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    Climate influences the genetic structure and niche differentiation among populations of the olive field mouse Abrothrix olivacea (Cricetidae: Abrotrichini)

    Charlesworth, B., Charlesworth, D. & Barton, N. H. The effects of genetic and geographic structure on neutral variation. Annu. Rev. Ecol. Evol. Syst. 34(1), 99–125 (2003).Article 

    Google Scholar 
    Bradburd, G. S., Ralph, P. L. & Coop, G. M. Disentangling the effects of geographic and ecological isolation on genetic differentiation. Evolution 67(11), 3258–3273 (2013).Article 

    Google Scholar 
    Orsini, L., Vanoverbeke, J., Swillen, I., Mergeay, J. & De Meester, L. Drivers of population genetic differentiation in the wild: Isolation by dispersal limitation, isolation by adaptation and isolation by colonization. Mol. Ecol. 22(24), 5983–5999 (2013).Article 

    Google Scholar 
    Ronce, O. How does it feel to be like a rolling stone? Ten questions about dispersal evolution. Annu. Rev. Ecol. Evol. Syst. 38, 231–253 (2007).Article 

    Google Scholar 
    Broquet, T. & Petit, E. J. Molecular estimation of dispersal for ecology and population genetics. Annu. Rev. Ecol. Evol. Syst. 40, 193–216 (2009).Article 

    Google Scholar 
    Sexton, J. P., McIntyre, P. J., Angert, A. L. & Rice, K. J. Evolution and ecology of species range limits. Annu. Rev. Ecol. Evol. Syst. 40, 415–436 (2009).Article 

    Google Scholar 
    Qiao, H., Saupe, E. E., Soberón, J., Peterson, A. T. & Myers, C. E. Impacts of niche breadth and dispersal ability on macroevolutionary patterns. Am. Nat. 188(2), 149–162 (2016).Article 

    Google Scholar 
    Mayr, E. Ecological factors in speciation. Evolution 1(4), 263–288 (1947).
    Google Scholar 
    Hua, X. & Wiens, J. J. How does climate influence speciation?. Am. Nat. 182(1), 1–12 (2013).Article 

    Google Scholar 
    Rundle, H. D. & Nosil, P. Ecological speciation. Ecol. Lett. 8(3), 336–352 (2005).Article 

    Google Scholar 
    Schluter, D. Evidence for ecological speciation and its alternative. Science 323(5915), 737–741 (2009).Article 
    ADS 

    Google Scholar 
    Wielstra, B. et al. Corresponding mitochondrial DNA and niche divergence for crested newt candidate species. PLoS ONE 7(9), e46671 (2012).Article 
    ADS 

    Google Scholar 
    Wiens, J. J. Speciation and ecology revisited: Phylogenetic niche conservatism and the origin of species. Evolution 58(1), 193–197 (2004).
    Google Scholar 
    Manel, S., Schwartz, M. K., Luikart, G. & Taberlet, P. Landscape genetics: combining landscape ecology and population genetics. Trends Ecol. Evol. 18(4), 189–197 (2003).Article 

    Google Scholar 
    Alvarado-Serrano, D. F. & Hickerson, M. J. Spatially explicit summary statistics for historical population genetic inference. Methods Ecol. Evol. 7(4), 418–427 (2016).Article 

    Google Scholar 
    Rissler, L. J. Union of phylogeography and landscape genetics. PNAS 113(29), 8079–8086 (2016).Article 
    ADS 

    Google Scholar 
    Pinho, C. & Hey, J. Divergence with gene flow: Models and data. Annu. Rev. Ecol. Evol. Syst. 41, 215–230 (2010).Article 

    Google Scholar 
    Sobel, J. M., Chen, G. F., Watt, L. R. & Schemske, D. W. The biology of speciation. Evolution 64(2), 295–315 (2010).Article 

    Google Scholar 
    Richards, C. L., Carstens, B. C. & Knowles, L. L. Distribution modelling and statistical phylogeography: An integrative framework for generating and testing alternative biogeographical hypotheses. J. Biogeogr. 34(11), 1833–1845 (2007).Article 

    Google Scholar 
    Alvarado-Serrano, D. F. & Knowles, L. L. Ecological niche models in phylogeographic studies: applications, advances and precautions. Mol. Ecol. 14(2), 233–248 (2014).Article 

    Google Scholar 
    Wang, I. J. Examining the full effects of landscape heterogeneity on spatial genetic variation: A multiple matrix regression approach for quantifying geographic and ecological isolation. Evolution 67(12), 3403–3411 (2013).Article 

    Google Scholar 
    Wright, S. Isolation by distance. Genetics 28(2), 114–138 (1943).Article 

    Google Scholar 
    Sexton, J. P., Hangartner, S. B. & Hoffmann, A. A. Genetic isolation by environment or distance: which pattern of gene flow is most common?. Evolution 68(1), 1–15 (2014).Article 

    Google Scholar 
    Wang, I. J. & Bradburd, G. S. Isolation by environment. Mol. Ecol. 23(23), 5649–5662 (2014).Article 

    Google Scholar 
    Lee, C. R. & Mitchell-Olds, T. Quantifying effects of environmental and geographical factors on patterns of genetic differentiation. Mol. Ecol. 20(22), 4631–4642 (2011).Article 

    Google Scholar 
    Moreira-Muñoz, A. Plant Geography of Chile Vol. 10, 978–990 (Springer, 2011).Book 

    Google Scholar 
    Orme, A. R. Tectonism, climate, and landscape change. Phys. Geogr. South Am. 1, 23–44 (2007).
    Google Scholar 
    Morando, M. et al. Diversification and evolutionary histories of Patagonian steppe lizards. in Lizards of Patagonia (pp. 217–254). (Springer, 2020).Rull, V. Neotropical diversification: historical overview and conceptual insights. In Neotropical Diversification: Patterns and Processes (eds Rull, V. & Carnaval, A. C.) (Springer, 2020).Chapter 

    Google Scholar 
    Lessa, E. P., D’Elía, G. & Pardiñas, U. F. J. Mammalian biogeography of Patagonia and Tierra del Fuego. In Bones, Clones and Biomes: The History and Recent Geography of Neotropical Animals (eds Patterson, B. D. & Costa, L. P.) 379–398 (University of Chicago Press, 2012).Chapter 

    Google Scholar 
    Pardiñas, U. F., D’Elía, G. & Lessa, E. P. The evolutionary history of sigmodontine rodents in Patagonia and Tierra del Fuego. Biol. J. Linn. Soc. 2(103), 495–513 (2011).Article 

    Google Scholar 
    Alarcón, O., D’Elía, G., Lessa, E. P. & Pardiñas, U. Phylogeographic structure of the Fossorial Long-Clawed Mouse Chelemys macronyx (Cricetidae: Sigmodontinae). Zool. Stud. 50(5), 682–688 (2011).
    Google Scholar 
    Lessa, E. P., D’Elía, G. & Pardiñas, U. F. J. Genetic footprints of late Quaternary climate change in the diversity of Patagonian-Fueguian rodents. Mol. Ecol. 19(15), 3031–3037 (2010).Article 

    Google Scholar 
    Valdez, L. & D’Elía, G. Genetic diversity and demographic history of the Shaggy Soft-Haired Mouse Abrothrix hirta (Cricetidae; Abrotrichini). Front. Genet. 12, 184 (2021).Article 

    Google Scholar 
    Valdez, L., Quiroga-Carmona, M. & D’Elía, G. Genetic variation of the Chilean endemic long-haired mouse Abrothrix longipilis (Rodentia, Supramyomorpha, Cricetidae) in a geographical and environmental context. PeerJ 8, e9517 (2020).Article 

    Google Scholar 
    Valdez, L. & D’Elía, G. Local persistence of Mann’s soft-haired mouse Abrothrix manni (Rodentia, Sigmodontinae) during Quaternary glaciations in southern Chile. PeerJ 6, e6130 (2018).Article 

    Google Scholar 
    Quiroga-Carmona, M., Abud, C., Lessa, E. P. & D’Elía, G. The mitochondrial genetic diversity of the olive field mouse Abrothrix olivacea (Cricetidae; Abrotrichini) is latitudinally structured across its geographic distribution. J. Mamm. Evol. 29, 431–433 (2022).Article 

    Google Scholar 
    Cañón, C., D’Elía, G., Pardiñas, U. F. & Lessa, E. P. Phylogeography of Loxodontomys micropus with comments on the alpha taxonomy of Loxodontomys (Cricetidae: Sigmodontinae). J. Mamm. 91(6), 1449–1458 (2010).Article 

    Google Scholar 
    Palma, R. E., Boric-Bargetto, D., Torres-Perez, F., Hernández, C. E. & Yates, T. L. Glaciation effects on the phylogeographic structure of Oligoryzomys longicaudatus (Rodentia: Sigmodontinae) in the Southern Andes. PLoS ONE 7(3), e32206 (2012).Article 
    ADS 

    Google Scholar 
    Rodríguez-Serrano, E., Cancino, R. & Palma, R. E. Molecular phylogeography of Abrothrix olivaceus (Rodentia: Sigmodontinae) in Chile. J. Mamm. 87(5), 971–980 (2006).Article 

    Google Scholar 
    Rodríguez-Serrano, E., Hernandez, C. & Palma, R. E. A new record and an evaluation of the phylogenetic relationships of Abrothrix olivaceus markhami (Rodentia: Sigmodontinae). Mamm. Biol. 73(4), 309–317 (2008).Article 

    Google Scholar 
    Sánchez, J., Poljak, S., Teta, P., Lanusse, L. & Lizarralde, M. S. A contribution to the knowledge of the taxonomy of the subgenus Abrothrix (Angelomys) (Rodentia, Cricetidae) in southernmost South America. Polar Biol. 45(4), 601–614 (2022).Article 

    Google Scholar 
    Patton, J., Pardiñas, U. F. & D’Elía, G. Mammals of South America Vol. 2 (The University of Chicago Press, 2015).Book 

    Google Scholar 
    Patterson, B. D., Smith, M. F. & Teta, P. Genus Abrothrix Waterhouse, 1837. In Mammals of South America Vol. 2 (eds Patton, J. L. et al.) 109–127 (The University of Chicago Press, 2015).
    Google Scholar 
    Jombart, T., Devillard, S. & Balloux, F. Discriminant analysis of principal components: A new method for the analysis of genetically structured populations. BMC Genet. 11, 94 (2010).Article 

    Google Scholar 
    Hijmans, R. J., Cameron, S. E., Parra, J. L., Jones, P. G. & Jarvis, A. Very high-resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 25(15), 1965–1978 (2005).Article 

    Google Scholar 
    Quantum GIS Development Team (2021) Quantum GIS Geographic Information System. Version 3.18.2-ZürichHijmans, R. J. et al. Package ‘raster’. R package. (2015).Kuhn, M. caret: Classification and Regression Training. (2019) https://CRAN.R-project.org/package=caret.Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.5–7. (2020). https://CRAN.R-project.org/package=vegan.Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35(6), 1547–1549 (2018).Article 

    Google Scholar 
    Wang, C. et al. Comparing spatial maps of human population-genetic variation using Procrustes analysis. Stat. Appl. Genet. Mol. Biol. 9(1), 13 (2010).Article 
    MathSciNet 

    Google Scholar 
    Wang, C., Zöllner, S. & Rosenberg, N. A. A quantitative comparison of the similarity between genes and geography in worldwide human populations. PLoS Genet. 8(8), e1002886 (2012).Article 

    Google Scholar 
    Bivand, R., Keitt, T. & Rowlingson, B. rgdal: Bindings for the ‘Geospatial’ Data Abstraction Library. R package version 1.5–28. (2021). https://CRAN.R-project.org/package=rgdal.Kierepka, M. E. & Latch, K. E. Performance of partial statistics in individual-based landscape genetics. Mol. Ecol. 15(3), 512–525 (2015).Article 

    Google Scholar 
    Legendre, P. & Legendre, L. Numerical Ecology (Elsevier, 2012).MATH 

    Google Scholar 
    Lê, S., Josse, J. & Husson, F. FactoMineR: An R package for multivariate analysis. J. Stat. Soft. 25(1), 1–8 (2008).Article 

    Google Scholar 
    Barria, A. M. et al. The importance of intraspecific variation for niche differentiation and species distribution models: the ecologically diverse frog Pleurodema thaul as study case. Evol. Biol. 47(3), 206–219 (2020).Article 

    Google Scholar 
    Blonder, B., Lamanna, C., Violle, C. & Enquist, B. J. The n-dimensional hypervolume. Glob. Ecol. Biol. 23(5), 595–609 (2014).Article 

    Google Scholar 
    Aiello-Lammens, M. E., Boria, R. A., Radosavljevic, A., Vilela, B. & Anderson, R. P. spThin: An R package for spatial thinning of species occurrence records for use in ecological niche models. Ecography 38(5), 541–545 (2015).Article 

    Google Scholar 
    Peterson, A. T. et al. Ecological Niches and Geographic Distributions (Princeton University Press, 2011).Book 

    Google Scholar 
    Viale, M. et al. Contrasting climates at both sides of the Andes in Argentina and Chile. Front. Environ. Sci. 7, 69 (2019).Article 

    Google Scholar 
    Pacifici, M. et al. Global correlates of range contractions and expansions in terrestrial mammals. Nat. Commun. 11(1), 1–9 (2020).Article 

    Google Scholar 
    Di Marco, M., Pacifici, M., Maiorano, L. & Rondinini, C. Drivers of change in the realised climatic niche of terrestrial mammals. Ecography 44(8), 1180–1190 (2021).Article 

    Google Scholar 
    Phillips, S. J., Anderson, R. P., Dudík, M., Schapire, R. E. & Blair, M. E. Opening the black box: An open-source release of Maxent. Ecography 40(7), 887–893 (2017).Article 

    Google Scholar 
    Phillips, S. J., Anderson, R. P. & Schapire, R. E. Maximum entropy modeling of species geographic distributions. Ecol. Model 190(3–4), 231–259 (2006).Article 

    Google Scholar 
    Phillips, S. J., Dudík, M. & Schapire, R. E. Maxent Software for Modeling Species Niches and Distributions. (American Museum of Natural History, 2018) http://biodiversityinformatics.amnh.org/opensource/maxent/.Muscarella, R. et al. ENMeval: An R package for conducting spatially independent evaluations and estimating optimal model complexity for Maxent ecological niche models. Methods Ecol. Evol. 5(11), 1198–1205 (2014).Article 

    Google Scholar 
    Radosavljevic, A. & Anderson, R. P. Making better Maxent models of species distributions: complexity, overfitting and evaluation. J. Biogeogr. 41(4), 629–643 (2014).Article 

    Google Scholar 
    Warren, D. L. & Seifert, S. N. Ecological niche modeling in Maxent: The importance of model complexity and the performance of model selection criteria. Ecol. Appl. 21(2), 335–342 (2011).Article 

    Google Scholar 
    Warren, D. L., Wright, A. N., Seifert, S. N. & Shaffer, H. B. Incorporating model complexity and spatial sampling bias into ecological niche models of climate change risks faced by 90 California vertebrate species of concern. Diver. Dist. 20(3), 334–343 (2014).Article 

    Google Scholar 
    Franklin, J. Mapping Species Distributions: Spatial Inference and Prediction (Cambridge University Press, 2010).Book 

    Google Scholar 
    Merow, C., Smith, M. J. & Silander, J. A. A practical guide to MaxEnt for modeling species’ distributions: What it does, and why inputs and settings matter. Ecography 36(10), 1058–1069 (2013).Article 

    Google Scholar 
    Elith, J., Kearney, M. & Phillips, S. The art of modelling range-shifting species. Methods Ecol. Evol. 1(4), 330–342 (2010).Article 

    Google Scholar 
    Osorio-Olvera, L. et al. ntbox: An r package with graphical user interface for modelling and evaluating multidimensional ecological niches. Methods Ecol. Evol. 11(10), 1199–1206 (2020).Article 

    Google Scholar 
    Guevara, L., Gerstner, B. E., Kass, J. M. & Anderson, R. P. Toward ecologically realistic predictions of species distributions: A cross-time example from tropical montane cloud forests. Glob. Change Biol. 24, 1511–1522 (2018).Article 
    ADS 

    Google Scholar 
    Otto-Bliesner, B. L., Marshall, S. J., Overpeck, J. T., Miller, G. H. & Hu, A. Simulating arctic climate warmth and icefield retreat in the last interglaciation. Science 311(5768), 1751–1753 (2008).Article 
    ADS 

    Google Scholar 
    Watanabe, S. et al. MIROC-ESM 2010: Model description and basic results of CMIP5-20c3m experiments. Geosci. Model Dev. 4(4), 845 (2011).Article 
    ADS 

    Google Scholar 
    Knowles, L. L., Massatti, R., He, Q., Olson, L. E. & Lanier, H. C. Quantifying the similarity between genes and geography across Alaska’s alpine small mammals. J. Biogeogr. 43(7), 1464–1476 (2016).Article 

    Google Scholar 
    McGaughran, A., Morgan, K. & Sommer, R. J. Environmental variables explain genetic structure in a beetle-associated nematode. PLoS ONE 9(1), e87317 (2014).Article 
    ADS 

    Google Scholar 
    Wang, I. J. Choosing appropriate genetic markers and analytical methods for testing landscape genetic hypotheses. Mol. Ecol. 20(12), 2480–2482 (2011).Article 

    Google Scholar 
    Bohonak, A. J. & Vandergast, A. G. The value of DNA sequence data for studying landscape genetics. Mol. Ecol. 20(12), 2477–2479 (2011).Article 

    Google Scholar 
    Vandergast, A. G., Bohonak, A. J., Weissman, D. B. & Fisher, R. N. Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: Phylogeography and landscape genetics of a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus). Mol. Ecol. 16(5), 977–992 (2007).Article 

    Google Scholar 
    Pearson, O. P. & Smith, M. F. Genetic similarity between Akodon olivaceus and Akodon xanthorhinus (Rodentia: Muridae) in Argentina. J. Zool. 247(1), 43–52 (1999).Article 

    Google Scholar 
    Smith, M. F., Kelt, D. A. & Patton, J. L. Testing models of diversification in mice in the Abrothrix olivaceus/xanthorhinus complex in Chile and Argentina. Mol. Ecol. 10(2), 397–405 (2001).Article 

    Google Scholar 
    Palma, R. E., Marquet, P. A. & Boric-Bargetto, D. Inter- and intraspecific phylogeography of small mammals in the Atacama Desert and adjacent areas of northern Chile. J. Biogeogr. 32(11), 1931–1941 (2005).Article 

    Google Scholar 
    Arroyo, M. T. K., Squeo, F. A., Armesto, J. J. & Villagran, C. Effects of aridity on plant diversity in the northern Chilean Andes: Results of a natural experiment. Ann. Mol. Bot. Gard. 1, 55–78 (1988).Article 

    Google Scholar 
    Del Pozo, A. H., Fuentes, E. R., Hajek, E. R. & Molina, J. D. Zonación microclimática por efecto de los manchones de arbustos en el matorral de Chile central. Rev. Chil. Hist. Nat. 62, 85–94 (1989).
    Google Scholar 
    Armesto, J. J., Vidiella, P. E. & Gutiérrez, J. R. Plant communities of the fog-free coastal desert of Chile: Plant strategies in a fluctuating environment. Rev. Chil. Hist. Nat. 66, 271–282 (1993).
    Google Scholar 
    Veblen, T. T., Young, K. R. & Orme, A. R. The Physical Geography of South America (Oxford University Press, 2015).
    Google Scholar 
    Kelt, D. A. et al. Community structure of desert small mammals: Comparisons across four continents. Ecology 77(3), 746–761 (1996).Article 

    Google Scholar 
    Shenbrot, G. B., Krasnov, B. R. & Rogovin, K. A. Spatial Ecology of Desert Rodent Communities (Springer, 1999).Book 

    Google Scholar 
    Van Strien, M. J., Holderegger, R. & Van Heck, H. J. Isolation-by-distance in landscapes: considerations for landscape genetics. Heredity 114(1), 27–37 (2015).Article 

    Google Scholar 
    Diniz-Filho, J. A. F. et al. Mantel test in population genetics. Genet. Mol. Biol. 36(4), 475–485 (2013).Article 

    Google Scholar 
    Blier, P. U., Dufresne, F. & Burton, R. S. Natural selection and the evolution of mtDNA-encoded peptides: Evidence for intergenomic co-adaptation. Trends Genet. 17(7), 400–406 (2001).Article 

    Google Scholar 
    Meiklejohn, C. D., Montooth, K. L. & Rand, D. M. Positive and negative selection on the mitochondrial genome. Trends Genet. 23(6), 259–263 (2007).Article 

    Google Scholar 
    Giorello, F. M. et al. An association between differential expression and genetic divergence in the Patagonian olive mouse (Abrothrix olivacea). Mol. Ecol. 27(16), 3274–3286 (2018).Article 

    Google Scholar 
    Soberón, J. Grinnellian and Eltonian niches and geographic distributions of species. Ecol. Lett. 10(12), 1115–1123 (2007).Article 

    Google Scholar 
    Holt, R. D. Bringing the Hutchinsonian niche into the 21st century: Ecological and evolutionary perspectives. PNAS 106(Supplement 2), 19659–19665 (2009).Article 
    ADS 

    Google Scholar 
    Soberón, J. & Nakamura, M. Niches and distributional areas: Concepts, methods, and assumptions. PNAS 106(Supplement 2), 19644–19650 (2009).Article 
    ADS 

    Google Scholar 
    Kearney, M. & Porter, W. P. Mapping the fundamental niche: Physiology, climate, and the distribution of a nocturnal lizard. Ecology 85(11), 3119–3131 (2004).Article 

    Google Scholar 
    Kearney, M. & Porter, W. P. Mechanistic niche modelling: Combining physiological and spatial data to predict species’ ranges. Ecol. Lett. 12(4), 334–350 (2009).Article 

    Google Scholar 
    Bonetti, M. F. & Wiens, J. J. Evolution of climatic niche specialization: A phylogenetic analysis in amphibians. Proc. R. Soc. B. 281(1795), 20133229 (2014).Article 

    Google Scholar 
    Sexton, J. P., Montiel, J., Shay, J. E., Stephens, M. R. & Slatyer, R. A. Evolution of ecological niche breadth. Annu. Rev. Ecol. Evol. Syst. 48, 183–206 (2017).Article 

    Google Scholar 
    Holt, R. D. On the evolutionary ecology of species’ ranges. Evol. Ecol. Res. 5(2), 159–178 (2003).
    Google Scholar 
    Merilä, J. & Hendry, A. P. Climate change, adaptation, and phenotypic plasticity: The problem and the evidence. Evol. Appl. 7(1), 1–14 (2014).Article 

    Google Scholar 
    Schmid, M. & Guillaume, F. The role of phenotypic plasticity on population differentiation. Heredity 119(4), 214–225 (2017).Article 

    Google Scholar 
    Novoa, F., Rivera, A., Rosenmann, M. & Sabat, P. Intraspecific differences in metabolic rate of Chroeomys olivaceus (Rodentia: Muridae): The effect of thermal acclimation in arid and mesic habitats. Rev. Chil. Hist. Nat. 78, 207–214 (2005).Article 

    Google Scholar 
    Bozinovic, F., Rojas, J. M., Maldonado, K., Sabat, P. & Naya, D. E. Between-population differences in digestive flexibility in the olivaceous field mouse. Zool 113(6), 373–377 (2010).Article 

    Google Scholar 
    Bozinovic, F., Rojas, J. M., Gallardo, P. A., Palma, R. E. & Gianoli, E. Body mass and water economy in the South American olivaceous field mouse along a latitudinal gradient: Implications for climate change. J. Arid. Environ. 75(5), 411–415 (2011).Article 
    ADS 

    Google Scholar 
    Naya, D. E. et al. Digestive morphology of two species of Abrothrix (Rodentia, Cricetidae): Comparison of populations from contrasting environments. J. Mammal. 95(6), 1222–1229 (2014).Article 

    Google Scholar 
    Warren, D. L., Glor, R. E. & Turelli, M. Environmental niche equivalency versus conservatism: Quantitative approaches to niche evolution. Evolution 62(11), 2868–2883 (2008).Article 

    Google Scholar 
    Goudarzi, F. et al. Geographic separation and genetic differentiation of populations are not coupled with niche differentiation in threatened Kaiser’s spotted newt (Neurergus kaiseri). Sci. Rep. 9(1), 1–12 (2019).Article 

    Google Scholar 
    Pyron, R. A., Costa, G. C., Patten, M. A. & Burbrink, F. T. Phylogenetic niche conservatism and the evolutionary basis of ecological speciation. Biol. Rev. 90(4), 1248–1262 (2015).Article 

    Google Scholar 
    Latorre, C. et al. Late Quaternary environments and paleoclimate. In The Geology of Chile (eds Moreno, T. & Gibbons, W.) 309–328 (Geological Society, 2007).Chapter 

    Google Scholar 
    Kaplan, M. R., Moreno, P. I. & Rojas, M. Glacial dynamics in southernmost South America during Marine Isotope Stage 5e to the Younger Dryas chron: A brief review with a focus on cosmogenic nuclide measurements. J. Quat. Sci. 23(6–7), 649–658 (2008).Article 

    Google Scholar 
    McCulloch, R. D. et al. Climatic inferences from glacial and palaeoecological evidence at the last glacial termination, southern South America. J. Quat. Sci. 15(4), 409–417 (2000).Article 

    Google Scholar 
    Giorello, F. M., D’Elía, G. & Lessa, E. P. Genomic footprints of Quaternary colonization and population expansion in the Patagonian-Fuegian region rules out a separate southern refugium in Tierra del Fuego. J. Biogeogr. 48(10), 2656–2670 (2021).Article 

    Google Scholar 
    Knowles, L. L., Carstens, B. C. & Keat, M. L. Coupling genetic and ecological-niche models to examine how past population distributions contribute to divergence. Curr. Biol. 17(11), 940–946 (2007).Article 

    Google Scholar 
    Diniz-Filho, J. A. F. et al. Correlation between genetic diversity and environmental suitability: Taking uncertainty from ecological niche models into account. Mol. Ecol. 15(5), 1059–1066 (2015).Article 

    Google Scholar 
    Guevara, L., León-Paniagua, L., Rios, J. & Anderson, R. P. Variación entre modelos de circulación global para reconstrucciones de distribuciones geográficas del Último Máximo Glacial: Relevancia en la filogeografía. Ecosistemas 27(1), 62–76 (2018).Article 

    Google Scholar 
    Guevara, L., Morrone, J. J. & León-Paniagua, L. Spatial variability in species’potential distributions during the Last Glacial Maximum under different Global Circulation Models: Relevance in evolutionary biology. J. Zool. Syst. Evol. Res. 57(1), 113–126 (2019).Article 

    Google Scholar 
    Cab-Sulub, L. & Álvarez-Castañeda, S. T. Genetic isolation between conspecific populations and their relationship to climate heterogeneity. Acta Oecol. 116, 103847 (2022).Article 

    Google Scholar 
    Teta, P., de la Sancha, N. U., D’Elía, G. & Patterson, B. D. Andean rain shadow effect drives phenotypic variation in a widely distributed Austral rodent. J. Biogeogr. 00, 1–12 (2022).
    Google Scholar 
    León-Tapia, M. A. DNA barcoding and demographic history of Peromyscus yucatanicus (Rodentia: Cricetidae) endemic to the Yucatan Peninsula, Mexico. J. Mammal. Evol. 28(2), 481–495 (2021).Article 

    Google Scholar 
    Lin, X. et al. Climatic-niche evolution with key morphological innovations across clades within Scutiger boulengeri (Anura: Megophryidae). Ecol. Evol. 11, 10353–10368 (2021).Article 

    Google Scholar  More

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    Evaluation of the current understanding of the impact of climate change on coral physiology after three decades of experimental research

    Hoegh-Guldberg, O. & Bruno, J. F. The impact of climate change on the world’s marine ecosystems. Science 328, 1523–1528 (2010).Article 
    CAS 

    Google Scholar 
    Hoegh-Guldberg, O. et al. Coral reefs under rapid climate change and ocean acidification. Science 318, 1737–1742 (2007).Article 
    CAS 

    Google Scholar 
    Brown, B. E. Coral bleaching: causes and consequences. Coral Reefs 16, 129–138 (1997).Article 

    Google Scholar 
    Hoegh-Guldberg, O. Climate change, coral bleaching and the future of the world’s coral reefs. Mar. Freshw. Res. 50, 839–866 (1999).
    Google Scholar 
    Scheufen, T., Krämer, W. E., Iglesias-Prieto, R. & Enríquez, S. Seasonal variation modulates coral sensibility to heat-stress and explains annual changes in coral productivity. Sci. Rep. 7, 4937 (2017).Article 

    Google Scholar 
    Hughes, T. P. et al. Global warming and recurrent mass bleaching of corals. Nature 543, 373–377 (2017).Article 
    CAS 

    Google Scholar 
    Hughes, T. P. et al. Global warming transforms coral reef assemblages. Nature 556, 492–496 (2018).Article 
    CAS 

    Google Scholar 
    Doney, S. C., Fabry, V. J., Feely, R. A. & Kleypas, J. A. Ocean acidification: the other CO2 problem. Annu. Rev. Mar. Sci. 1, 169–192 (2009).Article 

    Google Scholar 
    Warner, M. E., Fitt, W. K. & Schmidt, G. W. The effects of elevated temperature on the photosynthetic efficiency of zooxanthellae in hospite from four different species of reef coral: a novel approach. Plant Cell Environ. 19, 291–299 (1996).Article 

    Google Scholar 
    Iglesias-Prieto, R. Temperature-dependent inactivation of photosystem II in symbiotic dinoflagellates. in Proceedings of the 8th International Coral Reef Symposium (eds. Lessios, H. A. & MacIntyre, I. G.) Vol. 2, 1313–1318 (1997).Takahashi, S., Nakamura, T., Sakamizu, M., van Woesik, R. & Yamasaki, H. Repair machinery of symbiotic photosynthesis as the primary target of heat stress for reef-building corals. Plant Cell Physiol. 45, 251–255 (2004).Article 
    CAS 

    Google Scholar 
    Warner, M. E., Fitt, W. K. & Schmidt, G. W. Damage to photosystem II in symbiotic dinoflagellates: a determinant of coral bleaching. Proc. Natl Acad. Sci. USA 96, 8007–8012 (1999).Article 
    CAS 

    Google Scholar 
    Scheufen, T., Iglesias-Prieto, R. & Enríquez, S. Changes in the number of symbionts and Symbiodinium cell pigmentation modulate differentially coral light absorption and photosynthetic performance. Front. Mar. Sci. 4, 309 (2017).Gómez-Campo, K., Enríquez, S. & Iglesias-Prieto, R. A road map for the development of the bleached coral phenotype. Front. Mar. Sci. 9, 806491 (2022).Dahlhoff, E. A. & Somero, G. N. Effects of temperature on mitochondria from abalone (genus Haliotis): adaptive plasticity and its limits. J. Exp. Biol. 185, 151–168 (1993).Article 

    Google Scholar 
    Kajiwara, K., Nagai, A. & Ueno, S. Examination of the effect of temperature, light intensity and zooxanthellae concentration on calcification and photosynthesis of scleractinian coral Acropora pulchra. J. Sch. Mar. Sci. Technol. 40, 95–103 (1995).
    Google Scholar 
    Rodolfo-Metalpa, R., Huot, Y. & Ferrier-Pagès, C. Photosynthetic response of the Mediterranean zooxanthellate coral Cladocora caespitosa to the natural range of light and temperature. J. Exp. Biol. 211, 1579–1586 (2008).Article 
    CAS 

    Google Scholar 
    Marshall, A. T. & Clode, P. Calcification rate and the effect of temperature in a zooxanthellate and an azooxanthellate scleractinian reef coral. Coral Reefs 23, 218–224 (2004).Article 

    Google Scholar 
    Kleypas, J. A., Buddemeier, R. W. & Gattuso, J.-P. The future of coral reefs in an age of global change. Int. J. Earth Sci. 90, 426–437 (2001).Article 
    CAS 

    Google Scholar 
    Orr, J. C. et al. Anthropogenic ocean acidification over the twenty-first century and its impact on calcifying organisms. Nature 437, 681–686 (2005).Article 
    CAS 

    Google Scholar 
    Ries, J. B., Cohen, A. L. & McCorkle, D. C. Marine calcifiers exhibit mixed responses to CO2-induced ocean acidification. Geology 37, 1131–1134 (2009).Article 
    CAS 

    Google Scholar 
    Vasquez-Elizondo, R. M. & Enríquez, S. Coralline algal physiology is more adversely affected by elevated temperature than reduced pH. Sci. Rep. 6, 19030 (2016).Article 
    CAS 

    Google Scholar 
    Anthony, K. R., Kline, D. I., Diaz-Pulido, G., Dove, S. & Hoegh-Guldberg, O. Ocean acidification causes bleaching and productivity loss in coral reef builders. Proc. Natl Acad. Sci. USA 105, 17442–17446 (2008).Article 
    CAS 

    Google Scholar 
    Gattuso, J.-P., Allemand, D. & Frankignoulle, M. Photosynthesis and calcification at cellular, organismal and community levels in coral reefs: A review on interactions and control by carbonate chemistry. Am. Zool. 39, 160–183 (1999).Article 
    CAS 

    Google Scholar 
    Langdon, C. & Aktinson, M. J. Effect of elevated pCO2 on photosynthesis and calcification of corals and interactions with seasonal change in temperature/irradiance and nutrient enrichment. J. Geophys. Res. 110, https://doi.org/10.1029/2004JC002576 (2005).Iglesias-Rodriguez, M. D. et al. Phytoplankton calcification in a high-CO2 world. Science 320, 336–340 (2008).Article 
    CAS 

    Google Scholar 
    Krumhardt, K. M., Lovenduski, N. S., Iglesias-Rodriguez, M. D. & Kleypas, J. A. Coccolithophore growth and calcification in a changing ocean. Prog. Oceanogr. 159, 276–295 (2017).Article 

    Google Scholar 
    Kleypas, J. A. et al. Impact of Ocean Acidification on Coral Reefs and Other Marine Calcifiers: A Case Guide for Future Research Vol. 88 (2005).Comeau, S., Cornwall, C. E., DeCarlo, T. M., Krieger, E. & McCulloch, M. T. Similar controls on calcification under ocean acidification across unrelated coral reef taxa. Glob. Change Biol. 24, 4857–4868 (2018).Article 

    Google Scholar 
    Kroeker, K. J. et al. Impacts of ocean acidification on marine organisms: quantifying sensitivities and interaction with warming. Glob. Change Biol. 19, 1884–1896 (2013).Article 

    Google Scholar 
    Hoadley, K. D., Pettay, D. T., Dodge, D. & Warner, M. E. Contrasting physiological plasticity in response to environmental stress within different cnidarians and their respective symbionts. Coral Reefs 35, 529–542 (2016).Article 

    Google Scholar 
    Langdon, C., Albright, R., Baker, A. & Jones, P. Two threatened Caribbean coral species have contrasting responses to combined temperature and acidification stress. Limnol. Oceanogr. 63, 2450–2464 (2018).Article 
    CAS 

    Google Scholar 
    Agostini, S. et al. The effects of thermal and high-CO2 stresses on the metabolism and surrounding microenvironment of the coral Galaxea fascicularis. C. R. Biol. 336, 384–391 (2013).Article 
    CAS 

    Google Scholar 
    Reynaud, S. et al. Interacting effects of CO2 partial pressure and temperature on photosynthesis and calcification in a scleractinian coral. Glob. Change Biol. 9, 1660–1668 (2003).Article 

    Google Scholar 
    Klein, S. G. et al. Projecting coral responses to intensifying marine heatwaves under ocean acidification. Glob. Change Biol. 28, 1753–1765 (2022).Article 
    CAS 

    Google Scholar 
    Colombo-Pallotta, M. F., Rodríguez-Román, A. & Iglesias-Prieto, R. Calcification in bleached and unbleached Montastraea faveolata: evaluating the role of oxygen and glycerol. Coral Reefs 29, 899–907 (2010).Article 

    Google Scholar 
    Holcomb, M., Tambutte, E., Allemand, D. & Tambutte, S. Light enhanced calcification in Stylophora pistillata: effects of glucose, glycerol and oxygen. PeerJ 2, e375 (2014).Article 

    Google Scholar 
    Herfort, L., Thake, B. & Taubner, I. Bicarbonate stimulation of calcification and photosynthesis in two hermatypic corals. J. Phycol. 44, 91–98 (2008).Article 
    CAS 

    Google Scholar 
    Tremblay, P., Fine, M., Maguer, J. F., Grover, R. & Ferrier-Pagès, C. Photosynthate translocation increases in response to low seawater pH in a coral–dinoflagellate symbiosis. Biogeosciences 10, 3997–4007 (2013).Article 

    Google Scholar 
    Briggs, A. A. & Carpenter, R. C. Contrasting responses of photosynthesis and photochemical efficiency to ocean acidification under different light environments in a calcifying alga. Sci. Rep. 9, 3986 (2019).Suggett, D. J. et al. Light availability determines susceptibility of reef building corals to ocean acidification. Coral Reefs 32, 327–337 (2013).Article 

    Google Scholar 
    IPCC. Climate change 2007: The physical science basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change 747–845 (2007).IPCC. Climate change 2021: The physical science basis. Working Group I Contribution to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (2021).Wall, C. B., Fan, T. Y. & Edmunds, P. J. Ocean acidification has no effect on thermal bleaching in the coral Seriatopora caliendrum. Coral Reefs 33, 119–130 (2014).Article 

    Google Scholar 
    Kuffner, I. B., Andersson, A. J., Jokiel, P. L., Rodgers, K. S. & Mackenzie, F. T. Decreased abundance of crustose coralline algae due to ocean acidification. Nat. Geosci. 1, 114–117 (2008).Article 
    CAS 

    Google Scholar 
    LaJeunesse, T. C. et al. Systematic revision of Symbiodiniaceae highlights the antiquity and diversity of coral endosymbionts. Curr. Biol. 28, 2570–2580 (2018). e6.Article 
    CAS 

    Google Scholar 
    Kemp, D. W. et al. Spatially distinct and regionally endemic Symbiodinium assemblages in the threatened Caribbean reef-building coral Orbicella faveolata. Coral Reefs 34, 535–547 (2015).Article 

    Google Scholar 
    Enríquez, S., Méndez, E. R., Hoegh-Guldberg, O. & Iglesias-Prieto, R. Key functional role of the optical properties of coral skeletons in coral ecology and evolution. Proc. Biol. Sci. 284, 20161667 (2017).Enríquez, S., Méndez, E. R. & Iglesias-Prieto, R. Multiple scattering on coral skeletons enhances light absorption by symbiotic algae. Limnol. Oceanogr. 50, 1025–1032 (2005).Article 

    Google Scholar 
    Skirving, W. et al. Remote sensing of coral bleaching using temperature and light: progress towards an operational algorithm. Remote Sens 10, 18 (2017).Article 

    Google Scholar 
    Warner, M. E., LaJeunesse, T. C., Robison, J. D. & Thur, R. M. The ecological distribution and comparative photobiology of symbiotic dinoflagellates from reef corals in Belize: Potential implications for coral bleaching. Limnol. Oceanogr. 51, 1887–1897 (2006).Article 

    Google Scholar 
    Krämer, W., Caamaño-Ricken, I., Richter, C. & Bischof, K. Dynamic regulation of photoprotection determines thermal tolerance of two phylotypes of Symbiodinium clade A at two photon flux densities. Photochem. Photobio. 88, 398–413 (2012).Article 

    Google Scholar 
    Wall, C. B., Mason, R. A. B., Ellis, W. R., Cunning, R. & Gates, R. D. Elevated pCO2 affects tissue biomass composition, but not calcification, in a reef coral under two light regimes. R. Soc. Open Sci. 4, 170683 (2017).Article 
    CAS 

    Google Scholar 
    Baghdasarian, G. et al. Effects of temperature and pCO2 on population regulation of Symbiodinium spp. in a tropical reef coral. Biol. Bull. 232, 123–139 (2017).Article 

    Google Scholar 
    Cornwall, C. E. et al. Resistance of corals and coralline algae to ocean acidification: physiological control of calcification under natural pH variability. Proc. R. Soc. B Biol. Sci. 285, 20181168 (2018).Article 

    Google Scholar 
    DeCarlo, T. M., Comeau, S., Cornwall, C. E. & McCulloch, M. T. Coral resistance to ocean acidification linked to increased calcium at the site of calcification. Proc. R. Soc. B Biol. Sci. 285, 20180564 (2018).Article 

    Google Scholar 
    Davies, S. W., Marchetti, A., Ries, J. B. & Castillo, K. D. Thermal and pCO2 stress elicit divergent transcriptomic responses in a resilient coral. Front. Mar. Sci. 3, 112 (2016).Article 

    Google Scholar 
    Hernansanz-Agustín, P. & Enríquez, J. A. Generation of reactive oxygen species by mitochondria. Antioxidants 10, 415 (2021).Article 

    Google Scholar 
    Acín-Pérez, R. et al. ROS-triggered phosphorylation of complex II by Fgr kinase regulates cellular adaptation to fuel use. Cell Metab. 19, 1020–1033 (2014).Article 

    Google Scholar 
    Burris, J. E., Porter, J. W. & Laing, W. A. Effects of carbon dioxide concentration on coral photosynthesis. Mar. Biol. 75, 113–116 (1983).Article 
    CAS 

    Google Scholar 
    Muscatine, L., Falkowski, P. G., Dubinsky, Z., Cook, P. A. & McCloskey, L. R. The effect of external nutrient resources on the population dynamics of zooxanthellae in a reef coral. Proc. R. Soc. Lond. B Biol. Sci. 236, 311–324 (1989).Article 

    Google Scholar 
    Goiran, C., Al-Moghrabi, S., Allemand, D. & Jaubert, J. Inorganic carbon uptake for photosynthesis by the symbiotic coral/dinoflagellate association I. Photosynthetic performances of symbionts and dependence on sea water bicarbonate. J. Exp. Mar. Biol. Ecol. 199, 207–225 (1996).Article 
    CAS 

    Google Scholar 
    Buxton, L., Badger, M. & Ralph, P. Effects of moderate heat stress and dissolved inorganic carbon concentration on photosynthesis and respiration of Symbiodinium sp. (Dinophyceae) in culture and in symbiosis. J. Phycol. 45, 357–365 (2009).Article 
    CAS 

    Google Scholar 
    Lin, Z., Wang, L., Chen, M. & Chen, J. The acute transcriptomic response of coral-algae interactions to pH fluctuation. Mar. Genomics 42, 32–40 (2018).Article 

    Google Scholar 
    Ziegler, M. et al. Integrating environmental variability to broaden the research on coral responses to future ocean conditions. Glob. Change Biol. 27, 5532–5546 (2021).Article 
    CAS 

    Google Scholar 
    Cornwall, C. E. et al. Global declines in coral reef calcium carbonate production under ocean acidification and warming. Proc. Natl Acad. Sci. 118, e2015265118 (2021).Article 
    CAS 

    Google Scholar 
    Eyre, B. D. et al. Coral reefs will transition to net dissolving before end of century. Science 359, 908–911 (2018).Article 
    CAS 

    Google Scholar 
    Cyronak, T. & Eyre, B. D. The synergistic effects of ocean acidification and organic metabolism on calcium carbonate (CaCO3) dissolution in coral reef sediments. Mar. Chem. 183, 1–12 (2016).Article 
    CAS 

    Google Scholar 
    Eyre, B. D., Andersson, A. J. & Cyronak, T. Benthic coral reef calcium carbonate dissolution in an acidifying ocean. Nat. Clim. Change 4, 969–976 (2014).Article 
    CAS 

    Google Scholar 
    Bedwell-Ivers, H. E. et al. The role of in hospite zooxanthellae photophysiology and reef chemistry on elevated pCO2 effects in two branching Caribbean corals: Acropora cervicornis and Porites divaricata. ICES J. Mar. Sci. 74, 1103–1112 (2016).Article 

    Google Scholar 
    Pierrot, D., Lewis, E. & Wallace, D. W. R. MS excel program developed for CO2 system calculations (2006).Cayabyab, N. M. & Enríquez, S. Leaf photoacclimatory responses of the tropical seagrass Thalassia testudinum under mesocosm conditions: a mechanistic scaling-up study. N. Phytol. 176, 108–123 (2007).Article 

    Google Scholar 
    Smith, S. V. & Kinsey, D. W. In Coral Reefs: Research Methods (eds. Stoddart, D. R. & Johannes, R. E.) 469–484 (UNESCO, 1978).Yao, W. & Byrne, R. H. Simplified seawater alkalinity analysis—application to the potentiometric titration of the total alkalinity and carbonate content in sea water. Deep Sea Res. Part Oceanogr. Res. Pap. 45, 1383–1392 (1998).Article 
    CAS 

    Google Scholar 
    Vasquez-Elizondo, R. M. et al. Absorptance determinations on multicellular tissues. Photosynth. Res. 132, 311–324 (2017).Article 
    CAS 

    Google Scholar 
    Whitaker, J. R. & Granum, P. E. An absolute method for protein determination based on the difference in absorbance at 235 and 280 nm. Anal. Biochem. 109, 156–159 (1980).Article 
    CAS 

    Google Scholar 
    Iglesias-Prieto, R., Matta, J. L., Robins, W. A. & Trench, R. K. Photosynthetic response to elevated temperature in the symbiotic dinoflagellate Symbiodinium microadriaticum in culture. Proc. Natl Acad. Sci. USA 89, 10302–10305 (1992).Article 
    CAS 

    Google Scholar 
    Jeffrey, S. W. & Humphrey, G. F. New spectrophotometric equations for determining chlorophyll a, b, c1 and c2 in higher plants, algae and natural phytoplankton. Biochem. Physiol. Pflanz. 167, 191–194 (1975).Article 
    CAS 

    Google Scholar  More

  • in

    Validation of SNP markers for thermotolerance adaptation in Ovis aries adapted to different climatic regions using KASP-PCR technique

    IPCC. Summary for Policymakers. In (Masson-Delmotte, V., P. Zhai, H.-O. Pörtner, D. Roberts, J. Skea, P.R. Shukla, A. Pirani, W. Moufouma-Okia, C. Péan, R. Pidcock, S. Connors, J.B.R. Matthews, Y. Chen, X. Zhou, M.I. Gomis, E. Lonnoy, T. Maycock, M. Tignor, and T. Waterfield, eds) Global Warming of 1.5°C. An IPCC Special Report on the impacts of global warming of 1.5°C above pre-industrial levels and related global greenhouse gas emission pathways, in the context of strengthening the global response to the threat of climate change, sustainable development, and efforts to eradicate poverty. In Press (2018).Malhi, Y. et al. Climate change and ecosystems: Threats, opportunities and solutions. Philos. Trans. R. Soc. B Biol. Sci. 375(1794), 20190104. https://doi.org/10.1098/rstb.2019.0104 (2020).Article 
    CAS 

    Google Scholar 
    McElwee, P. Climate change and biodiversity loss. Curr. Hist. 120(829), 295–300. https://doi.org/10.1525/curh.2021.120.829.295 (2021).Article 

    Google Scholar 
    Dickinson, M. G., Orme, C. D. L., Suttle, K. B. & Mace, G. M. Separating sensitivity from exposure in assessing extinction risk from climate change. Sci. Rep. 4(1), 6898. https://doi.org/10.1038/srep06898 (2015).Article 
    CAS 

    Google Scholar 
    UNFCCC (United Nations Framework Convention on Climate Change). Global Warming Potentials http://unfccc.int/ghg_data/items/3825.php (2014).BelhadjSlimen, I., Chniter, M., Najar, T. & Ghram, A. Meta-analysis of some physiologic, metabolic and oxidative responses of sheep exposed to environmental heat stress. Livestock Sci. 229, 179–187. https://doi.org/10.1016/j.livsci.2019.09.026 (2019).Article 

    Google Scholar 
    Wojtas, K., Cwynar, P. & Kołacz, R. Effect of thermal stress on physiological and blood parameters in merino sheep. Bull. Vet. Inst. Pulawy 58(2), 283–288. https://doi.org/10.2478/bvip-2014-0043 (2014).Article 

    Google Scholar 
    Gavojdian, D., Cziszter, L. T., Budai, C. & Kusza, S. Effects of behavioral reactivity on production and reproduction traits in Dorper sheep breed. J. Vet. Behav. 10(4), 365–368. https://doi.org/10.1016/j.jveb.2015.03.012 (2015).Article 

    Google Scholar 
    Mehaba, N., Coloma-Garcia, W., Such, X., Caja, G. & Salama, A. A. K. Heat stress affects some physiological and productive variables and alters metabolism in dairy ewes. J. Dairy Sci. 104(1), 1099–1110. https://doi.org/10.3168/jds.2020-18943 (2021).Article 
    CAS 

    Google Scholar 
    Ramón, M., Díaz, C., Pérez-Guzman, M. D. & Carabaño, M. J. Effect of exposure to adverse climatic conditions on production in Manchega dairy sheep. J. Dairy Sci. 99(7), 5764–6577. https://doi.org/10.3168/jds.2016-10909 (2016).Article 
    CAS 

    Google Scholar 
    Mahjoubi, E. et al. The effect of cyclical and severe heat stress on growth performance and metabolism in Afshari lambs1. J. Anim. Sci. 93(4), 1632–1640. https://doi.org/10.2527/jas.2014-8641 (2015).Article 
    CAS 

    Google Scholar 
    dos Hamilton, T. R. S. et al. Evaluation of lasting effects of heat stress on sperm profile and oxidative status of ram semen and epididymal sperm. Oxid. Med. Cell. Longev. 1–12, 2016. https://doi.org/10.1155/2016/1687657 (2016).Article 
    CAS 

    Google Scholar 
    Romo-Barron, C. B. et al. Impact of heat stress on the reproductive performance and physiology of ewes: A systematic review and meta-analyses. Int. J. Biometeorol. 63(7), 949–962. https://doi.org/10.1007/s00484-019-01707-z (2019).Article 
    ADS 

    Google Scholar 
    Caroprese, M. et al. Glucocorticoid effects on sheep peripheral blood mononuclear cell proliferation and cytokine production under in vitro hyperthermia. J. Dairy Sci. 101(9), 8544–8551. https://doi.org/10.3168/jds.2018-14471 (2018).Article 
    CAS 

    Google Scholar 
    Marcone, G., Kaart, T., Piirsalu, P. & Arney, D. R. Panting scores as a measure of heat stress evaluation in sheep with access and with no access to shade. Appl. Anim. Behav. Sci. 240, 105350. https://doi.org/10.1016/j.applanim.2021.105350 (2021).Article 

    Google Scholar 
    Van Wettere, W. H. E. J. et al. Review of the impact of heat stress on reproductive performance of sheep. J. Anim. Sci. Biotechnol. 12(1), 26. https://doi.org/10.1186/s40104-020-00537-z (2021).Article 

    Google Scholar 
    Belhadj Slimen, I., Najar, T., Ghram, A. & Abdrrabba, M. Heat stress effects on livestock: Molecular, cellular and metabolic aspects, a review. J. Anim. Physiol. Anim. Nutr. 100(3), 401–412. https://doi.org/10.1111/jpn.12379 (2016).Article 
    CAS 

    Google Scholar 
    Guo, Z., Gao, S., Ouyang, J., Ma, L. & Bu, D. Impacts of heat stress-induced oxidative stress on the milk protein biosynthesis of dairy cows. Animals 11(3), 726. https://doi.org/10.3390/ani11030726 (2021).Article 

    Google Scholar 
    Liu, Z. et al. Heat stress in dairy cattle alters lipid composition of milk. Sci. Rep. 7(1), 961. https://doi.org/10.1038/s41598-017-01120-9 (2017).Article 
    ADS 
    CAS 

    Google Scholar 
    Krishnan, G. et al. Mitigation of the heat stress impact in Livestock reproduction. In Theriogenology (InTech, 2017).
    Google Scholar 
    Robertson, S. & Friend, M. Strategies to ameliorate heat stress effects on sheep reproduction. In Climate Change and Livestock Production: Recent Advances and Future Perspectives 175–183 (Springer, 2021). https://doi.org/10.1007/978-981-16-9836-1_15.Chapter 

    Google Scholar 
    Sawyer, G. & Narayan, E. J. A review on the influence of climate change on sheep reproduction. In Comparative Endocrinology of Animals (Intech Open, 2019). https://doi.org/10.5772/intechopen.86799.Chapter 

    Google Scholar 
    Maurya, V. P., Sejian, V., Kumar, D. & Naqvi, S. M. K. Biological ability of Malpura rams to counter heat stress challenges and its consequences on production performance in a semi-arid tropical environment. Biol. Rhythm. Res. 49(3), 479–493. https://doi.org/10.1080/09291016.2017.1381451 (2018).Article 

    Google Scholar 
    Shahat, A. M., Rizzoto, G. & Kastelic, J. P. Amelioration of heat stress-induced damage to testes and sperm quality. Theriogenology 158, 84–96. https://doi.org/10.1016/j.theriogenology.2020.08.034 (2020).Article 
    CAS 

    Google Scholar 
    Singh, K. M. et al. Association of heat stress protein 90 and 70 gene polymorphism with adaptability traits in Indian sheep (Ovis aries). Cell Stress Chaperones 22(5), 675–684. https://doi.org/10.1007/s12192-017-0770-4 (2017).Article 
    CAS 

    Google Scholar 
    Kim, E.-S. et al. Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment. Heredity 116(3), 255–264. https://doi.org/10.1038/hdy.2015.94 (2016).Article 
    CAS 

    Google Scholar 
    do Paim, T. P., Alves dos Santos, C., de Faria, D. A., Paiva, S. R. & McManus, C. Genomic selection signatures in Brazilian sheep breeds reared in a tropical environment. Livestock Sci. 258, 104865. https://doi.org/10.1016/j.livsci.2022.104865 (2022).Article 

    Google Scholar 
    Kusza, S. et al. Kompetitive Allele Specific PCR (KASPTM) genotyping of 48 polymorphisms at different caprine loci in French Alpine and Saanen goat breeds and their association with milk composition. PeerJ 6, e4416. https://doi.org/10.7717/peerj.4416 (2018).Article 
    CAS 

    Google Scholar 
    Zhang, Y. et al. Technical note: Development and application of KASP assays for rapid screening of 8 genetic defects in Holstein cattle. J. Dairy Sci. 103(1), 619–624. https://doi.org/10.3168/jds.2019-16345 (2020).Article 
    CAS 

    Google Scholar 
    Chaari, A. Molecular chaperones biochemistry and role in neurodegenerative diseases. Int. J. Biol. Macromol. 131, 396–411. https://doi.org/10.1016/j.ijbiomac.2019.02.148 (2019).Article 
    CAS 

    Google Scholar 
    Tripathy, K., Sodhi, M., Kataria, R. S., Chopra, M. & Mukesh, M. In silico analysis of HSP70 gene family in bovine genome. Biochem. Genet. 59(1), 134–158. https://doi.org/10.1007/s10528-020-09994-7 (2021).Article 
    CAS 

    Google Scholar 
    Rehman, S. et al. Genomic identification, evolution and sequence analysis of the heat-shock protein gene family in buffalo. Genes 11(11), 1388. https://doi.org/10.3390/genes11111388 (2020).Article 
    CAS 

    Google Scholar 
    Huo, C. et al. Chronic heat stress negatively affects the immune functions of both spleens and intestinal mucosal system in pigs through the inhibition of apoptosis. Microbial Pathog. 136, 103672. https://doi.org/10.1016/j.micpath.2019.103672 (2019).Article 
    CAS 

    Google Scholar 
    Morange, M. HSFs in development. In Molecular Chaperones in Health and Disease 153–169 (Springer, 2006). https://doi.org/10.1007/3-540-29717-0_7.Chapter 

    Google Scholar 
    Hoter, A., El-Sabban, M. & Naim, H. The HSP90 family: Structure, regulation, function, and implications in health and disease. Int. J. Mol. Sci. 19(9), 2560. https://doi.org/10.3390/ijms19092560 (2018).Article 
    CAS 

    Google Scholar 
    Vanselow, J., Vernunft, A., Koczan, D., Spitschak, M. & Kuhla, B. Exposure of lactating dairy cows to acute pre-ovulatory heat stress affects granulosa cell-specific gene expression profiles in dominant follicles. PLoS One 11(8), e0160600. https://doi.org/10.1371/journal.pone.0160600 (2016).Article 
    CAS 

    Google Scholar 
    Joy, A. et al. Resilience of small ruminants to climate change and increased environmental temperature: A review. Animals 10(5), 86. https://doi.org/10.3390/ani10050867 (2020).Article 

    Google Scholar 
    Saravanan, K. A. et al. Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in a variety of cattle breeds. Genomics 113(3), 955–963. https://doi.org/10.1016/j.ygeno.2021.02.009 (2021).Article 
    CAS 

    Google Scholar 
    Singh, A. K., Upadhyay, R. C., Malakar, D., Kumar, S. & Singh, S. V. Effect of thermal stress on HSP70 expression in dermal fibroblast of zebu (Tharparkar) and crossbred (Karan-Fries) cattle. J. Therm. Biol 43, 46–53. https://doi.org/10.1016/j.jtherbio.2014.04.006 (2014).Article 
    CAS 

    Google Scholar 
    Verma, N., Gupta, I. D., Verma, A., Kumar, R. & Das, R. Novel SNPs in HSPB8 gene and their association with heat tolerance traits in Sahiwal indigenous cattle. Trop. Anim. Health Prod. 48(1), 175–180. https://doi.org/10.1007/s11250-015-0938-9 (2016).Article 

    Google Scholar 
    Al-Thuwaini, T. M., Al-Shuhaib, M. B. S. & Hussein, Z. M. A novel T177P missense variant in the HSPA8 gene associated with the low tolerance of Awassi sheep to heat stress. Trop. Anim. Health Prod. 52(5), 2405–2416. https://doi.org/10.1007/s11250-020-02267-w (2020).Article 

    Google Scholar 
    Onasanya, G. O. et al. Heterozygous single-nucleotide polymorphism genotypes at heat shock protein 70 gene potentially influence thermo-tolerance among four Zebu breeds of Nigeria. Front. Genet. https://doi.org/10.3389/fgene.2021.642213 (2021).Article 

    Google Scholar 
    Pascal, C. Researches regarding quality of sheep skins obtained from Karakul from Botosani sheep. Biotechnol. Anim. Husband. 27(3), 1123–1130. https://doi.org/10.2298/BAH1103123P (2011).Article 

    Google Scholar 
    Kevorkian, S. E. M., Zǎuleţ, M., Manea, M. A., Georgescu, S. E. & Costache, M. Analysis of the ORF region of the prion protein gene in the Botosani Karakul sheep breed from Romania. Turk. J. Vet. Anim. Sci. 35(2), 105–109. https://doi.org/10.3906/vet-0909-124 (2011).Article 
    CAS 

    Google Scholar 
    Kusza, S. et al. Mitochondrial DNA variability in Gyimesi Racka and Turcana sheep breeds. Acta Biochim. Pol. 62(2), 273–280. https://doi.org/10.18388/abp.2015_978 (2015).Article 
    CAS 

    Google Scholar 
    Gavojdian, D. et al. Effects of using indigenous heritage sheep breeds in organic and low-input production systems on production efficiency and animal welfare in Romania. Landbauforschung Volkenrode 66(4), 290–297. https://doi.org/10.3220/LBF1483607712000 (2016).Article 

    Google Scholar 
    Gavojdian, D. et al. Reproduction efficiency and health traits in Dorper, White Dorper, and Tsigai sheep breeds under temperate European conditions. Asian Australas. J. Anim. Sci. 28(4), 599–603. https://doi.org/10.5713/ajas.14.0659 (2015).Article 
    CAS 

    Google Scholar 
    Kusza, S. et al. The genetic variability of Hungarian Tsigai sheep. Archiv Tierzuch 53(3), 309–317 (2010).
    Google Scholar 
    Kusza, S. et al. Study of genetic differences among Slovak Tsigai populations using microsatellite markers. Czeh J. Anim. Sci. 54(10), 468–474. https://doi.org/10.17221/1670-CJAS (2009).Article 
    CAS 

    Google Scholar 
    Marcos-Carcavilla, A. et al. Polymorphisms in the HSP90AA1 5′ flanking region are associated with scrapie incubation period in sheep. Cell Stress Chaperones 15(4), 343–349. https://doi.org/10.1007/s12192-009-0149-2 (2010).Article 
    CAS 

    Google Scholar 
    Salces-Ortiz, J. et al. Looking for adaptive footprints in the HSP90AA1 ovine gene. BMC Evol. Biol. 15(1), 7. https://doi.org/10.1186/s12862-015-0280-x (2015).Article 
    CAS 

    Google Scholar 
    Toscano, J. H. B. et al. Innate immune responses associated with resistance against Haemonchus contortus in Morada Nova Sheep. J. Immunol. Res. 2019, 1–10. https://doi.org/10.1155/2019/3562672 (2019).Article 
    CAS 

    Google Scholar 
    Estrada-Reyes, Z. M. et al. Signatures of selection for resistance to Haemonchus contortus in sheep and goats. BMC Genom. 20(1), 735. https://doi.org/10.1186/s12864-019-6150-y (2019).Article 
    CAS 

    Google Scholar 
    Caroprese, M., Bradford, B. J. & Rhoads, R. P. Editorial: Impact of climate change on immune responses in agricultural animals. Front. Vet. Sci. https://doi.org/10.3389/fvets.2021.732203 (2021).Article 

    Google Scholar 
    FAO/IAEA. Agriculture biotechnology laboratory—handbook of laboratory exercises. Seibersdorf: IAEA Laboratories, 18 (2004).Zsolnai, A. & Orbán, L. Accelerated separation of random complex DNA patterns in gels: Comparing the performance of discontinuous and continuous buffers. Electrophoresis 20(7), 1462–1468. https://doi.org/10.1002/(SICI)1522-2683(19990601)20:7%3c1462::AID-ELPS1462%3e3.0.CO;2-0 (1999).Article 
    CAS 

    Google Scholar 
    Cavalcanti, L. C. G. et al. Genetic characterization of coat color genes in Brazilian Crioula sheep from a conservation nucleus. Pesq. Agrop. Brasil. 52(8), 615–622. https://doi.org/10.1590/s0100-204×2017000800007 (2017).Article 

    Google Scholar 
    Li, Y. et al. Heat stress-responsive transcriptome analysis in the liver tissue of Hu sheep. Genes 10(5), 395. https://doi.org/10.3390/genes10050395 (2019).Article 
    CAS 

    Google Scholar 
    Younis, F. Expression pattern of heat shock protein genes in sheep. Mansoura Vet. Med. J. 21(1), 1–5. https://doi.org/10.35943/mvmj.2020.21.001 (2020).Article 

    Google Scholar 
    Yeh F. C., Boyle R., Yang R. C., Ye Z., Mao J. X. & Yeh D. POPGENE version 1.32. Computer program and documentation distributed by the author. http://www.ualberta.ca/∼fyeh/popgene.html (1999).Lê, S., Josse, J. & Husson, F. FactoMineR: A package for multivariate analysis. J. Stat. Softw. 25(1), 1–18. https://doi.org/10.18637/jss.v025.i01 (2008).Article 

    Google Scholar 
    Wickham H. ggplot2: Elegant Graphics for Data Analysis. Springer. https://ggplot2.tidyverse.org (2016) (ISBN 978-3-319-24277-4).R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/ (2020). More

  • in

    Permafrost in the Cretaceous supergreenhouse

    Biskaborn, B. K. et al. Permafrost is warming at a global scale. Nat. Commun. 10, 264 (2019).Article 
    ADS 

    Google Scholar 
    Murton, J. B. What and where are periglacial landscapes? Permaf. Periglac. Process. 32, 186–212 (2021).Article 

    Google Scholar 
    Woodcroft, B. J. et al. Genome-centric view of carbon processing in thawing permafrost. Nature 560, 49–54 (2018).Article 
    ADS 
    CAS 

    Google Scholar 
    Reyes, F. & Lougheed, V. L. Rapid nutrient release from permafrost thaw in Arctic aquatic ecosystems. Arct. Antarct. Alp. Res. 47, 35–48 (2015).Article 

    Google Scholar 
    Fouché, J., Christiansen, C. T., Lafrenière, M. J., Grogan, P. & Lamoureux, S. F. Canadian permafrost stores large pools of ammonium and optically distinct dissolved organic matter. Nat. Commun. 11, 4500 (2020).Article 
    ADS 

    Google Scholar 
    Alley, N. F., Hore, S. B. & Frakes, L. A. Glaciations at high-latitude Southern Australia during the Early Cretaceous. Aust. J. Earth Sci. 67, 1045–1095 (2020).Article 
    ADS 

    Google Scholar 
    Hore, S. B., Hill, S. M. & Alley, N. F. Early Cretaceous glacial environment and paleosurface evolution within the Mount Painter Inlier, northern Flinders Ranges, South Australia. Aust. J. Earth Sci. 67, 1117–1160 (2020).Article 
    ADS 
    CAS 

    Google Scholar 
    Rodríguez-López, J. P. et al. Glacial dropstones in the western Tethys during the late Aptian–early Albian cold snap: Palaeoclimate and palaeogeographic implications for the mid-Cretaceous. Palaeogeogr. Palaeoclimatol. Palaeoecol. 452, 11–27 (2016).Article 

    Google Scholar 
    Schneider, S. et al. Macrofauna and biostratigraphy of the Rollrock Section, northern Ellesmere Island, Canadian Arctic Islands e a comprehensive high latitude archive of the Jurassic–Cretaceous transition. Cret. Res. 114, 104508 (2020).Article 

    Google Scholar 
    Jeans, C. V. & Platten, I. M. The erratic rocks of the Upper Cretaceous Chalk of England: how did they get there, ice transport or other means? Acta Geol. Pol. 71, 287–304 (2021).
    Google Scholar 
    Wu, C. & Rodríguez-López, J. P. Cryospheric processes in Quaternary and Cretaceous hyper-arid oases. Sedimentology 68, 755–770 (2021).Article 

    Google Scholar 
    Grasby, S. E., McCune, G. E., Beauchamp, B. & Galloway, J. M. Lower Cretaceous cold snaps led to widespread glendonite occurrences in the Sverdrup Basin, Canadian High Arctic. GSA Bull. 129, 771–787 (2017).Article 
    CAS 

    Google Scholar 
    Galloway, J. M. et al. Finding the VOICE: organic carbon isotope chemostratigraphy of the Late Jurassic–Early Cretaceous of Arctic Canada. Geol. Mag. 1–15 https://doi.org/10.1017/S0016756819001316 (2019).Rogov, M. et al. Database of global glendonite and ikaite records throughout the Phanerozoic. Earth Syst. Sci. Data 13, 343–356 (2021).Article 
    ADS 

    Google Scholar 
    Price, G. D. The evidence and implications of polar ice during the Mesozoic. Earth–Sci. Rev. 48, 183–210 (1999).Article 
    ADS 

    Google Scholar 
    Savidge, R. A. Evidence of early glaciation of southeastern Beringia. Can. J. Earth Sci. 57, 199–226 (2020).Article 
    ADS 

    Google Scholar 
    Wang, Y. et al. Relict sand wedges suggest a high altitude and cold temperature during the Early Cretaceous in the Ordos Basin, North China. Int. Geol. Rev. https://doi.org/10.1080/00206814.2022.2081938 (2022).Nelson, D. A., Cottle, J. M., Bindeman, I. N. & Camacho, A. Ultra-depleted hydrogen isotopes in hydrated glass record Late Cretaceous glaciation in Antarctica. Nat. Commun. 13, 5209 (2022).Article 
    ADS 
    CAS 

    Google Scholar 
    Yang, W.-B. et al. Isotopic evidence for continental ice sheet in mid-latitude region in the supergreenhouse Early Cretaceous. Sci. Rep. 3, 2732 (2013).Article 

    Google Scholar 
    Gao, T. et al. Accelerating permafrost collapse on the eastern Tibetan Plateau. Environ. Res. Lett. 16, 054023 (2021).Article 
    ADS 

    Google Scholar 
    Huang, Y. B. The origin and evolution of the desert in southern Ordos in early Cretaceous: Constraint from Magnetostratigraphy of Zhidan Group and magnetic susceptibility of its sediment. Doctoral Dissertation. Lanzhou University (2010).Ma, J. Sedimentary Basin Analysis of the Cretaceous Ancient Desert in the Ordos Basin. Master’s thesis, China University of Geosciences (2020).Wu, C. H., Rodríguez-López, J. P. & Santosh, M. Plateau archives of lithosphere dynamics, cryosphere and paleoclimate: the formation of Cretaceous desert basins in east Asia. Geosci. Front. 13, 101454 (2022).Article 
    CAS 

    Google Scholar 
    Zhu, R. X., Chen, L., Wu, F. Y. & Liu, J. L. Timing, scale and mechanism of the destruction of the North China Craton. Sci. China Earth Sci. 54, 789–797 (2011).Article 
    ADS 
    CAS 

    Google Scholar 
    Rodríguez-López, J. P., Clemmensen, L. B., Lancaster, N., Mountney, N. P. & Veiga, G. D. Archean to Recent aeolian sand systems and their preserved successions: current understanding and way forward. Sedimentology 61, 1487–1534 (2014).Article 

    Google Scholar 
    Murton, J. B. in Encyclopedia of Quaternary Science Vol. 3 (eds Elias, S. A. & Mock, C. J.) 436–451 (Elsevier, Amsterdam, 2013).Rodríguez-López, J. P., Van Vliet-Lanöe, B., López-Martínez, J. & Martín-García, R. Scouring by rafted ice and cryogenic pattern ground preserved in a Palaeoproterozoic equatorial proglacial lagoon succession, eastern India, Nuna supercontinent. Mar. Pet. Geol. 123, 104766 (2021).Article 

    Google Scholar 
    Murton, J. B., Worsley, P. & Gozdzik, J. Sand veins and wedges in cold aeolian environments. Quat. Sci. Rev. 19, 899–922 (2000).Article 
    ADS 

    Google Scholar 
    Kovács, J., Fábián, S. A., Schweitzer, F. & Varga, G. A relict sand-wedge polygon site in north-central Hungary. Permafr. Periglac. Process. 18, 379–384 (2007).Article 

    Google Scholar 
    Fábián, S. Á. et al. Distribution of relict permafrost features in the Pannonian Basin, Hungary. Boreas 43, 722–732 (2014).Article 

    Google Scholar 
    Williams, G. E. Proterozoic (pre-Ediacaran) glaciation and the high obliquity, low-latitude ice, strong seasonality (HOLIST) hypothesis: principles and tests. Earth–Sci. Rev. 87, 61–93 (2008).Article 
    ADS 

    Google Scholar 
    Williams, G. E., Schmidt, P. W. & Young, G. M. Strongly seasonal Proterozoic glacial climate in low palaeolatitudes: radically different climate system on the pre-Ediacaran Earth. Geosci. Front. 7, 555–571 (2016).Article 

    Google Scholar 
    Van Vliet-Lanoë, B. Deformations in the active layer related with ice/soil wedge growth and decay in present day Arctic. Paleoclimate implications. Ann. Soc. Géol. Nord. 13, 81–95 (2005).
    Google Scholar 
    Remillard, A. M. et al. Chronology and palaeoenvironmental implications of the ice-wedge pseudomorphs and composite wedge casts on the Magdalen Islands (eastern Canada). Boreas 44, 658–675 (2015).Article 

    Google Scholar 
    Murton, J. B. Thermokarst sediments and sedimentary structures, Tuktoyaktuk Coastlands, western Arctic Canada. Glob. Planet. Change 28, 175–192 (2001).Article 
    ADS 

    Google Scholar 
    Harris, C., Murton, J. B. & Davies, M. C. R. An analysis of mechanisms of ice-wedge casting based on geotechnical centrifuge modelling. Geomorphology 71, 328–343 (2005).Article 
    ADS 

    Google Scholar 
    Houmark-Nielsen, M. et al. Early and Middle Valdaian glaciations, ice-dammed lakes and periglacial interstadials in northwest Russia: new evidence from the Pyoza River area. Glob. Planet. Change 31, 215–237 (2001).Article 
    ADS 

    Google Scholar 
    Murton, J. B. & Kolstrup, E. Ice-wedge casts as indicators of palaeotemperatures: precise proxy or wishful thinking? Prog. Phys. Geogr. 27, 155–170 (2003).Article 

    Google Scholar 
    Harry, D. G. & Gozdzik, J. S. Ice wedges: growth, thaw transformation, and palaeoenvironmental significance. J. Quat. Sci. 3, 39–55 (1988).Article 

    Google Scholar 
    Wolfe, S. A., Morse, P. D., Neudorf, C. M., Kokelj, S. V., Lian, O. B. & O’Neill, H. B. Contemporary sand wedge development in seasonally frozen ground and paleoenvironmental implications. Geomorphology 308, 215–229 (2018).Article 
    ADS 

    Google Scholar 
    Murton, J. B. & Bateman, M. D. Syngenetic sand veins and anti-syngenetic sand wedges, Tuktoyaktuk Coastlands, western Arctic Canada. Permafr. Periglac. Process. 18, 33–47 (2007).Article 

    Google Scholar 
    Obu, J., Westermann, S., Kääb, A., & Bartsch, A. Ground Temperature Map, 2000–2016, Northern Hemisphere Permafrost (Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, PANGAEA, 2018)Obu, J. et al. Northern Hemisphere permafrost map based on TTOP modelling for 2000–2016 at 1 km2 scale. Earth–Sci. Rev. 193, 299–316 (2019).Article 
    ADS 

    Google Scholar 
    Hock, R. et al. in IPCC Special Report on the Ocean and Cryosphere in a Changing Climate (eds Pörtner, H.-O. et al.) 131–202 (Cambridge University Press, Cambridge, UK and New York, NY, USA, 2019).Mackay, J. R. The origin of hummocks, western arctic coast, Canada. Can. J. Earth Sci. 17, 996–1006 (1980).Article 
    ADS 

    Google Scholar 
    Kokelj, S. V., Burn, C. R. & Tarnocai, C. The structure and dynamics of earth hummocks in the subarctic forest near Inuvik, Northwest Territories, Canada. Arct. Antarct. Alp. Res. 39, 99–109 (2007).Article 

    Google Scholar 
    Rodríguez-López, J. P., Meléndez, N., de Boer, P. L., Soria, A. R. & Liesa, C. L. Spatial variability of multicontrolled aeolian supersurfaces in central-erg and marine erg-margin systems. Aeolian Res. 11, 141–154 (2013).Article 
    ADS 

    Google Scholar 
    Lunt, D. J. et al. Palaeogeographic controls on climate and proxy interpretation. Clim. Past 12, 1181–1198 (2016).Article 

    Google Scholar 
    Cheng, G., Bai, Y. & Sun, Y. Paleomagnetic study on the tectonic evolution of the Ordos Block, North China. Seismol. Geol. 10, 81–87 (1988).
    Google Scholar 
    Zheng, Z. et al. The apparent polar wander path for the North China Block since the Jurassic. Geophys. J. Int. 104, 29–40 (1991).Article 
    ADS 

    Google Scholar 
    Malinverno, A., Hildebrandt, J., Tominaga, M. & Channell, J. E. T. M-sequence geomagnetic polarity time scale (MHTC12) that steadies global spreading rates and incorporates astrochronology constraints. J. Geophys. Res. 117, B06104 (2012).ADS 

    Google Scholar 
    Zachos, J. C., Shackleton, N. J., Revenaugh, J. S., Pälike, H. & Flower, B. P. Climate response to orbital forcing across the Oligocene–Miocene boundary. Science 292, 274–278 (2001).Article 
    ADS 
    CAS 

    Google Scholar 
    Li, M. et al. Astronomical tuning of the end-Permian extinction and the Early Triassic Epoch of South China and Germany. Earth Planet. Sci. Lett. 441, 10–25 (2016).Article 
    ADS 
    CAS 

    Google Scholar 
    Westall, F. The nature of fossil bacteria: a guide to the search for extraterrestial live. J. Geophys. Res. 104, 437–16,451 (1999).
    Google Scholar 
    Yang, H., Chen, Z.-Q. & Papineau, D. Cyanobacterial spheroids and other biosignatures from microdigitate stromatolites of Mesoproterozoic Wumishan Formation in Jixian, North China. Precambrian Res. 368, 106496 (2022).Article 
    ADS 
    CAS 

    Google Scholar 
    Kremer, B., Kazmierczak, J., Łukomska-Kowalczyk, M. & Kempe, S. Calcification and silicification: fossilization potential of cyanobacteria from stromatolites of Niuafo’ou’s caldera lakes (Tonga) and implications for the early fossil record. Astrobiology 12, 535–548 (2012).Article 
    ADS 
    CAS 

    Google Scholar 
    Astafieva M. M. et al. Fossil Bacteria and Other Microorganisms in Terrestrial Rocks and Astromaterials (Paleontological Institute Russian Academy of Science, Moscow, 2011).Rozanov, A. Y. & Zavarzin, G. A. Bacterial paleontology. Vestn. Akad. Med. Nauk 67, 241–245 (1997).
    Google Scholar 
    Perez-Mon, C., Stierli, B., Plötze, M. & Frey, B. Fast and persistent responses of alpine permafrost microbial communities to in situ warming. Sci. Total Environ. 807, 150–720 (2022).Article 

    Google Scholar 
    Rivkina, E. et al. Earth’s perennially frozen environments as a model of cryogenic planet ecosystems. Permafr. Periglac. Process. 29, 246–256 (2018).Article 

    Google Scholar 
    Vishnivetskaya, T. A. et al. Insights into community of photosynthetic microorganisms from permafrost. FEMS Microbiol. Ecol. 96, fiaa229 (2020).Article 
    CAS 

    Google Scholar 
    Hultman, J. et al. Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature 521, 208–212 (2015).Article 
    ADS 
    CAS 

    Google Scholar 
    Choe, Y. H. et al. Comparing rock-inhabiting microbial communities in different rock types from a high arctic polar desert. FEMS Microbiol. Ecol. 94, fiy070 (2018).ADS 

    Google Scholar 
    Wu, X. et al. Comparative metagenomics of the active layer and permafrost from low-carbon soil in the Canadian High Arctic. Environ. Sci. Technol. 55, 12683–12693 (2021).Article 
    ADS 
    CAS 

    Google Scholar 
    Vickers, M. L. et al. The duration and magnitude of Cretaceous cold events: evidence from the northern high latitudes. Geol. Soc. Am. Bull. 131, 1979–1994 (2019).Article 
    ADS 
    CAS 

    Google Scholar 
    Lehmann, J. in Ammonoid Palaeobiology: From Macroevolution to Palaeogeography (eds Klug, C. De Baets, K., Kruta I. & Mapes, R. H.) 403–429 (Springer, Amsterdam, 2015).Keller, M. A. & Macquaker, J. H. S. in Studies by the U.S. Geological Survey in Alaska: US Geological Survey Professional Paper 1814-B Vol. 15 (ed Dumoulin, J. A.) 1–35 (US Geological Survey, US Department of The Interior, Reston, 2015).Cavalheiro, L. et al. Impact of global cooling on Early Cretaceous high pCO2 world during the Weissert Event. Nat. Commun. 12, 5411 (2021).Article 
    ADS 
    CAS 

    Google Scholar 
    McArthur, J. M. et al. Palaeotemperatures, polar ice-volume, and isotope stratigraphy (Mg/Ca, d18O, d13C, 87Sr/86Sr): the Early Cretaceous (Berriasian, Valanginian, Hauterivian). Palaeogeogr. Palaeoclimatol. Palaeoecol. 248, 391–430 (2007).Article 

    Google Scholar 
    Lini, A., Weissert, H. & Erba, E. The Valanginian carbon isotope event: a first episode of greenhouse climate conditions during the Cretaceous. Terra Nova 4, 374–384 (1992).Article 
    ADS 

    Google Scholar 
    Li, X. et al. Carbon isotope signatures of pedogenic carbonates from SE China: rapid atmospheric pCO2 changes during middle–late Early Cretaceous time. Geol. Mag. 151, 830–849 (2014).Article 
    ADS 
    CAS 

    Google Scholar 
    O’Brien, Ch. L. et al. Cretaceous sea-surface temperature evolution: constraints from TEX86 and planktonic foraminiferal oxygen isotopes. Earth–Sci. Rev. 172, 224–247 (2017).Article 
    ADS 

    Google Scholar 
    Price, G. D. et al. A high-resolution Belemnite geochemical analysis of early Cretaceous (Valanginian–Hauterivian) environmental and climatic perturbations. Geochem. Geophys. Geosyst. 19, 3832–3843 (2018).Article 
    CAS 

    Google Scholar 
    Turetsky, M. R. et al. Carbon release through abrupt permafrost thaw. Nat. Geosci. 13, 138–143 (2020).Article 
    ADS 
    CAS 

    Google Scholar 
    Van der Kolk, D. A., Whalen, M. T., Wartes, M. A., Newberry, R. J. & McCarthy, P. in Arctic to the Cordillera: Unlocking the Potential. American Association of Petroleum Geologists Pacific Section Meeting, May 8–11, Anchorage, AK, USA, Search and Discovery Article 90125 (American Association of Petroleum Geologists, 2011).Walter Anthony, K. M. et al. 21st-century modeled permafrost carbon emissions accelerated by abrupt thaw beneath lakes. Nat. Commun. 9, 3262 (2018).Article 
    ADS 

    Google Scholar 
    Cheng, F. et al. Alpine permafrost could account for a quarter of thawed carbon based on Plio-Pleistocene palaeoclimate analogue. Nat. Commun. 13, 1329 (2022).Article 
    ADS 
    CAS 

    Google Scholar 
    Brouillette, M. How microbes in permafrost could trigger a massive carbon bomb. Nature 591, 360–362 (2021).Article 
    ADS 
    CAS 

    Google Scholar 
    Murton, J. B. in Climate Change, Observed Impacts on Planet Earth, 3rd edn (ed Letcher, T.) 281–326 (Elsevier, Amsterdam, 2021).Schnyder, J., Ruffell, A., Deconinck, J. F. & Baudin, F. Conjunctive use of spectral gamma-ray logs and clay mineralogy in defining late Jurassic–early Cretaceous palaeoclimate change (Dorset, UK). Palaeogeogr. Palaeoclimatol. Palaeoecol. 229, 303–320 (2006).Article 

    Google Scholar 
    Li, M. et al. Astrochronology of the Anisian stage (Middle Triassic) at the guandao reference section, south china. Earth Planet. Sci. Lett. 482, 591–606 (2018).Article 
    ADS 
    CAS 

    Google Scholar 
    Li, M. et al. Palaeoclimate proxies for cyclostratigraphy: comparative analysis using a Lower Triassic marine section in South China. Earth–Sci. Rev. 189, 125–146 (2019).Article 
    ADS 
    CAS 

    Google Scholar 
    Li, M., Hinnov, L. & Kump, L. Acycle: time–series analysis software for palaeoclimate research and education. Comput. Geosci. 127, 12–22 (2019).Article 
    ADS 
    CAS 

    Google Scholar 
    Laskar, J. et al. A long–term numerical solution for the insolation quantities of the Earth. Astron. Astrophys. 428, 261–285 (2004).Article 
    ADS 

    Google Scholar  More

  • in

    Responses to salinity in the littoral earthworm genus Pontodrilus

    Lavelle, P., Blanchart, E., Martin, A., Spain, A. V. & Martin, S. Impact of soil fauna on the properties of soils in the humid tropics. In Myths and Science of Soils of the Tropics (eds Lal, R. & Sanchez, P.) 157–185 (Soil Science Society of America, 1992).
    Google Scholar 
    Eisenhauer, N. The action of an animal ecosystem engineer: Identification of the main mechanisms of earthworm impacts on soil microarthropods. Pedobiologia 53, 343–352 (2010).Article 

    Google Scholar 
    Eisenhauer, N. & Eisenhauer, E. The “intestines of the soil”: The taxonomic and functional diversity of earthworms—A review for young ecologists. Preprint at https://doi.org/10.32942/osf.io/tfm5y (2020).Gates, G. E. Burmese earthworms, an introduction to the systematics and biology of megadrile oligochaetes with special reference to South-east Asia. Trans. Amer. Phil. Soc. 62, 1–326. https://doi.org/10.2307/1006214 (1972).Article 

    Google Scholar 
    Blakemore, R. J. Origin and means of dispersal of cosmopolitan Pontodrilus litoralis (Oligocaheta: Megascolecidae). Eur. J. Soil Biol. 443, S3–S8. https://doi.org/10.1016/j.ejsobi.2007.08.041 (2007).Article 

    Google Scholar 
    Seesamut, T., Sutcharit, C., Jirapatrasilp, P., Chanabun, R. & Panha, S. Morphological and molecular evidence reveal a new species of the earthworm genus Pontodrilus Perrier, 1874 (Clitellata, Megascolecidae) from Thailand and Peninsular Malaysia. Zootaxa 4496, 218–237. https://doi.org/10.11646/zootaxa.4496.1.18 (2018).Article 

    Google Scholar 
    Seesamut, T., Jirapatrasilp, P., Chanabun, R., Oba, Y. & Panha, S. Size variation and geographical distribution of the luminous earthworm Pontodrilus litoralis (Grube, 1855) (Clitellata, Megascolecidae) in Southeast Asia and Japan. Zookeys 862, 23–43. https://doi.org/10.3897/zookeys.862.35727 (2019).Article 

    Google Scholar 
    Seesamut, T., Jirapatrasilp, P., Sutcharit, C., Tongkerd, P. & Panha, S. Mitochondrial genetic population structure and variation of the littoral earthworm Pontodrilus longissimus Seesamut and Panha, 2018 along the coast of Thailand. Eur. J. Soil Biol. 93, 103091. https://doi.org/10.1016/j.ejsobi.2019.103091 (2019).Article 

    Google Scholar 
    Attrill, M. J. A testable linear model for diversity trends in estuaries. J. Anim. Ecol. 71, 262–269. https://doi.org/10.1046/j.1365-2656.2002.00593.x (2002).Article 

    Google Scholar 
    McLusky, D. S. & Elliott, M. The Estuarine Ecosystem: Ecology, Threats and Management 3rd edn. (Oxford University Press, 2004).Book 

    Google Scholar 
    Telesh, I. V. & Khlebovich, V. V. Principal processes within the estuarine salinity gradient: A review. Mar. Pollut. Bull. 61, 149–155. https://doi.org/10.1016/j.marpolbul.2010.02.008 (2010).Article 
    CAS 

    Google Scholar 
    Owojori, O. J. & Reinecke, A. J. Effects of natural (flooding and drought) and anthropogenic (copper and salinity) stressors on the earthworm Aporrectodea caliginosa under field conditions. Appl. Soil Ecol. 44, 156–163. https://doi.org/10.1016/j.apsoil.2009.11.006 (2010).Article 

    Google Scholar 
    Guzyte, G., Sujetoviene, G. & Zaltauskaite, J. Effects of salinity on earthworm (Eisenia fetida). Environ. Eng. 8, 111 (2011).
    Google Scholar 
    Ganapati, P. N. & Subba Rao, B. V. S. S. R. Salinity tolerance of a littoral oligochaete, Pontodrilus bermudensis Beddard. Proc. Ind. Nat. Sci. Acad. 38, 350–354 (1972).
    Google Scholar 
    Subba Rao, B. V. S. S. R. Volume regulation in a euryhaline oligochaete, Pontodrilus bermudensis Beddard. Proc. Indian Acad. Sci. 87, 339–347 (1978).Article 

    Google Scholar 
    Owojori, O. J., Reinecke, A. J. & Rozanov, A. B. Effects of salinity on partitioning, uptake and toxicity of zinc in the earthworm Eisenia fetida. Soil Biol. Biochem. 40, 2385–2393. https://doi.org/10.1016/j.soilbio.2008.05.019 (2008).Article 
    CAS 

    Google Scholar 
    Seesamut, T. et al. Occurrence of bioluminescent and nonbioluminescent species in the littoral earthworm genus Pontodrilus. Sci. Rep. 11, 8407 (2021).Article 
    CAS 

    Google Scholar 
    Sivinski, J. & Forrest, T. Luminous defense in an earthworm. Fla. Entomol. 66, 517 (1983).Article 

    Google Scholar 
    Verdes, A. & Gruber, D. F. Glowing worms: Biological, chemical, and functional diversity of bioluminescent annelids. Integr. Comp. Biol. 57, 18–32. https://doi.org/10.1093/icb/icx017 (2017).Article 
    CAS 

    Google Scholar 
    Shimomura, O. & Yampolsky, I. Bioluminescence: Chemical Principles and Methods 3rd edn. (World Scientific, 2019).Book 

    Google Scholar 
    Easton, E. G. Earthworms (Oligochaeta) from islands of the south-western Pacific, and a note on two species from Papua New Guinea. N. Z. J. Zool. 11, 111–128. https://doi.org/10.1080/03014223.1984.10423750 (1984).Article 

    Google Scholar 
    Shen, H.-P., Tsai, S.-C. & Tsai, C.-F. Occurrence of the earthworms Pontodrilus litoralis (Grube, 1855), Metaphire houlleti (Perrier, 1872), and Eiseniella tetraedra (Savigny, 1826) from Taiwan. Taiwania 50, 11–21 (2005).
    Google Scholar 
    Satheeshkumar, P., Khan, A. B. & Senthilkumar, D. Annelida, Oligochaeta, Megascolecidae, Pontodrilus litoralis (Grupe, 1985): First record from Pondicherry mangroves, southeast coast of India. Int. J. Zool. Res. 7, 406–409. https://doi.org/10.3923/ijzr.2011.406.409 (2011).Article 

    Google Scholar 
    Nguyen, T. T., Nguyen, D. A., Tran, T. T. B. & Blakemore, R. J. A comprehensive checklist of earthworm species and subspecies from Vietnam (Annelida: Clitellata: Oligochaeta: Almidae, Eudrilidae, Glossoscolecidae, Lumbricidae, Megascolecidae, Moniligastridae, Ocnerodrilidae, Octochaetidae). Zootaxa 4140, 1–92. https://doi.org/10.11646/zootaxa.4140.1.1 (2016).Article 

    Google Scholar 
    Chen, S.-Y., Hsu, C.-H. & Soong, K. How to cross the sea: Testing the dispersal mechanisms of the cosmopolitan earthworm Pontodrilus litoralis. R. Soc. Open Sci. 8, 202297. https://doi.org/10.1098/rsos.202297 (2021).Article 
    ADS 

    Google Scholar 
    Smyth, K. & Elliott, M. Effects of changing salinity on the ecology of the marine environment. In Stressors in the Marine Environment (eds Solan, M. & Whiteley, N. M.) 161–175 (Oxford University Press, 2016).Chapter 

    Google Scholar 
    Veiga, M. P. T., Gutierre, S. M. M., Castellano, G. C. & Freire, C. A. Tolerance of high and low salinity in the intertidal gastropod Stramonita brasiliensis (Muricidae): Behaviour and maintenance of tissue water content. J. Molluscan Stud. 82, 154–160. https://doi.org/10.1093/mollus/eyv044 (2016).Article 

    Google Scholar 
    Carley, W. W., Caracciolo, E. A. & Mason, R. T. Cell and coelomic fluid volume regulation in the earthworm Lumbricus terrestris. Comp. Biochem. Physiol. 74, 569–575 (1983).Article 

    Google Scholar 
    Sharif, F. et al. Salinity tolerance of earthworms and effects of salinity and vermi amendments on growth of Sorghum bicolor. Arch. Agron. Soil Sci. 62, 1169–1181. https://doi.org/10.1080/03650340.2015.1132838 (2016).Article 
    CAS 

    Google Scholar 
    Wu, Z. et al. Effects of salinity on earthworms and the product during vermicomposting of kitchen wastes. Int. J. Environ. Res. Public Health 16, 4737. https://doi.org/10.3390/ijerph16234737 (2019).Article 
    CAS 

    Google Scholar 
    Oglesby, L. C. Volume regulation in aquatic invertebrates. J. Exp. Zool. 215, 289–301 (1981).Article 
    CAS 

    Google Scholar 
    Generlich, O. & Giere, O. Osmoregulation in two aquatic oligochaetes from habitats with different salinity and comparison to other annelids. Hydrobiologia 334, 251–261. https://doi.org/10.1007/BF00017375 (1996).Article 

    Google Scholar 
    Carregosa, V. et al. Tolerance of Venerupis philippinarum to salinity: Osmotic and metabolic aspects. Comp. Biochem. Physiol. A 171, 36–43. https://doi.org/10.1016/j.cbpa.2014.02.009 (2014).Article 
    CAS 

    Google Scholar 
    Freitas, R. et al. The effects of salinity changes on the polychaete Diopatra neapolitana: Impacts on regenerative capacity and biochemical markers. Aquat. Toxicol. 163, 167–176. https://doi.org/10.1016/j.aquatox.2015.04.006 (2015).Article 
    CAS 

    Google Scholar 
    Rivera-Ingraham, G. A. & Lignot, J. H. Osmoregulation, bioenergetics and oxidative stress in coastal marine invertebrates: Raising the questions for future research. J. Exp. Biol. 220, 1749–1760. https://doi.org/10.1242/jeb.135624 (2017).Article 

    Google Scholar 
    Munnoli, P. M. & Bhosle, S. Effect of soil cow dung proportion of vermicomposting. J. Sci. Ind. Res. 68, 57–60 (2009).
    Google Scholar  More

  • in

    Multiscale responses and recovery of soils to wildfire in a sagebrush steppe ecosystem

    Odum, E. P. The strategy of ecosystem development. Science 164, 262–270 (1969).Article 
    ADS 
    CAS 

    Google Scholar 
    Gorham, E., Vitousek, P. M. & Reiners, W. A. The regulation of element budgets over the course of terrestrial ecosystem succession. Annu. Rev. Ecol. Syst. 10, 53–84 (1979).Article 
    CAS 

    Google Scholar 
    Corman, J. R. et al. Foundations and frontiers of ecosystem science: Legacy of a classic paper (Odum 1969). Ecosystems 22, 1160–1172. https://doi.org/10.1007/s10021-018-0316-3 (2019).Article 

    Google Scholar 
    Santín, C. et al. Towards a global assessment of pyrogenic carbon from vegetation fires. Glob. Change Biol. 22, 76–91. https://doi.org/10.1111/gcb.12985 (2016).Article 
    ADS 

    Google Scholar 
    Kominoski, J. S., Gaiser, E. E. & Baer, S. G. Advancing theories of ecosystem development through long-term ecological research. Bioscience 68, 554–562. https://doi.org/10.1093/biosci/biy070 (2018).Article 

    Google Scholar 
    Balch, J. K., Bradley, B. A., D’Antonio, C. M. & Gómez-Dans, J. Introduced annual grass increases regional fire activity across the arid western USA (1980–2009). Glob. Change Biol. 19, 173–183. https://doi.org/10.1111/gcb.12046 (2013).Article 
    ADS 

    Google Scholar 
    Abatzoglou, J. T. & Kolden, C. A. Climate change in Western US deserts: Potential for increased wildfire and invasive annual grasses. Rangeland Ecol. Manag. 64(5), 471–478 (2011).Article 

    Google Scholar 
    Shi, H. et al. Historical cover trends in a sagebrush steppe ecosystem from 1985 to 2013: Links with climate, disturbance, and management. Ecosystems 21, 913–929. https://doi.org/10.1007/s10021-017-0191-3 (2018).Article 

    Google Scholar 
    Seyfried, M. S. & Wilcox, B. P. Scale and the nature of spatial variability: Field examples having implications for hydrologic modeling. Water Resour. Res. 31, 173–184. https://doi.org/10.1029/94WR02025 (1995).Article 
    ADS 

    Google Scholar 
    Gasch, C. K., Huzurbazar, S. V. & Stahl, P. D. Description of vegetation and soil properties in sagebrush steppe following pipeline burial, reclamation, and recovery time. Geoderma 265, 19–26. https://doi.org/10.1016/j.geoderma.2015.11.013 (2016).Article 
    ADS 

    Google Scholar 
    Huber, D. P. et al. Vegetation and precipitation shifts interact to alter organic and inorganic carbon storage in desert soils. Ecosphere 10, e02655. https://doi.org/10.1002/ecs2.2655 (2019).Article 

    Google Scholar 
    Knight, D. H., Jones, G. P., Reiners, W. A. & Romme, W. H. Mountains and Plains: The Ecology of Wyoming Landscapes (Yale University Press, 2014).
    Google Scholar 
    Patton, N. R., Lohse, K. A., Seyfried, M. S., Godsey, S. E. & Parsons, S. Topographic controls on soil organic carbon on soil mantled landscapes. Sci. Rep. 9, 6390. https://doi.org/10.1038/s41598-019-42556-5 (2019).Article 
    ADS 
    CAS 

    Google Scholar 
    Schwabedissen, S. G., Lohse, K. A., Reed, S. C., Aho, K. A. & Magnuson, T. S. Nitrogenase activity by biological soil crusts in cold sagebrush steppe ecosystems. Biogeochemistry 134, 57–76. https://doi.org/10.1007/s10533-017-0342-9 (2017).Article 
    CAS 

    Google Scholar 
    You, Y. et al. Biological soil crust bacterial communities vary along climatic and shrub cover gradients within a sagebrush steppe ecosystem. Front. Microbiol. 12, 2365. https://doi.org/10.3389/fmicb.2021.569791 (2021).Article 

    Google Scholar 
    Burke, I. C., Reiners, W. A. & Olson, R. K. Topographic control of vegetation in a mountain big sagebrush steppe. Vegetation 84, 77–86 (1989).Article 

    Google Scholar 
    Poulos, M. J., Pierce, J. L., Flores, A. N. & Benner, S. G. Hillslope asymmetry maps reveal widespread, multi-scale organization. Geophys. Res. Lett. 39, 6. https://doi.org/10.1029/2012GL051283 (2012).Article 

    Google Scholar 
    Smith, T. & Bookhagen, B. Climatic and biotic controls on topographic asymmetry at the global scale. J. Geophys. Res.: Earth Surf. 126, e2020JF005692. https://doi.org/10.1029/2020JF005692Received22 (2021).Article 
    ADS 

    Google Scholar 
    Seyfried, M., Link, T., Marks, D. & Murdock, M. Soil temperature variability in complex terrain measured using fiber-optic distributed temperature sensing. Vadose Zone J. 15, 6. https://doi.org/10.2136/vzj2015.09.0128 (2016).Article 

    Google Scholar 
    Chambers, J. C. et al. Resilience and resistance of sagebrush ecosystems: Implications for state and transition models and management treatments. Rangel. Ecol. Manage. 67, 440–454. https://doi.org/10.2111/REM-D-13-00074.1 (2014).Article 

    Google Scholar 
    Chambers, J. C. et al. Operationalizing resilience and resistance concepts to address invasive grass-fire cycles. Front. Ecol. Evol. 7, 2369. https://doi.org/10.3389/fevo.2019.00185 (2019).Article 

    Google Scholar 
    Boehm, A. R. et al. Slope and aspect effects on seedbed microclimate and germination timing of fall-planted seeds. Rangel. Ecol. Manage. 75, 58–67. https://doi.org/10.1016/j.rama.2020.12.003 (2021).Article 

    Google Scholar 
    Sankey, J. B., Germino, M. J., Sankey, T. T. & Hoover, A. N. Fire effects on the spatial patterning of soil properties in sagebrush steppe, USA: A meta-analysis. Int. J. Wildl. Fire 21, 545–556. https://doi.org/10.1071/WF11092 (2012).Article 

    Google Scholar 
    Fellows, A., Flerchinger, G., Seyfried, M. S. & Lohse, K. A. Rapid recovery of mesic mountain big sagebrush gross production and respiration following prescribed fire. Ecosystems 21, 1283–1294. https://doi.org/10.1007/s10021-017-0218-9 (2018).Article 

    Google Scholar 
    Vega, S. P. et al. Interaction of wind and cold-season hydrologic processes on erosion from complex topography following wildfire in sagebrush steppe. Earth Surf. Process. Landforms https://doi.org/10.1002/esp.4778 (2019).Article 

    Google Scholar 
    Xie, J., Li, Y., Zhai, C., Li, C. & Lan, Z. CO2 absorption by alkaline soils and its implication to the global carbon cycle. Environ. Geol. 56, 953–961 (2009).Article 
    ADS 
    CAS 

    Google Scholar 
    Stanbery, C., Pierce, J. L., Benner, S. G. & Lohse, K. On the rocks: Quantifying storage of inorganic soil carbon on gravels and determining pedon-scale variability. CATENA 157, 436–442. https://doi.org/10.1016/j.catena.2017.06.011 (2017).Article 
    CAS 

    Google Scholar 
    Stanbery, C. et al. Controls on the presence and concentration of soil inorganic carbon in a semi-arid watershed. CATENA https://doi.org/10.2139/ssrn.4267018 (2023).Article 

    Google Scholar 
    Cerling, T. E. & Quade, J. Stable carbon and oxygen isotopes in soil carbonates. Geophys. Monogr. 78, 217–231 (1993).ADS 

    Google Scholar 
    Tappa, D. J., Kohn, M. J., McNamara, J. P., Benner, S. G. & Flores, A. N. Isotopic composition of precipitation in a topographically steep, seasonally snow-dominated watershed and implications of variations from the global meteoric water line. Hydrol. Process. 30, 4582–4592. https://doi.org/10.1002/hyp.10940 (2016).Article 
    ADS 
    CAS 

    Google Scholar 
    Salomons, W., Goudie, A. & Mook, W. G. Isotopic composition of calcrete deposits from Europe, Africa and India. Earth Surf. Process. 3, 43–57. https://doi.org/10.1002/esp.3290030105 (1978).Article 
    CAS 

    Google Scholar 
    Salomons, W. & Mook, W. G. In Handbook of Environmental Isotope Geochemistry (eds P. Fritz & J. Fontes) Ch. 6, 241–269 (Elsevier, 1986).Bodí, M. B. et al. Wildland fire ash: Production, composition and eco-hydro-geomorphic effects. Earth Sci. Rev. 130, 103–127. https://doi.org/10.1016/j.earscirev.2013.12.007 (2014).Article 
    ADS 
    CAS 

    Google Scholar 
    Kéraval, B. et al. Soil carbon dioxide emissions controlled by an extracellular oxidative metabolism identifiable by its isotope signature. Biogeosciences 13, 6353–6362. https://doi.org/10.5194/bg-13-6353-2016 (2016).Article 
    ADS 
    CAS 

    Google Scholar 
    Goforth, B. R., Graham, R. C., Hubbert, K. R., Zanner, C. W. & Minnich, R. A. Spatial distribution and properties of ash and thermally altered soils after high-severity forest fire, southern California. Int. J. Wildland Fire 14, 343–354 (2005).Article 

    Google Scholar 
    Glossner, K. L. et al. Long-term suspended sediment and particulate organic carbon yields from the Reynolds Creek Experimental Watershed and Critical Zone Observatory. Hydrol. Process. 36, e14484. https://doi.org/10.1002/hyp.14484 (2022).Article 
    CAS 

    Google Scholar 
    Seyfried, M. S. et al. Reynolds creek experimental watershed and critical zone observatory. Vadoze Zone J. 17, 180129. https://doi.org/10.2136/vzj2018.07.0129 (2018).Article 
    CAS 

    Google Scholar 
    McIntyre, D. H. Cenozoic geology of the Reynolds Creek Experimental Watershed, Owyhee County, Idaho (Idaho Bureau of Mines and Geology, 1972).Earth Resources Observation and Science (EROS) Center, U. Image of the week: Burned Area Analysis for the Soda Fire, Idaho, https://eros.usgs.gov/media-gallery/image-of-the-week/burned-area-analysis-the-soda-fire-idaho (2015).Jenny, H. Factors of Soil Formation (McGraw-Hill, 1941).Book 

    Google Scholar 
    Kormos, P. R. et al. 31 years of hourly spatially distributed air temperature, humidity, and precipitation amount and phase from Reynolds Critical Zone Observatory. Earth Syst. Sci. Data 10, 1197–1205. https://doi.org/10.5194/essd-10-1197-2018 (2018).Article 
    ADS 

    Google Scholar 
    Thomas, G. W. In Methods in Soil Analysis. Part 3. Chemical Methods (ed Sparks, D. L. ) (Soil Science Society of America and American Society of Agronomy, 1996).Brodie, C. R. et al. Evidence for bias in C and N concentrations and δ13C composition of terrestrial and aquatic organic materials due to pre-analysis acid preparation methods. Chem. Geol. 282, 67–83. https://doi.org/10.1016/j.chemgeo.2011.01.007 (2011).Article 
    ADS 
    CAS 

    Google Scholar 
    Patton, N. P., Lohse, K. A., Seyfried, M. S., Will, R. & Benner, S. G. Lithology and coarse fraction adjusted bulk density estimates for determining total organic carbon stocks in dryland soils. Geoderma 337, 844–852. https://doi.org/10.1016/j.geoderma.2018.10.036 (2019).Article 
    ADS 
    CAS 

    Google Scholar 
    McGuire, L. A., Rasmussen, C., Youberg, A. M., Sanderman, J. & Fenerty, B. Controls on the Spatial distribution of near-surface pyrogenic carbon on hillslopes 1 year following wildfire. J. Geophys. Res.: Earth Surf. 126, e2020JF005996. https://doi.org/10.1029/2020JF005996 (2021).Article 
    ADS 

    Google Scholar 
    Jiménez-González, M. A. et al. Spatial distribution of pyrogenic carbon in Iberian topsoils estimated by chemometric analysis of infrared spectra. Sci. Total Env. 790, 148170. https://doi.org/10.1016/j.scitotenv.2021.148170 (2021).Article 
    CAS 

    Google Scholar 
    Baldock, J. A. et al. Quantifying the allocation of soil organic carbon to biologically significant fractions. Soil Res. 51, 561–576. https://doi.org/10.1071/SR12374 (2013).Article 
    CAS 

    Google Scholar 
    Sanderman, J. et al. Soil organic carbon fractions in the Great Plains of the United States: An application of mid-infrared spectroscopy. Biogeochemistry 156, 97–114. https://doi.org/10.1007/s10533-021-00755-1 (2021).Article 
    CAS 

    Google Scholar 
    Sherrod, L. A., Dunn, G., Peterson, G. A. & Kolberg, R. L. Inorganic carbon analysis by modified pressure-calcimeter method. Soil Sci. Soc. Am. J. 66, 299–305 (2002).Article 
    ADS 
    CAS 

    Google Scholar 
    Mikutta, R., Kleber, M., Kaiser, K. & Jahn, R. Review. Soil Sci. Soc. Am. J. 69, 120–135. https://doi.org/10.2136/sssaj2005.0120 (2005).Article 
    ADS 
    CAS 

    Google Scholar 
    Risk, D., Nickerson, N., Creelman, C., McArthur, G. & Owens, J. Forced Diffusion soil flux: A new technique for continuous monitoring of soil gas efflux. Agric. For. Meteorol. 151, 1622–1631. https://doi.org/10.1016/j.agrformet.2011.06.020 (2011).Article 
    ADS 

    Google Scholar 
    Fierer, N. & Schimel, J. P. Effects of drying–rewetting frequency on soil carbon and nitrogen transformations. Soil Biol. Biochem. 34, 777–787. https://doi.org/10.1016/S0038-0717(02)00007-X (2002).Article 
    CAS 

    Google Scholar 
    Dane, J. H., Topp, G. C. & Campbell, G. S. In Methods of Soil Analysis: Physical Methods. Vol. 4 (ed SSSA) 721–738 (2002). More

  • in

    Incorporating dead material in ecosystem assessments and projections

    Stokland, J. N., Siitonen, J. & Jonsson, B. G. Biodiversity in Dead Wood (Cambridge Univ. Press, 2012).Turetsky, M. R. et al. Nat. Geosci. 8, 11–14 (2014).Article 

    Google Scholar 
    Wenger, S. J., Subalusky, A. L. & Freeman, M. C. Food Webs 18, e00106 (2019).Article 

    Google Scholar 
    Tomatsuri, M. & Kon, K. Hydrobiologia 790, 225–232 (2017).Article 

    Google Scholar 
    Henry, L. A. & Roberts, J. M. in Marine Animal Forests (eds Rossi, S. et al.) 235–256 (Springer, 2017).Walton, M. E. M. et al. Sci. Total Environ. 820, 153191 (2022).Article 
    CAS 

    Google Scholar 
    Wolfe, K., Kenyon, T. M. & Mumby, P. J. Coral Reefs 40, 1769–1806 (2021).Article 

    Google Scholar 
    Kim, H. et al. Glob. Change Biol. 28, 6180–6193 (2022).Jackson, R. B. et al. Annu. Rev. Ecol. Evol. Syst. 48, 419–445 (2017).Article 

    Google Scholar 
    Pan, Y. et al. Science 333, 988–993 (2011).Article 
    CAS 

    Google Scholar 
    Hedges, J. I., Keil, R. G. & Benner, R. Org. Geochem. 27, 195–212 (1997).Article 
    CAS 

    Google Scholar 
    Lønborg, C. et al. Front. Mar. Sci. 7, 466 (2020).Article 

    Google Scholar 
    Harden, J. W. et al. Glob. Change Biol. 6, 174–184 (2000).Davidson, E. A. & Janssens, I. A. Nature 440, 165–173 (2006).Article 
    CAS 

    Google Scholar 
    Hugelius, G. et al. Proc. Natl Acad. Sci. USA 117, 20438–20446 (2020).Article 
    CAS 

    Google Scholar 
    Hennige, S. J. et al. Front. Mar. Sci. https://doi.org/10.3389/fmars.2020.00668 (2020).Article 

    Google Scholar 
    Wolfram, U. et al. Sci. Rep. 12, 8052 (2022).Article 
    CAS 

    Google Scholar 
    Roberts, J. M., Wheeler, A. J. & Freiwald, A. Science 312, 543–547 (2006).Article 
    CAS 

    Google Scholar 
    Mortensen, P. B. & Fosså, J. H. Species diversity and spatial distribution of invertebrates on deep-water Lophelia reefs in Norway. In Proc. 10th Int. Coral Reef Symp. 1849–1868 (ICRS, 2006).Maier, S. R. et al. Deep Sea Res. I 175, 103574 (2021).. More

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    A metagenomic insight into the microbiomes of geothermal springs in the Subantarctic Kerguelen Islands

    MAG binning and general featuresFrom the four hot springs, we assembled four associated metagenomes and then binned a total of 42 MAGs. We recovered 12 MAGs from RB10 hot spring, 13 from RB13, 14 from RB32 and 3 from RB108. Out of these 42 MAGs, 7 were of high-quality, 25 of nearly-high quality, 9 of medium quality and 1 of low quality (Table 1) based on metagenomic standards26. The GC% was quite variable, ranging from 25.76 to 70.35% among all MAGs and between 32.15 and 69.21% only among the high- and near high-quality MAGs. With the exception of RB108 from which we only recovered bacterial MAGs, we retrieved both bacterial and archaeal MAGs in the other hot springs. Two thirds of the MAGs (26/42) were assigned to the domain Bacteria and the rest to the domain Archaea (16/42) (Table 2).Table 1 General characteristics of the 42 MAGs obtained from RB10, RB13, RB32 and RB108 samples.Full size tableTable 2 Classification of the MAGs based on the taxonomic classification of GTDB-Tk software (v2.1.0) and the Genome Taxonomy Database (07-RS207 release).Full size tableTaxonomic and phylogenomic analyses of MAGsThe taxonomic affiliation of the MAGs was investigated in detail through the workflow classify of GTDB-Tk (v 2.1.0; GTDB reference tree 07-RS207) (Table 2) and through de novo phylogenomic analyses (Fig. S1a–i). We also tried to classify MAGs on the basis of overall genome relatedness indices (OGRI), which is detailed in supplementary material (Text S1, Table S2, Fig. S2).De novo phylogenomic analyses globally confirmed the positioning of MAGs provided by GTDB-Tk, with high branching support. For Bacteria, GTDB-Tk analyses allowed us to place the MAGs in the following clades: six in the phylum Aquificota from the four different springs, comprising four MAGs belonging to the genus Hydrogenivirga (family Aquificaceae) (RB10-MAG07, RB13-MAG10, RB32-MAG07, RB108-MAG02), and two belonging to the family ‘Hydrogenobaculaceae’ (RB10-MAG12, RB32-MAG11) (Table 2, Fig. S1a). Their closest cultured relatives originated either from hot springs or from deep-sea hydrothermal vents27. Three MAGs from three geothermal springs belonged to the phylum Armatimonadota (RB10-MAG03, RB13-MAG04, RB32-MAG03) and had no close cultured relatives. Seven MAGs have been classified into the phylum Chloroflexota: three MAGs belonging to the genus Thermoflexus from three different springs (RB10-MAG04, RB13-MAG05, RB32-MAG02), one affiliating with the genus Thermomicrobium (RB32-MAG08), one falling into the family Ktedonobacteraceae (RB108-MAG03), one belonging to the class Dehalococcoidia (RB32-MAG04) and another one whose phylogenetic position is more difficult to assert because it is a MAG of medium quality (RB32-MAG14). Six MAGs from four various hot springs belonged to the phylum Deinococcota, and to the genera Thermus (RB10-MAG08, RB10-MAG11, RB13-MAG09, RB32-MAG10, RB108-MAG01) and Meiothermus (RB13-MAG13). One MAG belonged to the family ‘Sulfurifustaceae’ (RB13-MAG01), in the phylum Proteobacteria (Gamma-class). The MAG referenced as RB32-MAG13 was classified into the phylum ‘Patescibacteria’, in the class ‘Paceibacteria’, and was distantly related to MAGs originating from groundwater and from hot springs. Finally, two MAGs from two different springs belonged to the phylum WOR-3, in the Candidatus genus ‘Caldipriscus’ (RB32-MAG12, RB10-MAG09).For Archaea, almost all the MAGs reconstructed in this study, e.g. 15 of the 16 archaeal MAGs, belonged to the phylum Thermoproteota. Among them, four belonged to the genus Ignisphaera (RB10-MAG05, RB13-MAG08, RB13-MAG11, RB32-MAG05), three to the genus Infirmifilum (RB10-MAG06, RB13-MAG03, RB32-MAG09), two to the genus Zestosphaera (RB10-MAG02, RB13-MAG06), three to the family Acidilobaceae (RB10-MAG01, RB13-MAG02, RB32-MAG01) and two to the order Geoarchaeales (RB10-MAG10, RB32-MAG06). Additionally, one belonged to the family Thermocladiaceae (RB13-MAG07). Lastly, the MAG belonging to another phylum (RB13-MAG12) was affiliated with the ‘Aenigmatarchaeota’, class ‘Aenigmatarchaeia’, and was distantly related to MAGs from hot springs and from deep-sea hydrothermal vent sediments28,29.Out of these 42 MAGs, at least 19 MAGs corresponded to different taxa at the taxonomic rank of species or higher according to GTDB (Table 2). Eighteen of them belonged to lineages with several cultivated representatives including the species Thermus thermophilus. 13 new genomic species within the GTDB genera Hydrogenivirga, HRBIN17, Thermoflexus, SpSt-223, CADDYT01, Zestosphaera, Ignisphaera, Infirmifilum, Thermus, Thermus_A, Meiothermus_B, JAHLMO01 and Caldipriscus, and 6 putative new genomic genera belonging to the GTDB families Hydrogenobaculaceae, Acidilobaceae, WAQG01, Thermocladiaceae, Sulfurifustaceae and HR35 could be identified (Table 2). In addition, 9 MAGs belonged to lineages that are predominantly or exclusively known through environmental DNA sequences. Thus, these 42 MAGs comprised a broad phylogenetic range of Bacteria and Archaea at different levels of taxonomic organization, of which a large majority were not reported before.The approaches implemented here were not intended to describe the microbial diversity present in these sources in an exhaustive way or to compare them in a fine way, and cannot allow it because of a 2-year storage at 4 °C. This long storage has probably led to changes in the microbial communities and to the selective loss or enrichment of some taxa. As a result, no analysis of abundance or absence of taxa can be conducted from these metagenomes and the results are discussed taking this bias into account. However, they do provide an overview of the microbial diversity effectively present. If we compare the phylogenetic diversity of the MAGs found in the four hot springs, we can observe that 3 shared phyla (Deinococcota, Aquificota and Chloroflexota: phyla names according to GTDB), 2 shared families (Thermaceae and Aquificaceae), and one shared genus (Hydrogenivirga) were found among the four sources (Fig. 2). In addition, hot springs RB10, RB13 and RB32, that are geographically close ( More