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    Computational analysis and modeling of climate impact on Pteridium aquilinum (L.) populations

    AbstractPteridium aquilinum is a medicinally important fern with a limited range in northern Iran, increasingly threatened by climate change. Using morphological, genetic, and environmental data, we assessed differentiation, adaptive capacity, and vulnerability across 11 populations. Factor analysis of mixed data (FAMD) identified stipe indument, pinnule shape, and pinnae number as key traits distinguishing populations. Redundancy and association analyses (RDA/CCA) revealed strong links between both morphological and genetic variation and climatic gradients, particularly temperature and humidity, indicating local adaptation. Several SCoT loci were detected as adaptive outliers. Spatial PCA showed that variation is shaped by both global and local spatial factors, forming clines and local variants. Populations varied in sensitivity and adaptive capacity; populations 2, 3, 7, and 8 exhibited the lowest adaptive indices and highest vulnerability. Connectivity modeling suggested that while some populations (e.g., 2, 4, and 6) may maintain or slightly improve connectivity, others risk isolation under future climates. Structural equation modeling (SEM) indicated a positive genetic contribution to adaptation, while differential equation modeling (DEM) predicted logistic growth with temporary instability and genetic decline in vulnerable groups. Overall, findings highlight spatially uneven adaptive responses and recommend targeted conservation through connectivity enhancement, assisted gene flow, and ex-situ preservation of adaptive genotypes.

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    Data availability

    The datasets used and/ or analyzed during the current study available from the corresponding author on reasonable request.
    ReferencesIPCC. Climate Change 2022: Impacts, Adaptation and Vulnerability (Cambridge University Press, 2022).Kelly, S. A., Panhuis, T. M. & Stoehr, A. M. Phenotypic plasticity: molecular mechanisms and adaptive significance. Compreh Physiol. 9 (2), 259–303 (2019).
    Google Scholar 
    Parmesan, C. Ecological and evolutionary responses to recent climate change. Annu. Rev. Ecol. Evol. Syst. 37, 637–669 (2006).
    Google Scholar 
    Scheiner, S. M., Barfield, M. & Holt, R. D. The genetics of phenotypic plasticity. XVII. Response to climate change. Ecol. Evol. 9 (22), 12375–12389 (2019).
    Google Scholar 
    Christmas, M. J., Breed, M. F. & Lowe, A. J. Constraints to and conservation implications for climate change adaptation in plants. Conserv. Genet. 17 (2), 305–320 (2016).
    Google Scholar 
    Corlett, R. T. Climate change and the evolution of the next generation of tropical forest trees. Perspect. Plant. Ecol. Evol. Syst. 13 (1), 163–172 (2011).
    Google Scholar 
    Guan, B., Gao, J., Chen, W., Gong, X. & Ge, G. The effects of climate change on landscape connectivity and genetic clusters in a small subtropical and warm-temperate tree. Front. Plant. Sci. 12, 671336 (2021).
    Google Scholar 
    Foden, W. B. et al. Climate change vulnerability assessment of species. Wiley Interdiscip Rev. Clim. Change. 4 (3), 159–181 (2013).
    Google Scholar 
    Mair, L., O’Brien, G. S. D. W. & Purvis, A. The forgotten half of the species-area relationship. Ecol. Appl. 31 (8), e02447 (2021).Guisan, A., Edwards, T. C. & Hastie, T. Generalized linear and non-linear models for predicting species distributions. Ecol. Modell. 257, 1–17 (2013).
    Google Scholar 
    Moran, R. C. Diversity, biogeography, and floristics. In Biology and Evolution of Ferns and Lycophytes, 367–395 (Cambridge University Press, Cambridge, (2008).
    Google Scholar 
    Higgins, M. A. et al. Geological control of floristic composition in Amazonian forests. J. Biogeogr. 38 (11), 2136–2149 (2011).
    Google Scholar 
    Karst, J., Gilbert, B. & Lechowicz, M. J. Fern community assembly. Ecology 86 (9), 2473–2486 (2005).
    Google Scholar 
    Della, A. P. & Falkenberg, D. D. B. Pteridophytes as ecological indicators: an overview. Hoehnea 46 (1), e522018 (2019).
    Google Scholar 
    Sheidai, M., Alaeifar, M. & Koohdar, F. Integrating Geostatistical approaches into landscape genetics. Plant Mol. Biol. Rep. 1–12 (2025).Christenhusz, M. et al. Pteridium Pinetorum (The IUCN Red List of Threatened Species, 2017).CABI. Pteridium aquilinum (bracken). CABI Compendium. (2020).Davis, M. B. & Shaw, R. G. Range shifts and adaptive responses to quaternary climate change. Science 292 (5517), 673–679 (2001).
    Google Scholar 
    Nicotra, A. B. et al. Plant phenotypic plasticity in a changing climate. Trends Plant. Sci. 15 (12), 684–692 (2010).
    Google Scholar 
    Bradshaw, A. D. Unraveling phenotypic plasticity. New. Phytol. 170 (4), 644–648 (2006).
    Google Scholar 
    Reed, T. E., Schindler, D. E. & Waples, R. S. Phenotypic plasticity and evolution in population persistence. Conserv. Biol. 25 (1), 56–63 (2011).
    Google Scholar 
    Sheidai, M., Alaeifar, M. & Koohdar, F. PLS-SEM in plant ecological studies. Ecol. Modell. 500, 110–125 (2024).
    Google Scholar 
    Cruzan, M. B. & Hendrickson, E. C. Landscape genetics of plants. Plant. Commun. 1 (6), 100100 (2020).
    Google Scholar 
    Thurman, L. L., Stein, B. & Beever, E. A. Adaptive capacity of species to climate change. Front. Ecol. Environ. 18 (9), 499–507 (2020).
    Google Scholar 
    Fortini, L., Loehman, R. A. & Holsinger, L. M. Adaptive capacity of Pinus radiata. Glob Change Biol. 23 (1), 160–170 (2017).
    Google Scholar 
    Arnold, P. A., Kruuk, L. E. B. & Nicotra, A. B. Analyzing plant phenotypic plasticity. New. Phytol. 22 (3), 1235–1241 (2019).
    Google Scholar 
    Scheiner, S. M. Genetics and evolution of phenotypic plasticity. Annu. Rev. Ecol. Syst. 24, 35–68 (1993).
    Google Scholar 
    Thuiller, W. et al. Predicting global change impacts on plants. Perspect. Plant. Ecol. Evol. Syst. 9 (3–4), 137–152 (2008).
    Google Scholar 
    Jones, M. M. et al. Environmental heterogeneity and ferns. J. Ecol. 94 (1), 181–195 (2006).
    Google Scholar 
    FAO. GIEWS Country Brief: Iran (FAO, 2020).Zohary, M. Geobotanical Foundations of the Middle East (Gustav Fischer, 1973).Alaeifar, M., Sheidai, M. & Koohdar, F. Genetic diversity of Pteridium aquilinum. Plant Genet. Resour. 1–8 (2025).Ahmed, N. et al. Purchase intention toward organic food. J. Environ. Plan. Manag. 64 (5), 796–822 (2021).
    Google Scholar 
    Pagès, J. Multiple Factor Analysis by Example Using R (CRC, 2014).Lê, S., Josse, J. & Husson, F. FactoMineR: an R package. J. Stat. Softw. 25, 1–18 (2008).
    Google Scholar 
    Husson, F., Lê, S. & Pagès, J. Exploratory Multivariate Analysis Using R (CRC, 2011).Jolliffe, I. Principal component analysis. In International Encyclopedia of Statistical Science, 1094–1096 (Springer, (2011).
    Google Scholar 
    Legendre, P. & Legendre, L. F. L. Numerical Ecology (Elsevier, 2012).Forester, B. R. et al. Detecting multilocus adaptation. Mol. Ecol. 27 (9), 2215–2233 (2018).
    Google Scholar 
    Zuur, A. F. et al. Data exploration protocol. Methods Ecol. Evol. 1 (1), 3–14 (2010).
    Google Scholar 
    Jombart, T., Devillard, S. & Balloux, F. Spatial analysis of genetic variation. Genetics 178 (3), 1679–1691 (2008).
    Google Scholar 
    Hoban, S. et al. Genomic basis of local adaptation. Am. Nat. 188 (4), 379–397 (2016).
    Google Scholar 
    François, O. et al. Controlling false discoveries. Mol. Ecol. 25 (2), 454–469 (2016).
    Google Scholar 
    Andrews, K. R. et al. RADseq in genomics. Nat. Rev. Genet. 17 (2), 81–92 (2016).
    Google Scholar 
    Nussey, D. H. et al. Phenotypic plasticity in natural populations. J. Evol. Biol. 20 (2), 891–903 (2007).
    Google Scholar 
    Hadfield, J. D. MCMC methods for GLMM. (2009).Sexton, J. P. et al. Isolation by environment or distance. Evolution 68 (1), 1–15 (2014).
    Google Scholar 
    Sunday, J. M. et al. Thermal tolerance in ectotherms. Proc. R Soc. B. 278 (1713), 1823–1830 (2011).
    Google Scholar 
    Valladares, F., Matesanz, S. & Niinemets, Ü. Environmental stress and evolution. Biol. Rev. 89 (3), 564–582 (2014).
    Google Scholar 
    Dawson, T. P. et al. Biodiversity conservation in changing climate. Science 332 (6025), 53–58 (2011).
    Google Scholar 
    Young, B. E. et al. Climate change vulnerability index. Wildl. Soc. Bull. 39 (1), 174–181 (2015).
    Google Scholar 
    Wessels, C., Merow, C. & Trisos, C. H. Climate change risk to wild food plants. Reg. Environ. Change. 21 (2), 29 (2021).
    Google Scholar 
    Rinnan, D. S. & Lawler, J. Climate-niche factor analysis. Ecography 42 (9), 1494–1503 (2019).
    Google Scholar 
    Gienapp, P. et al. Environmental vs. genetic effects. Ecol. Lett. 11 (7), 633–643 (2008).
    Google Scholar 
    Wasserman, D. et al. EPA guidance on suicide treatment. Eur. Psychiatry. 27 (2), 129–141 (2012).
    Google Scholar 
    Krosby, M. et al. Ecological connectivity. Conserv. Biol. 24 (6), 1686–1689 (2010).
    Google Scholar 
    Fick, S. E. & Hijmans, R. J. WorldClim 2. Int. J. Climatol. 37 (12), 4302–4315 (2017).
    Google Scholar 
    Dormann, C. F. et al. Collinearity Rev. Ecography 36 (1), 27–46 (2013).
    Google Scholar 
    Dijkstra, E. W. A note on two problems in connection with graphs. Numer. Math. 1 (1), 269–271 (1959).
    Google Scholar 
    Inoue, K. & Berg, D. J. Climate change and Cumberlandia monodonta. Glob Change Biol. 23 (1), 94–107 (2017).
    Google Scholar 
    McRae, B. H. Isolation by resistance. Evolution 60 (8), 1551–1561 (2006).
    Google Scholar 
    Manel, S. et al. Landscape genetics. Trends Ecol. Evol. 18 (4), 189–197 (2003).
    Google Scholar 
    Balkenhol, N. et al. Landscape Genetics: Concepts, Methods, Applications (Wiley-Blackwell, 2015).Hoffmann, A. A. & Sgrò, C. M. Climate change and evolutionary adaptation. Nature 470 (7335), 479–485 (2011).
    Google Scholar 
    Spear, S. F. et al. Resistance surfaces in landscape genetics. Mol. Ecol. 19 (17), 3576–3591 (2010).
    Google Scholar 
    Grace, J. B. Structural Equation Modeling and Natural Systems (Cambridge University Press, 2010).Soetaert, K. et al. DeSolve package. J. Stat. Softw. 33 (9), 1–25 (2010).
    Google Scholar 
    Ixaru, L. G. & Vanden Berghe, G. Runge–Kutta solvers. In Exponential Fitting, 165–186 (Springer, 2004).
    Google Scholar 
    Transtrum, M. K. & Sethna, J. P. Improvements to Levenberg–Marquardt. https://arxiv.org/abs/1201.5885 (2012).Moré, J. J. The Levenberg–Marquardt algorithm. In Numerical Analysis, 105–116 (Springer, 1978).
    Google Scholar 
    Gao, X. et al. Climate change and firmiana Kwangsiensis. Ecol. Evol. 12 (8), e9165 (2022).
    Google Scholar 
    Mittal, S. Threats to biodiversity. Global Biodiversity Outlook 2 (United Nations Environment Programme, Nairobi, (2019).
    Google Scholar 
    Spathelf, P. et al. Adaptive forest management. Ann. Sci. 75, 55 (2018).
    Google Scholar 
    Li, Y. et al. Landscape genomics. Front. Plant. Sci. 8, 2136 (2017).
    Google Scholar 
    Buzatti, R. S. O. et al. Leaf trait variation. Front. Plant. Sci. 10, 1580 (2019).
    Google Scholar 
    Sexton, J. P. et al. Adaptive responses to climate change. Evol. Appl. 2 (2), 185–197 (2009).
    Google Scholar 
    Hampe, A. & Petit, R. J. Conserving biodiversity. Front. Ecol. Environ. 3 (10), 542–550 (2005).
    Google Scholar 
    Ghasemian, S. et al. Persian squirrel genetics. Ecol. Evol. 13 (7), e10318582 (2023).
    Google Scholar 
    Gholamali-Fard, N. et al. Gene flow barriers in lizards. Zool. Scr. 49 (6), 738–751 (2020).
    Google Scholar 
    Dolatkhahi, F. et al. Genetic diversity of Dracocephalum kotschyi. Hort Environ. Biotechnol. 60 (5), 767–777 (2019).
    Google Scholar 
    Matesanz, S., Gianoli, E. & Valladares, F. Global change and plant plasticity. Ann. N Y Acad. Sci. 1206 (1), 35–55 (2010).
    Google Scholar 
    Sultan, S. E. Phenotypic plasticity. Trends Plant. Sci. 5 (12), 537–542 (2000).
    Google Scholar 
    Agustí, J. & Blázquez, M. A. Plant vascular development. Cell. Mol. Life Sci. 77 (19), 3711–3728 (2020).
    Google Scholar 
    Ehleringer, J. R. Leaf morphology and stress. Oecologia 47 (3), 307–310 (1980).
    Google Scholar 
    Johnson, H. B. Plant pubescence. Bot. Rev. 41 (3), 233–258 (1975).
    Google Scholar 
    Levin, D. A. Role of trichomes. Q. Rev. Biol. 48 (1), 3–15 (1973).
    Google Scholar 
    Read, J., Sanson, G. D. & Watt, A. D. Leaf shape and function. New. Phytol. 204 (2), 263–278 (2014).
    Google Scholar 
    Nicotra, A. B. et al. Plasticity in changing climate. Funct. Ecol. 25 (1), 237–251 (2011).
    Google Scholar 
    Givnish, T. J. Leaf form significance. In Topics in Plant Population Biology. 375–404 (Cambridge University Press, 1979).
    Google Scholar 
    Vogel, S. Convective cooling and leaf shape. J. Exp. Bot. 21 (4), 91–101 (1970).
    Google Scholar 
    Nobel, P. S. Physicochemical and Environmental Plant Physiology (Academic, 2009).Parkhurst, D. F. & Mott, K. A. Gas exchange within leaves. Plant. Cell. Environ. 13 (7), 697–707 (1990).
    Google Scholar 
    Whitmore, T. C. Tropical Rain Forests of the Far East (Oxford University Press, 1984).Givnish, T. J. Leaf form. In Topics in Plant Population Biology. 375–407 (Cambridge University Press, 1978).
    Google Scholar 
    Habel, J. C. et al. Genetic drift in orchids. Biol. Conserv. 144 (12), 3020–3027 (2011).
    Google Scholar 
    Row, J. R. et al. Landscape features and salamander genetics. Conserv. Genet. 15 (3), 667–680 (2014).
    Google Scholar 
    Geffen, E., Anderson, M. J. & Wayne, R. K. Dispersal barriers in wolves. Mol. Ecol. 13 (10), 2481–2490 (2004).
    Google Scholar 
    Gosper, C. R. et al. Flora conservation and OCBIL theory. Biol. J. Linn. Soc. 133 (2), 373–393 (2021).
    Google Scholar 
    Download referencesAuthor informationAuthors and AffiliationsDepartment of Plant Sciences and Biotechnology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, IranMasoud Sheidai, Maedeh Alaeifar & Fahimeh KoohdarAuthorsMasoud SheidaiView author publicationsSearch author on:PubMed Google ScholarMaedeh AlaeifarView author publicationsSearch author on:PubMed Google ScholarFahimeh KoohdarView author publicationsSearch author on:PubMed Google ScholarContributionsM. Sh. and F. K. Conceptualization of the project, designed the research, analysis and wrote the manuscript and M. A. collected the samples and lab work. All authors reviewed the manuscript.Corresponding authorCorrespondence to
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    The authors declare no competing interests.

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    Reprints and permissionsAbout this articleCite this articleSheidai, M., Alaeifar, M. & Koohdar, F. Computational analysis and modeling of climate impact on Pteridium aquilinum (L.) populations.
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    Long-term effects of nitrogen fertilization on methane emissions in drained tropical peatland

    Abstract

    Nitrogen (N) fertilization improves crop productivity. However, the long-term effects of N application on methane (CH4) emissions in drained peat soils, particularly under different hydrological conditions, remain poorly understood. Accurate quantification of CH4 emissions from peatlands is essential for assessing carbon losses and formulating effective climate change mitigation strategies. This study was conducted to investigate the impact of N fertilization on CH4 emissions and identify the main factors influencing CH4 emissions from drained tropical peatlands. This study was conducted on an oil palm plantation in Sarawak, Malaysia, a randomized block design included four N fertilizer treatments: Control (0 kg N ha− 1 yr− 1) (T1); low (31.1 kg N ha⁻¹ yr⁻¹) (T2), moderate (62.2 kg N ha⁻¹ yr⁻¹) (T3), and high (124.3 kg N ha⁻¹ yr⁻¹) (T4). Soil CH4 fluxes showed no statistically significant differences between treatments or across years, with emissions ranging from − 163.6 to 320.7 µg C m− 2 hr− 1 at T1, -86.7 to 285.8 µg C m− 2 hr− 1 at T2, -131.6 to 274.1 µg C m− 2 hr− 1 at T3 and − 125.7 to 185.9 µg C m− 2 hr− 1 at T4 (p > 0.05). Although ammonium sulfate fertilization did not significantly alter CH4 emissions, its pronounced acidifying effect on soil pH, particularly at application rates above 62.2 kg N ha⁻¹ yr⁻¹ along with elevated sulfate (SO42−) inputs and nitrogen pools exceeding the critical threshold (> 400 ppm), likely suppressed methanogenic activity and constrained soil organic matter decomposition. Water-filled pore space (WFPS) influenced CH4 emissions more than groundwater level (GWL), with the low GWL at the site limiting its impact. Increased WFPS (60–80%) reduced nitrate (NO3−) through enhanced denitrification, lowering its inhibition on CH4 production and thus increasing emissions. This study highlights the key role of soil moisture and nitrogen cycling in regulating CH4 emissions in peatland.

    Data availability

    The datasets used and/or analyzed during the current study available from the corresponding author on reasonable request.
    ReferencesIPCC, A. Climate change 2013: The physical science basis. Contribution of working group I to the fifth assessment report of the intergovernmental panel on climate change, 1535. (2013). Wang, Z., Zeng, D. & Patrick, W. H. Methane emissions from natural wetlands. Environ. Monit. Assess. 42, 143–161. https://doi.org/10.1007/BF00394047 (1996).
    Google Scholar 
    Li, C., Grayson, R., Holden, J. & Li, P. Erosion in peatlands: recent research progress and future directions. Earth Sci. Rev. 185, 870–886. https://doi.org/10.1016/j.earscirev.2018.08.005 (2018).
    Google Scholar 
    Xu, J., Morris, P. J., Liu, J. & Holden, J. P. E. A. T. M. A. P. Refining estimates of global peatland distribution based on a meta-analysis. Catena 160, 134–140. https://doi.org/10.1016/j.catena.2017.09.010 (2018).
    Google Scholar 
    Ribeiro, K. et al. Tropical peatlands and their contribution to the global carbon cycle and climate change. Glob. Change Biol. 27 (3), 489–505. https://doi.org/10.1111/gcb.15408 (2021).
    Google Scholar 
    Mishra, S. et al. Degradation of Southeast Asian tropical peatlands and integrated strategies for their better management and restoration. J. Applied Ecology. 58 (7), 1370–1387. https://doi.org/10.1111/1365-2664.13905 (2021).
    Google Scholar 
    Omar, M. S. et al. Peatlands in Southeast asia: A comprehensive geological review. Earth Sci. Rev. 104149 https://doi.org/10.1016/j.earscirev.2022.104149 (2022).Page, S. et al. Anthropogenic impacts on lowland tropical peatland biogeochemistry. Nat. Reviews Earth Environ. 3 (7), 426–443. https://doi.org/10.1038/s43017-022-00289-6 (2022).
    Google Scholar 
    Hooijer, A. et al. Current and future CO2 emissions from drained peatlands in Southeast Asia. Biogeosciences 7 (5), 1505–1514. https://doi.org/10.5194/bg-7-1505-2010 (2010).
    Google Scholar 
    Oktarita, S., Hergoualc’h, K., Anwar, S. & Verchot, L. V. Substantial N2O emissions from peat decomposition and N fertilization in an oil palm plantation exacerbated by hotspots. Environ. Res. Lett. 12 (10), 104007. https://doi.org/10.1088/1748-9326/aa80f1 (2017).
    Google Scholar 
    Hergoualc’h, K. A. & Verchot, L. V. Changes in soil CH4 fluxes from the conversion of tropical peat swamp forests: a meta-analysis. J. Integr. Environ. Sci. 9 (2), 93–101. https://doi.org/10.1080/1943815X.2012.747252 (2012).
    Google Scholar 
    Hirano, T., Jauhiainen, J., Inoue, T. & Takahashi, H. Controls on the carbon balance of tropical peatlands. Ecosystems 12, 873–887. https://doi.org/10.1007/s10021-008-9209-1 (2009).
    Google Scholar 
    Deshmukh, C. S. et al. Impact of forest plantation on methane emissions from tropical peatland. Glob. Change Biol. 26 (4), 2477–2495. https://doi.org/10.1111/gcb.15019 (2020).
    Google Scholar 
    Le Mer, J. & Roger, P. Production, oxidation, emission and consumption of methane by soils: a review. Eur. J. Soil Biol. 37 (1), 25–50. https://doi.org/10.1016/S1164-5563(01)01067-6 (2001).
    Google Scholar 
    van Lent, J., Hergoualc’h, K., Verchot, L., Oenema, O. & van Groenigen, J. W. Greenhouse gas emissions along a peat swamp forest degradation gradient in the Peruvian amazon: soil moisture and palm roots effects. Mitig. Adapt. Strat. Glob. Change. 24, 625–643. https://doi.org/10.1007/s11027-018-9796-x (2019).
    Google Scholar 
    Watanabe, A. et al. CO2 fluxes from an Indonesian peatland used for Sago palm (Metroxylon Sagu Rottb.) cultivation: effects of fertilizer and groundwater level management. Agric. Ecosyst. Environ. 134 (1–2), 14–18. https://doi.org/10.1016/j.agee.2009.06.015 (2009).
    Google Scholar 
    Swails, E., Hergoualc’h, K., Verchot, L., Novita, N. & Lawrence, D. Spatio-temporal variability of peat CH4 and N2O fluxes and their contribution to peat GHG budgets in Indonesian forests and oil palm plantations. Front. Environ. Sci. 9, 617828. https://doi.org/10.3389/fenvs.2021.617828 (2021).
    Google Scholar 
    Luta, W. et al. Water table fluctuation and methane emission in pineapples (Ananas comosus (L.) Merr.) cultivated on a tropical peatland. Agronomy 11 (8), 1448. https://doi.org/10.3390/agronomy11081448 (2021).
    Google Scholar 
    Couwenberg, J., Dommain, R. & Joosten, H. Greenhouse gas fluxes from tropical peatlands in south-east Asia. Glob. Change Biol. 16 (6), 1715–1732. https://doi.org/10.1111/j.1365-2486.2009.02016.x (2010).
    Google Scholar 
    Hatano, R. Impact of land use change on greenhouse gases emissions in peatland: a review. Int. Agrophys. 33 (2), 167–173. https://doi.org/10.31545/intagr/109238 (2019).
    Google Scholar 
    Chaddy, A. et al. Effects of long-term nitrogen fertilization and ground water level changes on soil CO2 fluxes from oil palm plantation on tropical peatland. Atmosphere 12 (10), 1340. https://doi.org/10.3390/atmos12101340 (2021).
    Google Scholar 
    Hadi, A. et al. Greenhouse gas emissions from tropical peatlands of Kalimantan, Indonesia. Nutr. Cycl. Agrosyst. 71, 73–80. https://doi.org/10.1007/s10705-004-0380-2 (2005).
    Google Scholar 
    Li, Q., Peng, C., Zhang, J., Li, Y. & Song, X. Nitrogen addition decreases methane uptake caused by methanotroph and methanogen imbalances in a Moso bamboo forest. Sci. Rep. 11 (1), 1–14. https://doi.org/10.1038/s41598-021-84422-3 (2021).
    Google Scholar 
    Banger, K., Tian, H. & Lu, C. Do nitrogen fertilizers stimulate or inhibit methane emissions from rice fields? Glob. Change Biol. 18 (10), 3259–3267. https://doi.org/10.1111/j.1365-2486.2012.02762.x (2012).
    Google Scholar 
    Sun, B., Zhao, H., Lu, F. & Wang, X. The effects of nitrogen fertilizer application on methane and nitrous oxide emission/uptake in Chinese croplands. J. Integr. Agric. 15 (2), 440–450. https://doi.org/10.1016/S2095-3119(15)61063-2 (2016).
    Google Scholar 
    Conrad, R. Microbial ecology of methanogens and methanotrophs. Adv. Agron. 96, 1–63. https://doi.org/10.1016/S0065-2113(07)96005-8 (2007).
    Google Scholar 
    Laanbroek, H. J. Methane emission from natural wetlands: interplay between emergent macrophytes and soil microbial processes. Mini-Review Annals Bot. 105 (1), 141–153. https://doi.org/10.1093/aob/mcp201 (2010).
    Google Scholar 
    Bodelier, P. L. E. & Laanbroek, H. J. Nitrogen as a regulatory factor of methane oxidation in soils and sediments. FEMS Microbiol. Ecol. 47 (3), 265–277. https://doi.org/10.1016/S0168-6496(03)00304-0 (2004).
    Google Scholar 
    Kambara, H. et al. Environmental factors affecting the community of methane-oxidizing bacteria. Microbes Environ. 37 (1), ME21074. https://doi.org/10.1264/jsme2.ME21074 (2022).
    Google Scholar 
    Aulakh, M. S., Wassmann, R. & Rennenberg, H. Methane emissions from rice fields—quantification, mechanisms, role of management, and mitigation options. Adv. Agron. 70, 193–260. https://doi.org/10.1016/S0065-2113(01)70006-5 (2001).
    Google Scholar 
    Steudler, P. A., Bowden, R. D., Melillo, J. M. & Aber, J. D. Influence of nitrogen fertilization on methane uptake in temperate forest soils. Nature 341 (6240), 314–316. https://doi.org/10.1038/341314a0 (1989).
    Google Scholar 
    Mosier, A. R. & Delgado, J. A. Methane and nitrous oxide fluxes in grasslands in Western Puerto Rico. Chemosphere 35 (9), 2059–2082. https://doi.org/10.1016/S0045-6535(97)00231-2 (1997).
    Google Scholar 
    Wang, J. et al. Nitrate addition inhibited methanogenesis in paddy soils under long-term managements. Plant. Soil. Environ. 64 (8), 393–399. https://doi.org/10.17221/231/2018-PSE (2018).
    Google Scholar 
    Basiron, Y. Palm oil production through sustainable plantations. Eur. J. Lipid Sci. Technol. 109 (4), 289–295. https://doi.org/10.1002/ejlt.200600223 (2007).
    Google Scholar 
    Chaddy, A., Melling, L., Ishikura, K. & Hatano, R. Soil N2O emissions under different N rates in an oil palm plantation on tropical peatland. Agriculture 9 (10), 213. https://doi.org/10.3390/agriculture9100213 (2019).
    Google Scholar 
    Hasnol, O., Farawahida, M. D., Mohd, H. & Samsudin A Re-evaluation of nutrients requirements for oil palm planting on peat soil. Planter 90 (1056), 161–177 (2014).
    Google Scholar 
    Keeney, D. R. & Nelson, D. W. Nitrogen in organic forms. In (eds Page, A. L., Miller, R. H. & Keeney, D. R.) Methods of Soil Analysis. Part 2. Agronomy No. 9, American Society of Agronomy, Madison, WI, 643–698. (1982).
    Google Scholar 
    Salehi, M. H., Beni, O. H., Harchegani, H. B., Borujeni, I. E. & Motaghian, H. R. Refining soil organic matter determination by loss-on-ignition. Pedosphere 21 (4), 473–482. https://doi.org/10.1016/S1002-0160(11)60149-5 (2011).
    Google Scholar 
    Melling, L., Goh, K. J. & Hatano, R. Short-term effect of Urea on CH4 flux under the oil palm (Elaeis guineensis) on tropical peatland in Sarawak, Malaysia. Soil. Sci. Plant. Nutr. 52 (6), 788–792. https://doi.org/10.1111/j.1747-0765.2006.00092.x (2006).
    Google Scholar 
    Fageria, N. K., Dos Santos, A. B. & Moraes, M. F. Influence of Urea and ammonium sulfate on soil acidity indices in lowland rice production. Commun. Soil Sci. Plant Anal. 41 (13), 1565–1575. https://doi.org/10.1080/00103624.2010.485237 (2010).
    Google Scholar 
    Wang, Z. P., Delaune, R. D., Patrick, W. H. Jr & Masscheleyn, P. H. Soil redox and pH effects on methane production in a flooded rice soil. Soil Sci. Soc. Am. J. 57 (2), 382–385. https://doi.org/10.2136/sssaj1993.03615995005700020016x (1993).
    Google Scholar 
    Cai, Z. et al. Methane and nitrous oxide emissions from rice paddy fields as affected by nitrogen fertilizers and water management. Plant. Soil. 196, 7–14. https://doi.org/10.1023/A:1004263405020 (1997).
    Google Scholar 
    Minamikawa, K., Sakai, N. & Yagi, K. Methane emission from paddy fields and its mitigation options on a field scale. Microbes Environ. 21 (3), 135–147. https://doi.org/10.1264/jsme2.21.135 (2006).
    Google Scholar 
    Ro, S., Seanjan, P., Tulaphitak, T. & Inubushi, K. Sulfate content influencing methane production and emission from incubated soil and rice-planted soil in Northeast Thailand. Soil. Sci. Plant. Nutr. 57 (6), 833–842. https://doi.org/10.1080/00380768.2011.637302 (2011).
    Google Scholar 
    Kim, S. Y., Veraart, A. J., Meima-Franke, M. & Bodelier, P. L. Combined effects of carbon, nitrogen and phosphorus on CH4 production and denitrification in wetland sediments. Geoderma 259, 354–361. https://doi.org/10.1016/j.geoderma.2015.03.015 (2015).
    Google Scholar 
    Cai, Z., Shan, Y. & Xu, H. Effects of nitrogen fertilization on CH4 emissions from rice fields. Soil. Sci. Plant. Nutr. 53 (4), 353–361. https://doi.org/10.1111/j.1747-0765.2007.00153.x (2007).
    Google Scholar 
    Girkin, N. T., Turner, B. L., Ostle, N., Craigon, J. & Sjögersten, S. Root exudate analogues accelerate CO2 and CH4 production in tropical peat. Soil Biol. Biochem. 117, 48–55. https://doi.org/10.1016/j.soilbio.2017.11.008 (2018).
    Google Scholar 
    Ishikura, K. et al. Carbon dioxide and methane emissions from peat soil in an undrained tropical peat swamp forest. Ecosystems 22, 1852–1868. https://doi.org/10.1007/s10021-019-00376-8 (2019).
    Google Scholar 
    Azizan, S. N. F. et al. Comparing GHG emissions from drained oil palm and recovering tropical peatland forests in Malaysia. Water 13, 3372. https://doi.org/10.3390/w13233372 (2021).
    Google Scholar 
    Busman, N. A. et al. Soil CO2 and CH4 fluxes from different forest types in tropical peat swamp forest. Sci. Total Environ. 858, 159973. https://doi.org/10.1016/j.scitotenv.2022.159973 (2023).
    Google Scholar 
    Melling, L. & Hatano, R. Goh. K.J. Methane fluxes from three ecosystems in tropical peatland of Sarawak, Malaysia. Soil Biol. Biochem. 37 (8), 1445–1453. https://doi.org/10.1016/j.soilbio.2005.01.001 (2005).
    Google Scholar 
    Jovani-Sancho, A. J. et al. CH4 and N2O emissions from smallholder agricultural systems on tropical peatlands in Southeast Asia. Glob. Change Biol. 29 (15), 4279–4297. https://doi.org/10.1111/gcb.16747 (2023).
    Google Scholar 
    Murdiyarso, D., Hergoualc’h, K. & Verchot, L. V. Opportunities for reducing greenhouse gas emissions in tropical peatlands. Proc. Natl. Acad. Sci. 107 (46), 19655–19660. https://doi.org/10.1073/pnas.0911966107 (2010).
    Google Scholar 
    Sjögersten, S. et al. Temperature response of ex-situ greenhouse gas emissions from tropical peatlands: interactions between forest type and peat moisture conditions. Geoderma 324, 47–55. https://doi.org/10.1016/j.geoderma.2018.02.029 (2018).
    Google Scholar 
    Download referencesAcknowledgementsWe would like to express our sincere gratitude for the generous support from the Sarawak State Government and the Federal Government of Malaysia for making this research possible. We would also like to express our sincere appreciation to the dedicated staff of the Sarawak Tropical Peat Research Institute (TROPI) for their invaluable technical assistance and unwavering support throughout every phase of this study, including the challenging fieldwork. Their expertise and dedication contributed greatly to the successful completion of this study.FundingThis research was funded by the Federal Government of Malaysia and the Sarawak State Government.Author informationAuthors and AffiliationsSarawak Tropical Peat Research Institute, Kuching-Samarahan Expressway, Kota Samarahan, Sarawak, 94300, MalaysiaAuldry Chaddy, Faustina Elfrida Sangok, Sharon Yu Ling Lau & Lulie MellingAuthorsAuldry ChaddyView author publicationsSearch author on:PubMed Google ScholarFaustina Elfrida SangokView author publicationsSearch author on:PubMed Google ScholarSharon Yu Ling LauView author publicationsSearch author on:PubMed Google ScholarLulie MellingView author publicationsSearch author on:PubMed Google ScholarContributionsLiterature collection, data collection and analysis were performed by Auldry Chaddy, Faustina Elfrida Sangok, and Sharon Yu Ling Lau. The first draft of the manuscript was written by Auldry Chaddy. Faustina Elfrida Sangok, Sharon Lau Yu Ling and Lulie Melling revised the draft. All authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.Corresponding authorCorrespondence to
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    Reprints and permissionsAbout this articleCite this articleChaddy, A., Sangok, F.E., Lau, S.Y.L. et al. Long-term effects of nitrogen fertilization on methane emissions in drained tropical peatland.
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    Bridging agriculture, health and industry through plant molecular farming in the bioeconomic era

    AbstractGlobal food production requires a major upheaval to feed a burgeoning human population despite multiple disruptors, ranging from climate change to geopolitical instability. Innovation and a policy shift that focuses on the Bioeconomy could address these challenges. This Perspective highlights plant cellular agriculture, molecular farming, and plant cell culture as a potential “fourth pillar” that could diversify supply and produce high-value compounds associated with regulatory uncertainty, cost, and energy constraints.

    IntroductionEvery person deserves appropriate nutrition. Our world approaches a human population of 10 billion within the next 30 years, with global food demand increasing by more than 50% during this time period1.By 2050, global food demand is projected to increase by 50–60% compared to 2010 levels, with protein demand expected to double in some regions2. This growing demand encompasses diverse nutritional needs, including high-energy staples such as rice, wheat, and maize to ensure calorie sufficiency; high-quality proteins from sources like meat, dairy, plant-based alternatives, and novel proteins to support nutrition security3; and high-value foods such as functional ingredients and specialty crops that contribute to economic diversification. Global food systems are undergoing an upheaval, with vulnerabilities such as economic shocks due to tariff changes, the risk of zoonotic infectious diseases such as bovine influenza in the US, and geopolitical conflict such as grain shortages due to the Russian- Ukraine war. Collectively, these disruptions have greatly affected food prices and availability4. However, scaling up supply across these categories is challenged by the impacts of climate change, dietary shifts driven by urbanization and rising affluence, as well as policy and trade uncertainties5.In response, and due to concerns about global food security issues, many nations such as the US are trying to change the way they produce food, to mitigate global shocks of all nature, and to decentralize yet strengthen food supply chains to reduce their vulnerabilities6. The most noteworthy way this is taking place is by investing in novel strategies to produce alternative proteins. Alternative proteins, then, refer to those made that are equally as nutritious as conventional animal proteins, but are cheaper, require fewer inputs, have a lower carbon footprint, and are resilient to climate shocks7.Alternative protein production should reduce the load of zoonotic diseases as well as agricultural pest pressures and other exacerbating problems associated with livestock production, ranging from antimicrobial resistance to animal cruelty, from fair trade to bioterrorism8. Decentralizing our food production to an abundance of smaller locations would mitigate these problems substantially. The overall effect will be a shift in trade relations from one that is fixed due to geography, to one that is fluid and unconstrained.Alternative protein technologies for food are often placed into three main categories: cultivated meat, plant-based protein, and precision fermentation9. Cultivated, or cell-based meat, refers to the production of meat cells in culture to produce a food product such as hamburger, sausage or chicken nuggets. Plant-based proteins can be defined as proteins which have been processed in such a way that they resemble animal sourced products, such as oat milk. Precision fermentation covers the use of microbial fermentation systems to produce individual animal protein in a manner that more closely resembles the technology used in the past to produce pharmaceutical proteins. This synthetic biology approach includes the incorporation of a gene encoding an animal protein into the genome of a bacterial or fungal strain, which is then cultivated in a bioreactor to produce large amounts of target proteins, such as casein and whey. These three pillars represent the fundamentals of alternative protein production.A fourth ‘pillar’ has been defined as a facet of cellular agriculture based on plant molecular farming and plant cell culture technologies. Plant molecular farming refers to the use of plants themselves to replace microbial bioreactors, in such a way that a gene of interest is expressed and extracted from plants instead of from microbes10. Plant cellular agriculture, on the other hand, makes use of plant cell culture to produce large amounts of plant biomass which can be processed into food products, analogous to some of the cultivated meat production technologies11. Plant molecular farming and plant cell culture have been proposed as a potential “fourth pillar” of alternative proteins, though their precise definition and boundaries remain debated within the field.The following Perspective presents various examples of this fourth pillar of alternative plant cell-based technologies and describes the advantages that it has over the others. The Perspective concludes with a prediction of the prospects of plant cellular agriculture to address the widening cracks found within our current food system.Plant molecular farmingPlant molecular farming can be defined as the use of plants as a production platform to express a target protein12. Originally a production platform for pharmaceutical proteins (molecular pharming) that was developed over a quarter of a century ago, the technology has matured to such an extent that animal food proteins found in dairy, meat and eggs have become a more recent series of products under development. A great advantage of plant molecular farming is that in place of costly bioreactors, greenhouses or farm fields can be used to produce the protein of interest, thus mitigating the economic and environmental costs associated with farming livestock13. Plant molecular farming thus does not encounter scaling challenges the way other protein production platforms, such as precision fermentation, must face. Plants can perform post translational modifications that more resemble their animal counterparts, thus enabling them to follow a form and functionality that is superior to proteins produced in many microbial systems14. Animal proteins can be produced and stored in a wide diversity of plant tissues, such as potato tubers, rice grains, and legumes such as peas and soybeans15. Since these are edible tissues, it is feasible that partial purification of the protein in question may be sufficient, or, depending on the circumstances, completely unnecessary. Originally, this technology was adapted by companies such as Medicago, iBio and Kentucky Bioprocessing Co, to produce vaccines, monoclonal antibodies and other biologics16. Today, over 30 molecular farming companies can be found which produce different animal food proteins. Examples include Argentinian company Moolec (recently merged with Bioceres group limited), which produces the heme protein myoglobin in soybean and pea that can be processed into iron loaded products such as textured vegetable protein (valorasoy.com). Alpine Bio (formally Nobell Foods), based in San Francisco produces dairy proteins such as casein for cheese in soybean (alpbio.com). PoloPo is an Israeli company which produces the egg protein ovalbumin in potato tubers (PoLopo.tech). In Europe, molecular farming company Nambawan Spain produces and purifies sweet proteins such as thaumatin in transgenic tobacco seed (namba-wan.com).The key steps to plant molecular farming include determining the appropriate mode of animal gene delivery to crops, then optimizing expression levels, scaling-up to produce the desired amount of protein and finally, purification of protein, if required. Animal genes can be introduced via stable transformation to produce transgenic plants, or transiently, using replicating constructs based on virus expression vectors17. To date, largely transgenic plants have been created which express the target protein; these crops can be produced in the field or greenhouse and the protein extracted using standard agricultural techniques. Limitations for these processes include regulatory issues for GMOs (for plants grown in the open field) and scale up limitations (for plants grown in the greenhouse). Transient expression performed in the greenhouse using virus expression vectors can increase yield considerably and can be introduced to field crops using novel spray technologies, which are currently under development18.Expression levels can vary depending on the type of protein being produced (this problem exists for precision fermentation as well) and the tissue that it is expressed in, as well as environmental factors such as temperature and humidity. Oilseed crops, like soy, for example, have been shown to express myoglobin at 26.6% of the total soluble protein in the legume19; this can be easily stored at ambient temperatures and extracted later, whereas the level of protein expressed in a leafy crop like lettuce or tobacco may be considerably lower, but may not require extensive purification, depending on its future use. Existing agricultural infrastructure can be used whether the plants are produced in the greenhouse or in open field, and both farming practices can support local rural economies in a fashion that is more environmentally sustainable than livestock agriculture10.A comparison between plant molecular farming and precision fermentation indicates that on average, plant molecular farming requires a much lower initial investment, Capex and scaleup costs than precision fermentation. Precision fermentation, on the other hand, has lower land use requirements but also relies on sugar and other carbon sources, as well as continuous power to run the bioreactors13. These limitations make it more challenging to scale up to global demand, due to the inhibitory costs of bioreactors and in fact sufficient access to global steel to produce them20. While transgenic plants in the open field remain subject to GMO concerns (although protein purified from such sources is not considered to be a GMO), plants do not harbor mammalian pathogens and thus contain lower safety concerns than some microbial expression systems.Artificial intelligence (AI) and machine learning (ML) are now accelerating breakthroughs in plant molecular farming by enabling high-throughput strain optimization, metabolic pathway prediction, and the identification of gene-editing targets21,22. AI-driven algorithms are increasingly used to analyze large-scale omics datasets, predict optimal gene regulatory networks, and guide the design of synthetic constructs for enhanced metabolite production23. For instance, deep learning frameworks can assist in optimizing codon usage, protein folding stability, and promoter strength for cell factory development in plants or plant cells. When combined with CRISPR-based genome editing, these tools can significantly reduce the trial-and-error cycle in engineering high-yielding production strains, paving the way for scalable and cost-effective plant-based biofactories. Integrating AI into strain design thus not only enhances precision and efficiency but also supports predictive modeling for sustainable and economically viable molecular farming systems24.Plant cell-based productsCellular agriculture, a rising field focused on producing a plant-based product directly from a single cell rather than using whole organisms in their natural habitat, offers a transformative approach for the sustainable production of ingredients used in food, cosmetics, and nutraceuticals11. Within this framework, plant cell culture serves as a powerful platform for generating high-value bioactive compounds, flavors, pigments, and even staple ingredients through controlled, in vitro methods. Techniques such as micropropagation, adventitious shoot or root formation, and somatic embryogenesis are widely applied for the regeneration of whole plants and the production of targeted compounds from cultured cells25. The commercialization of these processes using bioreactor systems helps overcome major limitations of conventional methods, which are often labor-intensive and difficult to scale. Bioreactors enable precise control of physical and chemical conditions, improve nutrient distribution, reduce physiological disorders such as hyperhydricity, and support automation, making large-scale production more efficient and economically viable26.Thus, plant-based cellular agriculture not only reduces reliance on land, water, and traditional farming practices, but also supports global efforts toward a circular and sustainable bioeconomy, where biologically derived, renewable resources drive industrial innovation, environmental sustainability, and inclusive economic growth27.Plant tissue culture involves the sterile cultivation of plant parts under controlled conditions, first conceptualized by Gottlieb Haberlandt in 1902, and based on his pioneering work with single-cell cultures28. Initially developed at the beginning of the 20th Century, plant tissue culture has come a long way since then, and includes technologies that make use of root cultures, embryonic cultures, and many others29. Plant cell culture can assist in the production of a plethora of secondary metabolites, and their yields can be vastly improved using genome editing technologies for an increasing number of plant species30. Resembling a cross between cell-based meat and precision fermentation in terms of technology, plant cell culture will facilitate the production of ingredients which would reduce supply chain disruptions. Today, plant cell culture can be produced in bioreactors as great as 100,000 L31.The number of food products that can be produced in plant cell culture has exploded and will continue to expand as concerns about supply chain disruptions grow. For example, cocoa production in cell culture is now being explored as a viable option by several different cellular agriculture companies. Current cocoa production is restricted to tropical regions and is under pressure in terms of loss of land, human rights issues, pest pressures, and is not particularly environmentally friendly32. While these issues, when combined with predictive models of climate change, will undoubtedly reduce our future global cocoa supplies, the demand for cocoa is increasing at a rate that cannot be met using traditional manufacturing processes.Plant cell culture technology is emerging as a transformative platform for the sustainable production of high-value food ingredients. Cultivation of specific plant tissues or cells in a controlled system bypasses traditional agricultural constraints such as seasonal variation, climate vulnerability, and ethical concerns related to labor practices.A notable example is California Cultured (cacultured.com), a U.S.-based biotechnology company that is producing cocoa from cell cultures. Cocoa bean cell cultivation, rapid cell growth and maturation are all possible as well as scalable. This method also minimizes the use of water and labor. It avoids environmental and social issues commonly associated with cocoa farming in West Africa, where most global cocoa is sourced.Due to increasing cocoa demand and the vulnerability of the supply chain, cell culture-based cocoa offers a scalable and ethical alternative, providing substantial reductions in land use, water consumption, and labor requirements compared to conventional cultivation. To truly understand whether plant-based or cell-culture cocoa is more sustainable, the industry needs to apply life-cycle assessment (LCA) more widely. Future LCA studies on chocolate should clearly define their system boundaries, select functional units that are relevant to the purpose, and, where possible, combine both established and newer assessment methods. Adding steps such as uncertainty and sensitivity analysis can help ensure that the results are not only accurate but also reliable for guiding decisions33.Beyond cocoa, similar cellular agriculture technologies are also being applied to coffee production. Arabica coffee is the most widely consumed variety, and is threatened by climate-induced stress and fungal pathogens34. Pluri Biotech (pluri-biotech.com), an Israeli company, is developing coffee from plant cell cultures. Using bioreactors designed to support structured cell growth, the company cultivates coffee cells capable of synthesizing key bioactive compounds such as caffeine. The resulting biomass is harvested, dried, and roasted, yielding a product that visually and sensorial resembles conventional ground coffee.In Europe, the French startup Stem (s-tem.fr) is also working with coffee cell cultures. The cultured coffee powder with natural flavor extracts derived from coffee processing byproducts creates a final product that maintains the sensory characteristics of traditionally harvested beans35.Like cocoa and coffee, cellular agriculture is now an attractive alternative for the production of other bioactive and commercially valuable compounds, including vanillin, saffron, natural colorants, flavor compounds, and dietary supplements30. Growing consumer demand for traceable, sustainable and ethically produced food sources worldwide has fueled the development of plant cell-cultured products. Plant cell culture offers a promising platform for localized, scalable, and clean-label production of essential ingredients for food, cosmetics, and nutraceuticals, addressing both environmental challenges and evolving consumer expectations. Recent advances in plant cell culture and molecular farming are driving a growing number of startups to translate the science into commercial progress. These companies illustrate the technology’s potential through measurable funding rounds, strategic partnerships, and scale-up milestones (Table 1).Table 1 Key startups in plant cell culture and molecular farming with funding and progress metricsFull size tablePlant cell culture offers reduced land use and zero exposure to pests compared to open-field agriculture; however, it requires substantial energy, high-purity water, and refined media components, including sucrose and hormones, enabling the development of heterotrophic cultures. Life-cycle assessments indicate that although emissions per biomass unit may be lower, energy consumption remains a key barrier to economic scalability without renewable energy and media recycling15,36. Techno-economic analyses further emphasize electricity and sugar sourcing as critical factors that need optimization for commercial viability37.Regulatory and ethical considerations in molecular farmingRegulatory frameworks remain a critical consideration for the deployment of products derived from plant biotechnology. While open-field genetically modified (GM) crops typically undergo approval through distinct regulatory pathways, such as the Novel Food Regulation of European Union (EU 2015/2283) and the U.S. FDA approved Generally Recognized as Safe (GRAS) process, plant cell culture–derived products from controlled environments may follow different routes with unique timelines, transparency requirements, and public consultations38. Moreover, societal concerns regarding “laboratory-grown” or “genetically modified” ingredients could impact consumer acceptance and market adoption, highlighting the importance of proactive engagement and clear communication strategies to address public perception and ethical considerations39. Specifically, the molecular farming of animal proteins in plants raises additional public health, stewardship, religious, and ethical questions, underscoring the need for collaborative dialog among scientists, regulators, industry, and religious leaders to ensure responsible development and societal acceptance40.ConclusionsThe rise of cellular agriculture and plant molecular farming has the promise to transform global food systems by producing high-quality alternative proteins and novel ingredients with reduced land and water demands. The success of this growth is hindered by the cost, scalability, consumer acceptance, technical, regulatory, and societal hurdles. Life-cycle assessments and policy frameworks can facilitate the adoption of these technologies, which can complement alternative protein, fermentation, and conventional agriculture to form a resilient and diversified landscape of plant-based products. Strategic innovation, integrating advanced breeding, AI-driven optimization, genome editing, or other breakthrough modern technologies, helps scientists select better cell lines, tweak metabolic processes, and automate production steps, along with supportive policy, to accelerate their path to scale. Combining these advances as part of sustainable food production will ensure they complement, rather than compete with, other alternative protein pillars, positioning them to play a decisive role in meeting the nutritional and environmental challenges of the coming decades for both people and the planet.

    Data availability

    No datasets were generated or analysed during the current study.
    ReferencesFalcon, W. P., Naylor, R. L. & Shankar, N. D. Rethinking global food demand for 2050. Popul. Dev. Rev. 48, 921–957 (2022).Article 

    Google Scholar 
    Willett, W. et al. Food in the anthropocene: the EAT–Lancet Commission on healthy diets from sustainable food systems. Lancet 393, 447–492 (2019).Article 
    PubMed 

    Google Scholar 
    Béné, C. et al. When food systems meet sustainability—current narratives and implications for actions. World Dev. 113, 116–130 (2018).Article 

    Google Scholar 
    Hodgson, A., Alper, J. & Maxon, M. E. The U.S. bioeconomy: Charting a course for a resilient and competitive future. Ind. Biotechnol. 18, 115–136 (2022).Article 

    Google Scholar 
    Springmann, M., Godfray, H. C., Rayner, M. & Scarborough, P. Analysis and valuation of the health and climate change cobenefits of dietary change. Proc. Natl. Acad. Sci. USA 113, 4146–4151, https://doi.org/10.1073/pnas.1523119113 (2016).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kemp, L. et al. Point of view: Bioengineering horizon scan 2020. eLife 9, e54489 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Swanson, Z., Welsh, C. & Majkut, J. Mitigating risk and capturing opportunity: The future of alternative proteins. Center for Strategic & International Studies. Sponsored by The Good Food Institute (2023).Marsian, J. et al. Plant-made nervous necrosis virus-like particles protect fish against disease. Front. Plant Sci. 10, 880, https://doi.org/10.3389/fpls.2019.00880 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sim, S. Y. J., SRV, A., Chiang, J. H. & Henry, C. J. Plant proteins for future foods: a roadmap. Foods 10, 1967, https://doi.org/10.3390/foods10081967 (2021).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bresnahan, K. A. et al. Closed-loop systems for plants expressing animal proteins: a modernized framework to safeguard the future of agricultural innovation. Front. Plant Sci. 16, 1426290. https://doi.org/10.3389/fpls.2025.1426290 (2025).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Rischer, H., Szilvay, G. R. & Oksman-Caldentey, K.-M. Cellular agriculture — Industrial biotechnology for food and materials. Curr. Opin. Biotechnol. 61, 128–134, https://doi.org/10.1016/j.copbio.2019.12.003 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Shanmugaraj, B., Bulaon, C. J. I. & Phoolcharoen, W. Plant molecular farming: a viable platform for recombinant biopharmaceutical production. Plants 9, 842, https://doi.org/10.3390/plants9070842 (2020).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    The Good Food Institute. The state of alternative protein series (2025). https://gfi.org/state-of-alternative-protein/.Webster, D. E. & Thomas, M. C. Post-translational modification of plant-made foreign proteins; glycosylation and beyond. Biotechnol. Adv. 30, 410–418 (2012).Article 
    CAS 
    PubMed 

    Google Scholar 
    Buyel, J. F. Plant molecular farming—integration and exploitation of side streams to achieve sustainable biomanufacturing. Front. Plant Sci. 9, 1893 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Benvenuto, E. et al. Plant molecular farming in the wake of the closure of Medicago Inc. Nat. Biotechnol. 41, 893–894, https://doi.org/10.1038/s41587-023-01812-w (2023).Article 
    CAS 
    PubMed 

    Google Scholar 
    Nosaki, S., Hoshikawa, K., Ezura, H. & Miura, K. Transient protein expression systems in plants and their applications. Plant Biotechnol. (Tokyo) 38, 297–304, https://doi.org/10.5511/plantbiotechnology.21.0610a (2021).Article 
    CAS 
    PubMed 

    Google Scholar 
    Torti, S. et al. Transient reprogramming of crop plants for agronomic performance. Nat. Plants 7, 159–171, https://doi.org/10.1038/s41477-021-00851-y (2021).Article 
    CAS 
    PubMed 

    Google Scholar 
    LePage, M. Soya beans made more meat-like by adding genes for pig proteins. New Scientist https://www.newscientist.com/article/2345678-soya-beans-made-more-meat-like-by-adding-genes-for-pig-proteins/ (2023).Tubb, C., & Seba, T. Rethinking Food and Agriculture 2020-2030: A Rethinkx Sector Disruption Report https://www.rethinkx.com/food-and-agriculture (2019).Gupta, D. K., Pagani, A., Zamboni, P. & Singh, A. K. AI-powered revolution in plant sciences: advancements, applications, and challenges for sustainable agriculture and food security. Exploratory Foods Foodomics 2, 443–459 (2024).Article 

    Google Scholar 
    Jafar, A., Bibi, N., Naqvi, R. A., Sadeghi-Niaraki, A. & Jeong, D. Revolutionizing agriculture with artificial intelligence: plant disease detection methods, applications, and their limitations. Front. Plant Sci. 15, 1356260. https://doi.org/10.3389/fpls.2024.1356260 (2024).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Dublino, R., & Ercolano, M. Artificial intelligence redefines agricultural genetics by unlocking the enigma of genomic complexity. Crop J. https://doi.org/10.1016/j.cj.2025.05.008 (2025).Li, Z. et al. From code to life: the AI-driven revolution in genome editing. Adv. Sci. e17029 https://doi.org/10.1002/advs.202417029 (2025).Krasteva, G., Georgiev, V. & Pavlov, A. Recent applications of plant cell culture technology in cosmetics and foods. Eng. Life Sci. 21, 68–76 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Polivanova, O. B. & Bedarev, V. A. Hyperhydricity in plant tissue culture. Plants 11, 3313, https://doi.org/10.3390/plants11233313 (2022).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Engineering Biology Research Consortium (EBRC). Moonshots for the 21st-century bioeconomy: A policy paper. Compiled and edited by Emily R. Aurand (2022).Thorpe, T. A. History of plant tissue culture. Mol. Biotechnol. 37, 169–180, https://doi.org/10.1007/s12033-007-0031-3 (2007).Article 
    CAS 
    PubMed 

    Google Scholar 
    Ramírez-Mosqueda, M. A. Overview of somatic embryogenesis. In Methods in Molecular Biology (Vol. 2527, pp. 1–8). https://doi.org/10.1007/978-1-0716-2485-2_1 (2022).Wu, T., Kerbler, S. M., Fernie, A. R. & Zhang, Y. Plant cell cultures as heterologous bio-factories for secondary metabolite production. Plant Commun. 2, 100235 (2021).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Titova, M., Popova, E. & Nosov, A. Bioreactor systems for plant cell cultivation at the Institute of Plant Physiology of the Russian Academy of Sciences: 50 years of technology evolution from laboratory to industrial implications. Plants 13, 430, https://doi.org/10.3390/plants13030430 (2024).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chen, E. Bittersweet: The harsh realities of chocolate production in West Africa. Harvard International Review (2025).Wang, S. & Dong, Y. Applications of life cycle assessment in the chocolate industry: a state-of-the-art analysis based on systematic review. Foods 13, 915 (2024).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wright, D. R. et al. Sustainable coffee: a review of the diverse initiatives and governance dimensions of global coffee supply chains. Ambio 53, 984–1001 (2024).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Turrell, C. Cell-based coffee future-proofs world’s favorite brew. Nat. Biotechnol. 42, 350 (2024).Article 
    CAS 
    PubMed 

    Google Scholar 
    Puzanskiy, R. K., Romanyuk, D. A., Kirpichnikova, A. A., Yemelyanov, V. V. & Shishova, M. F. Plant heterotrophic cultures: No food, no growth. Plants 13, 277, https://doi.org/10.3390/plants13020277 (2024).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    McNulty, M. J. et al. Techno-economic analysis of a plant-based platform for manufacturing antimicrobial proteins for food safety. Biotechnol. Prog. 36, e2896. https://doi.org/10.1002/btpr.2896 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Lucht, J. M. Public acceptance of plant biotechnology and GM crops. Viruses 7, 4254–4281, https://doi.org/10.3390/v7082819 (2015).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Frewer, L. J., Scholderer, J. & Bredahl, L. Communicating about the risks and benefits of genetically modified foods: the mediating role of trust. Risk Anal. 23, 1117–1133 (2003).Article 
    PubMed 

    Google Scholar 
    Bobo, J. Molecular farming navigates a complex regulatory landscape. Front. Plant Sci. 15, 1411943, https://doi.org/10.3389/fpls.2024.1411943 (2024).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Download referencesAuthor informationAuthors and AffiliationsDepartment of Microbiology, Cornell University, Ithaca, NY, USAKathleen HefferonSchool of Integrative Plant Sciences, Cornell University, Ithaca, NY, USAAdam GannonDepartment of Biotechnology and Genetic Engineering, Jahangirnagar University, Dhaka, BangladeshAbdullah Mohammad ShohaelAuthorsKathleen HefferonView author publicationsSearch author on:PubMed Google ScholarAdam GannonView author publicationsSearch author on:PubMed Google ScholarAbdullah Mohammad ShohaelView author publicationsSearch author on:PubMed Google ScholarContributionsK.H. and A.S. wrote the main manuscript. A.G. revised and updated. All authors reviewed the manuscript.Corresponding authorCorrespondence to
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    Stochastic growth marks in Crocodylus niloticus

    Abstract

    Skeletochronology combined with growth curve reconstruction is routinely used to assess the age and growth dynamics of extinct and extant vertebrates. Here we performed in vivo labelling studies of the bone histology of four 2 years-old Crocodylus niloticus individuals. We found that all the crocodiles have more growth marks in their compacta than expected for their age, i.e., they deposited stochastic growth marks in their bones. Using the fluorochrome markers we determined that these stochastic growth marks were deposited during their favourable season of growth. The variable preservation of growth marks in the crocodile bones highlights developmental plasticity in their growth, which can be extrapolated to extinct archosaurs, and other reptiles. We caution the use of growth marks in fossil bones as a reliable estimator of age and discuss the far-reaching implications this has for growth curve reconstruction and life history assessments of extinct vertebrates, such as nonavian dinosaurs.

    Data availability

    High resolution images will be uploaded onto Morphobank. All thin sections will be deposited in the Vertebrate Comparative Collections of Iziko Museums of Cape Town.
    ReferencesCastanet, J., Newman, D. & Girons, H. S. Skeletochronological data on the growth, age, and population structure of the tuatara, Sphenodon punctatus, on Stephens and lady Alice Islands, New Zealand. Herpetologica 44, 25–37 (1988).
    Google Scholar 
    Castanet, J., Vieillot, H. F., Meunier, F. J. & De Ricqlès, A. Bone and individual aging. Bone 7, 245–283 (1993).
    Google Scholar 
    Chinsamy-Turan, A. The Microstructure of Dinosaur Bones: Deciphering Biology Through Fine Scale Techniques (John Hopkins University, 2005).Buffrenil, V. Q. & Castanet, A. J. in Vertebrate Skeletal Histology and Paleohistology. (eds de Buffrenil, V., de Ricqles, A. J., Zylberberg, L., Padian, K.) Ch. 31, 626–644 (CRC Press, 2021).Castanet, J., Francillon-Vieillot, H., Meunier, F., De Ricqles, A. & Hall, B. Bone and individual aging. Bone 7, 245–283 (1993).
    Google Scholar 
    Kohler, M., Marin-Moratalla, N., Jordana, X. & Aanes, R. Seasonal bone growth and physiology in endotherms shed light on dinosaur physiology. Nature 487, 358–361 (2012). https://doi.org/10.1038/nature11264
    Google Scholar 
    Hutton, J. M. Age determination of living Nile crocodiles from the cortical stratification of bone. Copeia 2, 332–341 (1986).
    Google Scholar 
    Roberts, E., Matlock, C., Joanen, T., McNease, L. & Bowen, M. Bone morphometrics and Tetracycline marking patterns in young growing American alligators (Alligator mississippiensis). J. Wildl. Dis. 24, 67–70 (1988).
    Google Scholar 
    Snover, M. L. & Hohn, A. A. Validation and interpretation of annual skeletal marks in loggerhead (Caretta caretta) and kemp’s ridley (Lepidochelys kempii) sea turtles. Fish. Bull. 102 (4), 682–693 (2004).
    Google Scholar 
    Cubo, J. et al. Phylogenetic, functional, and structural components of variation in bone growth rate of amniotes. Evol. Dev. 10, 217–227 (2008).
    Google Scholar 
    Ricqlès, A., Meunier, F. J., Castanet, J. & Francillon-Viellot, H. in Bone Matrix and Bone Specific Products, Vol. 31–78 (ed Hall B. K.) (CRC Press, Inc., 1991).Chinsamy, A. Palaeoecological deductions from osteohistology. Biol. Lett. 19, 20230245 (2023).
    Google Scholar 
    Caetano, M. & Castanet, J. Variability and microevolutionary patterns in Triturus marmoratus from Portugal: Age, size, longevity and individual growth. Amphibia-reptilia 14, 117–129 (1993).
    Google Scholar 
    Erismis, U. C. & Chinsamy, A. Ontogenetic changes in the epiphyseal cartilage of Rana (Pelophylax) Caralitana (Anura: Ranidae). Anat. Rec (Hoboken). 293, 1825–1837 (2010). https://doi.org/10.1002/ar.21241
    Google Scholar 
    Mattox, N. T. Annular rings in the long bones of turtles and their correlation with size. Trans. Ill. State Acad. Sci. 28, 255–256 (1936).
    Google Scholar 
    Avens, L., Taylor, J. C., Goshe, L. R., Jones, T. T. & Hastings, M. Use of skeletochronological analysis to estimate the age of leatherback sea turtles Dermochelys coriacea in the Western North Atlantic. Endanger. Species Res. 8, 165–177 (2009). https://doi.org/10.3354/esr00202
    Google Scholar 
    Pereyra, M. E. et al. Growth dynamics and body size evolution of South American long-necked chelid turtles: A bone histology approach. Acta Palaeontol. Pol. 65, 535–545 (2020).
    Google Scholar 
    Pereyra, M. E. Comparative postcranial osteohistology and bone histovariability of aquatic and terrestrial turtles: The case of the South American Phrynops hilarii, Hydromedusa tectifera (Pleurodira, Chelidae), and Chelonoidis Chilensis (Cryptodira, Testudinidae). Anat. Rec. 306, 1304–1322 (2023).
    Google Scholar 
    Bhat, M. S., Chinsamy, A. & Parkington, J. Long bone histology of Chersina angulata: Interelement variation and life history data. J. Morphol. 280, 1881–1899 (2019).
    Google Scholar 
    Bhat, M. S., Chinsamy, A. & Parkington, J. Bone histology of neogene angulate tortoises (Testudines: Testudinidae) from South africa: Palaeobiological and skeletochronological implications. R. Soc. Open. Sci. 10, 230064 (2023).
    Google Scholar 
    Bhat, M. S. & Cullen, T. M. Growth and life history of freshwater chelydrid turtles (Testudines: Cryptodira): A bone histological approach. J. Anat., 247(3-4), 518–541 .
    Google Scholar 
    Castanet, J. & Naulleau, G. Données expérimentales sur la Valeur des Marques squelettiques comme indicateur de l ‘âge Chez Vipera Aspis (L.)(Ophidia, Viperidae). Zoolog. Scr. 3, 201–208 (1974).
    Google Scholar 
    Castanet, J. & Baez, M. Data on age and longevity in Gallotia Galloti (Sauria, Lacertidae) assessed by skeletochronology. Herpetol. J. 1, 218–222 (1988).
    Google Scholar 
    Castanet, J. & Baez, M. Adaptation and evolution in Gallotia Lizard from the Canary islands: Age, growth, maturity and longevity. Amphibia-Reptilia 12, 81–102 (1991).
    Google Scholar 
    Chinsamy, A., Hanrahan, S. A., Neto, M. & Seely, M. Skeletochronological assessment of age in Angolosaurus skoogi, a cordylid Lizard living in an aseasonal environment. J. Herpetol. 29, 457–460 (1995).
    Google Scholar 
    Chinsamy, A. The Osteohistology of Femoral Growth within a Clade: A Comparison of the Crocodile, Crocodylus niloticus, the Dinosaurs, Massospondylus and Syntarsus, and the Birds, Struthio and Sagittarius, (Witwatersrand, 1991).Woodward, H. N., Horner, J. R. & Farlow, J. O. Quantification of intraskeletal histovariability in Alligator mississippiensis and implications for vertebrate osteohistology. PeerJ 2, e422 (2014).
    Google Scholar 
    Pereyra, M. E., Bona, P., Siroski, P. & Chinsamy, A. Ontogenetic and interelemental study of appendicular bones of Caiman latirostris Daudin, 1802 sheds light on osteohistological variability in crocodylians. J. Morphol. 285, e21687 (2024).
    Google Scholar 
    Pereyra, M. E., Bona, P., Siroski, P. & Chinsamy, A. Analyzing the life history of caimans: the growth dynamics of Caiman latirostris from an osteohistological approach. J. Morphol. 286, e70010 (2025).
    Google Scholar 
    Audije-Gil, J., Barroso‐Barcenilla, F. & Cambra‐Moo, O. Mapping histovariability and growth patterns of Crocodylus niloticus bred in captivity and their Paleobiological implications. Ruling Reptiles: Crocodylian Biology Archosaur Paleobiology, 284–299 (2023).Castanet, J. et al. Lines of arrested growth in bone and age Estimation in a small primate: Microcebus murinus. J. Zool. 263, 31–39 (2004). https://doi.org/10.1017/s0952836904004844
    Google Scholar 
    Morris, P. A. A method for determinng absolute age in the Hedgehog. J. Zool. 20, 277–281 (1970).
    Google Scholar 
    Bourdon, E. et al. Bone growth marks reveal protracted growth in New Zealand Kiwi (Aves, Apterygidae). Biol. Lett. 5, 639–642. (2009). https://doi.org/10.1098/rsbl.2009.0310
    Google Scholar 
    Chinsamy, A., Angst, D., Canoville, A. & Göhlich, U. B. Bone histology yields insights into the biology of the extinct elephant birds (Aepyornithidae) from Madagascar. Biol. J. Linn. Soc. 130, 268–295 (2020).
    Google Scholar 
    Chinsamy, A., Handley, W. D. & Worthy, T. H. Osteohistology of Dromornis stirtoni (Aves: Dromornithidae) and the biological implications of the bone histology of the Australian Mihirung birds. Anat. Rec. 306 (7), 1842–1863 (2022).
    Google Scholar 
    Weiss, B. M., Dollman, K. N., Choiniere, J. N., Browning, C. & Botha, J. The osteohistology of Orthosuchus stormbergi using synchrotron radiation microcomputed tomography. J. Anat. 247 (3-4), 587–607 (2024).
    Google Scholar 
    Fernández Dumont, M. L., Pereyra, M. E., Bona, P. & Apesteguía, S. New data on the palaeosteohistology and growth dynamic of the notosuchian Araripesuchus Price, 1959. Lethaia 54, 578–590 (2021).
    Google Scholar 
    Hoffman, D. et al. Evolution of growth strategy in alligators and Caimans informed by osteohistology of the late eocene early-diverging alligatoroid crocodylian Diplocynodon hantoniensis. J. Anat. 247, 165 (2025).
    Google Scholar 
    Chinsamy, A. Bone histology and growth trajectory of the prosauropod dinosaur Massospondylus carinatus Owen. Mod. Geol. 18, 319–329 (1993).
    Google Scholar 
    Varricchio, D. J. Bone microstructure of the upper cretaceous theropod dinosaur Troodon formosus. J. Vertebr. Paleontol. 13, 99–104 (1993).
    Google Scholar 
    Horner, J. R., De Ricqlès, A. & Padian, K. Long bone histology of the hadrosaurid dinosaur Maiasaura peeblesorum: Growth dynamics and physiology based on an ontogenetic series of skeletal elements. J. Vertebr. Paleontol. 20 (1), 115–129 (2000).
    Google Scholar 
    Erickson, G. M. Assessing dinosaur growth patterns: A microscopic revolution. Trends Ecol. Evol. 20, 677–684. (2005). https://doi.org/10.1016/j.tree.2005.08.012
    Google Scholar 
    Sander, M. Long bone histology of the Tendaguru sauropods: Implications for growth and biology. Paleobiology 26 (3), 466–488 (2000).
    Google Scholar 
    Woodward, H. N., Fowler, E. A. F., Farlow, J. O. & Horner, J. R. Maiasaura, a model organism for extinct vertebrate population biology: A large sample statistical assessment of growth dynamics and survivorship. Paleobiology 41, 503–527 (2015).
    Google Scholar 
    Bybee, P. J., Lee, A. H. & Lamm, E. T. Sizing the jurassic theropod dinosaur Allosaurus: Assessing growth strategy and evolution of ontogenetic scaling of limbs. J. Morphol. 267, 347–359. (2006). https://doi.org/10.1002/jmor.10406
    Google Scholar 
    Cullen, T. M. et al. Growth variability, dimensional scaling, and the interpretation of osteohistological growth data. Biol. Lett. 17, 20210383 (2021).
    Google Scholar 
    Cullen, T. M., Evans, D. C., Ryan, M. J., Currie, P. J. & Kobayashi, Y. Osteohistological variation in growth marks and osteocyte lacunar density in a theropod dinosaur (Coelurosauria: Ornithomimidae). BMC Evol. Biol. 14, 231 (2014).
    Google Scholar 
    Cerda, I. A., Pol, D., Otero, A. & Chinsamy, A. Palaeobiology of the early sauropodomorph Mussaurus patagonicus inferred from its long bone histology. Palaeontology 65, e12614 (2022).
    Google Scholar 
    SchuchtP.J., Klein, N. & Lambertz, M. What’s my age again? On the ambiguity of histology-based skeletochronology. Proc. R. Soc. B. 288, 20211166 (2021).
    Google Scholar 
    Bruce, R. C., Castanet, J. & Francillon-Vieillot, H. Skeletochronological analysis of variation in age structure, body size, and life history in three species of desmognathine salamanders. Herpetologica 58, 181–193 (2002).
    Google Scholar 
    Nacarino-Meneses, C. & Köhler, M. Limb bone histology records birth in mammals. PloS One. 13, e0198511 (2018).
    Google Scholar 
    Woolley, M. R., Chinsamy, A., Govender, R. & Bester, M. N. Microanatomy and histology of bone pathologies of extant and extinct phocid seals. Hist. Biol. 33 (8), 1231–1246 (2019).
    Google Scholar 
    Calderón, T., Arnold, W., Stalder, G., Painer, J. & Köhler, M. Labelling experiments in red deer provide a general model for early bone growth dynamics in ruminants. Sci. Rep. 11, 14074 (2021).
    Google Scholar 
    Klevezal, G. A. & Kleinenberg, S. E. Age Determination of Mammals from Annual Layers in Teeth and Bones. (Translated from Russian by Salkind J.) (Israel Program for Scientific Translations Press, Jerusalem, 1969).Köhler, M. et al. Insular giant leporid matured later than predicted by scaling. Iscience 26, 107654 (2023).
    Google Scholar 
    D’Emic, M. D. et al. Developmental strategies underlying gigantism and miniaturization in non-avialan theropod dinosaurs. Science 379, 811–814 (2023).
    Google Scholar 
    Chinsamy, A. R. Preparation of fossil bone for histological examination. Palaeontol. Afr. 29, 39–44 (1992).
    Google Scholar 
    Castanet, J. & Baez, M. Adaptation and evolution in Gallotia lizards from the Canary islands: Age, growth, maturity and longevity. Amphibia-Reptilia 12, 81–102 (1991).
    Google Scholar 
    Larriera, A. & Imhof, A. Proyecto yacaré. Manejo de Fauna Silvestre en Argentina. Ministerio de Salud y Ambiente de la Nación, Buenos Aires, 51–64 (2006).Viotto, E. V., Simoncini, M. S., Verdade, L. M., Navarro, J. L. & Piña, C. Winter survivorship of hatchling broad-snouted Caimans (Caiman latirostris) in Argentina. Ethnobiol. Conserv. 11 (2022).Petter-Rousseaux, A. Recherches Sur La croissance et Le cycle d’activité testiculaire de natrix natrix helvetica (Lacépède). Revue d’Écologie (La Terre Et La. Vie). 7, 175–223 (1953).
    Google Scholar 
    Saint Girons, H. Les critères d’âge Chez les reptiles et leurs applications à l’étude de La structure des populations sauvages. Revue d’Écologie, 342–358 (1965).Heck, C. T. & Woodward, H. N. Intraskeletal bone growth patterns in the North Island brown Kiwi (Apteryx mantelli): Growth mark discrepancy and implications for extinct taxa. J. Anat. 239, 1075–1095 (2021).
    Google Scholar 
    Collins, E. P. & Rodda, G. H. Bone layers associated with ecdysis in laboratory-reared Boiga irregularis (Colubridae). J. Herpetol. 28, 378–381 (1994).
    Google Scholar 
    Castanet, J. Les méthodes d’estimation de l’age Chez les chéloniens. Mesogee 48, 21–28 (1988).
    Google Scholar 
    de Buffrénil, V. & Castanet, J. Age Estimation by skeletochronology in the Nile monitor (Varanus niloticus), a highly exploited species. J. Herpetol. 34, 414–424 (2000).
    Google Scholar 
    Castanet, J., Rogers, K. C., Cubo, J. & Boisard, J. J. Periosteal bone growth rates in extant ratites (ostriche and emu). Implications for assessing growth in dinosaurs. C. R. Acad. Sci. 323, 543–550 (2000).
    Google Scholar 
    Starck, J. M. & Chinsamy, A. Bone microsructure and developmental plasticity in birds and other dinosaurs. J. Morphol. 254, 232–246 (2002).
    Google Scholar 
    Montes, L., Castanet, J. & Cubo, J. Relationship between bone growth rate and bone tissue organization in amniotes: First test of Amprino’s rule in a phylogenetic context. Anim. Biol. 60, 25–41 (2010).
    Google Scholar 
    Cubo, J. & Laurin, M. Perspectives on vertebrate evolution: Topics and problems. C.R. Palevol. 10, 285–292. (2011). https://doi.org/10.1016/j.crpv.2011.05.007
    Google Scholar 
    Montoya-Sanhueza, G., Bennett, N. C., Oosthuizen, M. K., Dengler‐Crish, C. M. & Chinsamy, A. Bone remodeling in the longest living rodent, the naked mole‐rat: Interelement variation and the effects of reproduction. J. Anat. 239 (1), 81–100 (2021).
    Google Scholar 
    Schlief, S. C., Richman, J. M. & Brink, K. S. Bone labeling experiments and intraskeletal growth patterns in captive Leopard geckos (Eublepharis macularius). J. Anat. 247 (3-4), 542–555 (2024).
    Google Scholar 
    Maloney, S. K. et al. Minimum daily core body temperature in Western grey kangaroos decreases as summer advances: A seasonal pattern, or a direct response to water, heat or energy supply? J. Exp. Biol. 214, 1813–1820 (2011).
    Google Scholar 
    Jacobsen, T. & Kushlan, J. A. Growth dynamics in the American alligator (Alligator mississippiensis). J. Zool. Lond. 219, 309–328 (1989).
    Google Scholar 
    Wilkinson, P. M. & Rhodes, W. E. Growth rates of American alligators in coastal South Carolina. J. Wildl. Manag. 61, 397–402 (1997).
    Google Scholar 
    Brito, J. C., Martinez-Freiria, F., Sierra, P., Sillero, N. & Tarroso, P. Crocodiles in the Sahara desert: An update of distribution, habitats and population status for conservation planning in Mauritania. PLoS One. 6, e14734 (2011).
    Google Scholar 
    Caetano, M. H. Use and results of skeletochronology in some urodeles (Triturus marmoratus, Latreille 1800 and Triturus boscai, lataste 1879. Ann. des. Sci. Nat. Zool. 11, 197–199 (1990).
    Google Scholar 
    Webb, G., Manolis, S. & Buckworth, R. Crocodylus Johnstoni in the McKinlay river area N. T, III.* Growth, movement and the population age structure. Wildl. Res. 10, 383–401 (1983).
    Google Scholar 
    Sander, P. M. & Klein, N. Developmental plasticity in the life history of a prosauropod dinosaur. Science 310, 1800–1802 (2005).
    Google Scholar 
    Chapelle, K. E., Botha, J. & Choiniere, J. N. Extreme growth plasticity in the early branching sauropodomorph Massospondylus carinatus. Biol. Lett. 17, 20200843 (2021).
    Google Scholar 
    Chinsamy, A., Marugán-Lobón, J., Serrano, F. J. & Chiappe, L. Osteohistology and Life History of the Basal Pygostylian, Confuciusornis sanctus. Anat. Record 303(4), 949–962 (2019).
    Google Scholar 
    Spiekman, S. N., Butler, R. J. & Maidment, S. C. The postcranial anatomy and osteohistology of Terrestrisuchus gracilis (Archosauria, Crocodylomorpha) from the late triassic of Wales. Papers Palaeontol. 10, e1577 (2024).
    Google Scholar 
    Pereyra, E. M., Bona, P., Siroski, P. & Chinsamy, A. Analyzing the life history of caimans: The growth dynamics of Caiman latirostris from an osteohistological approach. J. Morphol. 286, e70010 (2025).
    Google Scholar 
    Chinsamy, A. in Fifth Symposium on Mesozoic Terrestrial Ecosystems and Biota. (ed Z. Kielan-Jaworoska, Natascha Heitz and Hans Arne Nakrem) 13 (Paleontological Museum).Erickson, G. Growth curve of Psittacosaurus mongoliensis Osborn (Ceratopsia: Psittacosauridae) inferred from long bone histology. Zool. J. Linn. Soc. 130, 551–566 (2000). https://doi.org/10.1111/j.1096-3642.2000.tb02201.x
    Google Scholar 
    Erickson, G. M. et al. Gigantism and comparative life-history parameters of tyrannosaurid dinosaurs. Nature 430, 772–775 (2004).
    Google Scholar 
    Woodward, H. N. Maiasaura (Dinosauria: Hadrosauridae) tibia osteohistology reveals Non-annual cortical vascular rings in young of the year. Front. Earth Sci. 7, 50 (2019). https://doi.org/10.3389/feart.2019.00050
    Google Scholar 
    Horner, J. R. & Padian, K. Age and growth dynamics of Tyrannosaurus. Rex. Proc. Biol. Sci. 271, 1875–1880 (2004). https://doi.org/10.1098/rspb.2004.2829
    Google Scholar 
    Cullen, T. M., Simon, D. J., Benner, E. K. & Evans, D. C. Morphology and osteohistology of a large-bodied caenagnathid (Theropoda, Oviraptorosauria) from the hell creek formation (Montana): implications for size‐based classifications and growth reconstruction in theropods. Papers Palaeontol. 7, 751–767 (2021).
    Google Scholar 
    Kolb, C. et al. Growth in fossil and extant deer and implications for body size and life history evolution. BMC Evol. Biol. 15, 19 (2015). https://doi.org/10.1186/s12862-015-0295-3
    Google Scholar 
    Curry Rogers, K., Whitney, M., D’Emic, M. & Bagley, B. Precocity in a tiny titanosaur from the cretaceous of Madagascar. Science 352, 450–453 (2016).
    Google Scholar 
    Horner, J. R., Ricqlès, A. & Padian, K. Variation in dinosaur skeletochronology indicators: implications for age assessment and physiology. Paleobiology 25 (3), 295–304 (1999).
    Google Scholar 
    Campbell, D. L., Hewitt, L., Lee, C., Timmerhues, C. A. & Small, A. H. Behaviours of farmed saltwater crocodiles (Crocodylus porosus) housed individually or in groups. Front. Veterinary Sci. 11, 1394198 (2024).
    Google Scholar 
    Morpurgo, B., Gvaryahu, G. & Robinzon, B. Aggressive behaviour in immature captive nile crocodiles, Crocodylus niloticus, in relation to feeding. Physiol. Behav. 53, 1157–1161 (1993).
    Google Scholar 
    Download referencesAcknowledgementsWe are grateful to Le Bonheur Reptiles and Adventures for permitting access to the crocodiles investigated here. Aurore Canoville and Andrea Plos are warmly thanked for assisting with fieldwork. Vidushi Dabee is acknowledged for having prepared some of the thin sections. We thank Viantha Naidoo and Dirk Lang at the Confocal and Light Microscope Imaging Facility of the Faculty of Health Sciences at UCT. Shafi M. Bhat of the Department of Geosciences at Auburn University, Alabama, is acknowledged for having read an earlier draft of this manuscript. Devin Hoffman and two additional anonymous reviewers are thanked for their comments. The University of Cape Town Research Committee (URC) is thanked for the postdoctoral fellowship awarded to the second author.Author informationAuthors and AffiliationsDepartment of Biological Sciences, University of Cape Town, Private Bag, Rhodes Gift, Rondebosch, 7700, South AfricaAnusuya Chinsamy & Maria-Eugenia PereyraAuthorsAnusuya ChinsamyView author publicationsSearch author on:PubMed Google ScholarMaria-Eugenia PereyraView author publicationsSearch author on:PubMed Google ScholarContributionsAC conceived and designed the project and administered the fluorochrome labelling to the crocodiles. M-EP and AC analysed the histological thin sections, and both contributed to the data interpretation and analysis.  M-EP did the confocal and petrographic micrographs and figures for the manuscript. AC wrote the first draft, and M-EP contributed to the write up and made important suggestions. Both authors approved the final version of the manuscript.Corresponding authorCorrespondence to
    Anusuya Chinsamy.Ethics declarations

    Competing interests
    The authors declare no competing interests.

    Additional informationPublisher’s noteSpringer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.Supplementary InformationBelow is the link to the electronic supplementary material.Supplementary Material 1Supplementary Material 2Rights and permissions
    Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
    Reprints and permissionsAbout this articleCite this articleChinsamy, A., Pereyra, ME. Stochastic growth marks in Crocodylus niloticus.
    Sci Rep (2025). https://doi.org/10.1038/s41598-025-31384-5Download citationReceived: 28 July 2025Accepted: 02 December 2025Published: 18 December 2025DOI: https://doi.org/10.1038/s41598-025-31384-5Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy shareable link to clipboard
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    Author Correction: Sociality predicts orangutan vocal phenotype

    Correction to: Nature Ecology & Evolution https://doi.org/10.1038/s41559-022-01689-z, published online 21 March 2022.After publication of the article, an error was identified in the data entry of the maximum frequency parameter for the Suaq orangutan population. Recalculation of entropy measures and reanalysis of the mixed models revealed that, for maximum frequency, the previously reported effect of sociality is no longer statistically supported (Emergence and self-organization: F = 0.321, P = 0.573; Complexity: F = 0.009, P = 0.927). The original results for duration remain unchanged and continue to show a significant effect of sociality. While the loss of statistical support for one parameter is regrettable, the revised findings are scientifically meaningful. They align with recent findings in chimpanzees1, showing that control over vocal parameters such as frequency and duration may operate independently. This suggests that social influences on vocal phenotypes may target specific acoustic features, and that specific populations may deploy features of vocal novelty in culturally localized ways.The corrected analysis further reaffirms key methodological points raised in our original paper. In entropy-based analyses of behavioural novelty, low-probability events—sometimes mischaracterized as ‘outliers’—are not statistical noise but the core phenomena of interest. Their removal would bias entropy estimates and undermine the capacity to detect innovation. Given the nature of our study—multi-year, multi-site, and focused on a critically endangered species—each data point represents an irreplaceable behavioural observation. Removing such points without clear justification raises ethical concerns, including violation of IUCN data integrity guidelines and FAIR/TRUST data stewardship principles2,3. Our approach illustrates how ethical and methodological rigour must go hand-in-hand when working with vulnerable wild populations.For the calculation of entropy values from continuous acoustic data, equal-width binning at the individual level remains a necessary and appropriate step4. Our binning approach was selected to capture vocal originality at the level of individual phenotypes—what we term “vocal personalities”—in response to social input. Other binning choices, such as a global binning, would be unable to distinguish between individual differences and novelty; benchmarking individuals against each other would be an analysis of group conformity, not of individual originality or vocal personality.The Supplementary Information accompanying this amendment includes the original, uncorrected article for comparison (changes have been made to the Results and discussion, Methods, Table 1 and Fig. 2). Supplementary Data 3–5 have also been corrected and are available alongside the original article.The authors would like to thank Peng-Fei Fan and Zi-Di Wang for intially bringing the issue to their attention.

    ReferencesLameira, A. R., Caneco, B., Kershenbaum, A., Santamaría-Bonfil, G. & Call, J. Generative vocal plasticity in chimpanzees. iScience 112381 (2025).Wilkinson, M. D. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data 3, 160018 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lin, D. et al. The TRUST Principles for digital repositories. Sci. Data 7, 144 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Santamaría-Bonfil, G., Fernández, N. & Gershenson, C. Measuring the complexity of continuous distributions. Entropy 18, 72 (2016).Article 

    Google Scholar 
    Download referencesAuthor informationAuthors and AffiliationsDepartment of Psychology, University of Warwick, Coventry, UKAdriano R. LameiraSchool of Psychology and Neuroscience, University of St Andrews, St Andrews, UKAdriano R. LameiraInstituto Nacional de Electricidad y Energías Limpias, Gerencia de Tecnologías de la Información, Cuernavaca, MéxicoGuillermo Santamaría-BonfilDepartment of Life Sciences and Systems Biology, University of Torino, Turin, ItalyDeborah Galeone & Marco GambaIndependent researcher, Warwick, UKMadeleine E. HardusDepartment of Anthropology, Boston University, Boston, MA, USACheryl D. KnottBorneo Nature Foundation, Palangka Raya, IndonesiaHelen Morrogh-BernardCollege of Life and Environmental Sciences, University of Exeter, Penryn, UKHelen Morrogh-BernardThe PanEco Foundation—Sumatran Orangutan Conservation Programme, Berg am Irchel, SwitzerlandMatthew G. NowakDepartment of Anthropology, Southern Illinois University, Carbondale, IL, USAMatthew G. NowakYayasan Inisiasi Alam Rehabilitasi Indonesia, International Animal Rescue, Ketapang, IndonesiaGail Campbell-SmithSchool of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UKSerge A. WichFaculty of Science, University of Amsterdam, Amsterdam, NetherlandsSerge A. WichAuthorsAdriano R. LameiraView author publicationsSearch author on:PubMed Google ScholarGuillermo Santamaría-BonfilView author publicationsSearch author on:PubMed Google ScholarDeborah GaleoneView author publicationsSearch author on:PubMed Google ScholarMarco GambaView author publicationsSearch author on:PubMed Google ScholarMadeleine E. HardusView author publicationsSearch author on:PubMed Google ScholarCheryl D. KnottView author publicationsSearch author on:PubMed Google ScholarHelen Morrogh-BernardView author publicationsSearch author on:PubMed Google ScholarMatthew G. NowakView author publicationsSearch author on:PubMed Google ScholarGail Campbell-SmithView author publicationsSearch author on:PubMed Google ScholarSerge A. WichView author publicationsSearch author on:PubMed Google ScholarCorresponding authorCorrespondence to
    Adriano R. Lameira.Supplementary informationOriginal, uncorrected articleRights and permissions
    Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
    Reprints and permissionsAbout this articleCite this articleLameira, A.R., Santamaría-Bonfil, G., Galeone, D. et al. Author Correction: Sociality predicts orangutan vocal phenotype.
    Nat Ecol Evol (2025). https://doi.org/10.1038/s41559-025-02954-7Download citationPublished: 18 December 2025Version of record: 18 December 2025DOI: https://doi.org/10.1038/s41559-025-02954-7Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy shareable link to clipboard
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    De novo assembly of complete circular mitochondrial genomes from 2,695 fungal species

    AbstractFungal mitochondrial genomes are critical for understanding phylogenetics, evolution, and ecology of the Kingdom Fungi, yet they remain underrepresented in public databases. To address this, we developed a workflow to recover mitochondrial genomes from 12,902 fungal short read sequencing data housed in the Sequence Read Archive (SRA) records, assembling complete circular genomes from 2,695 species. This effort expanded fungal mitochondrial genome diversity by nearly 2.3X particularly in understudied phyla such as Mucoromycota (11X increase) and Zoopagomycota (8X increase). The new dataset contains novel yet undescribed mitochondrial genomes at numerous taxonomic levels, including 15 classes, 64 orders, 178 families, and 544 genera. Taxonomic analysis revealed broad ecological representation among the top-assembled species, including human pathogens (e.g., Cryptococcus tetragattii), plant pathogens (e.g., Melampsora larici-populina), edible mushrooms (e.g., Suillus luteus), and industrial fungi. By leveraging the not yet fully exploited SRA sequencing data, this study fills critical gaps in fungal mitochondrial genomics, tripling the currently known mitochondrial genome diversity of the Kingdom Fungi, and provides an extensive resource for phylogenetic and evolutionary research.

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    Code availability

    The assembly workflow was implemented in a python script (assembly_workflow.py) passing SRA run accession as input and outputting the assembly contigs and graphs, which are used by GetOrganelle for mitochondrial genome extraction (Methods). The script uses already published tools and explained in the Methods section. The script is available on GitHub at https://github.com/msabrysarhan/fungal_mtDNA.
    Data availability

    Nucleotide sequence data reported are available in the Third Party Annotation Section of the DDBJ/ENA/GenBank databases under the BioProject PRJNA1367877 and the accession numbers TPA: BK072095-BK074789, and the metadata is available at https://doi.org/10.6084/m9.figshare.28750034.
    ReferencesHawksworth, D. L. & Lücking, R. J. M. s. Fungal diversity revisited: 2.2 to 3.8 million species. 5, https://doi.org/10.1128/microbiolspec. funk-0052-2016 (2017).Paterson, R. R. M., Solaiman, Z. & Santamaria, O. J. S. R. Guest edited collection: fungal evolution and diversity. 13, 21438 (2023).James, T. Y., Stajich, J. E., Hittinger, C. T. & Rokas, A. J. A. R. O. M. Toward a fully resolved fungal tree of life. 74, 291-313 (2020).Chethana, K. T. et al. What are fungal species and how to delineate them? 109, 1-25 (2021).Li, Y. et al. A genome-scale phylogeny of the kingdom Fungi. 31, 1653-1665. e1655 (2021).Kouvelis, V. N., Kortsinoglou, A. M., James, T. Y. J. E. o. F. & Organisms, F.-L. The evolution of mitochondrial genomes in fungi. 65-90 (2023).Kulik, T., Van Diepeningen, A. D. & Hausner, G. J. F. i. M. Vol. 11 628579 (Frontiers Media SA, 2021).Song, N., Geng, Y. & Li, X. J. F. i. M. The mitochondrial genome of the phytopathogenic fungus Bipolaris sorokiniana and the utility of mitochondrial genome to infer phylogeny of Dothideomycetes. 11, 863 (2020).Zhang, S. et al. Dynamic evolution of eukaryotic mitochondrial and nuclear genomes: a case study in the gourmet pine mushroom Tricholoma matsutake. 23, 7214-7230 (2021).Sauters, T. J. & Rokas, A. J. C. B. Patterns and mechanisms of fungal genome plasticity. 35, R527-R544 (2025).Jung, H. et al. Twelve quick steps for genome assembly and annotation in the classroom. 16, e1008325 (2020).Persoons, A. et al. Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina identify pathogenesis-related factors. 5, 450 (2014).Schoch, C. L. et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. 2020, baaa062 (2020).Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890, https://doi.org/10.1093/bioinformatics/bty560 (2018).
    Google Scholar 
    Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome research 27, 824–834 (2017).
    Google Scholar 
    Jin, J.-J. et al. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology 21, 241, https://doi.org/10.1186/s13059-020-02154-5 (2020).
    Google Scholar 
    Lang, B. F. et al. Mitochondrial genome annotation with MFannot: a critical analysis of gene identification and gene model prediction. 14, 1222186 (2023).Katoh, K. & Standley, D. M. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution 30, 772–780, https://doi.org/10.1093/molbev/mst010 (2013).
    Google Scholar 
    Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. J. B. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. 25, 1972-1973 (2009).Borowiec, M. L. J. P. AMAS: a fast tool for alignment manipulation and computing of summary statistics. 4, e1660 (2016).Price, M. N., Dehal, P. S. & Arkin, A. P. J. P. O. FastTree 2–approximately maximum-likelihood trees for large alignments. 5, e9490 (2010).Sarhan, M. S., Abdalrahem, A., Maixner, F. & Fuchsberger, C. NCBI GenBank https://identifiers.org/ncbi/bioproject:PRJNA1367877 (2025).Sarhan, M. S., Abdalrahem, A., Maixner, F. & Fuchsberger, C. De novo assembly of complete circular mitochondrial genomes from 2,695 fungal species. figshare https://doi.org/10.6084/m9.figshare.28750034 (2025).Fonseca, P. L. et al. Global characterization of fungal mitogenomes: new insights on genomic diversity and dynamism of coding genes and accessory elements. 12, 787283 (2021).Wijayawardene, N. N. et al. Classes and phyla of the kingdom Fungi. 128, 1-165 (2024).Download referencesAcknowledgementsThis work was supported by the “MOC – MultiOmics Centre for Food and Health” project. The MOC project is co-funded by the European Union (European Regional Development Fund – EFRE). Ammar Abdalrahem was supported by a PhD fellowship from the French Ministry of Education and Research (MESR) and by the French Plan Investissement d’Avenir (PIA) Lab of Excellence ARBRE [ANR-11-LABX-0002- 01]. The authors thank the Department of Innovation, Research and University of the Autonomous Province of Bozen/Bolzano, Italy for covering the Open Access publication costs.Author informationAuthors and AffiliationsInstitute for Biomedicine, Eurac Research, Bolzano, 39100, ItalyMohamed S. Sarhan & Christian FuchsbergerDepartment CIBIO, University of Trento, Trento, ItalyMohamed S. SarhanUniversité de Lorraine, INRAE, IAM, F-54000, Nancy, FranceAmmar AbdalrahemPHIM, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, FranceAmmar AbdalrahemInstitute for Mummy Studies, Eurac Research, Bolzano, 39100, ItalyFrank MaixnerAuthorsMohamed S. SarhanView author publicationsSearch author on:PubMed Google ScholarAmmar AbdalrahemView author publicationsSearch author on:PubMed Google ScholarFrank MaixnerView author publicationsSearch author on:PubMed Google ScholarChristian FuchsbergerView author publicationsSearch author on:PubMed Google ScholarContributionsM.S.S. conceived the original idea. M.S.S. and A.A. designed and performed the computational analysis. M.S.S. performed the data visualization and wrote the first draft of the manuscript. M.S.S. and A.A. curated the data for public deposition. F.M. and C.F. edited and revised the manuscript. All authors read and approved the final version of the manuscript.Corresponding authorCorrespondence to
    Mohamed S. Sarhan.Ethics declarations

    Competing interests
    The authors declare no competing interests.

    Additional informationPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.Rights and permissions
    Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
    Reprints and permissionsAbout this articleCite this articleSarhan, M.S., Abdalrahem, A., Maixner, F. et al. De novo assembly of complete circular mitochondrial genomes from 2,695 fungal species.
    Sci Data (2025). https://doi.org/10.1038/s41597-025-06447-xDownload citationReceived: 10 April 2025Accepted: 09 December 2025Published: 18 December 2025DOI: https://doi.org/10.1038/s41597-025-06447-xShare this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy shareable link to clipboard
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    Telemetry reveals potential mating aggregation behavior of tiger sharks (Galeocerdo cuvier) in Hawaiʻi

    AbstractTiger sharks (Galeocerdo cuvier) are typically solitary marine predators that are rarely observed forming aggregations. We analyzed long-term acoustic telemetry data from the Hawaiian Archipelago that indicate that there are seasonal partial migrations within the population. We investigated whether these migrations are driven primarily by mating or foraging behaviors. Mature tiger sharks tagged around O ‘ahu migrated seasonally to Maui, with timing aligned with the known mating season in Hawai ‘i. In contrast, sharks tagged around Maui displayed year-round residency (no seasonal departures). Seasonal philopatry was most pronounced at Olowalu, Maui. At this site, we observed a high spatiotemporal overlap between mature males and females and physical signs of mating activity for both sexes, which suggested a mating aggregation. Shark abundance at Olowalu peaked approximately one month prior to the peak presence of adult humpback whales (Megaptera novaeangliae). Whale calf abundance was moderately correlated with shark detection rates, suggesting that foraging opportunities might also influence the timing of shark aggregations. These aggregations appear diffuse rather than dense, extending over several kilometers and persisting for several weeks. Our findings provide the first evidence of potential seasonal mating aggregations in tiger sharks, a behavior previously undocumented for this typically solitary species.

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    IntroductionTiger sharks (Galeocerdo cuvier) are marine top predators that play a crucial role in ecosystem function across their temperate and tropical circumglobal distribution1,2,3. By regulating prey abundance and behavior, suppressing mesopredators, scavenging large carrion, and transporting nutrients across habitats, they influence community structure and cross-ecosystem energy flow4,5. They are typically solitary in nature and rarely form aggregations except in the context of feeding events or possibly in gestation-related groupings6,7,8,9,10,11. Significant knowledge gaps remain in our understanding of their spatial ecology, especially regarding seasonal movements, reproductive behavior, and the occurrence of aggregations3. Although tiger sharks are known to mate seasonally12,13 it is unclear whether mating relies on opportunistic encounters between males and females, whether they aggregate at specific sites, or whether both factors contemporaneously drive their reproductive strategies. This lack of understanding complicates the identification of key habitats and hinders the prediction of behaviors that are important for informing their conservation and management.Meyer et al.14 observed increases in tiger shark presence around Maui that align with the mid-winter mating season, suggesting a possible link to reproductive behavior. However, the observed detection peaks may instead reflect foraging, as tiger sharks in other regions aggregate in response to seasonal prey pulses such as fledgling seabirds and nesting sea turtles5,15. Waters surrounding Maui also experience an influx of humpback whales (Megaptera novaeangliae) during the winter months16, offering potential seasonal scavenging opportunities from whale carcasses, placental remains, or neonate calves17,18,19. The coincidence of Hawaiʻi’s tiger shark mating season with the humpback whale arrival period makes it difficult to distinguish movements driven by mating from those linked to whale-related foraging.Meyer et al.14tagged tiger sharks with long-lasting acoustic tags, collecting a continuous six-year time series of detections around Maui and O ‘ahu from 2013 to 2019. This extensive dataset provides an unprecedented opportunity to assess whether seasonal movements to Maui are driven by mating, by foraging, or a combination of the two, as these may not be mutually exclusive activities. Tiger sharks could utilize the shelf of Maui Nui (the region encompassing the islands of Maui, Moloka ‘i, Lānaʻi, and Kahoʻolawe), for both purposes, and both could produce similar patterns of acoustic detections (i.e. clusters of individuals in space and time). The maturity status of the sharks present, as well as the temporal predictability of the clusters could provide further insight into the function of these aggregations. For example, a mating aggregation requires sexually mature adults of both sexes to be present simultaneously at a predictable time each year (tiger shark size at first reproduction: males ~ 292 cm TL, females ~ 330 cm TL13;). In contrast, a cluster of detections consisting of only one sex and/or immature individuals that closely tracks prey abundance may be more indicative of foraging activity.In this study we addressed five questions: (1) Do tiger sharks tagged around O ‘ahu and Maui exhibit repeated inter-island movements? (2) Are these movements seasonal? (3) What are the demographics of seasonal inter-island migrants? (4) Do specific Maui sites show seasonal shark aggregations and overlapping use by both sexes? (5) Does tiger shark seasonal presence correlate with humpback whale indicators (song intensity and calf counts)? By addressing these questions, we aim to clarify the ecological drivers behind tiger shark movements and possible aggregations, thereby advancing our understanding of tiger shark behavior and identifying potentially important habitats in the Hawaiian Islands.MethodsStudy siteThe Main Hawaiian Islands (MHI) consist of eight high volcanic islands. Shark capture and tagging efforts in this study were concentrated around O ‘ahu and Maui (Fig. 1). The MHI are each bordered by an insular shelf that gradually descends from the shoreline to a shelf break, occurring at depths between 100 and 200 m (Fig. 1). The width of this insular shelf differs across the islands, with the Maui Nui complex (Maui, Moloka ‘i, Lānaʻi, and Kahoʻolawe) having a more extensive shelf than the islands of Ni ‘ihau, Kaua ‘i, O ‘ahu, and Hawai ‘i combined (Fig. 1). The insular shelf hosts a variety of photic and mesophotic coral reefs, macroalgal beds, and sandy habitats20,21, and is the preferred habitat for tiger sharks in Hawaii waters14.Fig. 1Bathymetry of the Main Hawaiian Islands highlighting the insular shelf between depths of zero and 200 m (red shaded areas).Full size imageOlowalu, on Maui’s west coast (Fig. 2), features a diverse benthic habitat (coral reefs, sandy bottom, macroalgal beds) and a gentle slope to ~ 60 m depth22,23,24. Importantly, Olowalu’s sheltered waters host breeding, calving, and nursing humpback whales during their overwintering period25,26,27, making it an important seasonal habitat for this whale population.Fig. 2Receiver locations (red diamonds) around Maui (a) and O ‘ahu (b). Six sites with the most consistent temporal coverage are represented by solid filled red diamonds.Full size imageAcoustic monitoring systemWe used Vemco VR2W acoustic receivers (69 kHz frequency) to monitor tiger shark presence around Maui and O ‘ahu. These small, self-contained underwater receivers (∼ 34 cm length, 6 cm diameter) detect coded acoustic transmitters. Each tagged shark carried a V16-6H transmitter (16 × 94 mm, 14 g in water) that emits a unique ‘ping’ sequence lasting 3–5 s, with a random silent interval of 20–230 s between sequences. Each decoded transmission is logged by receivers with a timestamp and the shark’s ID code. Transmitters had nominal battery lives of 2–10 years (10-year tags were used on Maui sharks; O ‘ahu sharks had mixed 2–10 year tags), enabling multi-year tracking.We determined receiver detection ranges using a boat-mounted Vemco VR100 hydrophone and test transmitters. We dropped a transmitter from the surface directly above each VR2W receiver, recorded ~ 10 transmissions, then incrementally moved ~ 100 m away (up to 1.5 km) and repeated. By cross-referencing the VR100 GPS log with detections recorded on the stationary VR2W, we identified that VR2W receivers could detect tags at distances up to ~ 900 m.We deployed receivers at twenty-six monitoring sites around Maui (15 sites total, with data recovered from 14) and O ‘ahu (12 sites) (Fig. 2). The array spanned the depth range of the insular shelf, with inshore units deployed at depths of 5 to 20 m and offshore units deployed in deeper waters (100 to 200 m) up to several kilometers offshore. This array design allowed for the comparison of tiger shark presence between deep and shallow areas, between different coasts of the same island, and between Maui and O ‘ahu. Receivers were actively monitoring around Maui from October 2013 until April 2019, and around O ‘ahu throughout and beyond this period. Receivers were deployed on subsurface moorings.Shark capture and taggingShark handling and tagging activities were carried out in accordance with the animal use protocols of the University of Hawai’i at Manoa Institutional Animal Care and Use Committee (IACUC) and were approved under IACUC protocol #05–053. Sharks were captured and tagged around Maui from Oct 2013 to Feb 2015 (26 individuals: 3 M, 23 F) and around O ‘ahu from Apr 2013 to Oct 2018 (16 individuals: 6 M, 10 F). In addition, 17 ‘legacy’ tiger sharks (3 M, 14 F) originally tagged off O ‘ahu prior to this study were still transmitting during all or part of the monitoring period covered by the Maui receiver array. Following the methods of Meyer et al.14, we used demersal longlines baited with large tuna heads, which soaked for 2–4 h at depths of 10–100 m. Targeting these shallower depths typically resulted in a strong female bias in capture rates, as tiger sharks in Hawaiʻi exhibit sexual segregation—with females more commonly occupying nearshore habitats and males more frequently found offshore14. Captured sharks were brought alongside a 6 m skiff, tail-roped, and placed into tonic immobility by inversion. Acoustic transmitters were surgically implanted into the body cavity through a small incision in the abdominal wall, and the incision was closed with interrupted sutures28. Sharks were also tagged with unique external identification tags (Hallprint, Hindmarsh Valley, Australia), then released. The use of internal acoustic transmitters is widespread in shark movement studies and has been shown to have minimal impact on the study subjects29. The size of our acoustic transmitters was small (16 × 94 mm, weight in water 14 g) compared to the size range of the sharks tagged (183–464 cm TL), and surgical implantation procedures were quick and efficient (between 5 and 15 min duration). Our use of tonic immobility as an anesthetic has several advantages, including: rapid induction, minimal disruption to respiration, and immediate and full recovery30. Tiger sharks have been shown to be especially resilient to capture stress. Post-release mortality (PRM) in tiger sharks is very low (0–2% observed31,32,33,34;), and they rank as the least disturbed shark species in terms of capture stress35.Field observationsSharks captured in the field were photo-documented for evidence of recent mating activity, characterized as clasper abrasions or chafing on males and tooth gouges on females.Data analysisMaui receiver site selectionWe used a Gantt chart (Fig. S1) to visualize receiver deployment timelines and identify core sites with the longest continuous monitoring periods and the greatest temporal overlap. Limiting analyses to these core sites enabled us to compare seasonal patterns across the full six years of the study. Of the 14 receiver sites around Maui, six had the most consistent coverage throughout the monitoring period: Kalama Deep, Mākena Pt., Olowalu Shallow, Kalama Shallow, Honokōwai Shallow, and Palauea Shallow (Fig. 2). These sites were selected as the focus for further comparative analyses.Seasonal migration patterns and demography (Rayleigh and F-tests)We conducted a Rayleigh test using the R (v4.4.3; R Core Team 2025) package ‘circular’36 to evaluate whether seasonal migratory patterns differed between sharks captured and tagged around Maui and O ‘ahu. First, we calculated the total observed number of unique individuals from each tagging location (Maui or O ‘ahu) detected around Maui each month. The Rayleigh test identifies departures from uniformity in circular data, where one calendar year is represented as a complete circle. Under the null hypothesis of no seasonal migration, shark detections would be uniformly distributed across months (equal in each month). This test also assumes that any departure from the null hypothesis will be unimodal reflecting a single peak in the distribution. In addition to the Rayleigh test, we calculated the coefficient of variation, variance, and standard deviation to quantify the variability in the number of sharks detected each month for Maui- and O ‘ahu-tagged individuals. These statistics provided insight into the degree of seasonal variation, where high variability in the monthly number of sharks detected may indicate shifts in habitat use and possibly migratory behavior. We used an F-test to compare the variances between the two tagging locations, assessing whether the seasonal variation in the number of sharks detected monthly around Maui differed between Maui and O ‘ahu-tagged individuals. The maturity status of sharks making inter-island movements was determined using the estimated size at first detection, derived from capture size and adjusted based on average annual growth rates for Hawaiian tiger sharks (from37) (Table 1).Table 1 Sex, original tagging date, date of first Maui detection, total length (TL) at tagging, and estimated TL at first Maui detection for sharks originally captured and tagged around O ‘ahu.Full size tableSeasonal comparison using T-test for paired samples, independent T-test, and Rayleigh testMonths were categorized as “Summer” (April through September) or “Winter” (October through March), and monthly numbers of sharks detected at each receiver site were summed separately for each season. Before conducting the t-test, we verified key assumptions. Normality was assessed using the Shapiro–Wilk and Kolmogorov–Smirnov tests, supported by visual inspections of histograms and Q-Q plots38. Independence of observations was confirmed: for the independent t-test, we ensured no correlation between shark detections across sites39, and for the paired t-test, we verified logical pairing of Summer vs. Winter detections within each site40. Equality of variances was tested with Levene’s test41 and outliers were identified using box plots and z-scores42. A paired t-test assessed seasonal differences across all six receiver sites combined, while independent t-tests and Rayleigh tests evaluated seasonal patterns at individual sites. P-values were calculated for each test, and sites were ranked by probability (Tables 2, 3).Table 2 Total unique number, annual mean number (± standard deviation), and p-value of sharks detected during summer and winter at each receiver site.Full size tableTable 3 Rayleigh test of uniformity results for each of the 6 receiver sites, ranked from most to least significant with statistically significant p-values in bold (α = 0.05).Full size tableDiscrete Fourier transformation using fast Fourier transformationTo examine seasonal patterns at the top four ranked receiver sites (Olowalu, Kalama Deep, Kalama Shallow, and Honokōwai), we applied a Discrete Fourier Transformation (DFT) using the Fast Fourier Transformation (FFT) algorithm to time series data representing monthly shark detection counts over the full monitoring period. The DFT converts a time-domain signal into its constituent frequencies, enabling identification of underlying cyclical trends43. The FFT efficiently computes the DFT, allowing rapid analysis of complex temporal signals44. Peaks in the resulting magnitude spectrum indicate dominant frequencies and their corresponding amplitudes, highlighting the strongest periodic patterns in shark detections45.Seasonal trend decomposition using LoessWe used Seasonal Trend Decomposition using Loess (STL) to analyze the time series data of shark detections at Olowalu, the site that showed the most prominent seasonal philopatry. STL is a flexible and robust decomposition method that breaks down time series data into three distinct components: trend, seasonality, and residual46. The trend component reflects the overall direction of the data over time, the seasonality component captures recurring, predictable patterns that occur at fixed intervals (e.g., monthly or yearly), and the residual component represents the random fluctuations or noise that remain after removing the trend and seasonal elements. For our analysis, monthly counts of sharks detected were binned to create the time series data. STL was applied to understand how these counts varied over time, allowing us to distinguish long-term trends and recurring seasonal patterns from random variations.Analysis of diel patterns of shark presence at OlowaluWe used kernel density estimation (KDE)47 to quantify diel overlap in habitat use at Olowalu between male and female tiger sharks. Raw detection data, including detection timestamps, unique transmitter IDs, and sex, were analyzed for the entire monitoring period. To reduce pseudo-replication, we excluded consecutive detections of the same individual at the same receiver within 3 min. From each timestamp, we extracted the hour (0–23) as a numeric column. The kernel density of activity for each sex was estimated in R using the density function, which calculates probability density for activity times and produces a smooth distribution. Both densities were interpolated onto a shared 0–23 h grid and normalized to ensure total probabilities summed to 1 for each sex. Overlap was assessed using the Bhattacharyya Coefficient48, calculated as the sum of square roots of the product of the two densities at each point. This coefficient, ranging from 0 (no overlap) to 1 (perfect overlap), measures distribution similarity. Kernel density estimates were visualized with ggplot249.Median daily root-mean-squared sound pressure levels at Olowalu vs. sharks at OlowaluWe used whale song chorusing data provided by Oceanwide Science Institute’s Ecological Acoustic Recorders (EARs) in the 0.1–1.5 kHz frequency band as a proxy for humpback whale abundance at Olowalu26,27. Median daily root-mean-squared sound pressure levels (RMS SPL) were overlaid with monthly shark detection data at Olowalu to compare the timing of presence and abundance for both species (Fig. 8).To assess time-lagged relationships, we applied a Cross-Correlation Function (CCF) to the monthly maximum RMS SPL and the number of tiger sharks detected per month. This analysis identifies statistically significant correlations and the lag at which they are strongest, revealing whether peaks in shark presence typically precede or follow peaks in acoustic activity.We also conducted a linear regression analysis to directly evaluate the relationship between maximum monthly RMS SPL and monthly tiger shark detections at Olowalu. Model assumptions of normality and homoscedasticity were assessed using residual diagnostic plots. Statistical analyses were performed in R (v4.4.3; R Core Team 2025) using the base lm() function, with significance evaluated at α = 0.05 and model fit assessed via R2 and residual standard error.Land-based humpback whale calf survey data vs. sharks at OlowaluData from land-based visual scan surveys obtained by Kügler et al.27 were used as a proxy for humpback whale calf abundance near Olowalu. Observations were conducted from a cliff site approximately 1 km northwest of Olowalu. Calf counts were normalized by survey effort and overlaid with the monthly time series of tiger shark detections at Olowalu to assess the timing and potential overlap in species presence and abundance.We conducted a linear regression analysis comparing the number of individual tiger sharks detected per month with the average number of whale calves observed per hour, based on multiple daily 30 min scans. Data from 13 months spanning peak whale season (December–April) across three years (2017–2019) were included. Calf observations were normalized to account for variable survey effort. A linear model was fit to test whether monthly variation in tiger shark detections corresponded with changes in calf abundance. Model assumptions of normality and homoscedasticity were assessed using residual diagnostic plots. Statistical analyses were performed in R (v4.4.3; R Core Team 2025) using the base lm() function. Significance was set at α = 0.05, with model fit evaluated using R2 and the residual standard error.We also applied a Cross-Correlation Function (CCF) to the normalized monthly calf averages and tiger sharks detected to assess time-lagged relationships and determine whether peaks in shark presence consistently preceded or followed calf abundance.ResultsOverviewFrom 2013 to 2019, the Maui receiver array detected a total of 44 individual tiger sharks: 8 males (223–408 cm TL) and 36 females (183–464 cm TL). Of these, 21 sharks (48%) had been originally captured and tagged around O ‘ahu (5 of the 8 males and 16 of the 36 females). Detection spans (time between first and last detection on the array) ranged from 1 to 1,990 days (mean = 900 days) for individual sharks, and total detections per shark ranged from 2 to 5,899 (mean = 1,114). Only 5 Maui-tagged tiger sharks were ever detected on the O ‘ahu receiver array, and those detections were sparse (only 3–14 detections each), underscoring the rarity of inter-island movements for Maui-tagged sharks.Broad-scale seasonal movement patternsA comparison of monthly tiger shark detections around Maui revealed significant differences in seasonal patterns between sharks tagged on Maui versus those tagged around O ‘ahu. Sharks tagged around Maui were consistently detected across all months, with no significant seasonal variation in the number of unique individuals detected. In contrast, sharks tagged around O ‘ahu exhibited a clear seasonal cycle, with detections of individuals peaking around Maui in February and reaching their lowest point during the summer months. A Rayleigh test confirmed that detections of Maui-tagged sharks did not deviate significantly from a uniform distribution (R = 0.03, p = 0.71), while O ‘ahu-tagged sharks displayed a significant peak, indicating a non-uniform distribution and demonstrating their seasonal presence around Maui (R = 0.28, p = 0.006) (Fig. 3). Additionally, the coefficient of variation for O ‘ahu-tagged sharks was 49.5% compared to 5.7% for Maui-tagged sharks, indicating much higher variability in O ‘ahu sharks’ detection patterns. The variance of O ‘ahu-tagged sharks detected around Maui was 6.9, reflecting a greater spread from the mean, whereas Maui-tagged sharks had a variance of 1.5. The F-test confirmed a significant difference between the variances of the two groups (F(11,11) = 4.5, p = 0.01). Out of the 21 O ‘ahu-tagged sharks that visited Maui, 14 (67%) were later detected back at O ‘ahu at least once. The maximum number of roundtrips observed for any individual shark between O ‘ahu and Maui was four (Fig. S2). Seven O ‘ahu-tagged sharks were not detected anywhere following their detections around Maui; however, most had previously been detected around O ‘ahu before appearing around Maui. Eight O ‘ahu-tagged individuals (36%) were detected in Maui waters during the tiger shark mating season months (January–February), but only one of those appeared in multiple mating seasons.Fig. 3Total numbers of sharks detected per month on Maui receivers for all years combined. Maui-tagged sharks: sharks originally captured and tagged around Maui. O ‘ahu-tagged sharks: sharks originally captured and tagged around O ‘ahu.Full size imageDemographic patterns of inter-island movementsOf the 21 tiger sharks (16 females and 5 males) captured, tagged in O ‘ahu waters, and later detected around Maui at any time of year, 17 (80%) were sexually mature at the time of their first detection in Maui waters (Table 1). Six individuals were sexually immature when tagged and only detected around Maui after they reached sexual maturity (lengths at detection estimated using tiger shark growth curve from37 and maturity status at detection estimated from maturity data in13), 4 were sexually immature when tagged and still sexually immature when detected, and 11 were sexually mature when initially tagged. Among the 13 O ‘ahu individuals (12 females and 1 male) detected at any Maui receiver site during the peak mating season months of January and February 11 were sexually mature.Evidence for seasonal aggregations at specific Maui locationsThe total number of individuals detected seasonally at each of the 6 core Maui monitoring sites ranged from 8 (Honokowai, summer) to 32 (Kalama Deep, winter) (Table 2). The overall mean number of sharks detected at these sites during winter (25.5 ± 5.68) was significantly higher than during summer (20 ± 6.81) (paired t-test, t = − 4.68, df = 5, p = 0.015). A t-test for independent samples comparing summer and winter means at each site found that all six sites exhibited significantly higher mean shark counts during winter than summer months. However, the level of significance for these seasonal differences varied across sites (Table 2).Aggregate seasonal histograms showing the number of individuals detected in each calendar month across the entire 6 year monitoring period indicate that the seasonal pattern is more clearly defined at Olowalu than at any other site (Fig. 4). Rayleigh tests performed on each individual site confirmed Olowalu as having the most significant peak (Table 3).Fig. 4Aggregate monthly detections of individual sharks at each of the six receiver sites.Full size imageDiscrete Fourier Transforms (DFTs) performed on the four receiver sites with significant p-values revealed a clear peak in amplitude density at a 1-year (annual) frequency for Olowalu (Fig. 5). This dominant peak indicates that annual cycles are the strongest temporal pattern in the Olowalu time series of tiger shark detections. Kalama Deep showed a similar, though slightly weaker, annual peak, suggesting a comparable cyclical trend. In contrast, Kalama Shallow and Honokōwai exhibited only low-amplitude peaks, indicating a lack of strong or consistent seasonal patterns in shark detections at those sites.Fig. 5Fast Fourier Transformations (FFTs) for the 4 significant Rayleigh test sites. Left panel shows detrended time series for each receiver site, right panel shows the dominant frequency extracted from each time series.Full size imageSeasonal Trend Decomposition using Loess also identified a strong cyclical seasonal pattern of shark detections at Olowalu, combined with a long-term trend showing an initial rise in shark detections during the early tagging phase, followed by a gradual decline over the later years (Fig. 6). The remainder was confirmed to be residual noise using Shapiro–Wilk normality test and examination of QQ plot.Fig. 6Seasonal trend decomposition using Loess for sharks detected at Olowalu. Panels from top to bottom show the original time-series data of shark detections (Data – number of individuals detected), the long-term underlying trend indicating an initial increase during the shark tagging phase followed by a gradual decline (Trend), the seasonal component highlighting consistent cyclical variation in shark presence after removing the overall trend (Seasonal), and the residual variability (Remainder).Full size imageDiel activity patternsA kernel density plot (Fig. 7) revealed substantial temporal overlap between sexes at Olowalu. The Bhattacharyya coefficient of 0.983 for the diel activity patterns of males and females confirmed this overlap. Both sexes were more consistently present during the day than at night, with overlapping peaks in presence at approximately 1500 h. In addition, multiple sharks captured at this site had physical signs of recent mating activity (females with fresh mating scars and males with visibly chafed claspers (Figs. 8, 9)).Fig. 7Kernel density plot of activity by sex for male and female sharks detected at Olowalu.Full size imageFig. 8Male tiger shark captured at Olowalu, Maui during the known tiger shark mating season in Hawai’i. View the distinct abrasions on his right clasper.Full size imageFig. 9Multiple female tiger sharks captured at Olowalu, Maui during the known tiger shark mating season in Hawai’i. Tooth gouges can be seen on their dorsal fins, head, gills, and caudal fin.Full size imageSex, size and maturity status of sharks detected at Olowalu, MauiAmong the O ‘ahu-tagged individuals (8 females and 0 males) detected at Olowalu during the peak tiger shark mating season months of January and February, 7 (87.5%) were sexually mature. Outside of mating season, there were 7 O ‘ahu-tagged tiger sharks (6 females and 1 male) detected at Olowalu, 5 of which were sexually mature.Comparison of tiger shark detection patterns with humpback whale song intensityDaily RMS SPL values (used as a proxy for humpback whale presence) plotted against monthly shark detections at Olowalu revealed consistent but slightly offset peaks in abundance for each species (Fig. 10). Cross-correlation analysis confirmed this offset, indicating a one-month time lag in which peak tiger shark detections preceded peak whale call intensity (best lag = 1 month, r = 0.821; Fig. 11). Linear regression analysis showed a significant positive relationship between the number of tiger sharks detected per month and the monthly maximum RMS SPL (β = 0.387, SE = 0.059, t = 6.511, p < 0.001). Residual diagnostics indicated no clear violations of model assumptions, suggesting a good overall fit.Fig. 10Daily root mean square sound pressure levels (RMS SPL) in dB (black dots) recorded off Olowalu vs monthly acoustically tagged sharks (solid blue line) detected at Olowalu.Full size imageFig. 11Cross-correlation function for monthly maximum RMS SPL vs. the number of sharks detected per month at Olowalu. Dashed blue lines represent significance and solid black lines represent time lags.Full size imageComparison of tiger shark detection patterns with whale calf survey dataNormalized monthly averages of humpback whale calf counts plotted against monthly individual tiger shark detections at Olowalu show closely aligned peaks across the 13 months of available data (Fig. 12). Cross-correlation analysis confirmed this synchrony, indicating no time lag between the two patterns (best lag = 0 months, r = 0.749; Fig. 13). Linear regression analysis revealed a significant positive relationship between monthly tiger shark detections and average whale calf counts from shore-based surveys (p = 0.00316). The model explained 56.23% of the variance in shark presence (R2 = 0.5623, Adjusted R2 = 0.5225), suggesting a moderate association between the two variables. However, a residual standard error of 2.272 indicates that additional unmeasured factors likely influence tiger shark presence during peak winter months.Fig. 12Normalized monthly average of humpback whale calves per month (red) vs. monthly individual sharks detected (black) at Olowalu during three different whale seasons.Full size imageFig. 13Cross-correlation function for monthly average humpback whale calves vs. the number of sharks detected per month at Olowalu. Blue dashed lines represent significance; solid black lines represent time lags.Full size imageDiscussionUnderstanding the ecological drivers shaping apex predator distributions is essential for predicting species interactions, identifying important habitats, and informing effective marine conservation strategies4,50,51. Here, we combined long-term acoustic telemetry with demographic analyses to investigate the seasonal site-specific presence of tiger sharks in waters around Maui (Hawaiian Islands). Our findings suggest that the seasonal aggregation of tiger sharks around Maui, particularly at Olowalu, is consistent with a combination of reproductive activities and opportunistic foraging on whale associated biomass. Four main lines of evidence support this interpretation: (1) Seasonal inter-island migrations to Maui that coincide with the known tiger shark mating period (mid-winter) and overlap with humpback whale calving season; (2) Demographic patterns indicating migrating sharks are predominantly sexually mature (80% mature at first Maui detection) which is consistent with mating driven movement; (3) Spatially and temporally overlapping occurrences of mature males and females at Olowalu during mid-winter, together with independent evidence of recent mating (fresh mating scars on females and clasper chafing on males; Figs. 8 and 9), provide circumstantial support for potential mating interactions at this site; and (4) A temporal alignment between shark presence and peak whale calf abundance, implying that foraging opportunities (e.g., scavenging whale placentas or carcasses) may also influence shark aggregations.Seasonal inter-island movements indicating reproductive migrationsTiger sharks tagged around O ‘ahu showed distinct seasonal peaks near Maui, especially in January and February (mating season), whereas sharks tagged around Maui displayed year-round residency. Most O ‘ahu-tagged sharks returned to O ‘ahu after visiting Maui. Given the three-year gestation period described by Whitney and Crow13, successfully mated females would not be expected to revisit mating grounds for at least three years, allowing time to gestate, give birth, and recover. Thus, detection of adult females at suspected mating grounds in consecutive years would contradict the mating migration hypothesis. We observed only one instance of an adult female returning during mating season in back-to-back years (Fig. S3). All other sharks were detected during only one mating season (Fig. S3). Taken together, these observations indicate directed, seasonal partial migrations by O’ahu-tagged tiger sharks that coincide with Hawai ‘i’s mid-winter mating period13. This suggests reproduction as a driver for these seasonal migrations; the overlap of which peaks during whale calving events27.Partial migration describes the behavior of populations composed of individuals with varying degrees of site attachment due to factors such as reproductive status, local competition, predation risk, and body condition52. The contrasting patterns observed between O’ahu-tagged and Maui-resident sharks may reflect differences in the physical and ecological settings of each island. O’ahu and Maui differ in oceanography, bathymetry, coastal habitat structure, and levels of human activity, all of which could influence shark residency and movement. Maui’s extensive insular shelf and proximity to whale calving grounds may favor year-round occupancy, whereas O’ahu’s more developed coastline and narrower shelf may limit suitable habitats for tiger sharks, encouraging seasonal migration. There is evidence that some tiger shark migrations are driven by reproduction. In Hawai ‘i, mature females from the Northwestern Hawaiian Islands migrate to the Main Hawaiian Islands during the fall pupping season, highlighting parturition as a key migratory driver53. Similarly, in the northwest Atlantic, mature male tiger sharks migrate from open-ocean habitats to specific reef areas for the mating season, implicating mating as the primary driver54. Comparable reproduction-driven partial migrations occur in other shark species, including lemon sharks55, in which only a subset of the population migrates to distinct breeding locations.The observed seasonal influx of sharks from O ‘ahu combined with the high residency of Maui sharks suggests a spatially structured mating system. Sharks with core habitats located outside Maui Nui appear to specifically migrate to this region for mating opportunities, whereas local sharks remain resident year-round. However, given that Olowalu is also a known hotspot for whale calves and placental resources56,57, this dual timing and location may not be coincidental. Both mating and foraging may jointly influence tiger shark seasonal movements to Maui. Access to calorie-dense whale blubber during the breeding season could substantially improve female energetic condition, as large sharks readily scavenge whale carcasses and preferentially consume lipid-rich blubber58. Fecundity in many sharks scales with female body size (a proxy for energetic condition59;), and therefore access to high-calorie prey pulses (e.g. fledgling seabirds at French Frigate Shoals; migratory birds along the Gulf coast; or scavenged whale blubber) can subsidize females’ energy budgets and help meet the substantial costs of viviparous reproduction5,58,60.Demographic evidence supports mating hypothesisExtensive tagging and long-term monitoring, coupled with established tiger shark growth rates in Hawai ‘i37, allowed us to estimate size at first detection on Maui for several O ‘ahu-tagged individuals. We found that 80% of O ‘ahu-tagged sharks detected around Maui were already sexually mature at their initial detection. Notably, several sharks initially tagged as juveniles only appeared in Maui waters after reaching estimated maturity. Similar maturity-dependent migratory behaviors have been documented in tiger sharks from the northwest Atlantic, suggesting that these migrations are reproductive in nature54. Such ontogenetic shifts in habitat use and behavior are widespread among elasmobranchs61 and typically represent transitions from juvenile priorities, such as foraging or predation avoidance, to adult reproductive strategies. However, these patterns do not preclude additional drivers. Not all sharks arriving at Maui were mature, and the presence of some juvenile sharks suggest that factors like foraging could also play a role.Seasonal aggregation and diel synchrony at OlowaluAmong the six Maui shelf monitoring sites, Olowalu exhibited the strongest and most consistent seasonal pattern of tiger shark detections. Diel activity at Olowalu revealed near-complete overlap (98.3% overlap by kernel density) between male and female presence, possibly indicating synchronized habitat use during daytime that may facilitate mating interactions. This aligns with the current operational definition for aggregation in elasmobranch species, characterized by the co-occurrence of two or more individuals in space and time due to the deliberate use of a common driver62. Although males appeared underrepresented in our detections, this may reflect a sampling bias stemming from difficulties capturing mature males in nearshore habitats14, rather than their actual absence. The fresh mating scars observed on females and chafed claspers on males provide physical evidence of active mating at this site, similar to observations that have supported Fernando de Noronha as a reproductive area for tiger sharks in the South Atlantic63.Understanding the mating systems of tiger sharks is inherently challenging due to their large size, mobility, and generally solitary nature64. Our findings align with theoretical models proposing that even low-density aggregations can substantially enhance reproductive success in wide-ranging solitary species by increasing encounter rates among receptive individuals65,66. Rather than forming dense clusters, tiger sharks may form diffuse aggregations spanning several kilometers over extended periods. This coordinated yet dispersed aggregation at Olowalu appears to be a functionally significant reproductive strategy that balances mating opportunities against ecological constraints such as the energetic costs of migration, intra-specific competition, and the potential unpredictability of whale-derived food resources66,67. Such strategies are especially advantageous for sparsely distributed marine predators, reflecting an adaptive compromise between solitary lifestyles and reproductive needs.Correlations with whale biomass indicate trophic opportunitiesComparing the spatial and temporal patterns of predators and prey enables researchers to assess the likelihood of interactions between species68. To evaluate the whale biomass foraging hypothesis, we examined associations between tiger shark presence and proxies of humpback whale biomass—specifically adult humpback whale song chorusing intensity and calf counts. Our analysis revealed a positive relationship between monthly tiger shark abundance and humpback whale acoustic activity, predominantly reflecting adult male singing. However, peak shark abundance occurred one month before peak adult whale acoustic activity. There are multiple potential explanations for this phenomenon, namely (1) adult whales are unlikely to be the primary factor attracting sharks, (2) sharks may position themselves early to secure access to predictable resources, or (3) both sharks and whales may simply be responding to shared environmental cues (e.g. ocean temperature). Further fine-scale monitoring will be required to disentangle anticipatory behavior from coincidental timing. Conversely, tiger shark abundance closely aligned with peak calf numbers, suggesting calves, placentas, or stillborn and vulnerable neonates may provide important, low-risk foraging opportunities. The moderate explanatory power (R2 = 0.56) of whale biomass on shark abundance, observed across the 13 months when whale calf data were available within the broader six-year monitoring dataset, is noteworthy for ecological studies69. This relationship suggests that whale-derived nutrients may indeed influence shark aggregation, although coincidental timing driven by shared migratory cues again cannot be ruled out. Tiger sharks are known opportunistic scavengers of whale carcasses7 and potentially consume placental or neonatal tissues. The predictable seasonal presence of whale-derived resources off Olowalu aligns well with observed shark aggregations. Similar seasonal foraging-driven shark aggregations have been documented elsewhere. One example is at French Frigate Shoals Atoll (Kānemiloha ‘i) in the Northwest Hawaiian Islands where tiger sharks aggregate in early summer specifically to prey upon fledgling albatross chicks, with shark presence closely matching the narrow seasonal and diel timing of fledgling events, primarily between sunrise and noon5. Such precise foraging-driven aggregations may be relatively rare within the broader context of tiger shark long-term movement patterns. For example, tiger sharks showed low overall site fidelity and no increase in fidelity over time at an ecotourism provisioning site70; individual prey species occurrence patterns did not explain tiger shark residency patterns in the northern Great Barrier Reef71; tiger shark proximity to a turtle nesting island remained consistent between nesting and non-nesting seasons68; and, although tiger sharks preferred shallow habitats where prey was abundant in Australia, prey availability did not explain their broader-scale movements72.Given Olowalu’s role as a hotspot for whale-calf pairs56,57,73 tiger shark reproductive activities likely coincide with significant foraging opportunities provided by nutrient-rich whale-derived resources. Our findings collectively suggest that tiger shark aggregations around Olowalu are influenced by both reproductive strategies and seasonal availability of whale biomass.Ecological significance and future studiesExplicit identification of mating aggregations in elasmobranchs remains uncommon, with only a few documented cases, such as nurse sharks (Ginglymostoma cirratum74;), Port Jackson sharks (Heterodontus portusjacksoni75;), and potentially white sharks (Carcharodon carcharias) at Guadalupe Island76. Most studies, however, infer mating aggregations indirectly from observed spatial and temporal patterns77,78. Beyond identifying mating aggregations, it is also important to consider the ecological attributes that define breeding and nursery areas. Shark breeding and/or nursery sites may reflect a combination of predictable prey availability, benthos type, depth, and predation risk66. The year-round residency for Maui-tagged sharks may therefore reflect a convergence of both functions, offering reproductive opportunities and reliable access to food resources that make the region suitable for multiple life-history stages.The convergence of mature tiger sharks during a defined seasonal window, their pronounced site fidelity to Olowalu—including repeated returns by specific individuals over seven years—and clear diel synchrony between sexes collectively suggest that Olowalu serves as a reproductive site for tiger sharks in Hawai ‘i. Fidelity to mating areas has been documented in only a few shark species66; notably, nurse sharks exhibit strong long-term fidelity, returning annually to the Dry Tortugas mating site over periods spanning up to 16 mating seasons and nearly three decades79. Similarly, our findings suggest mating-site fidelity among tiger sharks at Olowalu. Future research should adopt multi-modal approaches, such as biologging tags with video capabilities to directly quantify conspecific interactions, verify mating events, and document shark-whale interactions14. Other promising approaches include cloacal swabbing to detect whale DNA to assess the importance of scavenging events80 and energetic modeling to evaluate the relative importance of whale-derived nutrients.ConclusionThe temporal overlap between tiger shark aggregation and peak whale-calf biomass suggests that Olowalu aggregations may serve dual roles—supporting both reproductive and foraging activities. As generalist and opportunistic predators, tiger sharks can readily exploit these whale-derived resources while concurrently engaging in mating behaviors. Our integrative analysis of movement patterns, demographic structure, diel behavior, and seasonal occurrence provides the first evidence of seasonal mating aggregations for tiger sharks and advances our understanding of their mating behavior in Hawai’i.

    Data availability

    The data and accompanying code are hosted on Zenodo and will be made publicly available upon publication. A private access link has been provided for peer review: https://doi.org/10.5281/zenodo.15558374.
    ReferencesCompagno, L. J. V. FAO species catalogue. Volume 4. Sharks of the world. An annotated and illustrated catalogue of shark species known to date. Part 2. Carcharhiniformes. FAO Species Catalogue 4(2), 251–655 (1984).
    Google Scholar 
    Ferreira, L. C. et al. The trophic role of a large marine predator, the tiger shark Galeocerdo cuvier. Sci. Rep. 7(1), https://doi.org/10.1038/s41598-017-07751-2 (2017).Holland, K. N. et al. A perspective on future tiger shark research. Front. Mar. Sci. 6, 37. https://doi.org/10.3389/fmars.2019.00037 (2019).Article 

    Google Scholar 
    Heithaus, M. R., Frid, A., Wirsing, A. J. & Worm, B. Predicting ecological consequences of marine top predator declines (Elsevier Ltd., 2008).Book 

    Google Scholar 
    Meyer, C. G., Papastamatiou, Y. P. & Holland, K. N. A multiple instrument approach to quantifying the movement patterns and habitat use of tiger (Galeocerdo cuvier) and Galapagos sharks (Carcharhinus galapagensis) at French Frigate Shoals, Hawaii. Mar. Biol. 157(8), 1857–1868. https://doi.org/10.1007/s00227-010-1457-x (2010).Article 

    Google Scholar 
    Vossgaetter, L. et al. Non-invasive methods characterise the world’s largest tiger shark aggregation in Fuvahmulah, Maldives. Sci. Rep. 14(1), 21998. https://doi.org/10.1038/s41598-024-73079-3 (2024).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Clua, E., Chauvet, C., Read, T., Werry, J. M. & Lee, S. Y. Behavioural patterns of a tiger shark (Galeocerdo cuvier) feeding aggregation at a blue whale carcass in Prony Bay, New Caledonia. Mar. Freshw. Behav. Physiol. 46(1), 1–20. https://doi.org/10.1080/10236244.2013.773127 (2013).Article 

    Google Scholar 
    Jacoby, D. M. P. et al. Social network analysis reveals the subtle impacts of tourist provisioning on the social behavior of a generalist Marine Apex Predator. Front. Mar. Sci. 8, 665726. https://doi.org/10.3389/fmars.2021.665726 (2021).Article 

    Google Scholar 
    Hammerschlag, N., Gutowsky, L. F. G., Gallagher, A. J., Matich, P. & Cooke, S. J. Diel habitat use patterns of a marine apex predator (tiger shark, Galeocerdo cuvier) at a high use area exposed to dive tourism. J. Exp. Mar. Biol. Ecol. 495, 24–34. https://doi.org/10.1016/j.jembe.2017.05.010 (2017).Article 

    Google Scholar 
    Sulikowski, J. A. et al. Identification of the first gestational ground for tiger sharks (Galeocerdo cuvier) in the Central Indian Ocean using a high-definition submersible ultrasound. Front. Mar. Sci. 11, 1500176. https://doi.org/10.3389/fmars.2024.1500176 (2024).Article 

    Google Scholar 
    Reinero, F. R. et al. First insights into social behavioral patterns between pairs of bait-attracted mature female tiger sharks from Fuvahmulah Island, Maldives. Behav. Proc. 229, 105216. https://doi.org/10.1016/j.beproc.2025.105216 (2025).Article 

    Google Scholar 
    Shields, C., Reproductive biology of the tiger shark in the Western Atlantic reproductive biology of the tiger shark in the Western Atlantic Ocean Ocean, (2018).Whitney, N. M. & Crow, G. L. Reproductive biology of the tiger shark (Galeocerdo cuvier) in Hawaii. Mar. Biol. 151(1), 63–70. https://doi.org/10.1007/s00227-006-0476-0 (2007).Article 

    Google Scholar 
    Meyer, C. G. et al. Habitat geography around Hawaii’s oceanic islands influences tiger shark (Galeocerdo cuvier) spatial behaviour and shark bite risk at ocean recreation sites. Sci. Rep. 8(1), 4945. https://doi.org/10.1038/s41598-018-23006-0 (2018).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Salinas-De-León, P. et al. A matter of taste: Spatial and ontogenetic variations on the trophic ecology of the tiger shark at the Galapagos marine reserve. PLoS ONE 14(9), e0222754. https://doi.org/10.1371/journal.pone.0222754 (2019).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Helweg, D. A., Daily and Seasonal patterns of behavior and Abundance of Humpback Whales (Megaptera novaeangliae) in Hawaiian Waters, University of Hawaii at Manoa, (1989).Tucker, J. P., Vercoe, B., Santos, I. R., Dujmovic, M. & Butcher, P. A. Whale carcass scavenging by sharks. Glob Ecol. Conserv. 19, e00655. https://doi.org/10.1016/j.gecco.2019.e00655 (2019).Article 

    Google Scholar 
    Gallagher, A. J., Papastamatiou, Y. P. & Barnett, A. Apex predatory sharks and crocodiles simultaneously scavenge a whale carcass. J Ethol 36(2), 205–209. https://doi.org/10.1007/s10164-018-0543-2 (2018).Article 

    Google Scholar 
    Dicken, M. L. et al. Diet and trophic ecology of the tiger shark (Galeocerdo cuvier) from South African waters. PLoS ONE 12(6), e0177897. https://doi.org/10.1371/journal.pone.0177897 (2017).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Fletcher, C. H. et al. Geology of Hawaii Reefs. In Coral Reefs of the USA, Springer Netherlands, pp. 435–487. https://doi.org/10.1007/978-1-4020-6847-8_11 (2008).Jokiel, P. L. Biology and ecological functioning of Coral Reefs in the Main Hawaiian Islands. In Coral Reefs of the USA, Springer Netherlands, pp. 489–517. https://doi.org/10.1007/978-1-4020-6847-8_12 (2008).Brown, D. An ecological comparison of turf algae between two sites on West Maui that differ in anthropogenic impacts,” University of Hawaii at Manoa, (2019).Brown, E. K. Reef Coral populations: Spatial and temporal differences observed on six Reefs Off West Maui,” University of Hawaii at Manoa, (2004).Wei, J. et al. Shallow water bathymetry with multi-spectral satellite ocean color sensors: Leveraging temporal variation in image data. Remote Sens. Environ. 250, 112035. https://doi.org/10.1016/j.rse.2020.112035 (2020).Article 

    Google Scholar 
    Salden, D. R. Humpback Whale encounter rates Offshore of Maui, Hawaii, (1988).Kugler, A., Lammers, M. O., Zang, E. J., Kaplan, M. B. & Aran Mooney, T. Fluctuations in Hawaii’S Humpback Whale Megaptera Novaeangliae population inferred from male song Chorusing Off Maui. Endanger Species Res 43, 421–434. https://doi.org/10.3354/ESR01080 (2020).Article 

    Google Scholar 
    Kügler, A., Lammers, M. O., Zang, E. J., Pack, A. A., Male Humpback Whale Chorusing in Hawai‘i and its Relationship with Whale abundance and density. Front Mar Sci, 8, https://doi.org/10.3389/fmars.2021.735664 (2021).Holland, K. N., Wetherbee, B. M., Lowe, C. G. & Meyer, C. G. Movements of tiger sharks (Galeocerdo cuvier ) in coastal Hawaiian waters. Mar Biol 134, 665–673. https://doi.org/10.1007/s002270050582 (1999).Article 

    Google Scholar 
    Heim, V., van Zinnicq Bergmann, M. P. M., Smukall, M. J. & Guttridge, T. L. Multiyear tourism-related feeding reduces short- and long-term local space use in a marine apex predator. Anim. Behav. 217, 81–107. https://doi.org/10.1016/j.anbehav.2024.08.012 (2024).Article 

    Google Scholar 
    Kessel, S. T. & Hussey, N. E. Tonic immobility as an anaesthetic for elasmobranchs during surgical implantation procedures. Can. J. Fish. Aquat. Sci. 72(9), 1287–1291. https://doi.org/10.1139/cjfas-2015-0136 (2015).Article 

    Google Scholar 
    Afonso, A. S. & Hazin, F. H. V. Post-release survival and behavior and exposure to fisheries in juvenile tiger sharks, Galeocerdo cuvier, from the South Atlantic. J. Exp. Mar. Biol. Ecol. 454, 55–62. https://doi.org/10.1016/j.jembe.2014.02.008 (2014).Article 

    Google Scholar 
    Binstock, A. L. et al. Variable post-release mortality in common shark species captured in Texas shore-based recreational fisheries. PLoS ONE 18(2), e0281441. https://doi.org/10.1371/journal.pone.0281441 (2023).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Grosse, T. A. Assessing survival rates of discarded sandbar (Carcharhinus plumbeus), tiger sharks (Galeocerdo cuvier), Port Jackson sharks (Heterodontus portusjacksoni) and dusky sharks (Carcharhinus obscurus),” Curtin University, (2023).Whitney, N. M. et al. Connecting post-release mortality to the physiological stress response of large coastal sharks in a commercial longline fishery. PLoS ONE 16(9), e0255673. https://doi.org/10.1371/journal.pone.0255673 (2021).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gallagher, A. J., Serafy, J. E., Cooke, S. J. & Hammerschlag, N. Physiological stress response, reflex impairment, and survival of five sympatric shark species following experimental capture and release. Mar Ecol Prog Ser 496, 207–218. https://doi.org/10.3354/meps10490 (2014).Article 
    ADS 

    Google Scholar 
    Lund, U., Agostinelli, C. Package ‘circular,’” 2017, Repository CRAN 775.5. [Online]. Available: https://orcid.org/0000-0001-6702-4312Meyer, C. G. et al. Growth and maximum size of tiger sharks (Galeocerdo cuvier) in Hawaii. PLoS ONE 9(1), e84799. https://doi.org/10.1371/journal.pone.0084799 (2014).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Shapiro, S. S., Wilk, M. B. An analysis of variance test for normality (complete samples),” Biometrika, vol. 52, no. 3–4, pp. 591–611, 1965, [Online]. Available: https://academic.oup.com/biomet/article/52/3-4/591/336553Field, A. Discovering statistics using IBM SPSS statistics. Sage publications limited, (2013).Hurlbert, S. H. Pseudoreplication and the design of ecological field experiments. Ecol. Monogr. 54(2), 187–211. https://doi.org/10.2307/1942661 (1984).Article 

    Google Scholar 
    Levene, H., Robust tests for equality of variances,” (1960).Tukey, J. W., Exploratory data analysis, Reading/Addison-Wesley, (1977).Bracewell, R. N., The fourier transform and its applications, 3rd ed. McGraw-Hill Science/Engineering/Math, (1999).Cooley, J. W., Tukey, J. W. An algorithm for the machine calculation of complex fourier series, 1965. [Online]. Available: https://www.jstor.org/stable/2003354?seq=1&cid=pdf-Oppenheimer, A., Schafer, R. Discrete-time signal processing, 3rd ed. Pearson, (2009).Cleveland, R. B., Cleveland, W. S., McRae, J. E. & Terpenning, I. STL: A seasonal-trend decomposition procedure based on Loess. J. Off. Stat. 6(1), 3–73 (1990).
    Google Scholar 
    Ridout, M. S. & Linkie, M. Estimating overlap of daily activity patterns from camera trap data. J. Agric. Biol. Environ. Stat. 14(3), 322–337. https://doi.org/10.1198/jabes.2009.08038 (2009).Article 
    MathSciNet 

    Google Scholar 
    Bhattacharyya, A. On a measure of divergence between two statistical populations defined by their probability distribution. Bull. Calcutta. Math. Soc. 35, 99–110 (1943).MathSciNet 

    Google Scholar 
    Wickham, H. et al. ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics, The R Foundation. https://doi.org/10.32614/CRAN.package.ggplot2. (2007).Block, B. A. et al. Tracking apex marine predator movements in a dynamic ocean. Nature 475(7354), 86–90. https://doi.org/10.1038/nature10082 (2011).Article 
    CAS 
    PubMed 

    Google Scholar 
    Estes, J. A. et al., Trophic downgrading of planet Earth,” 2011. [Online]. Available: https://www.science.orgChapman, B. B., Brönmark, C., Nilsson, J. Å. & Hansson, L. A. The ecology and evolution of partial migration. Oikos 120(12), 1764–1775. https://doi.org/10.1111/j.1600-0706.2011.20131.x (2011).Article 
    ADS 

    Google Scholar 
    Papastamatiou Y. P., Meyer, C. G., Carvalho, F., Dale, J. J., Hutchinson, M. R., Holland, K. N. Telemetry and random-walk models reveal complex patterns of partial migration in a, (2013).Lea, J. S. E. et al. Repeated, long-distance migrations by a philopatric predator targeting highly contrasting ecosystems. Sci. Rep. 5, 11202. https://doi.org/10.1038/srep11202 (2015).Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Pillans, R. D. et al. Long-term acoustic monitoring reveals site fidelity, reproductive migrations, and sex specific differences in habitat use and migratory timing in a large Coastal shark (Negaprion acutidens). Front. Mar. Sci. 8, 616633. https://doi.org/10.3389/fmars.2021.616633 (2021).Article 

    Google Scholar 
    Cartwright, R. et al. Between a rock and a hard place: Habitat selection in female-calf humpback whale (megaptera novaeangliae) pairs on the hawaiian breeding grounds. PLoS ONE 7(5), e38004. https://doi.org/10.1371/journal.pone.0038004 (2012).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Pack, A. A. et al. Comparing depth and seabed terrain preferences of individually identified female humpback whales (Megaptera novaeangliae), with and without calf, off Maui, Hawaii. Mar. Mamm Sci. 34(4), 1097–1110. https://doi.org/10.1111/mms.12495 (2018).Article 

    Google Scholar 
    Fallows, C., Gallagher, A. J. & Hammerschlag, N. White sharks (Carcharodon carcharias) Scavenging on Whales and its potential role in further shaping the ecology of an apex predator. PLoS ONE 8(4), e60797. https://doi.org/10.1371/journal.pone.0060797 (2013).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Cortés, E. Life history patterns and correlations in sharks. Rev. Fish. Sci. 8(4), 299–344. https://doi.org/10.1080/10408340308951115 (2000).Article 

    Google Scholar 
    Drymon, J. M. et al. Tiger sharks eat songbirds: scavenging a windfall of nutrients from the sky. Ecology 100(9), 1–4. https://doi.org/10.1002/ecy.2728 (2019).Article 

    Google Scholar 
    Grubbs, R. D., 7 Ontogenetic shifts in movements and Habitat Use.McInturf, A. G. A. et al. A unified paradigm for defining elasmobranch aggregations. ICES J. Mar. Sci. 80(6), 1551–1566. https://doi.org/10.1093/icesjms/fsad099 (2023).Article 

    Google Scholar 
    Rangel, B. S. et al. Evidence of mating scars in female tiger sharks (Galeocerdo cuvier) at the Fernando de Noronha Archipelago, Brazilian Equatorial Atlantic. Environ. Biol. Fishes 106(1), 107–115. https://doi.org/10.1007/s10641-022-01380-z (2023).Article 

    Google Scholar 
    Sulikowski, J. A. et al. Seasonal and life-stage variation in the reproductive ecology of a marine apex predator, the tiger shark Galeocerdo cuvier, at a protected female-dominated site. Aquat Biol 24(3), 175–184. https://doi.org/10.3354/ab00648 (2016).Article 

    Google Scholar 
    Kokko, H. Rankin, D. J. Lonely hearts or sex in the city? Density-dependent effects in mating systems. In Philosophical transactions of the royal society B: Biological sciences, Royal society, pp. 319–334. https://doi.org/10.1098/rstb.2005.1784 (2006).Speed, C. W., Field, I. C. Meekan, M. G., Bradshaw, C. J. A. Complexities of coastal shark movements and their implications for management, https://doi.org/10.3354/meps08581 (2010).Chapman, D. D., Feldheim, K. A., Papastamatiou, Y. P. & Hueter, R. E. There and back again: A review of residency and return migrations in sharks, with implications for population structure and management. Ann Rev Mar Sci 7, 547–570. https://doi.org/10.1146/annurev-marine-010814-015730 (2015).Article 
    PubMed 

    Google Scholar 
    Fitzpatrick, R. et al. A comparison of the seasonal movements of tiger sharks and green turtles provides insight into their predator-prey relationship. PLoS ONE 7(12), e51927. https://doi.org/10.1371/journal.pone.0051927 (2012).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Low-Décarie, E., Chivers, C. & Granados, M. Rising complexity and falling explanatory power in ecology. Front Ecol Environ 12(7), 412–418. https://doi.org/10.1890/130230 (2014).Article 

    Google Scholar 
    Séguigne, C., Bègue, M., Meyer, C., Mourier, J. & Clua, É. Provisioning ecotourism does not increase tiger shark site fidelity. Sci. Rep. 13(1), 7785. https://doi.org/10.1038/s41598-023-34446-8 (2023).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Werry, J. M. et al. Reef-fidelity and migration of tiger sharks, Galeocerdo cuvier, across the coral sea. PLoS ONE 9(1), e83249. https://doi.org/10.1371/journal.pone.0083249 (2014).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Heithaus, M. R., Wirsing, A. J., Dill, L. M. & Heithaus, L. I. Long-term movements of tiger sharks satellite-tagged in Shark Bay, Western Australia. Mar Biol 151(4), 1455–1461. https://doi.org/10.1007/s00227-006-0583-y (2007).Article 

    Google Scholar 
    Kugler, A. Male humpback whale chorusing and what it reveals about the species’ ecology in Hawaiʻi,” University of Hawaii at Manoa, (2022).Whitney, N. M., Pratt, H. L. & Carrier, J. C. Group courtship, mating behaviour and siphon sac function in the whitetip reef shark, Triaenodon obesus. Anim Behav 68(6), 1435–1442. https://doi.org/10.1016/j.anbehav.2004.02.018 (2004).Article 

    Google Scholar 
    Mourier, J., Bass, N. C., Guttridge, T. L., Day, J. & Brown, C. Does detection range matter for inferring social networks in a benthic shark using acoustic telemetry?. R Soc Open Sci 4(9), 170485. https://doi.org/10.1098/rsos.170485 (2017).Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Domeier, M. L. & Nasby-Lucas, N. Two-year migration of adult female white sharks (Carcharodon carcharias) reveals widely separated nursery areas and conservation concerns. Animal Biotelemetry 1(1), 2. https://doi.org/10.1186/2050-3385-1-2 (2013).Article 
    ADS 

    Google Scholar 
    Jacoby, D. M. P., Croft, D. P. & Sims, D. W. Social behaviour in sharks and rays: Analysis, patterns and implications for conservation. Fish Fish. 13(4), 399–417. https://doi.org/10.1111/j.1467-2979.2011.00436.x (2012).Article 

    Google Scholar 
    Palacios, M. D. et al., Manta and devil ray aggregations: conservation challenges and developments in the field, Frontiers Media S.A. https://doi.org/10.3389/fmars.2023.1148234. (2023).Pratt, H. L., Pratt, T. C., Knotek, R. J., Carrier, J. C. & Whitney, N. M. Long-term use of a shark breeding ground: Three decades of mating site fidelity in the nurse shark, Ginglymostoma cirratum. PLoS ONE 17(10), e0275323. https://doi.org/10.1371/journal.pone.0275323 (2022).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    van Zinnicq Bergmann, M. P. M. et al. Elucidating shark diets with DNA metabarcoding from cloacal swabs. Mol. Ecol. Resour. 21(4), 1056–1067. https://doi.org/10.1111/1755-0998.13315 (2021).Article 
    CAS 
    PubMed 

    Google Scholar 
    Download referencesAcknowledgementsWe would like to thank the staff of the Maui Division of Aquatic Resources for logistical support for the Maui fieldwork component of the study. We are especially grateful to Daniel Coffey, Melanie Hutchinson, and James Anderson for their contributions to the fishing and tagging efforts that resulted in this data set, as well as the many volunteers who helped with collecting the acoustic and visual humpback whale data. Special thanks to the Hawaii Institute of Marine Biology.FundingWe thank the Hawaii Department of Land and Natural Resources and the Pacific Islands Ocean Observing System for funding this study.Author informationAuthors and AffiliationsHawaiʻi Institute of Marine Biology, University of Hawaiʻi at Mānoa, 46-007 Lilipuna Rd, Kaneohe, HI, 96744, USAPaige Wernli, Mark Royer, Anke Kügler, Kim Holland & Carl MeyerHawaiian Islands Humpback Whale National Marine Sanctuary, NOAA, Kihei, HI, USAMarc LammersAuthorsPaige WernliView author publicationsSearch author on:PubMed Google ScholarMark RoyerView author publicationsSearch author on:PubMed Google ScholarAnke KüglerView author publicationsSearch author on:PubMed Google ScholarMarc LammersView author publicationsSearch author on:PubMed Google ScholarKim HollandView author publicationsSearch author on:PubMed Google ScholarCarl MeyerView author publicationsSearch author on:PubMed Google ScholarContributionsPW analyzed the data and wrote the first draft under the direct supervision and guidance of CM, who continued to review and edit subsequent drafts. MR and KM reviewed and edited subsequent drafts as well as suggested further analyses, ML and AK reviewed and edited subsequent drafts, provided data, as well as suggested further analyses. All authors substantially contributed to the conception/design of this work and have approved this submitted version.Corresponding authorCorrespondence to
    Paige Wernli.Ethics declarations

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    Reprints and permissionsAbout this articleCite this articleWernli, P., Royer, M., Kügler, A. et al. Telemetry reveals potential mating aggregation behavior of tiger sharks (Galeocerdo cuvier) in Hawaiʻi.
    Sci Rep 15, 44076 (2025). https://doi.org/10.1038/s41598-025-27742-yDownload citationReceived: 23 July 2025Accepted: 05 November 2025Published: 18 December 2025Version of record: 18 December 2025DOI: https://doi.org/10.1038/s41598-025-27742-yShare this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy shareable link to clipboard
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    KeywordsDiel patternsElasmobranchHawai ‘iPartial migrationPhilopatryPredator-prey interactionsReproductive ecologySeasonal movementsSite fidelitySpatial ecology More

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    Environmentally adjusted δ13C thresholds for accurate detection of C4 plant consumption in Europe

    AbstractDetecting C4 plants consumption is central to investigating animal ecology, agriculture, dietary transitions, and socio-environmental adaptations, and can be done using carbon isotope analysis. The conventional δ¹³C threshold used to identify C4 plant intake does not consider substantial ecological variability across Europe. By analyzing over 4,000 δ13C values from archaeological C3 and C4 grains, we present a European-wide C3 grain δ13C baseline and establish adjusted δ13C threshold estimations for C4 consumption from the site to the ecozone scale using multicomponent environmental models and ecozone cluster analysis. We show that a fixed threshold lead to under- or overestimation of C4 plant consumption, particularly in northern/humid and southern/arid regions, where the threshold needs to be revised downwards or upwards by up to 2‰. This refined framework offers a more accurate baseline for interpreting human and animal diet and enhances our understanding of the spread, adoption and consumption of C4 crops across Europe.

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    IntroductionEstimating the proportion of C3 versus C4 plants in human and animal diet is a key part of bioarchaeological, palaeontological and ecological research. Scholars worldwide have been investigating the spread of millet across Eurasia because this highly nutritious and drought-resistant C4 plant can address various questions about past societies1,2. This includes complex social structures, the adoption of new subsistence strategies, the adaptation to challenging climatic and environmental settings, as well as mobility and health status3,4,5,6,7. In ecology and palaeontology, identifying C3 and C4 diets provides insight into (past) habitats, niche partitioning, and animal behaviours8,9,10,11,12.Stable carbon (C) isotope analyses—paired with nitrogen (N) isotope analyses when investigating collagen—represent the most efficient and preferred method to identify C4 plant consumption from bioarchaeological and palaeontological skeletal remains. Due to different photosynthetic pathways between C3 and C4 plants, the ratio of 13C/12C isotopes (expressed as δ13C in ‰) is significantly more negative in C3 plants (−35 to −23‰) compared to C4 plants (−14 to −10‰)13,14,15. Plant δ13C is transferred to the consumer’s body tissues along the food chain, following well-described and quantified fractionation processes16,17, which leads to enriched δ13C values in the tissues of C4 plant consumers compared to C3 plant consumers. In general, bone or dentine collagen δ13C values above −18‰ and enamel or bone apatite δ13C values above −10‰ indicate a mixed diet of C3 and C4 plants13,18,19. In contrast, δ13C values above −12‰ and −4‰, respectively, represent a pure C4 diet13,18,19.However, specific environmental and climatic settings influence the plant’s δ13C value20. For instance, C3 plant δ13C values are more depleted under oceanic or Mediterranean climates, forest soil, dense canopy, elevated humidity or increased CO2 concentration20,21. Conversely, continental climate, aridity, salinity (including sea-spray effect), elevated temperature or high altitude tend to enrich plant δ¹³C values, which are the basis of the terrestrial food chain20,21. The geographical location of the investigated site is also determinant. On average, skeletal tissues can be 1 to 2‰ lower in high latitudes compared to low latitudes in Europe21,22,23. Although C4 plants react differently to environmental and climatic factors14,24, their δ13C values can vary across latitude as well25,26. This implies that the threshold value for C4 plant consumption needs to be adapted depending on the geographical location and environmental settings to avoid misinterpretations of body tissue isotopic composition. This paper fills this research gap to avoid an over- or underestimation of C4 plants dietary intakes of premodern animals and human communities across Europe.The main research questions addressed here are: (i) In which regions of Europe is it required to apply an environmentally adjusted δ13C threshold value for identifying C3 versus C4 plant consumption? (ii) What is the magnitude of this adjustment? (iii) Can we identify specific biogeographic parameters related to this isotope variability in Europe? This study draws on over 400027 published δ13C values from charred archaeological C3 and C4 grains derived from Isotope-Ratio Mass Spectrometry (IRMS)28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101. We present an innovative and, to the best of our knowledge, unprecedented ecozone-based model framework that integrates multivariate environmental data to facilitate the identification of C3 versus C4 plant diets in bioarchaeological, palaeontological and ecological research.ResultsEcozone cluster modelUsing multicomponent environmental datasets from topographical and climatic variables, we applied k-means cluster analysis to determine zones of similar environmental conditions across Europe. The model provides 20 spatial clusters including one cluster with unclassified values where not all conditions were equally met (Figs. 1 and  S1, Table 1). Due to numeric quantization of k observations, we labelled the clusters based on the percentiles of the respective data ranges using expressional combinations of temperature, climatic moisture index (CMI), and topography. Some of them are geographically restricted to specific regions, such as the cold and humid ecozones 4 and 5 in North-Eastern Europe, the mild and very humid ecozone 8 at the Atlantic coast, or the hot and arid ecozones in the south of Europe, northern Africa and the Near East (e.g., clusters 10, 16 and 18). Other ecozones are spatially more scattered, for example European high mountain ranges (e.g., clusters 11 and 15). The results can be compared to the biome-based ecoregions from the literature102 despite the reduced number of modelled ecozones.Fig. 1: Site distribution over the European Ecozone clusters.20 clusters based on temperature (TMP), moisture availability (CWB), and topography (DEM) were defined using k-means cluster analysis (with k = 20), including unclassified NA values (i.e., inland water). See the methods and material section for a description of the open source TMP, CWB and DEM data and their provenience. The sites are distributed over 15 clusters. See Table 1 for the ecozone descriptions and numbering and Fig. S1 for the ecozones displayed without sites. Figure by Michael Kempf, created using the open source R and QGIS software.Full size imageTable 1 K-means cluster ecozone cluster summary table including descriptionFull size tableThe sites from which the investigated grains originate cover 15 out of 20 modelled ecozones (Fig. 1, Supplementary data 1), representing most of the European geographical and ecological diversity. However, their distribution is biased by past and modern human activity, archaeological sampling and analytical strategies. Not all ecozones are equally represented in the sample and the ecozones 3, 12, 14, 15 and 18 were excluded from the analyses due to small sample sizes.Isotope diversity among grain speciesDespite the isotopic diversity between the main C3 grain species included in this study (Fig. S2A, B, Supplementary data 2), the two dominant crops of this sample, i.e. the Triticum (wheat, n = 1923) and Hordeum (barley, n = 1843) species, are largely overlapping in the northern and southern parts of Europe (Fig. S2B, Supplementary data 2). Differences from the Central/Western European samples are mostly caused by the wide geographical area represented by this region. In the UK, however, the two crops show notably distinct δ13C values (Fig. S2B, Supplementary data 2), which possibly reflects species-specific differences (e.g., the different timing of the vegetation period, which is earlier for barley, while wheat is more impacted by the summer conditions)28,103 or the environmental diversity of the fields used to grow the different crops29. Because human and animal diet is never based on one single crop, the C3 grain sample was kept as one entity for the rest of the analyses. In contrast, the C3 and C4 grains show distinct δ13C values (Fig. S3C, Supplementary data 2), as expected from their different photosynthetic pathways13,14,15. They are thus considered separately in the rest of the study.Temporal isotope variabilityAmong the entire C3 grains dataset, there is hardly any evolution of δ13C over time (linear model [lm] R² = 0.017, p = 1.75e-17; Pearson’s r value = 0.13, p = <2.2e-16; Fig. S3, Supplementary data 2). When distinguishing between the geographical subsets UK (lm R² = 0.044, p = 0.000276; Pearson’s r value = −0.21, p = 0.000276), Southern (lm R² = 0.03, p = 3.43e-17; Pearson’s r value = 0.17, p = <2.2e-16), Central/Western (lm R² = 0.215, p = 1.80e-32; Pearson’s r value = 0.46, p = <2.2e-16) and Northern Europe (including Denmark: lm R² = 0.078, p = 4.13e-18; Pearson’s r value = 0.28, p = <2.2e-16; and excluding Denmark: lm R² = 0.059, p = 1.55e-09; Pearson’s r value = 0.34, p = <2.2e-16), the positive correlation between C3 grain δ13C values and the grain mean date is particularly weak (Fig. S4A–E, Supplementary data 2). In particular, the slightly stronger relationship observed for Central/Western Europe (Fig. S4B) is biased by the youngest samples from Central France, which exhibit particularly enriched δ13C values (Fig. S4C). At the ecozone level, a weak to moderate and significant increase in C3 grains δ13C values can be observed for ecozone 1 (lm R² = 0.359, p = 5.39e-15; Pearson’s r value = 0.60, p = 5.39e-15) and ecozone 17 only (lm R² = 0.223, p = 0.00157; Pearson’s r value = 0.47, p = 1.57e-03) (Figs. 1 and  S5, Supplementary data 2). The C4 grains dataset has a small sample size and each geographical area is represented by short chronologies, which does not enable any proper diachronic analysis (Fig. S6A). The slight decrease in C4 δ13C values over time might thus be only considered statistically significant in Southern Europe despite the chronological gap of nearly a thousand years between the oldest and youngest cluster (Fig. S6B, Supplementary data 2). This implies that the C3 and the C4 grains datasets were not subdivided into different chronological phases for the subsequent analyses.Geographical isotope variabilitySplitting the C3 grain dataset into geographical subsets (UK, Northern, Southern, and Central/Western Europe) shows that the median δ13C value of C3 grains from Northern Europe is approximately 1‰ lower than that from Southern Europe (Fig. 2A, Table 2). This confirms the previous observations made on different types of samples such as faunal remains22,23 and modern plants21. Yet it has to be stressed that the standard deviation (1 SD) is quite large for both regions (±1.35 and ±1.05, respectively), implying some overlap. Despite the high latitude, C3 grains from the UK exhibit among the highest δ13C values across time (Figs. 2A and  S4), which can be related to the oceanic climate22,23. In Denmark, the low δ13C values of the oldest half of the sample (c. 3700–3000 BCE) shift to particularly enriched δ13C values for the most recent half of the sample (c. 1000 BCE–1000 CE) (Fig. S7, Supplementary data 2). This might reflect changes in agricultural practices and soil management following its decrease in quality starting from the Neolithic period30,31.Fig. 2: Geographical isotopic variability in C3 grains.A C3 grains δ13C values in Europe. B C3 grain δ13C variability compared to latitudinal bins within Europe. The middle line of the box represents the median value, the box is delimited by the quartiles Q1 on the left and Q3 on the right and contains the middle half of the sample, the horizontal lines completed by the outlier dots represent the extent of the data. The mean, median, mean absolute deviation (MAD) and standard deviation (1 SD) values for each region and each latitudinal bin are listed in Table 2. The results of the one-way ANOVA tests related to (A) and (B) and of the Pearson’s correlations related to the C3 grain δ13C versus latitude for the whole dataset and for specific subsets are reported in Supplementary data 2. Figure by Margaux L. C. Depaermentier, created using the open source R software.Full size imageTable 2 Statistical summary for the C3 and C4 grain δ13C values over the latitude bins, regions, modern countries and ecozonesFull size tableUsing the whole dataset, we observe a significant decrease in C3 grain δ13C values with increasing latitude (Fig. 2B, Supplementary data 2). From the median values calculated for each latitudinal bin (Table 2, Fig. 2B), the C3 grains δ13C values from sites above 50° latitude are on average 0.54 to 1.72‰ lower than those of grains from sites at latitudes below 50° (Fig. 2B, Table 2). This confirms the mean offset of around 1–2‰ between Southern and Northern Europe. In comparison, there is a mean variation of 0.46‰ among the median δ13C values of the latitudinal bins above 50° and approximately 0.33‰ among the median δ13C values of the bins below 50°. The difference between southern and northern sites is therefore substantial, yet related to an increasing degree of variability towards the north. When excluding the UK and/or Denmark from this dataset due to the overall elevated values in these regions despite their northern latitude, the decrease in δ13C values with increasing latitude is accordingly even stronger and more significant (Pearson’s r value: −0.25 for the whole sample, −0.27 excluding UK and −0.30 excluding UK and Denmark, with a p-value < 2.2e-16 in each case; see Supplementary data 2).At the modern country level, the C3 grains from Lithuania (median −25.18 ± 1.16‰, n = 153) are on average nearly 2.5‰ lower than those from Jordan (median −22.86 ± 0.74‰, n = 46) (Fig. 3A, Table 2) which exceeds the previously defined offset of 1–2‰ between Southern and Northern Europe21,22,23. On the contrary, the Jordan sample is on average 0.80‰ more enriched than those from Greece (median −23.50 ± 0.82‰, n = 383) or Italy (median −23.50 ± 0.97‰, n = 497) despite their shared southern location. Consequently, the North–South-dichotomy is not enough to characterize the different isotopic composition of grains from diverse parts of Europe and does not account for micro-regional environmental diversity. Moreover, the northernmost countries show standard deviations (SD) of 1.29‰ on average (1.12 to 1.67‰ in total), which is sensibly more than in most of the southern (from 0.40 to 1.43‰; mean: 0.92‰) and of the central/western countries (from 0.39 to 1.51‰, mean: 0.90‰) (see the ANOVA test in Supplementary data 2).Fig. 3: Differences in archaeological charred C3 and C4 grain δ13C values in Europe.A C3 grain δ13C values over the modern countries. B C4 grain δ13C values over modern countries. C The comparison between latitude and C4 grain δ13C values shows a weak but significant negative correlation. Boxplots are defined in Fig. 2. The mean, median, MAD and SD values for each modern country are listed in Table 2. The results of the related one-way ANOVA tests and Pearson’s correlations are available from Supplementary data 2. The red labels show non-representative sample sizes (n < 10). Figure by Margaux L. C. Depaermentier, created using the open source R software.Full size imageSimilarly, the C4 grain δ13C values from Lithuania (median: −10.83 ± 0.48‰, n = 20) are on average nearly 1‰ lower than those from Greece (median: −10.19 ± 0.15‰, n = 12), France (median: −10.15‰, n = 16) or Poland (median: −10.19 ± 0.15‰, n = 9) (Fig. 3B, C; Table 2). The sample sizes from Spain (n = 3, median: −10.69 ± 0.15‰) and from the Czech Republic (n = 1) are too low to be considered representative. This trend confirms previous studies from China with depleted C4 grain δ13C values recorded at higher latitudes25,26. The pattern is further supported by the larger C4 grain δ13C dataset resulting from Alpha Magnetic Spectrometer (AMS) in Europe104, showing generally lower δ13C values in Northern compared to Southern or Central Europe (Fig. S8). However, AMS stable isotopic data lack precision due to differences in calibration compared to IRMS and provide particularly wide and unusual δ13C ranges for C4 grains105. Therefore, these data cannot be used to extend the IRMS dataset in this study. Differences in local plant genotypes are considered more likely triggers for the isotopic variability than climate and water availability24. Both C3 and C4 grains exhibit lower δ13C values in some northern regions relative to the rest of Europe, leading to regional variation in the δ¹³C threshold for identifying C4 consumption.Ecological isotopic variabilityThe geographical isotopic variability is related to environmental factors captured in the ecozone model. C3 grain samples from Lithuania (n = 153), Estonia (n = 11), Finland (n = 44), and from parts of Denmark (n = 86) fall into the subhumid temperate lowlands of North-Eastern Europe represented by ecozone 5 (n = 294). Together with ecozone 17 (n = 42)—represented by grains from Norway only—these samples exhibit the lowest median δ13C values (−25.01 ± 1.25‰ and −25.08 ± 1.20‰, respectively) for charred C3 grains in Europe (Fig. 4, Table 2). The high humidity, low temperature and low to moderately elevated topography of these ecozones can explain the depleted δ13C values20. Ecozone 20 (n = 717), represented by balanced temperate plains scattered over Europe and including samples mostly from Denmark, northern Germany and England, exhibit a much higher median δ13C value (−23.00 ± 1.16‰) and its range hardly overlaps with the other northern samples. Beyond the influence of agricultural practices mentioned above30,31, this can be explained by higher temperatures and moderate humidity characterizing this ecozone. In contrast, the 1007 samples from ecozone 17 and the 140 samples from ecozone 1 show the lowest median δ13C values among the sites below 50° latitude (−23.47 ± 0.82‰ and −23.35 ± 1.41‰, respectively). This reflects the mild and moist conditions of these transition zones at a mid-range altitude. In Southern Europe, the ecozones 7 and 13, representing warm highlands in the Mediterranean area, show the highest median δ13C values (−22.93 ± 1.35‰ and −22.56 ± 0.87‰, respectively), deriving from the drier and warmer climatic conditions. The ecozones 2, 8 and 19 are scattered over wide areas of Europe and are not related to extreme temperatures. Their isotopic ratios show intermediate values (Table 2). Ecozones 3, 12, 14, 15 and 18 cannot be included in this isotope investigation due to their small sample size.Fig. 4: C3 grains δ13C values over the European ecozones clusters.The ecozone numbers refer to the numbering in Table 1. Boxplots are defined in Fig. 2. The boxplots are ordered from top to bottom according to decreasing latitude and to increasing temperature within the ecozone. The red labels underline non-representative sample sizes (n < 10). The mean, median, MAD and SD values for each ecozone can be found in Table 2. The results of the one-way ANOVA test are available from Supplementary data 2. Figure by Margaux L. C. Depaermentier, created using the open source R software.Full size imageDiscussionBuilding on the substantial geographical and ecological variation in isotope values within C3 (and to a lesser extent C4) plants, it is essential to revise the commonly used δ13C threshold for identifying C4 consumption, such as −18.0‰ for mammal collagen (for example, ref. 7). At each investigated site, the C3 and C4 grain δ13C values from this dataset (Fig. 5A) were used to create theoretical collagen δ13C values for a diet based exclusively on these crops (Fig. 5B)—which is no realistic diet for humans or animals and was only used for a first theoretical model. This resulted in site-specific estimations for an overall C3 grain-based diet with 10% to 20% C4 grain inputs (Fig. 5B and Supplementary data 1). Our model shows that at several sites from the Baltic and Nordic countries, human or animal collagen δ13C values below −19.0‰ (with a mean SD of 0.59‰)—and up to −19.68 ± 0.94‰ at Bėlis lake, Lithuania (n = 10), for example—already reflect a low C4 input within a primarily C3-grain-based diet. In the Mediterranean, the same C4 input would result in collagen δ13C values above −17.0 ± 0.77 or −16.0 ± 0.57‰ (Fig. 5B and Supplementary data 1).Fig. 5: Point-based approach for baseline C3 grain δ13C values and estimated threshold values for C4 diet identification in mammal collagen at sites with n ≥ 10 grains.A Median C3 grain δ¹³C values (left) and related SD (right). B Median estimated threshold δ¹³C values for mammal collagen (left) and related SD (right) based on a theoretical 100%-grain-based-diet. The mean, median, SD and MAD values for each site are listed in Supplementary data 1. The same maps including even site with n < 10 are in Fig. S9. Figure by Margaux L. C. Depaermentier, created using the open source R software.Full size imageIt is generally accepted that at least 20% of dietary protein from an alternative source (such as C4 compared to C3 crops) is required to be detected in collagen106. However, with a model based on theoretical grain-based diets, a 20% C4 input produces excessively elevated δ13C estimates for mammal collagen (Supplementary data 1). This highlights the limits of a model based on non-realistic grain-based diets, as despite the important role of grains in human diet, both humans and animals have more varied diets in reality—the latter even consuming mostly other parts of the plant and only rarely grains. And with collagen δ13C values reflecting the protein component of the diet16, plant intake contributes less to collagen isotopic composition than animal-derived proteins, which may alter this threshold value in omnivorous diets. Moreover, in regions where the diet includes significant proportions of mushrooms107, forest-derived foods influenced by the canopy effect108,109, and/or freshwater fish110,111,112, consumers are exposed to more depleted δ13C values. These foods have a much stronger influence on collagen δ13C values than any enrichment from C4 plants. And since such conditions are highly plausible in the Baltics and in Scandinavia, the threshold δ13C value for C4 consumption might be even lower than those suggested by the model with 10% C4 input (Figs. 5A, B and  6). On the contrary, potential marine food consumption17 or sea-spray effects in coastal areas113 need to be considered to avoid any over-estimation of C4 plant intake.Fig. 6: Ecozone-based interpolation of the C3 grain δ13C baseline and of the estimated threshold δ13C values for detecting C4 consumers.A Median δ13C (left) and SD values (right) of charred C3 grains interpolated at the ecozone level. B Median δ13C (left) and SD values (right) of the estimated threshold ranges for C4 consumption for each ecozone. Ecozones 3, 12, 14, 15 and 18 are left grey due to their too small sample sizes. Ecozones 4, 9, 10, 11 and 15 are left grey due to the absence of data. The ecozone’s mean, median, SD and MAD values for C3 grains and for C4 consumption are listed in Table 2 and Tab. S1, respectively. Figure by Michael Kempf, created using the open source R and QGIS software.Full size imageA model involving all other food resources would go beyond the scope of this paper. But to accurately estimate the actual local threshold values for C4 consumption, it is essential to use δ13C and δ15N values from as many local and contemporaneous food resources as possible, including crops (for example32). Wild plants would further represent a better baseline for herbivore’s diets. Yet these are much more seldom in archaeological remains and their isotopic ratios are hardly represented in bioarchaeological studies so far. A model based on modern plants21 or on tree δ13C values114 can thus further serve as comparison δ13C baseline for herbivore’s diets. The combination of various isotope systems113,115,116 and/or the application of mixing models117 are further powerful approaches to disentangle the diverse dietary sources.Considerable isotopic variability is observed within each site, region and ecozone (Figs. 2–4 and 5A, Supplementary data 1–2), indicating that a range rather than a sharp threshold value is more appropriate (Figs. 5B and 6B). This isotopic variability is not only related to the gradual and complex variation of environmental settings across Europe, but is also intrinsic to the grains, as grain δ13C may vary for up to 0.5‰ within one ear despite same species and same growing conditions33. Differing growing conditions, in particular various watering practices, can further impact local grain δ13C values by up to 1.7‰24,28. Wild plants δ13C values may be good comparison references to disentangle anthropogenic and natural differences in water regimes21,118,119. Another variability might be induced by diverging analytical uncertainty between datasets, as the data result from different laboratories and protocols and were obtained with different calibrations—which are relevant information to make sure that the datasets are comparable120. Unfortunately, information on calibration, precision and accuracy of the published isotope data were mostly missing, thus it was not possible to assess the impact on the presented results. Yet when available, the error value for replicated samples was very low and still within the range of analytical errors.An evolution of the grain δ13C values might be expected over time as well, especially when considering the various climatic phases that implied a great variation in moisture and temperature throughout Europe over the investigated time frame. The presented regional differences in grain δ13C values have therefore varied between the climatic phases (Fig. S10), yet the isotopic variations within each region over the various climatic phases is overall significantly weak (Supplementary data 2). A larger dataset for the most recent periods might reveal more effective trends. In this study, the impact of the chronological depth and imbalance covered by this dataset can be considered weak (Figs. S2–S5 and S10).The isotopic difference reported in this study between regions and ecozone therefore remains strong enough to highlight environmentally-driven differences (Figs. 2–7, Table 2) even from grains that were possibly undergoing various cultivation practices. Our approach thus demonstrates that the threshold at −18.0‰ for consumer’s collagen is not universal and is mostly valid in the ecozone 2 (−17.51 ± 1.28‰), whereas the northern ecozone 5 and the widespread ecozone 17 require a threshold δ13C value closer to −19.0‰, i.e., −18.59 ± 1.12 and −18.67 ± 1.08‰, respectively. In high-temperature Mediterranean lowlands (ecozone 16), European plains (ecozone 19), and Atlantic regions (ecozone 20), the threshold shifts to −17.0‰ (i.e., −16.88 ± 0.90‰, −17.15 ± 0.74‰, and −16.71 ± 1.05‰, respectively; Figs. 6, 7, Tab. S1). In the arid southern regions (ecozone 13 [−16.31 ± 0.78‰], and partially ecozones 7 and 16), it approaches −16.0‰ (Fig. 7, Tab. S1). Yet in each case, the SD ranges from 0.74 to 1.26‰, stressing again the isotopic variability within ecozones.Fig. 7: Theoretical δ13C threshold ranges for C4 consumption across the European ecozone clusters.The ecozone numbers refer to the numbering in Table 1. Boxplots are defined in Fig. 1. The boxplots are ordered from top to bottom according to decreasing latitude and to increasing temperature within the ecozone. The red labels underline non-representative sample sizes (n < 10). The mean, median, MAD and SD values for each ecozone are listed in Tab. S1. The purple line represents the revised δ13C threshold value for C4 consumption in mammal collagen (i.e., −18.0‰). Figure by Margaux L. C. Depaermentier, created using the open source R software.Full size imageTo conclude, this paper offers both a European-wide δ13C baseline from archaeological charred C3 grains and a threshold-value-model for environmentally adjusted identification of C4 consumption from the site to the ecozone level across Europe (Fig. 7, Tab. S1). The grain baseline offers the advantage to consider a fundamental dietary resource (in particular for humans) as reference data and can be completed by local foods resources at the site level for more holistic and accurate interpretations. A comparison to wild proxies further enhances the results for animal diets. The threshold estimations are particularly suitable in bioarchaeological, ecological or palaeontological studies for which local plants or food resources are unavailable for calculating an isotopic baseline. However, it requires to account for the great degree of isotopic variability within each geographical entity as underlined by the SD values—a variability slightly increasing with latitude. In this context, the point-based approach (Fig. 5) provides more accurate yet geographically discrete data, while the interpolation-based approach (Fig. 6) offers ecologically sensitive estimates over large areas at the ecozone level, both related to some degree of uncertainty or variability. Future datasets could be used to test (and if necessary adjust) the interpolated values in areas of currently low site density. This innovative and context-sensitive ecozone clustering model based on temperature, humidity, and elevation thus enables more accurate interpretations of both animal ecologies and anthropogenic social and agricultural dynamics across Europe by avoiding over- or underestimation of C4 consumption.Methods and materialIsotopic datasetThe material used in this study consists of published δ13C values from charred grains derived from archaeological context, compiled into one single dataset27. The data was collected from 75 publications until September 202528,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101, also using the open access online repositories IsoArch121, MAIA122, Isotòpia123, IsoMedIta124 and CIMA125. In total, this represents 4,210 δ13C values of C3 and C4 grains derived from 260 sites dated between 8000 BCE and 1800 CE. The represented C3 plants are oat (Avena species, n = 58), rye (Secale species, n = 325), barley (Hordeum species, n = 1843), and wheat (Triticum species, n = 1923). Broomcorn millet (Panicum miliaceum, n = 57) and foxtail millet (Setaria italica, n = 4) represent the C4 crops from this dataset. To facilitate visualization and pattern-recognition, the C3 and C4 grain datasets were considered separately for the various analyses due to their distinct δ13C values and due to the particularly small C4 grain sample size. C3 and C4 grain δ13C values were then combined to address the question of identifying the introduction of C4 crops in C3 plants-based diets. Despite the fact that anthropogenic agricultural practices such as irrigation can impact grain δ13C values24,28, altering the natural and ecological signal, crops remain an important proxy for human diet regardless of agricultural practices, as their isotopic composition would be transferred to human tissues all the same. The ecological differences are considered important enough across Europe to be detectable from grain isotopic composition despite anthropogenic alterations. Wild plants would have represented a better proxy for animal diet, however, this proxy is lacking from archaeological contexts—or could be derived from tree δ13C values for the most recent periods114.Geographically, the research area spans modern Europe and the Mediterranean countries of the Near East, i.e., between 30 and 63° (N) latitude and between −8 and 45° (E) longitude. Yet the data is not evenly distributed and Denmark is over-represented in terms of sites, while Greece is over-represented in terms of number of samples. There are considerable gaps in several regions of Europe (see Fig. 1 and the isotopic dataset27). Chronologically, this dataset covers most archaeological and historical periods and ranges from 8000 BCE to 1800 CE. In this context, it is important to stress that the oldest samples (8000–6000 BCE) exclusively originate from Greece, whereas samples from Northern Europe are predominantly younger than 1000 BCE—except for some larger site samples dated between 4000 BCE and 2000 BCE. Modern data created in the framework of experimental archaeology were not included in the dataset because of the controlled conditions in which they were produced and because of the different present-day atmospheric composition compared to pre-industrial periods126.Only data obtained from Isotope-Ratio Mass Spectrometry (IRMS) were selected for analyses. Despite the fact that these values are not comparable to IRMS isotopic values due to different calibrations105, a European-wide dataset obtained from Accelerator Mass Spectrometry (AMS) in the context of radiocarbon measurements104 was also used as a comparison dataset to verify whether the same trend is visible among both datasets. Importantly, grain δ13C values are sometimes (i.e., in 12 out of 64 publications used in this study) published in form of corrected values to consider the charring effect on the carbon isotope composition of archaeological C3127,128 and C4 grains129,130. But following the approach by Gron et al.30, we are considering here only uncorrected values in order to enhance the comparability between datasets. This is considered to have no significant impact on this study’s results, as the charring effect is not systematic33 particularly low on grain δ13C values (i.e., 0.06 to 0.18‰33,127,128,129,130 on C3 and C4 grains for a heat up to 300 °C) and remains below analytical errors for isotope analyses131.Statistical analysesAll statistical analyses were performed using R software132 and the results and relevant values are summarised in Supplementary data 2. To determine the relationship between grain δ13C values and chronology or geographical location, we applied both Pearson’s correlation tests and linear models—the latter using the lme4 package133. The Pearson correlation coefficient (Pearson’s r value) indicated the strength and direction of a linear relationship between two tested variables, the confidence interval gives the uncertainty range for the true correlation. While in the linear model, the R-squared values show the percentage of the dataset affected by the relationship and the p-values show the significance of the results. To determine the geographical scale at which significant changes in grain values occur, the dataset was divided into various bins. At the largest scale, the main regions of Europe, split into Northern Europe, Southern Europe, Central/Western Europe and the UK. This is not only convenient but also follows expectations based on previous research21,22,23. At the smallest geographical scale, the dataset was binned according to the borders of modern countries. Boxplots were used for data visualization and one-way ANOVA tests were performed to test the difference in grain δ13C values between the investigated clusters. The results and relevant values for the ANOVA tests are summarised in Supplementary data 2). Because our dataset shows a particularly important isotopic variability, the results for each considered bin or entity/group are presented in the text using the median value (since the mean value is more sensitive to extreme outliers) and the related one standard deviation (1 SD). The tables are showing the mean, median, median absolute deviation (MAD) and 1 SD for each category/bin. In order to integrate an ecological dimension to the investigation of grain δ13C variability, the dataset was also binned into newly determined ecozones, as presented in the section below.Environmental clusterFor the cluster analysis, we used these R-packages: terra134, sf 135,136, gtools137, dplyr138 and ggplot2139, ggspatial140, gridExtra141 for plotting, as described in the R-code provided in the open access repository to this paper142. We used an unsupervised k-means clustering approach based on three spatial predictors to differentiate environmental ecozones across Europe. Components include elevation (DEM), mean temperature (T), and the Climatic Moisture Index (CMI). A DEM derived from the USGS (United States Geological Survey, Global Multi-resolution Terrain Elevation Data 2010, https://earthexplorer.usgs.gov/; last accessed 19th of June 2025). Monthly resolved climate variables for the period 1980-2018 were downloaded from CHELSA143. The CMI represents a standardized water availability index, calculated as the ratio of precipitation (P) to potential evapotranspiration (PET) with CMI = P − PET. We used CHELSA v2.1 monthly CMI data based on the Penman-Monteith equation for PET and downscaled from ERA5 reanalysis. The grids were reprojected to a meter-based projection (EPSG:3857) and cropped to the extent of the geographic European landmass. The dataset (n = 468) were aggregated to a 1000 m resolution using bilinear interpolation prior to clustering. Monthly layers were averaged to create a multiannual mean (1980–2018). To allow comparison between variables with different scales and units, all raster layers were standardized using z-score normalization with mean and standard deviation (sd) of the raster (z = cell value − mean_raster / sd_raster). A regular grid of 1 km spacing was generated across the study area and the centroid of each grid cell was calculated for regular point sampling. To reduce edge effects and avoid NA values near the coast, centroids were restricted to land areas using a simplified buffer around the European landmass boundaries. At each centroid location, the values were extracted from the normalized rasters.
    K-Means clusteringK-means clustering was performed using the extracted values, with the determined number of clusters k = 20. This dimensionality was chosen to balance regional ecological resolution with model interpretability, including NA values (replaced by −99999 during the cluster analysis to protect correct geographical raster reassignment). Each centroid was assigned a cluster label based on the combined environmental profile of elevation, temperature, and moisture availability. Cluster labels were spatially joined to centroid coordinates and rasterized back into a continuous spatial layer using the DEM grid as a template. The resulting map classifies observational sites into discrete clustered ecozones (Fig. 1).To characterize each of the 20 ecozone clusters based on the data variability, we summarized the environmental properties of each cluster using the mean and standard deviation of the three input variables: Elevation (ELEV), T, and CMI. All values were normalized using z-scores prior to clustering, enabling direct comparison across variables. The clusters were then qualitatively interpreted based on their relative environmental signatures. For example, clusters with low temperatures, moderately dry conditions and high elevations were categorized as Cool|Moderately Dry|Alpine zones. Clusters with high temperatures and low moisture availability in low areas were described as Very Hot|Very Dry|Moderately Low. Intermediate clusters were labeled based on transitional or temperate climate conditions (Table 1).Determining consumer’s δ
    13C valuesTo determine the theoretically expected δ13C values of consumer tissues from a mixed C3-C4 diet, we first associated each C3 grain δ13C value to a measured or assumed C4 grain δ13C value. This means that for each site at which δ13C values of both C3 and C4 grains were available, each C3 grain δ13C value got associated with the mean C4 grain δ13C value of the site. However, most of the sites included in this study provided no C4 grain. In this case, a theoretical C4 grain δ13C value was determined for the site based on the observed values from this dataset. In most regions of Europe, the C4 grain δ13C value is thus expected to be −10‰32,72,87. Yet we observed that the C4 grain δ13C values in Lithuania—and by extension presumably in the northernmost latitudes of Europe—were rather around −11‰68. Similarly, C4 grain δ13C values from the western Mediterranean area seem to be closer to −10.5‰35,47. These regional values were thus used as theoretical C4 grain δ13C values associated with the measured C3 grain δ13C values at each site lacking C4 grains (see summary in Supplementary data 1).In a second step, 5‰ was added to each measured or theoretical grain δ13C value to mimic the fractionation offset that applies between the diet and the consumer’s collagenous tissues after consumption16,17. We applied this to both C3 and C4 grains, resulting in theoretical end-members collagen δ13C values for 100% C3 and 100% C4 based diet, respectively. In a third step, we used these end-members values for each grain to create theoretical collagen δ13C values for a C3-grain-based diet including either 10% or 20% C4 grains. These three first steps were done at the grain level to minimize the loss of resolution and information when working with mean values. In a fourth step, we eventually calculated a mean δ13C value for these two types of diet at the site level (Supplementary data 1). It is fundamental to note that these fictitious diets based on 100% grains are not existing in nature and only represent a theoretical model using grains only.Because a 100% grain-based diet does not exist in nature, the model using 10% of C4 input was considered the most reliable basis for estimating the related collagen δ13C values with low C4 input in a normal mixed diet. These results are presented at the site-level to account for local variability in threshold δ13C values for C4 consumption (Fig. 5). The ecozone cluster model was used to create a map of interpolated threshold δ13C values for C4 consumption and hence suggest environmentally adjusted threshold δ13C values for C4 consumption (Fig. 6C). The European background maps used to create Figs. 5 and 6 are vector map data from https://www.naturalearthdata.com/, implemented using the package rnaturalearth in R-Software132,144.Materials & correspondenceThe corresponding authors are MLCD and MK. The isotopic dataset used in this study is available from the open access repository: Depaermentier, M. L. C. (2025). Isotopic Dataset to: Depaermentier, MLC, Kempf, M, Motuzaitė Matuzevičiūtė, G. “Environmentally adjusted δ13C thresholds for accurate detection of C4 plant consumption in Europe” [Data set]. In Communications Earth & Environment. Zenodo. https://doi.org/10.5281/zenodo.17571650 [ref. 27 in this paper]. The data to reproduce the ecozone clusters is available from this open access repository: Kempf, M. (2025): Related files to: Depaermentier, MLC; Kempf, M; Motuzaitė Matuzevičiūtė, G: Environmentally adjusted δ13C thresholds for accurate detection of C4 plant consumption in Europe (2025) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.15695070 [ref. 147 in this paper]. Climate variables used in this article are freely available from Karger et al. (2017): https://chelsa-climate.org/ (last accessed 19th of June 2025) [ref. 143 in this paper]. The Digital Elevation Model (DEM) can be downloaded from the USGS earthexplorer server: https://earthexplorer.usgs.gov/, last accessed 19th of June 2025.Reporting summaryFurther information on research design is available in the Nature Portfolio Reporting Summary linked to this article.

    Data availability

    The compiled isotopic dataset used in this study is available from the open access repository: Depaermentier, M. L. C. (2025). Isotopic Dataset to: Depaermentier, MLC, Kempf, M, Motuzaitė Matuzevičiūtė, G. “Environmentally adjusted δ13C thresholds for accurate detection of C4 plant consumption in Europe” [Data set]. In Communications Earth & Environment. Zenodo. https://doi.org/10.5281/zenodo.17571650 [ref. 27 in this paper]. The data to reproduce the ecozone clusters is available from this open access repository: Kempf, M. (2025): Related files to: Depaermentier, MLC; Kempf, M; Motuzaitė Matuzevičiūtė, G: Environmentally adjusted δ13C thresholds for accurate detection of C4 plant consumption in Europe (2025) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.15695070 [ref. 147 in this paper]. Climate variables used in this article are freely available from Karger et al. (2017)143: https://chelsa-climate.org/ (last accessed 19th of June 2025). The Digital Elevation Model (DEM) can be downloaded from the USGS earthexplorer server: https://earthexplorer.usgs.gov/, last accessed 19th of June 2025.
    Code availability

    The code to reproduce the ecozone clusters is available from this open access repository: Kempf, M. (2025): Related files to: Depaermentier, MLC; Kempf, M; Motuzaitė Matuzevičiūtė, G: Environmentally adjusted δ13C thresholds for accurate detection of C4 plant consumption in Europe (2025) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.15695070 [ref. 147 in this paper].
    ReferencesVentresca-Miller, A. R. et al. Adaptability of millets and landscapes: ancient cultivation in North-Central Asia. Agronomy 13, 2848 (2023).Article 
    CAS 

    Google Scholar 
    Motuzaitė Matuzevičiūtė, G. Broomcorn millet: from the past to the future. AFF 2, 177–198 (2025).Article 

    Google Scholar 
    Hakenbeck, S. E., Evans, J., Chapman, H. & Fothi, E. Practising pastoralism in an agricultural environment: an isotopic analysis of the impact of the Hunnic incursions on Pannonian populations. PloS One 12, e0173079 (2017).Article 

    Google Scholar 
    Kaupová, S. et al. Dukes, elites, and commoners: dietary reconstruction of the early medieval population of Bohemia (9th–11th Century AD, Czech Republic). Archaeol. Anthropol. Sci. 11, 1887–1909 (2019).Article 

    Google Scholar 
    Martin, L. et al. The place of millet in food globalization during Late Prehistory as evidenced by new bioarchaeological data from the Caucasus. Sci. Rep. 11, 13124 (2021).Article 
    CAS 

    Google Scholar 
    Sneha, M. L. & Arjun, R. Medicinal knowledge In South India (during neolithic to early historic period): an analysis of staple plant dietary nutrition. CMDR J. Soc. Res. 1, 35–48 (2024).
    Google Scholar 
    Lightfoot, E., Liu, X. & Jones, M. K. Why move starchy cereals? A review of the isotopic evidence for prehistoric millet consumption across Eurasia. World Archaeol. 45, 574–623 (2013).Article 

    Google Scholar 
    Drucker, D. G. The isotopic ecology of the mammoth steppe. Annu. Rev. Earth Planet. Sci. 50, 395–418 (2022).Article 
    CAS 

    Google Scholar 
    Drucker, D. G. et al. Ecology of large ungulates in the northeastern Iberian Peninsula during the Upper Palaeolithic through stable isotopes and tooth wear analysis. Quat. Environ. Hum. 2, 100011 (2024).
    Google Scholar 
    Terry, R. C., Guerre, M. E. & Taylor, D. S. How specialized is a diet specialist? Niche flexibility and local persistence through time of the Chisel-toothed kangaroo rat. Funct. Ecol. 31, 1921–1932 (2017).Article 

    Google Scholar 
    Saarinen, J., Mantzouka, D. & Sakala, J. Aridity, cooling, open vegetation, and the evolution of plants and animals during the cenozoic. In Nature through Time, edited by E. Martinetto, E. Tschopp & R. A. Gastaldo, pp. 83–107 (Springer International Publishing, Cham, 2020).Prasifka, J. & Heinz, K. The use of C3 and C4 plants to study natural enemy movement and ecology, and its application to pest management. Int. J. Pest Manag. 50, 177–181 (2004).Article 

    Google Scholar 
    Cerling, T. E., Wang, Y. & Quade, J. Expansion of C4 ecosystems as an indicator of global ecological change in the late Miocene. Nature 361, 344–345 (1993).Article 

    Google Scholar 
    Farquhar, G. D. On the nature of carbon isotope discrimination in C4 species. Funct. Plant Biol. 10, 205 (1983).CAS 

    Google Scholar 
    O’Leary, M. H. Carbon isotope fractionation in plants. Phytochemistry 20, 553–567 (1981).Article 

    Google Scholar 
    Ambrose, S. H. Isotopic Analysis of Paleodiets: Methodological and Interpretative Considerations. In Investigations of ancient human tissue. Chemical analyses in anthropology, edited by M. K. Sandford, pp. 59–130 (Gordon and Breach, Philadelphia, 1993).Lee-Thorp, J. A. On isotopes and old bones. Archaeometry 50, 925–950 (2008).Article 
    CAS 

    Google Scholar 
    Kellner, C. M. & Schoeninger, M. J. A simple carbon isotope model for reconstructing prehistoric human diet. Am. J. Phys. Anthropol. 133, 1112–1127 (2007).Article 

    Google Scholar 
    Froehle, A. W., Kellner, C. M. & Schoeninger, M. J. Multivariate carbon and nitrogen stable isotope model for the reconstruction of prehistoric human diet. Am. J. Phys. Anthropol. 147, 352–369 (2012).Article 
    CAS 

    Google Scholar 
    van Klinken, G. J., Richards, M. P. & Hedges, R. E. M. An Overview of Causes for Stable Isotopic Variations in Past European Human Populations. Environmental, Ecophysiological, and Cultural Effects. In Biogeochemical approaches to paleodietary analysis. Advances in archaeological and museum science, edited by S. H. Ambrose & M. A. Katzenberg, pp. 39–63 (New York, London, 2002).Cooper, C. G., Cooper, M. D., Richards, M. P. & Schmitt, J. Geographic and seasonal variation in δ13C values of C3 plant arabidopsis: Archaeological implications. J. Archaeol. Sci. 149, 105709 (2023).Article 
    CAS 

    Google Scholar 
    van Klinken, G. J., van der Plicht, J. & Hedges, R. E. M. Bone 13C/12C ratios reflect (palaeo) climatic variations. Geophys. Res. Lett. 21, 445–448 (1994).Article 

    Google Scholar 
    Hedges, R. E., Stevens, R. E. & Richards, M. Bone as a stable isotope archive for local climatic information. Quat. Sci. Rev. 23, 959–965 (2004).Article 

    Google Scholar 
    Lightfoot, E. et al. Carbon and nitrogen isotopic variability in foxtail millet (Setaria italica) with watering regime. Rapid Commun. Mass Spectrom. 34, e8615 (2020).Article 
    CAS 

    Google Scholar 
    An, C.-B. et al. Variability of the stable carbon isotope ratio in modern and archaeological millets: evidence from northern China. J. Archaeol. Sci. 53, 316–322 (2015).Article 

    Google Scholar 
    Dong, Y. et al. The potential of stable carbon and nitrogen isotope analysis of foxtail and broomcorn millets for investigating ancient farming systems. Front. plant Sci. 13, 1018312 (2022).Article 
    CAS 

    Google Scholar 
    Depaermentier, M. L. C. Isotopic dataset to: Depaermentier, MLC, Kempf, M, Motuzaitė Matuzevičiūtė, G. “Environmentally adjusted δ13C thresholds for accurate detection of C4 plant consumption in Europe” (2025).Araus, J. L. et al. Identification of Ancient Irrigation Practices based on the Carbon Isotope Discrimination of Plant Seeds: a Case Study from the South-East Iberian Peninsula. J. Archaeol. Sci. 24, 729–740 (1997).Article 

    Google Scholar 
    Lightfoot, E. & Stevens, R. E. Stable isotope investigations of charred barley (Hordeum vulgare) and wheat (Triticum spelta) grains from Danebury Hillfort: implications for palaeodietary reconstructions. J. Archaeol. Sci. 39, 656–662 (2012).Article 
    CAS 

    Google Scholar 
    Gron, K. J. et al. Archaeological cereals as an isotope record of long-term soil health and anthropogenic amendment in southern Scandinavia. Quat. Sci. Rev. 253, 106762 (2021).Article 

    Google Scholar 
    Hald, M. M. et al. Farming during turbulent times: agriculture, food crops, and manuring practices in bronze age to viking age Denmark. J. Archaeol. Sci. Rep. 58, 104736 (2024).
    Google Scholar 
    Nitsch, E. et al. A bottom-up view of food surplus: using stable carbon and nitrogen isotope analysis to investigate agricultural strategies and diet at Bronze Age Archontiko and Thessaloniki Toumba, northern Greece. World Archaeol. 49, 105–137 (2017).Article 

    Google Scholar 
    Heaton, T. H., Jones, G., Halstead, P. & Tsipropoulos, T. Variations in the 13C/12C ratios of modern wheat grain, and implications for interpreting data from Bronze Age Assiros Toumba, Greece. J. Archaeol. Sci. 36, 2224–2233 (2009).Article 

    Google Scholar 
    Aguilera, M., Zech-Matterne, V., Lepetz, S. & Balasse, M. Crop fertility conditions in north-eastern Gaul during the la tène and roman periods: a combined stable isotope analysis of archaeobotanical and archaeozoological remains. Environ. Archaeol. 23, 323–337 (2018).Article 

    Google Scholar 
    Alagich, R., Gardeisen, A., Alonso, N., Rovira, N. & Bogaard, A. Using stable isotopes and functional weed ecology to explore social differences in early urban contexts: the case of Lattara in mediterranean France. J. Archaeol. Sci. 93, 135–149 (2018).Article 

    Google Scholar 
    Antanaitis, I. & Ogrinc, N. Chemical analysis of bone: stable isotope evidence of the diet of Neolithic and Bronze Age people In Lithuania. Istorija XLV, 3–12 (2000).
    Google Scholar 
    Araus, J. L. & Buxó, R. Changes in carbon isotope discrimination in grain cereals from the north-western mediterranean basin during the past seven millenia. Funct. Plant Biol. 20, 117 (1993).CAS 

    Google Scholar 
    Araus, J. L. et al. Changes in carbon isotope discrimination in grain cereals from different regions of the western Mediterranean Basin during the past seven millennia. Palaeoenvironmental evidence of a differential change in aridity during the late Holocene. Glob. Change Biol. 3, 107–118 (1997).Article 

    Google Scholar 
    Araus, J. L. et al. Isotope and morphometrical evidence reveals the technological package associated with agriculture adoption in western Europe. PNAS 121, e2401065121 (2024).Article 
    CAS 

    Google Scholar 
    Ben Makhad, S. et al. Crop manuring on the Beauce plateau (France) during the second iron age. J. Archaeol. Sci.: Rep. 43, 103463 (2022).
    Google Scholar 
    Bernardini, S. et al. New multi-proxy isotopic data on the copper age of eastern Liguria. Riv. di Sci. Preistoriche LXXIII S3, 1037–1043 (2023).
    Google Scholar 
    Bogaard, A. et al. From traditional farming in morocco to early urban agroecology in northern mesopotamia: combining present-day arable weed surveys and crop isotope analysis to reconstruct past agrosystems in (semi-)arid regions. Environ. Archaeol. 23, 303–322 (2018).Article 

    Google Scholar 
    Bogaard, A. et al. Crop manuring and intensive land management by Europe’s first farmers. Proc. Natl. Acad. Sci. USA 110, 12589–12594 (2013).Article 
    CAS 

    Google Scholar 
    Cortese, F. et al. Isotopic reconstruction of the subsistence strategy for a Central Italian Bronze Age community (Pastena cave, 2 nd millennium BCE) (2022).DiBenedetto, K. E. Investigating Land Use by the Inhabitants of Western Cyprus During the Early Neolithic (2018).Eklund, M. Changing Agriculture. Stable isotope analysis of charred cereals from Iron Age Öland. (Master thesis, Stockholm University, Stockholm, 2019).Fernández-Crespo, T., Ordoño, J., Bogaard, A., Llanos, A. & Schulting, R. A snapshot of subsistence in Iron Age Iberia: the case of La Hoya village. J. Archaeol. Sci.: Rep. 28, 102037 (2019).
    Google Scholar 
    Fiorentino, G. et al. Third millennium B.C. climate change in Syria highlighted by Carbon stable isotope analysis of 14C-AMS dated plant remains from Ebla. Palaeogeogr. Palaeoclimatol. Palaeoecol. 266, 51–58 (2008).Article 

    Google Scholar 
    Fiorentino, G., Caracuta, V., Casiello, G., Longobardi, F. & Sacco, A. Studying ancient crop provenance: implications from δ(13)C and δ(15)N values of charred barley in a Middle Bronze Age silo at Ebla(NW Syria). Rapid Commun. Mass Spectrom. 26, 327–335 (2012).Article 
    CAS 

    Google Scholar 
    García-Collado, M. I. et al. First direct evidence of agrarian practices in the alava plateau (northern Iiberia) during the middle ages through carbon and nitrogen stable isotope analyses of charred seeds. Environ. Archaeol. 1–11 (2022).Gavériaux, F. et al. L’alimentation des premières sociétés agropastorales du Sud de la France: premières données isotopiques sur des graines et fruits carbonisés néolithiques et essais de modélisation. Comptes Rendus. Palevol. (2021).Gavériaux, F., Motta, L., Bailey, P., Brilli, M. & Sadori, L. Crop husbandry at gabii during the iron age and archaic period: the archaeobotanical and stable isotope evidence. Environ. Archaeol. 29, 370–383 (2024).Article 

    Google Scholar 
    Gillis, R. E. et al. Stable isotopic insights into crop cultivation, animal husbandry, and land use at the Linearbandkeramik site of Vráble-Veľké Lehemby (Slovakia). Archaeol. Anthropol. Sci. 12; https://doi.org/10.1007/s12520-020-01210-2 (2020).Gron, K. J. et al. Nitrogen isotope evidence for manuring of early Neolithic Funnel Beaker Culture cereals from Stensborg, Sweden. J. Archaeol. Sci.: Rep. 14, 575–579 (2017).
    Google Scholar 
    Halvorsen, L. S., Mørkved, P. T. & Hjelle, K. L. Were prehistoric cereal fields in western Norway manured? Evidence from stable isotope values (δ15N) of charred modern and fossil cereals. Veget. Hist. Archaeobot. 32, 583–596 (2023).Article 

    Google Scholar 
    Fraser, R. A., Bogaard, A., Schäfer, M., Arbogast, R. & Heaton, T. H. E. Integrating botanical, faunal and human stable carbon and nitrogen isotope values to reconstruct land use and palaeodiet at LBK Vaihingen an der Enz, Baden-Württemberg. World Archaeol. 45, 492–517 (2013).Article 

    Google Scholar 
    Isaakidou, V. et al. Changing land use and political economy at neolithic and bronze Age Knossos, Crete: stable carbon (δ 13 C) and nitrogen (δ 15 N) isotope analysis of charred crop grains and faunal bone collagen. Proc. Prehist. Soc. 88, 155–191 (2022).Article 

    Google Scholar 
    Kanstrup, M. When δ15N values reveal manuring practice. Empirical evidence from fieldwork, charring experiments and archaeobotanical remains (Aarhus Universitet, Institut for Agroøkologi, Aarhus, 2012).Karakaya, D. Botanical Aspects of the Environment and Economy at Tell Tayinat from the Bronze to Iron Ages (ca. 2.200–600 BCE), In south-central Turkey (Doctoral Dissertation, Universität Tübingen (Germany), Doctoral Dissertation, Universität Tübingen (Germany, 2020).Karaliūtė, R., Motuzaitė Matuzevičiūtė, G., Styring, A. & Stroud, E. 2600 Years of farming in Eastern Lithuania: soil management according to ancient barley isotopic values. Quaternary Environments and Humans (in preparation).Knipper, C. et al. What is on the menu in a Celtic town? Iron age diet reconstructed at Basel-Gasfabrik, Switzerland. Archaeol. Anthropol. Sci. 9, 1307–1326 (2017).Article 

    Google Scholar 
    Knipper, C. et al. Reconstructing Bronze Age diets and farming strategies at the early Bronze Age sites of La Bastida and Gatas (southeast Iberia) using stable isotope analysis. PloS One 15, e0229398 (2020).Article 
    CAS 

    Google Scholar 
    Lodwick, L. Cultivating villa economies: archaeobotanical and isotopic evidence for iron age to roman agricultural practices on the chalk downlands of Southern Britain. Eur. j. archaeol. 26, 445–466 (2023).Article 

    Google Scholar 
    Lodwick, L., Campbell, G., Crosby, V. & Müldner, G. Isotopic evidence for changes in cereal production strategies in iron age and Roman Britain. Environ. Archaeol. 26, 13–28 (2021).Article 

    Google Scholar 
    Maltas, T., Şahoğlu, V., Erkanal, H. & Tuncel, R. From horticulture to agriculture: New data on farming practices in Late Chalcolithic western Anatolia. J. Archaeol. Sci.: Rep. 43, 103482 (2022).
    Google Scholar 
    Martínez Sánchez, R. M. et al. Archaeology, chronology, and age-diet insights of two late fourth millennium cal BC pit graves from central southern Iberia (Córdoba, Spain). Int. J. Osteoarchaeol. 30, 245–255 (2020).Article 

    Google Scholar 
    Messager, E. et al. Archaeobotanical and isotopic evidence of Early Bronze Age farming activities and diet in the mountainous environment of the South Caucasus: a pilot study of Chobareti site (Samtskhe–Javakheti region). J. Archaeol. Sci. 53, 214–226 (2015).Article 
    CAS 

    Google Scholar 
    Minkevičius, K. et al. New insights into the subsistence economy of the Late Bronze Age (1100–400 cal BC) communities in the southeastern Baltic. Archaeol. Balt. 30, 58–79 (2023).Article 

    Google Scholar 
    Mnich, B. et al. Terrestrial diet in prehistoric human groups from southern Poland based on human, faunal and botanical stable isotope evidence. J. Archaeol. Sci.: Rep. 32, 102382 (2020).
    Google Scholar 
    Mora-González, A. et al. The isotopic footprint of irrigation in the western Mediterranean basin during the Bronze Age: the settlement of Terlinques, southeast Iberian Peninsula. Veget Hist. Archaeobot. 25, 459–468 (2016).Article 

    Google Scholar 
    Mora-González, A., Teira-Brión, A., Granados-Torres, A., Contreras-Cortés, F. & Delgado-Huertas, A. Agricultural production in the 1st millennium BCE in Northwest Iberia: results of carbon isotope analysis. Archaeol. Anthropol. Sci. 11, 2897–2909 (2019).Article 

    Google Scholar 
    Mueller-Bieniek, A. et al. Spatial and temporal patterns in Neolithic and Bronze Age agriculture in Poland based on the stable carbon and nitrogen isotopic composition of cereal grains. J. Archaeol. Sci.: Rep. 27, 101993 (2019).
    Google Scholar 
    Niekamp, A. N. Crop growing conditions and agricultural practices in bronze age greece: a stable isotope analysis of archaeobotanical remains from Tsoungiza (Master’s thesis, University of Cincinnati, 2016).Nitsch, E. K., Jones, G., Sarpaki, A., Hald, M. M. & Bogaard, A. Farming practice and land management at Knossos, Crete: new insights from δ13C and δ15N analysis of Neolithic and Bronze Age crop remains. In Country in the City: Agricultural functions of protohistoric urban settlements (Aegean and Western Mediterranean), edited by D. Garcia, R. Orgeolet, M. Pomadère & J. Zurbach (Archaeopress, Oxford, 2019), pp. 159–173.O’connell, T. C. et al. Living and dying at the Portus Romae. Antiquity 93, 719–734 (2019).Article 

    Google Scholar 
    Pate, F. D., Henneberg, R. J. & Henneberg, M. Stable carbon and nitrogen isotope evidence for dietary variability at ancient Pompeii, Italy; https://doi.org/10.5281/zenodo.35526 (2015).Pilaar Birch, S. E. et al. Herd management and subsistence practices as inferred from isotopic analysis of animals and plants at Bronze Age Politiko-Troullia, Cyprus. PloS One 17, e0275757 (2022).Article 
    CAS 

    Google Scholar 
    Piličiauskas, G. et al. The earliest evidence for crop cultivation during the Early Bronze Age in the southeastern Baltic. J. Archaeol. Sci.: Rep. 36, 102881 (2021).
    Google Scholar 
    Riehl, S., Bryson, R. & Pustovoytov, K. Changing growing conditions for crops during the Near Eastern Bronze Age (3000–1200 BC): the stable carbon isotope evidence. J. Archaeol. Sci. 35, 1011–1022 (2008).Article 

    Google Scholar 
    Speciale, C. et al. The case study of Case Bastione: first analyses of 3rd millennium cal BC paleoenvironmental and subsistence systems in central Sicily. J. Archaeol. Sci.: Rep. 31, 102332 (2020).
    Google Scholar 
    Styring, A. K. et al. Urban form and scale shaped the agroecology of early ‘cities’ in northern Mesopotamia, the Aegean and Central Europe. J. Agrar. Change 22, 831–854 (2022).Article 

    Google Scholar 
    Vaiglova, P. et al. An integrated stable isotope study of plants and animals from Kouphovouno, southern Greece: a new look at Neolithic farming. J. Archaeol. Sci. 42, 201–215 (2014).Article 
    CAS 

    Google Scholar 
    Vaiglova, P. et al. Of cattle and feasts: Multi-isotope investigation of animal husbandry and communal feasting at Neolithic Makriyalos, northern Greece. PloS One 13, e0194474 (2018).Article 

    Google Scholar 
    Vaiglova, P. et al. Exploring diversity in neolithic agropastoral management in mainland greece using stable isotope analysis. Environ. Archaeol. 28, 62–85 (2021).Article 

    Google Scholar 
    Vanhanen, S. & Ilves, K. Flax use, weeds and manuring in Viking Age Åland: archaeobotanical and stable isotope analysis. Veget. Hist. Archaeobot. 34, 501–517 (2025).Article 

    Google Scholar 
    Varalli, A. et al. Bronze Age innovations and impact on human diet: a multi-isotopic and multi-proxy study of western Switzerland. PloS One 16, e0245726 (2021).Article 
    CAS 

    Google Scholar 
    Varalli, A. et al. Insights into the frontier zone of Upper Seine Valley (France) during the Bronze Age through subsistence strategies and dietary patterns. Archaeol. Anthropol. Sci. 15; https://doi.org/10.1007/s12520-023-01721-8 (2023).Wallace, M. P. et al. Stable carbon isotope evidence for neolithic and bronze age crop water management in the Eastern Mediterranean and Southwest Asia. PloS One 10, e0127085 (2015).Article 

    Google Scholar 
    Lempiäinen-Avci, M. et al. New insight into medieval cultivation at the village of Mankby in Espoo, Finland – comparing stable isotopes of carbon δ¹³C and nitrogen δ¹⁵N of Secale and Hordeum from Mankby to 14th century grain materials from Estonia. In Shattered and Scattered Pasts. Festschrift for Professor Georg Haggrén, edited by T. Heinonen, et al., pp. 68–85 (Waasa Graphics, Vaasa, 2025).Ferrio, J. P., Alonso, N., Voltas, J. & Araus, J. L. Grain weight changes over time in ancient cereal crops: Potential roles of climate and genetic improvement. J. Cereal Sci. 44, 323–332 (2006).Article 

    Google Scholar 
    Della Penna, V. Tradizione e modernità delle pratiche agricole nei Monti dauni: storia e archeologia dei sistemi agroalimentari subappenninici (Unpublished dissertation, Università degli Studi di Foggia, 2022).Dreslerová, D. et al. Maintaining soil productivity as the key factor in European prehistoric and Medieval farming. J. Archaeol. Sci.: Rep. 35, 102633 (2021).
    Google Scholar 
    Drtikolová Kaupová, S. et al. Stav izotopových výzkumů stravy, rezidenční mobility a zemědělského hospodaření populace Velké Moravy (9.–10. století). Arch. Rozhl. 74, 203–240 (2022).Article 

    Google Scholar 
    Hamerow, H. et al. An integrated bioarchaeological approach to the medieval ‘agricultural revolution’: a case study from Stafford, England, c.ad 800–1200. Eur. j. archaeol. 23, 585–609 (2020).Article 

    Google Scholar 
    Herrscher, E. et al. Dietary practices, cultural and social identity in the Early Bronze Age southern Caucasus. Paléorient, 151–174; (2021).Látková, M., Skála, R. & Drtikolová Kaupová, S. Bioarchaeological characteristics of the wheat (triticum aestivum) consumed at different parts of the early medieval settlement agglomeration of Mikulčice-Kopčany (9th–10th Century AD, Czech Republic). Environ. Archaeol. 30, 267–279 (2025).Article 

    Google Scholar 
    Reed, K. & Wallace, M. To pretreat, or not to pretreat, that is the question. The value of pretreatment protocols in the stable carbon and nitrogen isotope analysis of archaeobotanical cereal grains from Croatia and Serbia. Sci. Technol. Archaeol. Res. 10; https://doi.org/10.1080/20548923.2024.2410092 (2024).Russell, N., Cook, G. T., Ascough, P., Barrett, J. H. & Dugmore, A. Species specific marine radiocarbon reservoir effect: a comparison of ΔR values between Patella vulgata (limpet) shell carbonate and Gadus morhua (Atlantic cod) bone collagen. J. Archaeol. Sci. 38, 1008–1015 (2011).Article 

    Google Scholar 
    Schlütz, F. et al. Stable isotope analyses (δ15N, δ34S, δ13C) locate early rye cultivation in northern Europe within diverse manuring practices. Philos. Trans. R. Soc. Lond. Ser. B, Biol. Sci. 380, 20240195 (2025).
    Google Scholar 
    Treasure, E. R. The frontier of Islam: an archaeobotanical study of agriculture in the Iberian Peninsula (c.700 – 1500 CE) (Unpublished dissertation, Durham University, 2020).Vaiglova, P. Neolithic agricultural management in the Eastern Mediterranean: new insight from a multi-isotope approach (Doctoral dissertation, University of Oxford, 2016).Olson, D. M. et al. Terrestrial ecoregions of the world: a new map of life on earth. BioScience 51, 933 (2001).Article 

    Google Scholar 
    Larsson, M., Bergman, J. & Olsson, P. A. Soil, fertilizer and plant density: Exploring the influence of environmental factors to stable nitrogen and carbon isotope composition in cereal grain. J. Archaeol. Sci. 163, 105935 (2024).Article 
    CAS 

    Google Scholar 
    Filipović, D. et al. New AMS 14C dates track the arrival and spread of broomcorn millet cultivation and agricultural change in prehistoric Europe. Sci. Rep. 10, 13698 (2020).Article 

    Google Scholar 
    Vaiglova, P., Lazar, N. A., Stroud, E. A., Loftus, E. & Makarewicz, C. A. Best practices for selecting samples, analyzing data, and publishing results in isotope archaeology. Quat. Int.; https://doi.org/10.1016/j.quaint.2022.02.027 (2023).Hedges, R. E. M. Isotopes and red herrings: comments on Milner et al. and Lidén et al. Antiquity 78, 34–37 (2004).Article 

    Google Scholar 
    O’Regan, H. J., Lamb, A. L. & Wilkinson, D. M. The missing mushrooms: Searching for fungi in ancient human dietary analysis. J. Archaeol. Sci. 75, 139–143 (2016).Article 

    Google Scholar 
    Drucker, D. G., Bridault, A., Hobson, K. A., Szuma, E. & Bocherens, H. Can carbon-13 in large herbivores reflect the canopy effect in temperate and boreal ecosystems? Evidence from modern and ancient ungulates. Palaeogeogr. Palaeoclimatol. Palaeoecol. 266, 69–82 (2008).Article 

    Google Scholar 
    Bonafini, M., Pellegrini, M., Ditchfield, P. & Pollard, A. M. Investigation of the ‘canopy effect’ in the isotope ecology of temperate woodlands. J. Archaeol. Sci. 40, 3926–3935 (2013).Article 

    Google Scholar 
    Häberle, S. et al. Carbon and nitrogen isotopic ratios in archaeological and modern Swiss fish as possible markers for diachronic anthropogenic activity in freshwater ecosystems. J. Archaeol. Sci.: Rep. 10, 411–423 (2016).
    Google Scholar 
    Guiry, E. Complexities of stable carbon and nitrogen isotope biogeochemistry in ancient freshwater ecosystems: implications for the study of past subsistence and environmental change. Front. Ecol. Evol. 7; https://doi.org/10.3389/fevo.2019.00313 (2019).Robson, H. K. et al. Carbon and nitrogen stable isotope values in freshwater, brackish and marine fish bone collagen from Mesolithic and Neolithic sites in central and northern Europe. Environ. Archaeol. 21, 105–118 (2016).Article 

    Google Scholar 
    Göhring, A., Hölzl, S., Mayr, C. & Strauss, H. Identification and quantification of the sea spray effect on isotopic systems in α-cellulose (δ13C, δ18O), total sulfur (δ34S), and 87Sr/86Sr of European beach grass (Ammophila arenaria, L.) in a greenhouse experiment. Sci. Total Environ. 856, 158840 (2023).Article 

    Google Scholar 
    Büntgen, U. Scrutinizing tree-ring parameters for Holocene climate reconstructions. WIREs Clim. Change 13; https://doi.org/10.1002/wcc.778 (2022).Montgomery, J. et al. Strategic and sporadic marine consumption at the onset of the Neolithic: increasing temporal resolution in the isotope evidence. Antiquity 87, 1060–1072 (2013).Article 

    Google Scholar 
    Göhring, A., Hölzl, S., Mayr, C. & Strauss, H. Multi-isotope fingerprints of recent environmental samples from the Baltic coast and their implications for bioarchaeological studies. Sci. Total Environ. 874, 162513 (2023).Article 

    Google Scholar 
    Hopkins, J. B. & Ferguson, J. M. Correction: estimating the diets of animals using stable isotopes and a comprehensive bayesian mixing model. PloS One 7; https://doi.org/10.1371/annotation/d222580b-4f36-4403-bb1f-cfd449a5ed74 (2012).Ferrio, J. P., Araus, J. L., Buxó, R., Voltas, J. & Bort, J. Water management practices and climate in ancient agriculture: inferences from the stable isotope composition of archaeobotanical remains. Veget. Hist. Archaeobot. 14, 510–517 (2005).Article 

    Google Scholar 
    Jones, P. J., O’Connell, T. C., Jones, M. K., Singh, R. N. & Petrie, C. A. Crop water status from plant stable carbon isotope values: a test case for monsoonal climates. Holocene 31, 993–1004 (2021).Article 

    Google Scholar 
    Szpak, P., Metcalfe, J. Z. & Macdonald, R. A. Best practices for calibrating and reporting stable isotope measurements in archaeology. J. Archaeol. Sci.: Rep. 13, 609–616 (2017).
    Google Scholar 
    Salesse, K. et al. IsoArcH.eu: an open-access and collaborative isotope database for bioarchaeological samples from the Graeco-Roman world and its margins. J. Archaeol. Sci.: Rep. 19, 1050–1055 (2018).
    Google Scholar 
    Farese, M. MAIA: mediterranean archive of isotopic dAta. Pandora https://doi.org/10.48493/55v1-xg54 (2023).Article 

    Google Scholar 
    Formichella, G., Soncin, S. & Cocozza, C. Isotòpia: a stable isotope database for classical antiquity. Pandora v.1 19.09.2023; https://doi.org/10.48493/m0m0-b436 (2023).Mantile, N., Fernandes, R., Lubritto, C. & Cocozza, C. IsoMedIta: a stable isotope database for Medieval Italy. Res. Data J. Humanit. Soc. Sci. 8, 1–13 (2023).Article 

    Google Scholar 
    Cocozza, C., Cirelli, E., Groß, M., Teegen, W.-R. & Fernandes, R. Presenting the compendium isotoporum medii aevi, a multi-isotope database for Medieval Europe. Sci. Data 9, 354 (2022).Article 

    Google Scholar 
    Graven, H., Keeling, R. F. & Rogelj, J. Changes to carbon isotopes in atmospheric CO2 over the industrial era and into the future. Glob. Biogeochem. Cycles 34, e2019GB006170 (2020).Article 
    CAS 

    Google Scholar 
    Nitsch, E. K., Charles, M. & Bogaard, A. Calculating a statistically robust δ 13 C and δ 15 N offset for charred cereal and pulse seeds. Sci. Technol. Archaeol. Res. 1, 1–8 (2015).
    Google Scholar 
    Stroud, E., Charles, M., Bogaard, A. & Hamerow, H. Turning up the heat: Assessing the impact of charring regime on the morphology and stable isotopic values of cereal grains. J. Archaeol. Sci. 153, 105754 (2023).Article 

    Google Scholar 
    Teira-Brión, A., Stroud, E., Charles, M. & Bogaard, A. The effects of charring on morphology and stable carbon and nitrogen isotope values of common and foxtail millet grains. Front. Environ. Archaeol. 3; https://doi.org/10.3389/fearc.2024.1473593 (2024).Varalli, A., D’Agostini, F., Madella, M., Fiorentino, G. & Lancelotti, C. Charring effects on stable carbon and nitrogen isotope values on C4 plants: Inferences for archaeological investigations. J. Archaeol. Sci. 156, 105821 (2023).Article 
    CAS 

    Google Scholar 
    Styring, A. K. et al. Recommendations for stable isotope analysis of charred archaeological crop remains. Front. Environ. Archaeol. 3; https://doi.org/10.3389/fearc.2024.1470375 (2024).R. Core Team. R: A language and environment for statistical (R Foundation for Statistical Computing, Vienna, 2021).Bates, D., Mächler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Soft. 67; https://doi.org/10.18637/jss.v067.i01 (2015).Hijmans, R. J. _terra: Spatial Data Analysis_ (2024).Pebesma, E. & Bivand, R. Spatial Data Science (Chapman and Hall/CRC, New York, 2023).Pebesma, E. Simple Features for R: standardized support for spatial vector data. R. J. 10, 439 (2018).Article 

    Google Scholar 
    Warnes, G. et al. _gtools: Various R Programming Tools_ (2023).Wickham, H., François, R., Henry, L., Müller, K. & Vaughan, D. _dplyr: A Grammar of Data Manipulation_ (2023).Wickham, H. Ggplot2. Elegant graphics for data analysis (Springer Science+Business Media, LLC, New York, NY, 2016).Dunnington, D. _ggspatial: Spatial Data Framework for ggplot2_ (2023).Auguie, B. _gridExtra: Miscellaneous Functions for “Grid” Graphics (2017).Kempf, M. Environmental data to: Depaermentier, MLC; Kempf, M; Motuzaitė Matuzevičiūtė, G: environmentally adjusted δ13C thresholds for accurate detection of C4 plant consumption in Europe (2025).Karger, D. N. et al. Climatologies at high resolution for the earth’s land surface areas. Sci. Data 4, 170122 (2017).Article 

    Google Scholar 
    South, A., Michael, S. & Massicotte, P. rnaturalearthdata: world vector map data from natural earth used in ‘rnaturalearth’ (2017).Download referencesAcknowledgementsM.L.C.D. and G.M.M. were funded by the European Union with a Consolidator Grant awarded to Giedrė Motuzaitė Matuzevičiūtė (ERC-CoG, MILWAYS, 101087964). Views and opinions expressed are those of the authors only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. MK’s research is funded by the Swiss National Science Foundation (SNSF/SNF): Project EXOCHAINS − Exploring Holocene Climate Change and Human Innovations across Eurasia (SNSF grant number: TMPFP2_217358).Author informationAuthor notesThese authors contributed equally: Margaux L. C. Depaermentier, Michael Kempf.Authors and AffiliationsFaculty of History, Vilnius University, Vilnius, LithuaniaMargaux L. C. Depaermentier & Giedrė Motuzaitė MatuzevičiūtėDepartment of Environmental Sciences, University of Basel, Basel, SwitzerlandMichael KempfAuthorsMargaux L. C. DepaermentierView author publicationsSearch author on:PubMed Google ScholarMichael KempfView author publicationsSearch author on:PubMed Google ScholarGiedrė Motuzaitė MatuzevičiūtėView author publicationsSearch author on:PubMed Google ScholarContributionsConceptualization: M.L.C.D., M.K. and G.M.M. Isotope data collection and formal analyses: M.L.C.D. Environmental and cluster analyses: M.K. Writing: M.L.C.D and M.K. Editing: M.L.C.D., M.K., G.M.M. Visualisation: M.K. and M.L.C.D. Revision: M.L.C.D., M.K.Corresponding authorsCorrespondence to
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    Reprints and permissionsAbout this articleCite this articleDepaermentier, M.L.C., Kempf, M. & Motuzaitė Matuzevičiūtė, G. Environmentally adjusted δ13C thresholds for accurate detection of C4 plant consumption in Europe.
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