More stories

  • in

    Reply to: Methods matter in repeating ocean acidification studies

    1.
    Dixson, D. L., Munday, P. L. & Jones, G. P. Ocean acidification disrupts the innate ability of fish to detect predator olfactory cues. Ecol. Lett. 13, 68–75 (2010).
    Article  Google Scholar 
    2.
    Munday, P. L. et al. Replenishment of fish populations is threatened by ocean acidification. Proc. Natl Acad. Sci. USA 107, 12930–12934 (2010).
    ADS  CAS  Article  Google Scholar 

    3.
    Clements, J. C. & Hunt, H. L. Marine animal behaviour in a high CO2 ocean. Mar. Ecol. Prog. Ser. 536, 259–279 (2015).
    ADS  CAS  Article  Google Scholar 

    4.
    Watson, S.-A. et al. Marine mollusc predator-escape behaviour altered by near-future carbon dioxide levels. Proc. R. Soc. B 281, 20132377 (2014).
    Article  Google Scholar 

    5.
    Clark, T. D. et al. Ocean acidification does not impair the behaviour of coral reef fishes. Nature 577, 370–375 (2020).
    ADS  CAS  Article  Google Scholar 

    6.
    Munday, P. L. et al. Methods matter in repeating ocean acidification studies. Nature https://doi.org/10.1038/s41586-020-2803-x (2020).
    Article  Google Scholar 

    7.
    Nosek, B. A. & Errington, T. M. What is replication? PLoS Biol. 18, e3000691 (2020).
    CAS  Article  Google Scholar 

    8.
    Munday, P. L. et al. Elevated CO2 affects the behavior of an ecologically and economically important coral reef fish. Mar. Biol. 160, 2137–2144 (2013).
    CAS  Article  Google Scholar 

    9.
    Munday, P. L., Cheal, A. J., Dixson, D. L., Rummer, J. L. & Fabricius, K. E. Behavioural impairment in reef fishes caused by ocean acidification at CO2 seeps. Nat. Clim. Change 4, 487–492 (2014).
    ADS  CAS  Article  Google Scholar 

    10.
    Munday, P. L. et al. Effects of elevated CO2 on predator avoidance behaviour by reef fishes is not altered by experimental test water. PeerJ 4, e2501 (2016).
    Article  Google Scholar 

    11.
    Ioannidis, J. P. A. Why science is not necessarily self-correcting. Perspect. Psychol. Sci. 7, 645–654 (2012).
    Article  Google Scholar 

    12.
    Browman, H. I. Applying organized scepticism to ocean acidification research. ICES J. Mar. Sci. 73, 529–536 (2016).
    Article  Google Scholar 

    13.
    Nissen, S. B., Magidson, T., Gross, K. & Bergstrom, C. T. Publication bias and the canonization of false facts. eLife 5, e21451 (2016).
    Article  Google Scholar  More

  • in

    Bacteria incorporated with calcium lactate pentahydrate to improve the mortar properties and self-healing occurrence

    1.
    Monteiro, P. J. M., Miller, S. A. & Horvath, A. Towards sustainable concrete. Nat. Mater. 16, 698–699 (2017).
    ADS  CAS  Article  Google Scholar 
    2.
    Schneider, M., Romer, M., Tschudin, M. & Bolio, H. Sustainable cement production—Present and future. Cem. Concr. Res. 41, 642–650 (2011).
    CAS  Article  Google Scholar 

    3.
    Worrell, E., Price, L., Martin, N., Hendriks, C. & Meida, L. O. Carbon dioxide emissions from the global cement industry. Annu. Rev. Energy Environ. 26, 303–329 (2001).
    Article  Google Scholar 

    4.
    Mehta, P. K. & Monteiro, P. J. M. Concrete: Microstructure, Properties, and Materials (McGraw-Hill, New York, 2005).
    Google Scholar 

    5.
    Chen, C., Habert, G., Bouzidi, Y. & Jullien, A. Environmental impact of cement production: Detail of the different processes and cement plant variability evaluation. J. Clean. Prod. 18, 478–485 (2010).
    CAS  Article  Google Scholar 

    6.
    Bu, J., Tian, Z., Zheng, S. & Tang, Z. Effect of sand content on strength and pore structure of cement mortar. J. Wuhan Univ. Technol. Mater. Sci. Ed. 32, 382–390 (2017).
    CAS  Article  Google Scholar 

    7.
    Khaliq, W. & Ehsan, M. B. Crack healing in concrete using various bio influenced self-healing techniques. Constr. Build. Mater. 102, 349–357 (2016).
    CAS  Article  Google Scholar 

    8.
    Vijay, K. & Murmu, M. Effect of calcium lactate on compressive strength and self-healing of cracks in microbial concrete. Front. Struct. Civ. Eng. https://doi.org/10.1007/s11709-018-0494-2 (2018).
    Article  Google Scholar 

    9.
    Vahabi, A., Ramezanianpour, A. A. & Noghabi, K. A. A preliminary insight into the revolutionary new line in improving concrete properties using an indigenous bacterial strain Bacillus licheniformis AK01, as a healing agent. Eur. J. Environ. Civ. Eng. 19, 614–627 (2015).
    Article  Google Scholar 

    10.
    Schlangen, E. & Joseph, C. Self-Healing Processes in Concrete. Self-Healing Materials: Fundamentals, Design Strategies, and Applications (WILEY-VCH Verlag Gmbh & Co. KGaA, New York, 2009). https://doi.org/10.1002/9783527625376.ch5.
    Google Scholar 

    11.
    Mehta, P. K. High-performance, high-volume fly ash concrete for sustainable development. Int. Work. Sustain. Dev. Concr. Technol. 31, 3–14 (2008).
    Google Scholar 

    12.
    Achal, V. & Mukherjee, A. A review of microbial precipitation for sustainable construction. Constr. Build. Mater. 93, 1224–1235 (2015).
    Article  Google Scholar 

    13.
    Burne, R. A. & Chen, Y. Y. M. Bacterial ureases in infectious diseases. Microbes Infect. 2, 533–542 (2000).
    CAS  Article  Google Scholar 

    14.
    Dick, J. et al. Bio-deposition of a calcium carbonate layer on degraded limestone by Bacillus species. Biodegradation 17, 357–367 (2006).
    CAS  Article  Google Scholar 

    15.
    De Muynck, W., De Belie, N. & Verstraete, W. Microbial carbonate precipitation in construction materials: A review. Ecol. Eng. 36, 118–136 (2010).
    Article  Google Scholar 

    16.
    Van Tittelboom, K., De Belie, N., De Muynck, W. & Verstraete, W. Use of bacteria to repair cracks in concrete. Cem. Concr. Res. 40, 157–166 (2010).
    Article  Google Scholar 

    17.
    Dhami, N. K., Reddy, M. S. & Mukherjee, M. S. Biomineralization of calcium carbonates and their engineered applications: A review. Front. Microbiol. 4, 1–13 (2013).
    Article  Google Scholar 

    18.
    Ramachandran, S. K., Ramakrishnan, V. & Bang, S. S. Remediation of concrete using micro-organism. Aci Mater. J. 1, 1. https://doi.org/10.14359/10154 (2001).
    Article  Google Scholar 

    19.
    Dhami, N. K., Reddy, M. S. & Mukherjee, A. Bacillus megaterium mediated mineralization of calcium carbonate as biogenic surface treatment of green building materials. World J. Microbiol. Biotechnol. 29, 2397–2406 (2013).
    CAS  Article  Google Scholar 

    20.
    De Muynck, W., Cox, K., De Belie, N. & Verstraete, W. Bacterial carbonate precipitation as an alternative surface treatment for concrete. Constr. Build. Mater. 22, 875–885 (2008).
    Article  Google Scholar 

    21.
    Achal, V., Mukerjee, A. & Reddy, M. S. Biogenic treatment improves the durability and remediates the cracks of concrete structures. Constr. Build. Mater. 48, 1–5 (2013).
    Article  Google Scholar 

    22.
    Chahal, N., Siddique, R. & Rajor, A. Influence of bacteria on the compressive strength, water absorption and rapid chloride permeability of concrete incorporating silica fume. Constr. Build. Mater. 37, 645–651 (2012).
    Article  Google Scholar 

    23.
    van Paassen, L. A. et al. Potential soil reinforcement by biological denitrification. Ecol. Eng. 36, 168–175 (2010).
    Article  Google Scholar 

    24.
    Erşan, Y. Ç, Hernandez-Sanabria, E., Boon, N. & De Belie, N. Enhanced crack closure performance of microbial mortar through nitrate reduction. Cem. Concr. Compos. 70, 159–170 (2016).
    Article  Google Scholar 

    25.
    Glass, C. & Silverstein, J. Denitrification kinetics of high nitrate concentration water: pH effect on inhibition and nitrite accumulation. Water Res. 32, 831–839 (1998).
    CAS  Article  Google Scholar 

    26.
    van Paassen, L. Biogrout: Ground Improvement by Microbially Induced Carbonate Precipitation (Delft University of Technology, Delft, 2009).
    Google Scholar 

    27.
    Li, M., Fu, Q. L., Zhang, Q., Achal, V. & Kawasaki, S. Bio-grout based on microbially induced sand solidification by means of asparaginase activity. Sci. Rep. 5, 1–9 (2015).
    Google Scholar 

    28.
    Jonkers, H. M. & Schlangen, E. A two component bacteria-based self-healing concrete. In Concrete Repair, Rehabilitation and Retroftting II (eds Alexander, M. G. et al.) (CRC Press, Taylor and Francis Group, Boca Raton, 2009).
    Google Scholar 

    29.
    Jonkers, H. M., Thijssen, A., Muyzer, G., Copuroglu, O. & Schlangen, E. Application of bacteria as self-healing agent for the development of sustainable concrete. Ecol. Eng. 36, 230–235 (2010).
    Article  Google Scholar 

    30.
    Jonkers, H. M. Bacteria-based self-healing concrete. Heron 56, 1–12 (2011).
    Google Scholar 

    31.
    Chaurasia, L., Bisht, V., Singh, L. P. & Gupta, S. A novel approach of biomineralization for improving micro and macro-properties of concrete. Constr. Build. Mater. 195, 340–351 (2019).
    CAS  Article  Google Scholar 

    32.
    Seifan, M., Samani, A. K. & Berenjian, A. Induced calcium carbonate precipitation using Bacillus species. Appl. Microbiol. Biotechnol. 100, 9895–9906 (2016).
    CAS  Article  Google Scholar 

    33.
    Wang, J., Ersan, Y. C., Boon, N. & De Belie, N. Application of microorganisms in concrete: A promising sustainable strategy to improve concrete durability. Appl. Microbiol. Biotechnol. 100, 2993–3007 (2016).
    CAS  Article  Google Scholar 

    34.
    Mondal, S. & Ghosh, A. Investigation into the optimal bacterial concentration for compressive strength enhancement of microbial concrete. Constr. Build. Mater. 183, 202–214 (2018).
    Article  Google Scholar 

    35.
    Andalib, R. et al. Optimum concentration of Bacillus megaterium for strengthening structural concrete. Constr. Build. Mater. 118, 180–193 (2016).
    CAS  Article  Google Scholar 

    36.
    Achal, V. & Pan, X. Characterization of urease and carbonic anhydrase producing bacteria and their role in calcite precipitation. Curr. Microbiol. 62, 894–902 (2011).
    CAS  Article  Google Scholar 

    37.
    Sharma, A. & Bhattacharya, A. Enhanced biomimetic sequestration of CO2 into CaCO3 using purified carbonic anhydrase from indigenous bacterial strains. J. Mol. Catal. B Enzym. 67, 122–128 (2010).
    CAS  Article  Google Scholar 

    38.
    Morandeau, A., Thiéry, M. & Dangla, P. Investigation of the carbonation mechanism of CH and C–S–H in terms of kinetics, microstructure changes and moisture properties. Cem. Concr. Res. 56, 153–170 (2014).
    CAS  Article  Google Scholar 

    39.
    Ameri, F., Shoaei, P., Bahrami, N., Vaezi, M. & Ozbakkaloglu, T. Optimum rice husk ash content and bacterial concentration in self-compacting concrete. Constr. Build. Mater. 222, 796–813 (2019).
    CAS  Article  Google Scholar 

    40.
    Syarif, R., Rizki, I. N., Wattimena, R. K. & Chaerun, S. K. Selection of bacteria inducing calcium carbonate precipitation for self-healing concrete application. Curr. Res. Biosci. Biotechnol. 1, 26–30 (2019).
    Google Scholar 

    41.
    SNI 15-2049-2004. Semen Portland. BSN – National Standardization Agency of Indonesia (2004).

    42.
    Stephen, H. & Stephen, T. Solubilities of Inorganic and Organic Compounds. Binary Systems Part 1 Vol. 1 (Pergamon Press, Oxford, 1979).
    Google Scholar 

    43.
    ASTM C642-13. Standard test method for density, absorption, and voids in hardened concrete. Am. Society Testing Mater. https://doi.org/10.1520/C0642-13.5 (2013).
    Article  Google Scholar 

    44.
    ISRM. Suggested methods for determining the uniaxial compressive strength and deformability of rock materials. Int. J. Rock Mech. Min. Sci. Geomech. 16, 137–140 (1979).
    Google Scholar 

    45.
    ISRM. Suggested methods for determining tensile strength of rock materials. Int. J. Rock Mech. Min. Sci. Geomech. 15, 99–103 (1978).
    Article  Google Scholar  More

  • in

    The transboundary nature of the world’s exploited marine species

    1.
    Hutchinson, G. E. Concluding remarks. Cold Spring Harbor Symp. Quant. Biol. 22, 415–427 (1957).
    Article  Google Scholar 
    2.
    Nelson, J. S., Grande, T. C. & Wilson, M. V. H. Fishes of the World (Wiley, Hoboken, 2016).
    Google Scholar 

    3.
    Song, A. M., Scholtens, J., Stephen, J., Bavinck, M. & Chuenpagdee, R. Transboundary research in fisheries. Mar. Policy 76, 8–18 (2017).
    Article  Google Scholar 

    4.
    Fredston-Hermann, A., Gaines, S. D. & Halpern, B. S. Biogeographic constraints to marine conservation in a changing climate. Ann. N. Y. Acad. Sci. 367, 49–13 (2018).
    Google Scholar 

    5.
    Østhagen, A. Maritime boundary disputes: what are they and why do they matter?. Mar. Policy 120, 104118 (2020).
    Article  Google Scholar 

    6.
    United Nations. United Nations Convention on the Law of the Sea (UNCLOS)—Part V. (1986).

    7.
    Munro, G., Van Houtte, A. & Willmann, R. The Conservation and Management of Shared Fish Stocks: Legal and Economic Aspects. FAO Fisheries Technical Paper No. 456. Food and Agriculture Organization of the United Nations, Rome (2004).

    8.
    Miller, K. & Munro, G. Cooperation and Conflicts in the Management of Transboundary Fishery Resources. (Proceeding of the Second World Conference of the Second World Congress of the American; European Associations of Environmental; Resource Economics, 2002).

    9.
    Englander, G. Property rights and the protection of global marine resources. Nature Sustainability 2, 981–987 (2019).
    Article  Google Scholar 

    10.
    Spijkers, J. & Boonstra, W. J. Environmental change and social conflict: the northeast Atlantic mackerel dispute. Reg. Environ. Change 17, 1835–1851 (2017).
    Article  Google Scholar 

    11.
    Pinsky, M. L. et al. Preparing ocean governance for species on the move. Science 360, 1189–1191 (2018).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    12.
    Miller, K. A., Munro, G. R., Sumaila, U. R. & Cheung, W. W. L. Governing marine fisheries in a changing climate: a game-theoretic perspective. Can J Agric Econ 61, 309–334 (2013).
    Article  Google Scholar 

    13.
    United Nations. Agreement for the Implementation of the Provisions of the United Nations Convention on the Law of the Sea of 10 December 1982 Relating to the Conservation and Management of Straddling Fish Stocks and Highly Migratory Fish Stocks. (1995).

    14.
    Caddy, J. Establishing a consultative mechanism or arrangement for managing shared stocks within the jurisdiction of contiguous states. In Taking stock Defining and Managing Shared Resources (ed. Hancock, D. A.) 80–123 (Australian Society for Fish Biology, Adelaide, 1997).
    Google Scholar 

    15.
    Teh, L. S. L. & Sumaila, U. R. Trends in global shared fisheries. Mar. Ecol. Prog. Ser. 530, 243–254 (2015).
    ADS  Article  Google Scholar 

    16.
    Diario Oficial de la Federación (DOF). Carta Nacional Pesquera. Poder Ejecutivo—Secreataría de Agricultura, Ganadería, Desarrollo Rural, Pesca (SAGARPA). Diario Oficial de la Federación DOF, 1–268 (2018).

    17.
    MAP. Dictamen de Extracción No Perjudicial (DENP) de la población de “tiburón martillo” Sphyrna zygaena. Oficio N. 1038–2017-PRODUCE/DGPCHDI (Tra. N. 18254–2017). Ministerio del Ambiente, Viceministerio de Desarrollo Estratégico de los Recursos Naturales, Peru (2017).

    18.
    Ramesh, N., Rising, J. A. & Oremus, K. L. The small world of global marine fisheries: The cross-boundary consequences of larval dispersal. Science 364, 1192–1196 (2019).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    19.
    Levin, N., Beger, M., Maina, J., McClanahan, T. & Kark, S. Evaluating the potential for transboundary management of marine biodiversity in the Western Indian Ocean. Australas. J. Environ.Manag. 25, 62–85 (2018).
    Article  Google Scholar 

    20.
    Popova, E. et al. Ecological connectivity between the areas beyond national jurisdiction and coastal waters: safeguarding interests of coastal communities in developing countries. Mar. Policy 104, 90–102 (2019).
    Article  Google Scholar 

    21.
    Dunn, D. C. et al. The importance of migratory connectivity for global ocean policy. Proc. R. Soc. B: Biol. Sci. 286, 20191472 (2019).
    Article  Google Scholar 

    22.
    Kaplan, D. M. et al. Uncertainty in empirical estimates of marine larval connectivity. ICES J. Mar. Sci. 74, 1723–1734 (2016).
    Article  Google Scholar 

    23.
    Archambault, B. et al. Adult-mediated connectivity affects inferences on population dynamics and stock assessment of nursery-dependent fish populations. Global Environ. Change 181, 198–213 (2016).
    Google Scholar 

    24.
    Cashion, T. et al. Establishing company level fishing revenue and profit losses from fisheries: A bottom-up approach. Journals Plos.Org 13, e0207768 (2018).
    Google Scholar 

    25.
    FAO. The State of World Fisheries and Aquaculture: Meeting the Sustainable Development Goals. 1–227 (2018).

    26.
    UNDP. Chile and Peru sign Landmark Agreement to Sustain world’s Largest Single Species Fishery (2016).

    27.
    NOAA FIsheries. Bilateral Agreement Between the United States and Russia (2019).

    28.
    Kleisner, K. & Pauly, D. Stock-Status Plots of Fisheries for Regional Seas. in The State of Biodiversity and Fisheries in Regional Seas (eds. Christensen, V., Lai, S., Palomares, M. L. D., Zeller, D. & Pauly, D.) 37–40 (The Fisheries Center, University of British Columbia; Fisheries Centre Research Reports, 2011).

    29.
    Jensen, F., Frost, H., Thogersen, T., Andersen, P. & Andersen, J. L. Game theory and fish wars: the case of the Northeast Atlantic mackerel fishery. Fisheries 172, 7–16 (2015).
    Google Scholar 

    30.
    Munro, G. R. The management of shared fishery resources under extended jurisdiction. Mar. Resour. Econ. 3, 271–296 (2015).
    Article  Google Scholar 

    31.
    Eide, A., Heen, K., Armstrong, C., Flaaten, O. & Vasiliev, A. Challenges and successes in the management of a shared fish stock—the case of the Russian-Norwegian barents sea cod fishery. Acta Borealia 30, 1–20 (2013).
    Article  Google Scholar 

    32.
    Sumaila, U. R., Ninnes, C. & Oelofsen, B. Management of Shared Hake Stocks in the Benguela Marine Ecosystem. In Papers presented at the norway-fao expert consultation on the management of shared fish stocks, 143–159 (2003).

    33.
    Clark, C. W. Restricted Access to Common-Property Fishery Resources: A Game-Theoretic Analysis. In Dynamic optimization and mathematical economics, 117–132 (Springer, Boston, MA, 1980).

    34.
    Spijkers, J. et al. Global patterns of fisheries conflict: forty years of data. Global Environ. Change 57, 101921 (2019).
    Article  Google Scholar 

    35.
    Oremus, K. L. et al. Governance challenges for tropical nations losing fish species due to climate change. Nat. Sustain. 6, 1–4 (2020).
    Google Scholar 

    36.
    Palacios-Abrantes, J., Rashid Sumaila, U. & Cheung, W. W. L. Challenges to transboundary fisheries management in North America under climate change. Ecol. Soc. (in press).

    37.
    Sumaila, U. R., Palacios-Abrantes, J. & Cheung, W. W. L. Climate change, shifting threat points and the management of transboundary fish stocks. Ecol. Soc. (in press).

    38.
    Reygondeau, G. Current and future biogeography of marine exploited groups under climate change. In Predicting Future Oceans Sustainability of Ocean and Human Systems Amidst Global Environmental Change (eds. Cheung, W. W. L., Ota, Y. & Cisneros-Montemayor, A. M.) 87–99 (2019).

    39.
    Schill, S. R. et al. No reef is an island: integrating coral reef connectivity data into the design of regional-scale marine protected area networks. PLoS ONE 10, e0144199 (2015).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    40.
    Perez, A. U., Schmitter-Soto, J. J., Adams, A. J. & Heyman, W. D. Connectivity mediated by seasonal bonefish (Albula vulpes) migration between the Caribbean Sea and a tropical estuary of Belize and Mexico. Environ. Biol. Fishes 102, 197–207 (2019).
    Article  Google Scholar 

    41.
    Cisneros-Montemayor, A. M., Pauly, D., Weatherdon, L. V. & Ota, Y. A Global estimate of seafood consumption by coastal indigenous peoples. PLoS ONE 11, e0166681 (2016).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    42.
    Hanich, Q. et al. Small-scale fisheries under climate change in the Pacific Islands region. Mar. Policy 88, 279–284 (2018).
    Article  Google Scholar 

    43.
    Cabral, R. B. & Geronimo, R. C. How important are coral reefs to food security in the Philippines? Diving deeper than national aggregates and averages. Mar. Policy 91, 136–141 (2018).
    Article  Google Scholar 

    44.
    Zeller, D. et al. Still catching attention: Sea Around Us reconstructed global catch data, their spatial expression and public accessibility. Mar. Policy 70, 145–152 (2016).
    Article  Google Scholar 

    45.
    Thuiller, W., Lafourcade, B., Engler, R. & Araújo, M. B. BIOMOD—a platform for ensemble forecasting of species distributions. Ecography 32, 369–373 (2009).
    Article  Google Scholar 

    46.
    Phillips, S. J., Anderson, R. P. & Schapire, R. E. Maximum entropy modeling of species geographic distributions. Ecol. Model. 190, 231–259 (2006).
    Article  Google Scholar 

    47.
    Beaugrand, G., Lenoir, S., Ibanez, F. & Manté, C. A new model to assess the probability of occurrence of a species, based on presence-only data. Mar. Ecol. Prog. Ser. 424, 175–190 (2011).
    ADS  Article  Google Scholar 

    48.
    Asch, R. G., Cheung, W. W. L. & Reygondeau, G. Future marine ecosystem drivers, biodiversity, and fisheries maximum catch potential in Pacific Island countries and territories under climate change. Mar. Policy 88, 285–294 (2018).
    Article  Google Scholar 

    49.
    Close, C. et al. Distribution ranges of commercial fishes and invertebrates. In Fisheries Centre Research Reports. Fishes in Databases and Ecosystems (eds. Palomares, M. D., Stergiou, K. I. & Pauly, D.) 27–37 (2006).

    50.
    Pauly, D. & Zeller, D. Global Atlas of Marine Fisheries 1–520 (Island Press, Washington, D.C., 2016).
    Google Scholar 

    51.
    Kaschner, K. et al. AquaMaps: Predicted range maps for aquatic species www.aquamaps.org (2016).

    52.
    Pauly, D. & Zeller, D. Catch reconstructions reveal that global marine fisheries catches are higher than reported and declining. Nat. Commun. 7:10244,1–9 (2019).

    53.
    Pebesma, E. et al. Package sf; Simple Features for R. R ( >= 3.3.0), (2018).

    54.
    Tai, T. C., Cashion, T., Lam, V. W. Y. & Sumaila, U. R. Ex-vessel fish price database: disaggregating prices for low-priced species from reduction fisheries. Front. Mar. Sci. 4, 1–10 (2017).
    Article  Google Scholar 

    55.
    Sumaila, U. R., Teh, L., Zeller, D. & Pauly, D. The global ex-vessel fish price database. In Catch Reconstructions: Concepts, Methods and Data Sources (eds. Pauly D., & Zeller, S.) www.searoundus.org (2015).

    56.
    Grainger, R. J. R. & Garcia, S. M. Chronicles of Marine Fishery Landings (1950 1994) Trend Analysis and Fisheries Potential (1996).

    57.
    Pauly, D., Hilborn, R. & Branch, T. A. Fisheries: does catch reflect abundance?. Nature 494, 303–306 (2013).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    58.
    Branch, T. A. Not all fisheries will be collapsed in 2048. Mar. Policy 32, 38–39 (2008).
    Article  Google Scholar 

    59.
    Dowle, M. et al. Package data.table; Extension of ‘data.frame‘. R ( >= 3.1.0), MPL–2.0 | file LICENSE (2019).

    60.
    Firke, S., Haid, C., Knight, R. & Denney, B. Package janitor; Simple tools for examining and cleaning dirty data. R ( >= 3.1.2), (2018).

    61.
    Ram, K., Wickham, H., Richards, C. & Baggett, A. Package wesanderson; A Wes Anderson Palette Generator. R ( >= 3.0), MIT + file LICENSE (2018).

    62.
    Boettiger, C., Chamberlain, S., Lang, D. T. & Wainwright, P. Package rfishbase; R Interface to ’FishBase’. R ( >= 3.0), (2019).

    63.
    Bengtsson, H., Jacobson, A. & Riedy, J. Package R.matlab: Read and Write MAT Files and Call MATLAB from Within R. R ( 2.14.0), LGPL–2.1 | LGPL–3 (2018).

    64.
    Pebesma, E. et al. Package sp; Classes and methods for Spatial Data. R ( 3.0.0), GPL–2 | GPL–3 (2019).

    65.
    Wickham, H. Package tidyverse; Easily Install and Load the ’Tidyverse’. R (3.5.0), MIT + file LICENSE (2017).

    66.
    De Queiroz, G. et al. Package tidytext; Text Mining using ’dplyr’, ’ggplot2’, and Other Tidy Tools. R ( 2.10), MIT (2019).

    67.
    Zeileis, A., Grothendieck, G., Ryan, J. A., Ulrich, J. M. & Andrews, F. Package zoo; S3 Infrastructure for Regular and Irregular Time Series (Z’s Ordered Observations). R ( >= 3.1.0), GPL–2 | GPL–3 (2019).

    68.
    Chambers, J. M., Freeny, A. E. & Heiberger, R. M. Analysis of Variance; Designed Experiments. In Statistical models in s (eds Chambers, J. M. & Hastie, T. J.) 145–193 (Routledge, London, 1992).
    Google Scholar 

    69.
    Krzanowski, W. J. Principles of Multivariate Analysis (Oxford University Press, Oxford, 1990).
    Google Scholar 

    70.
    Hollander, M. & Wolfe, D. A. Nonparametric Statistical Methods (Wiley, Hoboken, 2013).
    Google Scholar 

    71.
    Moore, B. R. et al. Defining the stock structures of key commercial tunas in the Pacific Ocean I: current knowledge and main uncertainties. Global Environ. Change 230, 105525 (2020).
    Google Scholar 

    72.
    Sepulveda, C. A., Wang, M., Aalbers, S. A. & Alvarado-Bremer, J. R. Insights into the horizontal movements, migration patterns, and stock affiliation of California swordfish. Fish. Oceanogr. 29, 152–168 (2019).
    Article  Google Scholar 

    73.
    Vandeperre, F. et al. Movements of Blue Sharks (Prionace glauca) across Their Life History. PLoS ONE 9, e103538–e103614 (2014).
    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

    74.
    Chavez, F. P., Ryan, J., Lluch-Cota, S. E. & Niquen, C. M. From anchovies to sardines and back: multidecadal change in the Pacific Ocean. Science 299, 217–221 (2003).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar  More

  • in

    Linking structural and compositional changes in archaeological human bone collagen: an FTIR-ATR approach

    1.
    Boskey, A. L., Wright, T. M. & Blank, R. D. Collagen and bone strength. J. Bone Miner. Res. 14, 330–335. https://doi.org/10.1359/jbmr.1999.14.3.330 (1999).
    CAS  Article  PubMed  Google Scholar 
    2.
    Fratzl, P. In Collagen (ed Fratzl, P.) 1–13 (Springer, Berlin, 2008).

    3.
    Dehring, K. A., Smukler, A. R., Roessler, B. J. & Morris, M. D. correlating changes in collagen secondary structure with aging and defective type II collagen by Raman spectroscopy. Appl. Spectrosc. 60, 366–372 (2006).
    ADS  CAS  Article  Google Scholar 

    4.
    Shoulders, M. D. & Raines, R. T. Collagen structure and stability. Annu. Rev. Biochem. 78, 929–958. https://doi.org/10.1146/annurev.biochem.77.032207.120833 (2009).
    CAS  Article  PubMed  PubMed Central  Google Scholar 

    5.
    Mostaço-Guidolin, L. B. et al. Collagen morphology and texture analysis: From statistics to classification. Sci. Rep. 3, 2190. https://doi.org/10.1038/srep02190 (2013).
    Article  PubMed  PubMed Central  Google Scholar 

    6.
    Schrof, S., Varga, P., Galvis, L., Raum, K. & Masic, A. 3D Raman mapping of the collagen fibril orientation in human osteonal lamellae. J. Struct. Biol. 187, 266–275. https://doi.org/10.1016/j.jsb.2014.07.001 (2014).
    CAS  Article  PubMed  Google Scholar 

    7.
    Viguet-Carrin, S., Garnero, P. & Delmas, P. D. The role of collagen in bone strength. Osteoporos. Int. 17, 319–336. https://doi.org/10.1007/s00198-005-2035-9 (2006).
    CAS  Article  PubMed  Google Scholar 

    8.
    West, P., Torzilli, P., Chen, C., Lin, P. & Camacho, N. Fourier transform infrared imaging spectroscopy analysis of collagenase-induced cartilage degradation. J. Biomed. Opt. 10, 014015 (2005).
    ADS  CAS  Article  Google Scholar 

    9.
    Wang, X., Zhai, M., Zhao, Y. & Yin, J. A review of articular cartilage and osteoarthritis studies by Fourier transform infrared spectroscopic imaging. Ann. Joint 3, 1–9 (2018).
    Article  Google Scholar 

    10.
    Lee, Y.-C. et al. Evidence of preserved collagen in an Early Jurassic sauropodomorph dinosaur revealed by synchrotron FTIR microspectroscopy. Nat. Commun. 8, 14220. https://doi.org/10.1038/ncomms14220 (2017).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    11.
    Longin, R. New method of collagen extraction for radiocarbon dating. Nature 230, 241–242 (1971).
    ADS  CAS  Article  Google Scholar 

    12.
    Ambrose, S. H. & Krigbaum, J. Bone chemistry and bioarchaeology. J. Anthropol. Archaeol. 22, 193–199. https://doi.org/10.1016/S0278-4165(03)00033-3 (2003).
    Article  Google Scholar 

    13.
    13Katzenberg, M. A. In Biological Anthropology of the Human Skeleton (eds M. Katzenberg, A. & Saunders, S. R.) 413–441 (Wiley-Liss, Hoboken, 2000).

    14.
    Fewlass, H. et al. Pretreatment and gaseous radiocarbon dating of 40–100 mg archaeological bone. Sci. Rep. 9, 5342. https://doi.org/10.1038/s41598-019-41557-8 (2019).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    15.
    Pothier Bouchard, G. et al. Portable FTIR for on-site screening of archaeological bone intended for ZooMS collagen fingerprint analysis. J. Archaeol. Sci. Rep. 26, 101862. https://doi.org/10.1016/j.jasrep.2019.05.027 (2019).
    Article  Google Scholar 

    16.
    Kaal, J., López-Costas, O. & Martínez, A. Diagenetic effects on pyrolysis fingerprints of extracted collagen in archaeological human bones from NW Spain, as determined by pyrolysis-GC-MS. J. Archaeol. Sci. 65, 1–10. https://doi.org/10.1016/j.jas.2015.11.001 (2016).
    CAS  Article  Google Scholar 

    17.
    Van Klinken, G. J. Bone collagen quality indicators for palaeodietary and radiocarbon measurements. J. Archaeol. Sci. 26, 687–695 (1999).
    Article  Google Scholar 

    18.
    Dobberstein, R. C. et al. Archaeological collagen: Why worry about collagen diagenesis?. Archaeol. Anthropol. Sci. 1, 31–42. https://doi.org/10.1007/s12520-009-0002-7 (2009).
    Article  Google Scholar 

    19.
    Harbeck, M. & Grupe, G. Experimental chemical degradation compared to natural diagenetic alteration of collagen: Implications for collagen quality indicators for stable isotope analysis. Archaeol. Anthropol. Sci. 1, 43–57. https://doi.org/10.1007/s12520-009-0004-5 (2009).
    Article  Google Scholar 

    20.
    Collins, M. J., Riley, M. S., Child, A. M. & Turner-Walker, G. A basic mathematical simulation of the chemical degradation of ancient collagen. J. Archaeol. Sci. 22, 175–183. https://doi.org/10.1006/jasc.1995.0019 (1995).
    Article  Google Scholar 

    21.
    France, C. A. M., Thomas, D. B., Doney, C. R. & Madden, O. FT-Raman spectroscopy as a method for screening collagen diagenesis in bone. J. Archaeol. Sci. 42, 346–355. https://doi.org/10.1016/j.jas.2013.11.020 (2014).
    CAS  Article  Google Scholar 

    22.
    Chadefaux, C., Le Hô, A.-S., Bellot-Gurlet, L. & Reiche, I. Curve-fitting Micro-ATR-FTIR studies of the amide I and II bands of type I collagen in archaeological bone materials. E-Preserv. Sci. Morana RTD 6, 129–137 (2009).
    CAS  Google Scholar 

    23.
    Sponheimer, M. et al. Saving old bones: A non-destructive method for bone collagen prescreening. Sci. Rep. 9, 13928. https://doi.org/10.1038/s41598-019-50443-2 (2019).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    24.
    Goldenberg, L., Regev, L., Mintz, E. & Boaretto, E. Dating reassembled collagen from fossil bones. Radiocarbon 59, 1487–1496. https://doi.org/10.1017/rdc.2017.69 (2017).
    CAS  Article  Google Scholar 

    25.
    Yizhaq, M. et al. Quality controlled radiocarbon dating of bones and charcoal from the early pre-pottery neolithic B (PPNB) of Motza (Israel). Radiocarbon 47, 193–206. https://doi.org/10.1017/s003382220001969x (2005).
    CAS  Article  Google Scholar 

    26.
    Baker, M. J. et al. Using Fourier transform IR spectroscopy to analyze biological materials. Nat. Protoc. 9, 1771–1791. https://doi.org/10.1038/nprot.2014.110 (2014).
    CAS  Article  PubMed  PubMed Central  Google Scholar 

    27.
    Belbachir, K., Noreen, R., Gouspillou, G. & Petibois, C. Collagen types analysis and differentiation by FTIR spectroscopy. Anal. Bioanal. Chem. 395, 829–837. https://doi.org/10.1007/s00216-009-3019-y (2009).
    CAS  Article  PubMed  Google Scholar 

    28.
    de Campos Vidal, B. & Mello, M. L. S. Collagen type I amide I band infrared spectroscopy. Micron 42, 283–289. https://doi.org/10.1016/j.micron.2010.09.010 (2011).
    CAS  Article  Google Scholar 

    29.
    Figueiredo, M., Gamelas, J. & Martins, A. In Infrared Spectroscopy-Life and Biomedical Sciences (ed Theophile, T.) (InTech, 2012).

    30.
    Hanifi, A., McCarthy, H., Roberts, S. & Pleshko, N. Fourier transform infrared imaging and infrared fiber optic probe spectroscopy identify collagen type in connective tissues. PLoS ONE 8, e64822. https://doi.org/10.1371/journal.pone.0064822 (2013).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    31.
    Kong, J. & Yu, S. Fourier transform infrared spectroscopic analysis of protein secondary structures. Acta Biochim. Biophys. Sin. 39, 549–559. https://doi.org/10.1111/j.1745-7270.2007.00320.x (2007).
    CAS  Article  PubMed  Google Scholar 

    32.
    Stani, C., Vaccari, L., Mitri, E. & Birarda, G. FTIR investigation of the secondary structure of type I collagen: New insight into the amide III band. Spectrochim. Acta Part A Mol. Biomol. Spectrosc. 229, 118006. https://doi.org/10.1016/j.saa.2019.118006 (2020).
    CAS  Article  Google Scholar 

    33.
    Ramachandran, G. & Kartha, G. Structure of collagen. Nature 174, 269–270 (1954).
    ADS  CAS  Article  Google Scholar 

    34.
    Ramachandran, G. & Kartha, G. Structure of collagen. Nature 176, 593–595 (1955).
    ADS  CAS  Article  Google Scholar 

    35.
    Rich, A. & Crick, F. The molecular structure of collagen. J. Mol. Biol. 3, 483–484 (1961).
    CAS  Article  Google Scholar 

    36.
    Egli, J., Schnitzer, T., Dietschreit, J. C., Ochsenfeld, C. & Wennemers, H. Why proline? Influence of ring-size on the collagen triple helix. Org. Lett. 22, 348–351 (2019).
    Article  Google Scholar 

    37.
    Barth, A. Infrared spectroscopy of proteins. Biochim. Biophys. Acta Bioenergetics 1767, 1073–1101. https://doi.org/10.1016/j.bbabio.2007.06.004 (2007).
    CAS  Article  Google Scholar 

    38.
    Surovell, T. A. & Stiner, M. C. Standardizing infra-red measures of bone mineral crystallinity: An experimental approach. J. Archaeol. Sci. 28, 633–642. https://doi.org/10.1006/jasc.2000.0633 (2001).
    Article  Google Scholar 

    39.
    Garvie-Lok, S. J., Varney, T. L. & Katzenberg, M. A. Preparation of bone carbonate for stable isotope analysis: The effects of treatment time and acid concentration. J. Archaeol. Sci. 31, 763–776. https://doi.org/10.1016/j.jas.2003.10.014 (2004).
    Article  Google Scholar 

    40.
    Hollund, H. I., Ariese, F., Fernandes, R., Jans, M. M. E. & Kars, H. Testing an alternative high-throughput tool for investigating bone diagenesis: FTIR in attenuated total reflection (ATR) mode. Archaeometry 55, 507–532. https://doi.org/10.1111/j.1475-4754.2012.00695.x (2013).
    CAS  Article  Google Scholar 

    41.
    Berna, F., Matthews, A. & Weiner, S. Solubilities of bone mineral from archaeological sites: The recrystallization window. J. Archaeol. Sci. 31, 867–882. https://doi.org/10.1016/j.jas.2003.12.003 (2004).
    Article  Google Scholar 

    42.
    Lebon, M., Reiche, I., Frohlich, F., Bahain, J. J. & Falgueres, C. Characterization of archaeological burnt bones: Contribution of a new analytical protocol based on derivative FTIR spectroscopy and curve fitting of the nu1nu3 PO4 domain. Anal. Bioanal. Chem. 392, 1479–1488 (2008).
    CAS  Article  Google Scholar 

    43.
    Thompson, T. J. U., Gauthier, M. & Islam, M. The application of a new method of Fourier Transform Infrared Spectroscopy to the analysis of burned bone. J. Archaeol. Sci. 36, 910–914. https://doi.org/10.1016/j.jas.2008.11.013 (2009).
    Article  Google Scholar 

    44.
    Lebon, M. et al. New parameters for the characterization of diagenetic alterations and heat-induced changes of fossil bone mineral using Fourier transform infrared spectrometry. J. Archaeol. Sci. 37, 2265–2276. https://doi.org/10.1016/j.jas.2010.03.024 (2010).
    Article  Google Scholar 

    45.
    Dal Sasso, G. et al. Bone diagenesis variability among multiple burial phases at Al Khiday (Sudan) investigated by ATR-FTIR spectroscopy. Palaeogeogr. Palaeoclimatol. Palaeoecol. 463, 168–179. https://doi.org/10.1016/j.palaeo.2016.10.005 (2016).
    Article  Google Scholar 

    46.
    Toffolo, M. B., Brink, J. S. & Berna, F. Bone diagenesis at the Florisbad spring site, Free State Province (South Africa): Implications for the taphonomy of the Middle and Late Pleistocene faunal assemblages. J. Archaeol. Sci. Rep. 4, 152–163. https://doi.org/10.1016/j.jasrep.2015.09.001 (2015).
    Article  Google Scholar 

    47.
    Lebon, M., Reiche, I., Gallet, X., Bellot-Gurlet, L. & Zazzo, A. Rapid quantification of bone collagen content by ATR-FTIR spectroscopy. Radiocarbon 58, 131–145. https://doi.org/10.1017/rdc.2015.11 (2016).
    CAS  Article  Google Scholar 

    48.
    Pestle, W. J. et al. Hand-held Raman spectroscopy as a pre-screening tool for archaeological bone. J. Archaeol. Sci. 58, 113–120. https://doi.org/10.1016/j.jas.2015.03.027 (2015).
    CAS  Article  Google Scholar 

    49.
    Madden, O., Chan, D. M. W., Dundon, M. & France, C. A. M. Quantifying collagen quality in archaeological bone: Improving data accuracy with benchtop and handheld Raman spectrometers. J. Archaeol. Sci. Rep. 18, 596–605. https://doi.org/10.1016/j.jasrep.2017.11.034 (2018).
    Article  Google Scholar 

    50.
    Dal Sasso, G., Angelini, I., Maritan, L. & Artioli, G. Raman hyperspectral imaging as an effective and highly informative tool to study the diagenetic alteration of fossil bones. Talanta 179, 167–176. https://doi.org/10.1016/j.talanta.2017.10.059 (2018).
    CAS  Article  Google Scholar 

    51.
    López-Costas, O. & Müldner, G. Fringes of the empire: Diet and cultural change at the Roman to post-Roman transition in NW Iberia. Am. J. Phys. Anthropol. 161, 141–154. https://doi.org/10.1002/ajpa.23016 (2016).
    Article  PubMed  Google Scholar 

    52.
    López-Costas, O. Antropología de los restos óseos humanos de Galicia: estudio de la población romano y medieval gallega. Doctoral thesis, University of Granada, (2012).

    53.
    Petibois, C., Gouspillou, G., Wehbe, K., Delage, J.-P. & Déléris, G. Analysis of type I and IV collagens by FT-IR spectroscopy and imaging for a molecular investigation of skeletal muscle connective tissue. Anal. Bioanal. Chem. 386, 1961–1966. https://doi.org/10.1007/s00216-006-0828-0 (2006).
    CAS  Article  PubMed  Google Scholar 

    54.
    Haris, P. I. & Severcan, F. FTIR spectroscopic characterization of protein structure in aqueous and non-aqueous media. J. Mol. Catal. B Enzym. 7, 207–221. https://doi.org/10.1016/S1381-1177(99)00030-2 (1999).
    CAS  Article  Google Scholar 

    55.
    Goormaghtigh, E., Ruysschaert, J.-M. & Raussens, V. Evaluation of the information content in infrared spectra for protein secondary structure determination. Biophys. J . 90, 2946–2957. https://doi.org/10.1529/biophysj.105.072017 (2006).
    CAS  Article  PubMed  PubMed Central  Google Scholar 

    56.
    Paschalis, E. P. et al. Spectroscopic characterization of collagen cross-links in bone. J. Bone Miner. Res. 16, 1821–1828. https://doi.org/10.1359/jbmr.2001.16.10.1821 (2001).
    CAS  Article  PubMed  Google Scholar 

    57.
    D’Elia, M. et al. Evaluation of possible contamination sources in the 14C analysis of bone samples by FTIR spectroscopy. Radiocarbon 49, 201–210. https://doi.org/10.1017/s0033822200042120 (2007).
    CAS  Article  Google Scholar 

    58.
    Karkanas, P., Bar-Yosef, O., Goldberg, P. & Weiner, S. Diagenesis in prehistoric caves: The use of minerals that form in situ to assess the completeness of the archaeological record. J. Archaeol. Sci. 27, 915–929. https://doi.org/10.1006/jasc.1999.0506 (2000).
    Article  Google Scholar 

    59.
    López-Costas, O., Lantes-Suárez, Ó. & Martínez Cortizas, A. Chemical compositional changes in archaeological human bones due to diagenesis: Type of bone vs soil environment. J. Archaeol. Sci. 67, 43–51. https://doi.org/10.1016/j.jas.2016.02.001 (2016).
    CAS  Article  Google Scholar 

    60.
    Trueman, C. N., Privat, K. & Field, J. Why do crystallinity values fail to predict the extent of diagenetic alteration of bone mineral?. Palaeogeogr. Palaeoclimatol. Palaeoecol. 266, 160–167. https://doi.org/10.1016/j.palaeo.2008.03.038 (2008).
    Article  Google Scholar 

    61.
    Trueman, C. N. G., Behrensmeyer, A. K., Tuross, N. & Weiner, S. Mineralogical and compositional changes in bones exposed on soil surfaces in Amboseli National Park, Kenya: Diagenetic mechanisms and the role of sediment pore fluids. J. Archaeol. Sci. 31, 721–739. https://doi.org/10.1016/j.jas.2003.11.003 (2004).
    Article  Google Scholar 

    62.
    Salesse, K. et al. Variability of bone preservation in a confined environment: The case of the catacomb of Sts Peter and Marcellinus (Rome, Italy). Palaeogeogr. Palaeoclimatol. Palaeoecol. 416, 43–54. https://doi.org/10.1016/j.palaeo.2014.07.021 (2014).
    Article  Google Scholar 

    63.
    Weiner, S. Microarchaeology: Beyond the Visible Archaeological Record (Cambridge University Press, Cambridge, 2010).
    Google Scholar 

    64.
    Pate, F. D., Hutton, J. T. & Norrish, K. Ionic exchange between soil solution and bone: Toward a predictive model. Appl. Geochem. 4, 303–316. https://doi.org/10.1016/0883-2927(89)90034-6 (1989).
    CAS  Article  Google Scholar 

    65.
    Nielsen-Marsh, C. M. & Hedges, R. E. M. Patterns of diagenesis in bone I: The effects of site environments. J. Archaeol. Sci. 27, 1139–1150. https://doi.org/10.1006/jasc.1999.0537 (2000).
    Article  Google Scholar 

    66.
    Weiner, S. & Bar-Yosef, O. States of preservation of bones from prehistoric sites in the Near East: A survey. J. Archaeol. Sci. 17, 187–196. https://doi.org/10.1016/0305-4403(90)90058-D (1990).
    Article  Google Scholar 

    67.
    Weiner, S., Goldberg, P. & Bar-Yosef, O. Bone preservation in Kebara cave, Israel using on-site Fourier transform infrared spectrometry. J. Archaeol. Sci. 20, 613–627. https://doi.org/10.1006/jasc.1993.1037 (1993).
    Article  Google Scholar 

    68.
    Weiner, S., Goldberg, P. & Bar-Yosef, O. Three-dimensional distribution of minerals in the sediments of Hayonim Cave, Israel: Diagenetic processes and archaeological implications. J. Archaeol. Sci. 29, 1289–1308. https://doi.org/10.1006/jasc.2001.0790 (2002).
    Article  Google Scholar 

    69.
    Jans, M. M. E., Nielsen-Marsh, C. M., Smith, C. I., Collins, M. J. & Kars, H. Characterisation of microbial attack on archaeological bone. J. Archaeol. Sci. 31, 87–95. https://doi.org/10.1016/j.jas.2003.07.007 (2004).
    Article  Google Scholar 

    70.
    Ambrose, S. H. Preparation and characterization of bone and tooth collagen for isotopic analysis. J. Archaeol. Sci. 17, 431–451. https://doi.org/10.1016/0305-4403(90)90007-r (1990).
    Article  Google Scholar 

    71.
    López-Costas, O., Müldner, G. & Martínez Cortizas, A. Diet and lifestyle in Bronze Age Northwest Spain: The collective burial of Cova do Santo. J. Archaeol. Sci. 55, 209–218. https://doi.org/10.1016/j.jas.2015.01.009 (2015).
    Article  Google Scholar 

    72.
    Lopez-Costas, O. Taphonomy and burial context of the Roman/post-Roman funerary areas (2nd to 6th centuries AD) of A Lanzada, NW Spain. Estudos do Quaternário, APEQ 12, 55–67 (2015).
    Article  Google Scholar 

    73.
    Collins, M. J. & Galley, P. Towards an optimal method of archaeological collagen extraction: The influence of pH and grinding. Ancient Biomolecules 2, 209–222 (1998).
    CAS  Google Scholar 

    74.
    Boskey, A. & Camacho, N. P. FT-IR imaging of native and tissue-engineered bone and cartilage. Biomaterials 28, 2465–2478. https://doi.org/10.1016/j.biomaterials.2006.11.043 (2007).
    CAS  Article  PubMed  Google Scholar 

    75.
    Kim, M., Bi, X., Horton, W., Spencer, R. & Camacho, N. Fourier transform infrared imaging spectroscopic analysis of tissue engineered cartilage: Histologic and biochemical correlations. J. Biomed. Opt. 10, 031105 (2005).
    ADS  Article  Google Scholar 

    76.
    Heinly, J. H., Guerin, H. L., Auerbach, J. D., Siskey, R. L. & Villarraga, M. L. In 56th Annual Meeting of the Orthopaedic Research Society Poster No. 1466 (2010.).

    77.
    Mark, H. & Workman, J. Jr. Chemometrics: Derivatives in spectroscopy, Part I-the behavior of the derivative. Spectrosc. Eugene 18, 32–37 (2003).
    CAS  Google Scholar 

    78.
    Rieppo, L. et al. Application of second derivative spectroscopy for increasing molecular specificity of fourier transform infrared spectroscopic imaging of articular cartilage. Osteoarthr. Cartil. 20, 451–459. https://doi.org/10.1016/j.joca.2012.01.010 (2012).
    CAS  Article  Google Scholar 

    79.
    Ami, D., Mereghetti, P. & Doglia, S. M. In Multivariate Analysis in Management, Engineering and the Sciences (eds de Freitas, L. V. & de Freitas, A. P. B. R.) https://www.intechopen.com/books/multivariate-analysis-in-management-engineering-and-the-sciences/multivariate-analysis-for-fourier-transform-infrared-spectra-of-complex-biological-systems-and-proce (Intech Open, 2013).

    80.
    Saarakkala, S., Rieppo, L., Rieppo, J. & Jurvelin, J. In Microscopy: Science, Technology, Applications and Education Vol. 1 (eds Méndez-Vilas, A. & Díaz, J.) 403–414 (Formatex, 2010).

    81.
    Smith, B. C. (CRC Press, Boca Raton, 2011).

    82.
    Eriksson, L., Johansson, E., Kettaneh-Wold, N. & Wold, S. Introduction to Multi- and Megavariate Data Analysis using Projection Methods (PCA & PLS) (Umetrics AB, Umeå, 1999).
    Google Scholar 

    83.
    Garson, G. D. In Blue Book Series (Statistical Associates Publishers, Asheboro, 2016).

    84.
    SmartPLS 3 (SmartPLS GmbH, Boenningstedt, 2015). More

  • in

    Behaviours indicating cannibalistic necrophagy in ants are modulated by the perception of pathogen infection level

    1.
    Fox, L. R. Cannibalism in natural populations. Annu. Rev. Ecol. Syst. 6, 87–106 (1975).
    Article  Google Scholar 
    2.
    Polis, G. A. The evolution and dynamics of intraspecific predation. Annu. Rev. Ecol. Evol. Syst. 12, 225–251 (1981).
    Article  Google Scholar 

    3.
    Elgar, M. A. & Crespi, B. J. Ecology and evolution of cannibalism. In Cannibalism: ecology and evolution among diverse taxa (eds Elgar, M. A. & Crespi, B. J.) 1–12 (Oxford University Press, Oxford, 1992).
    Google Scholar 

    4.
    Richardson, M. L., Mitchell, R. F., Reagel, P. F. & Hanks, L. M. Causes and consequences of cannibalism in noncarnivorous insects. Annu. Rev. Entomol. 55, 39–53 (2010).
    CAS  PubMed  Article  Google Scholar 

    5.
    Vilaça, A. Relations between funerary cannibalism and warfare cannibalism: The question of predation. Ethnos 65, 83–106 (2000).
    Article  Google Scholar 

    6.
    Lopez-Riquelme, G. O. & Fanjul-Moles, M. L. The funeral ways of social insects. Social strategies for corpse disposal. Trends Entomol. 9, 71–129 (2013).
    Google Scholar 

    7.
    Walls, S. C. & Roudebush, R. E. Reduced aggression toward siblings as evidence of kin recognition in cannibalistic salamanders. Am. Nat 138, 1027–1038 (1991).
    Article  Google Scholar 

    8.
    Pfennig, D. W. Cannibalistic tadpoles that pose the greatest threat to kin are most likely to discriminate kin. Proc. R. Soc. Lond. B 266, 57–61 (1999).
    Article  Google Scholar 

    9.
    Bilde, T. & Lubin, Y. Kin recognition and cannibalism in a subsocial spider. J. Evolut. Biol. 14, 959–966 (2001).
    Article  Google Scholar 

    10.
    Santana, A. F. K., Roselino, A. C., Cappelari, F. A. & Zucoloto, F. S. Cannibalism in insects. In Insect bioecology and nutrition for integrated pest management (eds Panizzi, A. R. & Parra, J. R. P.) 177–190 (CRC Press, Boca Raton, 2012).
    Google Scholar 

    11.
    Hölldobler, B. & Wilson, E. O. The ants (The Belknap Press of Harvard University, London, 1990).
    Google Scholar 

    12.
    Schmickl, T. & Crailsheim, K. Cannibalism and early capping: strategy of honeybee colonies in times of experimental pollen shortage. J. Comput. Physiol. A 187, 541–547 (2001).
    CAS  Article  Google Scholar 

    13.
    Sun, Q. & Zhou, X. Corpse management in social insects. Int. J. Biol. Sci. 9, 313–321 (2013).
    PubMed  PubMed Central  Article  Google Scholar 

    14.
    Davis, H. E., Meconcelli, S., Rudek, R. & McMahon, D. P. Termites shape their collective behavioural response based on stage of infection. Sci. Rep. 8, 14433. https://doi.org/10.1038/s41598-018-32721-7 (2018).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    15.
    Mabelis, A. A. Wood ant wars: the relationship between aggression and predation in the red wood ant (Formica polyctena Först.). Neth. J. Zool. 29, 451–620 (1979).
    Article  Google Scholar 

    16.
    Driessen, G. J. J., Van Raalte, ATh. & De Bruyn, G. Cannibalism in the red wood ant, Formica polyctena (Hymenoptera: Formicidae). Oecologia 63, 13–22 (1984).
    ADS  PubMed  Article  Google Scholar 

    17.
    Yao, M. et al. The ancient chemistry of avoiding risks of predation and disease. Evol. Biol. 36, 267–281 (2009).
    Article  Google Scholar 

    18.
    Visscher, P. K. The honey bee way of death: Necrophoric behaviour in Apis mellifera colonies. Anim. Behav. 31, 1070–1076 (1983).
    Article  Google Scholar 

    19.
    Oi, D. H. & Pereira, R. M. Ant behavior and microbial pathogens (Hymenoptera: Formicidae). Florida Entomol. 76, 63–74 (1993).
    Article  Google Scholar 

    20.
    Nazzi, F., Della Vedova, G. & D’Agaro, M. A semiochemical from brood cells infested by Varroa destructor triggers hygienic behaviour in Apis mellifera. Apidologie 35, 65–70 (2004).
    CAS  Article  Google Scholar 

    21.
    Renucci, M., Tirrard, A. & Provost, E. Complex undertaking behavior in Temnothorax lichtensteini ant colonies: From corpse-burying behavior to necrophoric behavior. Insect. Soc. 58, 9–16 (2011).
    Article  Google Scholar 

    22.
    Diez, L., Le Borgne, H., Lejeune, P. & Detrain, C. Who brings out the dead? Necrophoresis in the red ant Myrmica rubra. Anim. Behav. 6, 1259–1264 (2013).
    Article  Google Scholar 

    23.
    Baracchi, D., Fadda, A. & Turillazzi, S. Evidence for antiseptic behaviour towards sick adult bees in honey bee colonies. J. Insect. Physiol. 58, 1589–1596 (2012).
    CAS  PubMed  Article  Google Scholar 

    24.
    Pull, Ch. D. et al. Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. eLife 7, e32073. https://doi.org/10.7554/eLife.32073 (2018).
    Article  PubMed  PubMed Central  Google Scholar 

    25.
    Leclerc, J.-B. & Detrain, C. Ants detect but do not discriminate diseased workers within their nest. Sci. Nat. 103, 70. https://doi.org/10.1007/s00114-016-1394-8 (2016).
    CAS  Article  Google Scholar 

    26.
    Williams, T. & Hernandez, O. Costs of cannibalism in the presence of an iridovirus pathogen of Spodoptera frugiperda. Ecol. Entomol. 31, 106–113 (2006).
    Article  Google Scholar 

    27.
    Rudolf, V. H. W. & Antonovics, J. Disease transmission by cannibalism: rare event or common occurrence?. Proc. R. Soc. Lond. B 274, 1205–1210 (2007).
    Google Scholar 

    28.
    Sadeh, A. & Rosenheim, J. A. Cannibalism amplifies the spread of vertically transmitted pathogens. Ecology 97, 1994–2002 (2016).
    PubMed  Article  Google Scholar 

    29.
    Claessen, D., de Roos, A. M. & Persson, L. Population dynamic theory of size-dependent cannibalism. Proc. R. Soc. Lond. B 271, 333–340 (2004).
    Article  Google Scholar 

    30.
    Pfennig, D. W., Ho, S. G. & Hoffman, E. A. Pathogen transmission as a selective force against cannibalism. Anim. Behav. 55, 1255–1261 (1998).
    CAS  PubMed  Article  Google Scholar 

    31.
    Loreto, R. G. & Hughes, D. P. Disease in the society: infectious cadavers result in collapse of ant sub-colonies. PLoS ONE 11, e0160820 (2016).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    32.
    Hughes, W. H., Eilenberg, J. & Boomsmal, J. J. Trade-offs in group living: Transmission and disease resistance in leaf-cutting ants. Proc. R. Soc. Lond. B 269, 1811–1819 (2002).
    Article  Google Scholar 

    33.
    Cremer, S. & Sixt, M. Analogies in the evolution of individual and social immunity. Proc. R. Soc. Lond. B 364, 129–142 (2009).
    Google Scholar 

    34.
    Konrad, M. et al. Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS ONE 10, 1–15 (2012).
    Google Scholar 

    35.
    Liu, L., Ganghua, L., Pengdong, S., Chaoliang, L. & Quiying, H. Experimental verification and molecular basis of active immunization against fungal pathogens in termites. Sci. Rep. 5, 15106. https://doi.org/10.1038/srep15106 (2015).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    36.
    Marikovsky, P. I. On some features of behaviour of the ants Formica rufa L. infected with fungus disease. Insect. Soc. 2, 173–179 (1962).
    Article  Google Scholar 

    37.
    Rutkowski, T. et al. Ants trapped for years in an old bunker; survival by cannibalism and eventual escape. J. Hymenopt. Res. 72, 177–184 (2019).
    Article  Google Scholar 

    38.
    Seifert, B. Die Ameisen Mittel- und Nordeuropas (Lutra-Verlags-und Vertriebsgesellschaft, Görlitz, 2007).
    Google Scholar 

    39.
    Czechowski, W., Radchenko, A., Czechowska, W. & Vepsäläinen, K. The ants of Poland with reference to the myrmecofauna of Europe. Fauna Poloniae (n.s.) 4. (Natura Optima Dux Foundation, 2012).

    40.
    Meyling, N. V. & Eilenberg, J. Ecology of the entomopathogenic fungi Beauveria bassiana and Metarhizium anisopliae in temperate agroecosystems: Potential for conservation biological control. Biol. Control 43, 145–155 (2007).
    Article  Google Scholar 

    41.
    Reber, A. & Chapuisat, M. Diversity, prevalence and virulence of fungal entomopathogens in colonies of the ant Formica selysi. Insect. Soc. 59, 231–239 (2012).
    Article  Google Scholar 

    42.
    Hajek, A. E. & St. Leger, R. J. Interactions between fungal pathogens and insect hosts. Annu. Rev. Entomol. 39, 293–322 (1994).
    Article  Google Scholar 

    43.
    Maák, I. et al. Cues or meaningless objects? Differential responses of the ant Formica cinerea to corpses of competitors and enslavers. Anim. Behav. 91, 53–59 (2014).
    Article  Google Scholar 

    44.
    Csata, E. & Dussutour, A. Nutrient regulation in ants (Hymenoptera: Formicidae): A review. Myrmecol. News 29, 111–124 (2019).
    Google Scholar 

    45.
    Nonacs, P. Death in the distance: Mortality risk as information for foraging ants. Behaviour 112, 23–35 (1990).
    Article  Google Scholar 

    46.
    Roces, F. & Núṅez, J. A. Information about food quality influences load-size selection in recruited leaf-cutting ants. Anim. Behav. 45, 135–143 (1993).
    Article  Google Scholar 

    47.
    Song, D., Hu, X. P. & Su, N.-Y. Survivorship, cannibalism, body weight loss, necrophagy, and entombement in laboratory groups of the Formosan subterranean termite, Coptotermes formosanus under starvation (Isoptera: Rhinotermitidae). Sociobiology 47, 27–39 (2006).
    Google Scholar 

    48.
    Heifig, I., Lima, J. T., Janei, V. & Costa-Leonardo, A. M. Effects of group size and starvation on survival of the Asian subterranean termite Coptotermes gestroi (Isoptera: Rhinotermitidae). Austral Entomol. 57, 279–284 (2017).
    Article  Google Scholar 

    49.
    Pompilio, L., Kacelnik, A. & Behmer, S. T. State-dependent learned valuation drives choice in an invertebrate. Science 311, 1613–1615 (2006).
    ADS  CAS  PubMed  Article  Google Scholar 

    50.
    Akino, T. & Yamaoka, R. Origin of oleic acid: Corpse recognition signal in the ant Formica japonica Motschlsky (Hymenoptera: Formicidae). Jpn. J. Appl. Entomol. Z. 40, 265–271 (1996).
    CAS  Article  Google Scholar 

    51.
    Chouvenc, T., Robert, A., Sémon, E. & Bordereau, C. Burial behaviour by dealates of the termite Pseudacanthotermes spiniger (Termitidae, Macrotermitinae) induced by chemical signals from termite corpses. Insect. Soc. 59, 119–125 (2012).
    Article  Google Scholar 

    52.
    Kok-Boon, N., Beng-Keok, Y., Kunio, T., Tsuyoshi, Y. & Chow-Yang, L. Do termites avoid carcasses? Behavioral responses depend on the nature of the carcasses. PLoS ONE 7, 1–11 (2012).
    Google Scholar 

    53.
    Diez, L., Moquet, L. & Detrain, C. Post-mortem changes in chemical profile and their influence on corpse removal in ants. J. Chem. Ecol. 39, 1424–1432 (2013).
    CAS  PubMed  Article  Google Scholar 

    54.
    Bignell, D. E., Roisin, Y. & Lo, N. Biology of Termites: A modern synthesis (Springer, Berlin, 2010).
    Google Scholar 

    55.
    Dlusskij, G. M. Ants of the genus Formica (Hymenoptera, Formicidae, g. Formica) (Nauka, Moscow, 1967) (in Russian).
    Google Scholar 

    56.
    Czechowski, W. Ants cemeteries. Przegląd Zoologiczny 20, 417–427 (1976) (in Polish with English summary).
    Google Scholar 

    57.
    Czechowski, W. Around nest cemeteries of Myrmica schencki Em. (Hymenoptera: Formicidae): their origin and a possible significance. Pol. J. Ecol. 56, 359–363 (2008).
    Google Scholar 

    58.
    Gibb, H. Experimental evidence for mediation of competition by habitat succession. Ecology 92, 1871–1878 (2011).
    CAS  PubMed  Article  Google Scholar 

    59.
    Chouvenc, T., Su, N.-Y. & Elliott, M. L. Interaction between the subterranean termite Reticulitermes flavipes (Isoptera: Rhinotermitidae) and the entomopathogenic fungus Metarhizium anisopliae in foraging arenas. J. Econ. Entomol. 101, 885–893 (2008).
    CAS  PubMed  Article  Google Scholar 

    60.
    Yanagawa, A., Yokohari, F. & Shimizu, S. The role of antennae in removing entomopathogenic fungi from cuticle of the termite Coptotermes formosanus. . J. Insect Sci. 9, 1–9 (2009).
    Article  Google Scholar 

    61.
    Tranter, Ch., LeFevre, L., Evison, S. E. F. & Hughes, W. O. H. Threat detection: Contextual recognition and response to parasites by ants. Behav. Ecol. 26, 396–405 (2015).
    Article  Google Scholar 

    62.
    Bonadies, E., Wcislo, W. T., Gálvez, D., Hughes, W. O. H. & Fernández-Marin, H. Hygiene defense behaviors used by a fungus-growing ant depend on the fungal pathogen stages. Insects 10, 130 (2019).
    PubMed Central  Article  PubMed  Google Scholar 

    63.
    Simone-Finstrom, M. D. & Spivak, M. Increased resin collection after parasite challenge: A case of self-medication in honey bees?. PLoS ONE 7, e34601. https://doi.org/10.1371/journal.pone.0034601 (2012).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    64.
    Brütsch, T. & Chapuisat, M. Wood ants protect their brood with tree resin. Anim. Behav. 93, 157–161 (2014).
    Article  Google Scholar 

    65.
    Ormond, E. L., Thomas, A. P. M., Pell, J. K., Freeman, S. N. & Roy, H. E. Avoidance of a generalist entomopathogenic fungus by the ladybird Coccinella septempunctata. FEMS Microbiol. Ecol. 77, 229–237 (2011).
    CAS  PubMed  Article  Google Scholar 

    66.
    Fernández-Marín, H., Zimmerman, J. K., Rehner, S. A. & Wcislo, W. T. Active use of the metapleural glands by ants in controlling fungal infection. Proc. R. Soc. Lond. B 273, 1689–1695 (2006).
    Google Scholar 

    67.
    Tragust, S. et al. Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. Curr. Biol. 23, 1–7 (2013).
    Article  CAS  Google Scholar 

    68.
    Tragust, S., Herrmann, C., Häfner, J., Braasch, R., Tilgen, Ch., Hoock, M., Milidakis, M. A., Gross, R. & Feldhaar, H. Formicine ants swallow their highly acidic poison for gut microbial selection and control. bioRxiv preprint https://doi.org/10.1101/2020.02.13.947432 (2020).

    69.
    Cremer, S., Pull, Ch. D. & Fürst, M. A. Social immunity: emergence and evolution of colony-level disease protection. Annu. Rev. Entomol. 63, 105–123 (2018).
    CAS  PubMed  Article  Google Scholar 

    70.
    Rosengaus, R. B., Jordan, C., Lefebvre, M. L. & Traniello, J. F. A. Pathogen alarm behavior in a termite: A new form of communication in social insects. Naturwissenschaften 86, 544–548 (1999).
    ADS  CAS  PubMed  Article  Google Scholar 

    71.
    Hernandez-Lopez, J., Reissberger-Gallé, U., Crailsheim, K. & Schuehly, W. Cuticular hydrocarbon cues of immune-challenged workers elicit immune activation in honeybee queens. Mol. Ecol. 26, 3062–3073 (2017).
    CAS  PubMed  Article  Google Scholar 

    72.
    Chouvenc, T. & Su, N.-Y. When subterranean termites challenge the rules of fungal epizootics. PLoS ONE 7, 84. https://doi.org/10.1371/journal.pone.0034484 (2012).
    CAS  Article  Google Scholar 

    73.
    Csata, E., Erős, K. & Markó, B. Effects of the ectoparasitic fungus Rickia wasmannii on its ant host Myrmica scabrinodis: changes in host mortality and behavior. Insect. Soc. 61, 247–252 (2014).
    Article  Google Scholar 

    74.
    Diez, L., Urbain, L., Lejeune, Ph. & Detrain, C. Emergency measures: adaptive response to pathogen intrusion in the ant nest. Behav. Process. 116, 80–86 (2015).
    Article  Google Scholar 

    75.
    Qui, H.-L. et al. Differential necrophoric behaviour of the ant Solenopsis invicta towards fungal infected corpses of workers and pupae. Bull. Entomol. Res. 105, 607–614 (2015).
    Article  CAS  Google Scholar 

    76.
    Pereira, H. & Detrain, C. Pathogen avoidance and prey discrimination in ants. R. Soc. Open Sci. 7, 191705 (2020).
    ADS  PubMed  PubMed Central  Article  Google Scholar 

    77.
    Cremer, S., Armitage, S. A. O. & Schmid-Hempel, P. Social immunity. Curr. Biol. 17, 693–702 (2007).
    Article  CAS  Google Scholar 

    78.
    Pull, Ch. D. & Cremer, S. Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour. BMC Evol. Biol. 219, 17. https://doi.org/10.1186/s12862-017-1062-4 (2017).
    Article  Google Scholar 

    79.
    Kramm, K. R., West, D. F. & Rockenbach, P. G. Pathogens of termites: transfer of the entomopathogen Metarhizium anisopliae between the termites of Reticulitermes sp.. J. Invertebr. Pathol. 40, 1–6 (1982).
    Article  Google Scholar 

    80.
    Kesäniemi, J., Koskimäki, J. J. & Jurvansuu, J. Corpse management of the invasive Argentine ant inhibits growth of pathogenic fungi. Sci. Rep. 9, 7593. https://doi.org/10.1038/s41598-019-44144-z (2019).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    81.
    Greenwald, E. E., Baltiansky, L. & Feinerman, O. Individual crop loads provide local control for collective food intake in ant colonies. eLife 7, e31730 (2018).
    PubMed  PubMed Central  Article  Google Scholar 

    82.
    Horstmann, K. Untersuchungen über den Nahrungserwerb der Waldameisen (Formica polyctena Foerster) im Eichenwald. Oecologia 5, 138–157 (1970).
    ADS  PubMed  Article  Google Scholar 

    83.
    Bhatkar, A. & Whitcomb, W. H. Artificial diet for rearing various species of ants. Florida Entomol. 53, 229–232 (1970).
    Article  Google Scholar 

    84.
    Choe, D. H. & Rust, M. K. Horizontal transfer of insecticides in laboratory colonies of the argentine ant (Hymenoptera: Formicidae). J. Econ. Entomol. 101, 1397–1405 (2008).
    CAS  PubMed  Article  Google Scholar 

    85.
    Pereira, R. M. & Stimac, J. L. Transmission of Beauveria bassiana within nests of Solenopsis invicta (Hymenoptera: Formicidae) in the laboratory. Environ. Entomol. 21, 1427–1432 (1992).
    Article  Google Scholar 

    86.
    Liu, H., Skinner, M., Parker, B. L. & Brownbridge, M. Pathogenicity of Beauveria bassiana, Metarhizium anisopliae (Deuteromycotina: Hyphomycetes), and other entomopathogenic fungi against Lygus lineolaris (Hemiptera: Miridae). J. Econ. Entomol. 95, 675–681 (2002).
    PubMed  Article  Google Scholar 

    87.
    Loreto, R. G. & Hughes, D. P. Disease dynamics in ants. Adv. Genet. 94, 287–306. https://doi.org/10.1016/bs.adgen.2015.12.005 (2016).
    CAS  Article  PubMed  Google Scholar 

    88.
    R Core Team. R: A language and environment for statistical computing. (R Foundation for Statistical Computing, 2017). https://www.R-project.org/.

    89.
    Therneau, T. coxme: Mixed Effects Cox Models. R package version 2.2-5. https://CRAN.R-project.org/package=coxme (2015).

    90.
    Bates, D., Maechler, M., Bolker, B. & Walker, S. lme4: Linear mixed-effects models using Eigen and S4. R package version 1.0-5. https://CRAN.R-project.org/package=lme4 (2013).

    91.
    Bartoń, K. MuMIn: Multi-model inference. R package version 1.9.13. https://CRAN.R-project.org/package=MuMIn (2013).

    92.
    Grueber, C. E., Nakagawa, S., Laws, R. J. & Jamieson, I. G. Multimodel inference in ecology and evolution: Challenges and solutions. J. Evol. Biol. 24, 699–711 (2011).
    CAS  PubMed  Article  Google Scholar  More

  • in

    Long-term surveys of age structure in 13 ungulate and one ostrich species in the Serengeti, 1926–2018

    There were three methods of sampling the populations. For Methods 1 and 2, records were obtained by driving along the road transects, and stopping to score the age groups in herds within some 100 m of the road. There were three road transects, entirely in the administrative boundaries of Serengeti National Park and consistent every year (1962–2018), with records summed over the three for each data entry. Transect 1 was from Seronera (34.823°E, 2.428°S) west to Kirawira (34.208°E, 2.151°S; 120 km), Transect 2 from Seronera to Bologonja (35.173°E, 1.757°S; 115 km), and Transect 3 from Seronera to Olduvai Gorge (35.35°E, 2.993°S; 75 km) (Fig. 1). The first two transects were in similar savanna ecosystems, and comparison of samples from these two showed close similarity.
    Fig. 1

    Ungulate and ostrich sampling transects in the Serengeti ecosystem.

    Full size image

    The criteria for age classes in each species are given in Online-only Table 1. The sample was the herd within view (such as a group of impalas (Ae. melampus) or hartebeests (Al. buselaphus), which occur in discrete groups), or a subset of it if the herd was very large. One observer, using 8–10 x magnification binoculars, called out the age category while a recorder entered the records on data sheets. These were later entered digitally.
    Two exceptions to this were the immense herds of migrant wildebeest (C. taurinus) and zebra (Eq. quagga). Because they were numerous and extensive, herds had to be sampled in a systematic way. A vehicle drove through the herds, stopping every half kilometer, where a 180 degree scan out to 100 m was conducted to count the sample within view. The transects were from the start to the end of the herd, with some being 30 km long through a single, continuous herd. Method 3 used aerial pictures of the herds to score age groups. Although the sampling protocol was different in the three methods (due to different distributions of each species) the same criteria for identifying age classes was used in all methods. All methods used either systematic or random sampling of the populations.
    All species were either migrants, if the species shows seasonal variation in habitat, or residents, if the species remains in the same area of the park year-round. A notable exception to this is the wildebeest (C. taurinus). In fact, there were two populations of wildebeest, a large migrant herd and a small resident herd at the far western end of the ecosystem. These two were sampled separately and scored as either migrant or resident.
    Method 1
    This method was used in all sampling years for impala (Ae. melampus), Coke’s kongoni (Al. buselaphus), topi (D. lunatus), warthog (P. africanus), Defassa waterbuck (K. defassa), and zebra (Eq. quagga). Sampling years 1984–1994 for African buffalo (Sy. caffer), 1965–2012 for giraffe (G. camelopardalus), and 1964–2016 for wildebeest (C. taurinus).
    Populations were sampled once or twice a year at specific times, depending on the availability of different age classes in the areas near transects. Because ungulates had different birth seasons samples were collected at two time periods, once in mid-year and once at year-end. Only one time period per year was used for each species. The early age group, “infants”, was sampled usually near the end of the rainy season (March–June) since many species give birth during the rainy season. For some species, there was a second sampling period (August-December) at the end of the dry season, to measure the survival of juveniles during this period of ecological stress. There are a few cases where more than two samples were obtained in a single year, so as to track the survival of the whole cohort throughout a year.
    Method 2
    This method was used in all sampling years for eland (T. oryx), elephant (L. africana), Grant’s gazelle (N. granti), ostrich (S. camelus), and waterbuck (K. defassa).
    These species were sufficiently scarce that an adequate sample could not be obtained at specific times. For these, records were scored whenever the species was seen in a sampling period, and then records for all sampling periods of a single given year were summed. A special case was Thomson’s gazelle (Eu. thomsonii), which, although numerous, was scored only during one short time period (1992–1994) for the months of August and September.
    Method 3
    This method was used in sample years 1965–1973 for African buffalo (Sy. caffer), and 1926–1933 for giraffe (G. camelopardalus tippelskirchi), wildebeest (C. taurinus), and zebra (Eq. quagga). The area covered was in all cases within the Serengeti ecosystem. Buffalo and giraffe were only found in the savanna, while wildebeest were sampled when they were on the plains. Flights were made systematically over the area, wildebeest was sampled using photographs at regular intervals, buffalo and giraffe were sampled when they were encountered.
    The third method, applied only in the very early years, used aerial photographs to identify age classes and females. The same criteria for identifying age classes was used as those for Methods 1 and 2 (Online-only Table 1), with an emphasis on the shape and size of horns for the wildebeest and African buffalo2, and of the relative sizes of young giraffe. The early samples in 1926–1933, were obtained from photographs taken by Martin Johnson. These photos reside in the Martin and Osa Johnson Safari Museum, Chanute, Kansas. Unfortunately, the 1965–1973 photographs of buffalo herds have now all been lost or destroyed. More

  • in

    Movement patterns of the grey field slug (Deroceras reticulatum) in an arable field

    The nature of the slug movement data collected in our field experiment (i.e. position on or beneath the soil surface observed at discrete moments of time) makes it possible to analyse the slug locomotory track in terms of the discrete-time random movement framework12,16,35,36. Within this framework, a curvilinear movement path is approximated by a broken line (see Fig. 2) and the movement of an individual slug is parameterized by the following frequency distributions:
    1.
    The distribution of the step sizes along the movement path (i.e. the distance between sequential pairs of recorded positions; Fig. 2) or the corresponding average speed

    2.
    The distribution of turning angle (the angle between the straight lines drawn between sequential pairs of recorded positions; Fig. 2).

    Figure 2

    A sketch of animal movement path and its discretization (adapted from36). (a) The original movement path is normally curvilinear. (b) Due to the limitations of the radio-tracking technique, position of the animal is only known at certain discrete moments of time; correspondingly, the curve is approximated by a broken line. (c) The movement path as a broken line is fully described by the sequence of the step sizes (lengths) along the path, i.e. the distances travelled between any two sequential recorded positions, and the sequence of the corresponding turning angles.

    Full size image

    Once all the information is available, it is possible to calculate the mean squared displacement as a function of time12,37. Additionally, in case the movement consists of alternating periods of active movement and immobility (periods with no recorded displacement resulting from feeding or inactivity, hereafter referred to as“resting time”), one should also consider the distribution of the corresponding periods.
    Speed, squared displacements and the straightness index
    It is apparent from the data that slug movement is intermittent, with periods of locomotion interspersed between periods in which they remain motionless. Tables 1 and 2 show, for the sparse and dense releases respectively, the number of ‘active’ time intervals when the slugs were moving. Periods during which slugs were motionless are marked by the zeros in Tables 1 and 2, but all these individuals resumed their movement during the following hours, confirming that they were alive throughout the assessment period. We therefore retain the zeros in the data for the subsequent analysis.
    Table 1 Slug mean speed (averaged over the whole movement path), the mean SSD (see Eqs. (3) and (5), respectively) and the straightness index in the case of sparse release for each of 17 slugs used in the experiment. Here the straightness index is calculated using Eq. (4) where the values of the step size are immediately available from our field data.
    Full size table

    Table 2 Slug mean speed (averaged over the whole movement path), the mean SSD (see Eqs. (3) and (5), respectively) and the straightness index in the case of dense release for each of 11 slugs used in the experiment. Here the straightness index is calculated using Eq. (4) where the values of the step size are immediately available from our field data.
    Full size table

    The baseline discrete-time framework considers animal position at equidistant moments of time. However, in the field experiment (as described in the previous section), time taken to locate slugs at each assessment resulted in the time interval varying between measurements (sparse release treatment: 27–87 mins; dense release treatment: 20–103 mins). The step size, i.e. the displacement during one time interval, depends in part on the duration of that interval, hence risking bias in the results. We address this issue by scaling the step size by the duration of the corresponding time interval, i.e. by considering the average speed during the step:

    $$begin{aligned} v_k(i)=, & {} frac{|Delta {mathbf{r}|_k(i)}}{Delta {t}_k(i)}, quad i=1,2,ldots ,N, end{aligned}$$
    (1)

    where

    $$begin{aligned} |Delta {mathbf{r}|_k(i)}=, & {} |mathbf{r}_k(t_i)-mathbf{r}_k(t_{i-1})|, end{aligned}$$
    (2)

    is the displacement of the kth slug during the ith time interval, i.e. the distance between the two sequential positions in the field. Here N is the total number of steps made by the given slug during the full period of the experiment (in our field data, for all slugs (N=10)).
    For each individual slug, we then calculate the mean speed over all steps along the movement path:

    $$begin{aligned} _k=, & {} frac{1}{N} sum ^{N}_{i=1} v_k(i). end{aligned}$$
    (3)

    The results for the sparse and dense releases are shown in Tables 1 and 2, respectively; see also Fig. 3a.
    The mean speed of slug movement, although being an important factor for slug dispersal, does not provide enough information about the rate at which the slug increases its linear distance from the point of release, because it does not provide information on the frequency of turning or the turning angle. In order to take that into account, we calculate the straightness index35, i.e. the ratio of the total displacement (distance between the point of release and the final position at the end of the experiment) to the total distance travelled along the path:

    $$begin{aligned} s_k= & {} |mathbf{r}_k(t_N)-mathbf{r}_k(t_0)|/left( sum ^{N}_{i=1}|Delta {mathbf{r}}|_k(i) right) , end{aligned}$$
    (4)

    where (t_0) is the time of slug release and (t_N) is the time of the final observation. The actual distance travelled is approximated by the length of the corresponding broken line (see the dark solid line in Fig. 2).
    Figure 3

    (a) Slug mean spead and (b) slug mean SSD, black diamonds for the sparse release and red circles for the dense release.

    Full size image

    The straightness index quantifies the amount of turning (a combination of the frequency and angles of turns) along the whole movement path, i.e. over the whole observation time, but it says nothing about the rate of turning on the shorter time scale of a single ‘step’ along the movement path. To account for this, along with the mean speed we calculate the mean scaled squared displacement (SSD):

    $$begin{aligned} langle sigma ^2 rangle _k=, & {} frac{1}{N} sum ^{N}_{i=1} sigma ^2_k(i) qquad text{ where }qquad sigma ^2_k(i)~=~frac{|Delta {mathbf{r}|^2_k(i)}}{Delta {t}_k(i)}, end{aligned}$$
    (5)

    see Tables 1 and 2 and Fig. 3b. For the same value of mean speed, a larger value of the SSD corresponds to a straighter movement on the timescale of a single step, with a smaller turning rate.
    An immediate observation from visual analysis of the data shown in Fig. 3 is that both slug speed and the SSD are smaller in the case of dense release than in the sparse release. Therefore, a preliminary conclusion can be drawn that average slug movement is slower in the dense release compared to the sparse release treatment.
    Turning angles
    Figure 4

    Frequency distribution of the turning angle in the case of (a) sparse and (b) dense releases of slugs. In calculating the turning angle, the periods of no movement were disregarded. The red curve shows the best-fitting of the data with the exponential function; see details in the text.

    Full size image

    We now proceed to analyse the distribution of turning angles. The histogram of different values of the angle is shown in Fig. 4. Let us consider first the case of sparse release (see Fig. 4a). We readily observe that the distribution is roughly symmetrical and has a clear maximum at (theta _T=0). The latter indicates that, on this timescale, slug movement is better described as the CRW than the standard diffusion1,16. Indeed, the standard diffusion (also known as the simple random walk) assumes that there is no bias in the movement direction, in particular there is no correlation in the movement direction in the intervals before and after the recorded position, which means that the turning angle is uniformly distributed over the whole circle. On the contrary, in the case where a correlation between the movement directions exists (hence resulting in the CRW), the distribution of the turning angle becomes hump-shaped. This is in agreement with the results of previous studies on animal movement (in particular, invertebrates12,38) as well as a general theoretical argument13.
    In order to provide a more quantitative insight, we look for a functional description of the turning angle distribution using several distributions that are commonly used in movement ecology. The results are shown in Table 3. We establish that the turning angle data are best described by the exponential distribution. Somewhat unexpectedly, it outperforms the Von Mises distribution, although the latter is often regarded as a benchmark and its use has some theoretical justification1. However, the exponential distribution of the turning angle has previously been observed in movement data on some other species, e.g. on swimming invertebrates39.
    Table 3 The (r^2) values for the turning angle movement data (in case of sparsely released slugs) described by different standard frequency distributions. The corresponding data are shown in Fig. 4a.
    Full size table

    The distribution of turning angle obtained in the case of dense release exhibit different features; see Fig. 4b. However, in this case, the distribution is not symmetric and has a clear bias towards positive values: the mean turning angle corresponding to the data shown in Fig. 4b is (langle theta _T rangle = 0.772approx pi /4). Since the slugs used in the dense release are from the same cohort as those used in the sparse release, we consider this bias as an effect of the slug density: the movement pattern of an individual slug is affected by the presence of con-specifics. We discuss possible specific mechanisms for the responsiveness to this factor in the Discussion.
    An attempt to describe the turning angle data from the dense release by a symmetric distribution returns low values of (r^2) (see Suppl. Appendix A.1). However, the accuracy of data fitting comparable with the sparse release can be achieved by using an asymmetric distribution, i.e. where the corresponding function has different parameters for the positive and negative values of the angle. The results are shown in Table 4.
    Table 4 The (r^2) values for the turning angle movement data (in case of densely released slugs) described by asymmetric frequency distributions. In calculating the turning angle, the periods of no movement were disregarded; the corresponding data are shown in Fig. 4b.
    Full size table

    The turning angle data shown in Fig. 4 were obtained using all active steps along the movement paths. However, since periods of slug movement alternate with periods of resting, it may raise the question of the relevance of the turning angle at the locations where slugs remained motionless for some time. In order to check the robustness of our results, we now repeat the analysis to calculate the turning angle differently by omitting the segments adjoined with the rest position. The results are shown in Fig. 5. In this case, a reliable fit may not be possible due to there being insufficient data. However, a visual inspection of the corresponding histograms suggests that the main properties of the turning angle distribution agree with those observed above for the bigger data set. Namely, in both cases the distribution has a clear maximum at (theta _T=0) (this is seen particularly well in the case of sparse release). In the case of sparse release the distribution is approximately symmetric, while in the case of dense release there is a clear bias towards positive values. We therefore conclude that the properties of the turning angle distribution are robust with regard to the details of its definition.
    Figure 5

    Frequency distribution of the turning angle in case of (a) sparse release, (b) dense release. The turning angle is only calculated for consecutive movements, i.e. if a slug does not move during a time step then its previous angle of movement is not used.

    Full size image

    Movement and resting times
    Figure 6

    Distribution of the proportion of the total time spent in movement in case of (a) sparse release and (b) dense release. The red curve shows the best-fit of the data with the normal distribution; see details in the text.

    Full size image

    Our field data shows that, while foraging, slugs do not move continuously but alternate periods of movement and rest; see the second column in Tables 1 and 2. Such behaviour is typical of many animal species38,40. In this section, we analyse the proportion of time that slugs spend moving, in particular to reveal the differences, if any, between the sparse and dense release.
    Figure 6 shows the corresponding data where for the convenience of analysis the slugs are renumbered in a hierarchical order, so that slug 1 spends the highest proportion of time moving, slug 2 has the second highest, etc. We readily observe that the sparse release slugs tend to move more frequently than those from the dense release treatment: slugs that move for more than half of the total observation time constitute about 50% of the group in the case of sparse release but less than 30% in the case of dense release.
    Figure 7

    Distribution of the movement frequencies in case of (a) sparse release and (b) dense release.

    Full size image

    In order to make a more quantitative insight, we endeavour to describe the data using several standard distributions; see Tables 5 and 6. We find that the normal distribution performs better than others both in sparse and dense release treatments. Importantly, however, the parameters of the distribution are significantly different between the two cases; in particular, the standard deviation appears to be approximately twice as large in the case of sparse release. Arguably, it confirms the above conclusion that slugs move more frequently or for longer in the case of sparse release. Slugs released as a group tend to spend considerably more time at rest compared to the slugs released individually.
    Table 5 The (r^2) values for the proportion of movement time described by different standard frequency distributions in the case of sparse release.
    Full size table

    To avoid a possible bias due to the different group size (17 slugs in the sparse release and 11 in the dense release), we now rearrange the data in terms of the proportion of the group that moves with a given frequency. The results are shown in Fig. 7. Although the amount of data in this case does not allow us to describe them using a particular function, the two cases clearly exhibit distributions with different properties. In particular, the average movement frequency is 0.467 for the sparse release and 0.264 for the dense release, and the corresponding variances are 0.090 and 0.065, respectively.
    Table 6 The (r^2) values for the proportion of movement time described by different standard frequency distributions in the case of dense release.
    Full size table

    To further quantify the differences, Fig. 8 shows the number of slugs moving in each observation interval. Once again, we observe that the graph exhibits essentially different properties between the two releases. In particular, over the first interval, the majority of slugs (14 out of 17) move in the case of sparse release but none of the slugs move in the case of dense release. In the second half of the observation time (intervals 6–10) on average about 50% of slugs (8 out of 17) move in the case of sparse release but only about 25% of slugs (2–3 out of 11) move in the case of dense release.
    Based on the differences between the two releases, we conclude that the presence of con-specifics is the factor that affects the distribution of slug movement time. Thus, along with the results of the previous sections, it suggests that slug movement is density dependent.
    Figure 8

    The number of moving slugs at each observation moment in case of (a) sparse release and (b) dense release.

    Full size image More

  • in

    Long-term capture and handling effects on body condition, reproduction and survival in a semi-aquatic mammal

    1.
    Jobling, M. Are compensatory growth and catch-up growth two sides of the same coin?. Aquacult. Int. 18, 501–510. https://doi.org/10.1007/s10499-009-9260-8 (2010).
    Article  Google Scholar 
    2.
    Rebke, M., Coulson, T., Becker, P. H. & Vaupel, J. W. Reproductive improvement and senescence in a long-lived bird. Proc. Natl. Acad. Sci. 107, 7841–7846. https://doi.org/10.1073/pnas.1002645107 (2010).
    ADS  Article  PubMed  Google Scholar 

    3.
    Farias, V., Fuller, T. K., Wayne, R. K. & Sauvajot, R. M. Survival and cause-specific mortality of gray foxes (Urocyon cinereoargenteus) in southern California. J. Zool. 266, 249–254. https://doi.org/10.1017/S0952836905006850 (2005).
    Article  Google Scholar 

    4.
    Clutton-Brock, T. & Sheldon, B. C. Individuals and populations: the role of long-term, individual-based studies of animals in ecology and evolutionary biology. Trends Ecol. Evol. 25, 562–573. https://doi.org/10.1016/j.tree.2010.08.002 (2010).
    Article  PubMed  Google Scholar 

    5.
    Arnemo, J. M. et al. Risk of capture-related mortality in large free-ranging mammals: experiences from Scandinavia. Wildl. Biol. 12, 109–113. https://doi.org/10.1017/S0952836901000309 (2006).
    Article  Google Scholar 

    6.
    Harcourt, R. G., Turner, E., Hall, A., Waas, J. R. & Hindell, M. Effects of capture stress on free-ranging, reproductively active male Weddell seals. J. Comp. Physiol. A. 196, 147–154. https://doi.org/10.1007/s00359-009-0501-0 (2010).
    Article  Google Scholar 

    7.
    Pelletier, F., Hogg, J. T. & Festa-Bianchet, M. Effect of chemical immobilization on social status of bighorn rams. Anim. Behav. 67, 1163–1165. https://doi.org/10.1016/j.anbehav.2003.07.009 (2004).
    Article  Google Scholar 

    8.
    Brivio, F., Grignolio, S., Sica, N., Cerise, S. & Bassano, B. Assessing the impact of capture on wild animals: the case study of chemical immobilisation on alpine ibex. PLoS ONE 10, e0130957. https://doi.org/10.1371/journal.pone.0130957 (2015).
    CAS  Article  PubMed  PubMed Central  Google Scholar 

    9.
    Cattet, M., Boulanger, J., Stenhouse, G., Powell, R. A. & Reynolds-Hogland, M. J. An evaluation of long-term capture effects in ursids: implications for wildlife welfare and research. J. Mammal. 89, 973–990. https://doi.org/10.1644/08-MAMM-A-095.1 (2008).
    Article  Google Scholar 

    10.
    Holt, R. D. et al. Estimating duration of short-term acute effects of capture handling and radiomarking. J. Wildl. Manag. 73, 989–995. https://doi.org/10.2193/2008-073 (2009).
    Article  Google Scholar 

    11.
    Jordan, B. Science-based assessment of animal welfare: wild and captive animals. Revue Sci. Tech. Office Int. Des. Epizooties 24, 515. https://doi.org/10.20506/rst.24.2.1588 (2005).
    CAS  Article  Google Scholar 

    12.
    Jewell, Z. Effect of monitoring technique on quality of conservation science. Conserv Biol 27, 501–508. https://doi.org/10.1111/cobi.12066 (2013).
    Article  PubMed  Google Scholar 

    13.
    Wilson, R. P. & McMahon, C. R. Measuring devices on wild animals: what constitutes acceptable practice?. Front Ecol. Environ. 4, 147–154 (2006).
    Article  Google Scholar 

    14.
    Bourbonnais, M. L. et al. Environmental factors and habitat use influence body condition of individuals in a species at risk, the grizzly bear. Conserv. Physiol. 2, 1. https://doi.org/10.1093/conphys/cou043 (2014).
    CAS  Article  Google Scholar 

    15.
    Pearson, E., Ortega, Y. K. & Ruggiero, L. F. Trap-induced mass declines in small mammals: mass as a population index. J. Wildl. Manag. 1, 684–691. https://doi.org/10.2307/3802675 (2003).
    Article  Google Scholar 

    16.
    Smith, J. B., Windels, S. K., Wolf, T., Klaver, R. W. & Belant, J. L. Do transmitters affect survival and body condition of American beavers Castor canadensis?. Wildl. Biol 22, 117–123. https://doi.org/10.2981/wlb.00160 (2016).
    Article  Google Scholar 

    17.
    Alibhai, S. K., Jewell, Z. C. & Towindo, S. S. Effects of immobilization on fertility in female black rhino (Diceros bicornis). J. Zool. 253, 333–345 (2001).
    Article  Google Scholar 

    18.
    Carey, M. J. The effects of investigator disturbance on procellariiform seabirds: a review. N. Z. J. Zool. 36, 367–377. https://doi.org/10.1080/03014220909510161 (2009).
    Article  Google Scholar 

    19.
    Côté, S. D., Festa-Bianchet, M. & Fournier, F. Life-history effects of chemical immobilization and radiocollars on mountain goats. J. Wildl. Manag. 1, 745–752. https://doi.org/10.2307/3802351 (1998).
    Article  Google Scholar 

    20.
    Omsjoe, E. H. et al. Evaluating capture stress and its effects on reproductive success in Svalbard reindeer. Can. J. Zool. 87, 73–85. https://doi.org/10.1139/Z08-139 (2009).
    Article  Google Scholar 

    21.
    Sharpe, F., Bolton, M., Sheldon, R. & Ratcliffe, N. Effects of color banding, radio tagging, and repeated handling on the condition and survival of Lapwing chicks and consequences for estimates of breeding productivity. J. Field Ornithol. 80, 101–110. https://doi.org/10.1111/j.1557-9263.2009.00211.x (2009).
    Article  Google Scholar 

    22.
    Igual, J. M. et al. Short-term effects of data-loggers on Cory’s shearwater (Calonectris diomedea). Mar. Biol. 146, 619–624 (2005).
    Article  Google Scholar 

    23.
    Casas, F. et al. Assessing the short-term effects of capture, handling and tagging of sandgrouse. Ibis 157, 115–124. https://doi.org/10.1111/ibi.12222 (2015).
    Article  Google Scholar 

    24.
    Clinchy, M., Krebs, C. J. & Jarman, P. J. Dispersal sinks and handling effects: interpreting the role of immigration in common brushtail possum populations. J. Anim. Ecol. 70, 515–526. https://doi.org/10.1046/j.1365-2656.2001.00510.x (2001).
    Article  Google Scholar 

    25.
    Dugger, K. M., Ballard, G., Ainley, D. G. & Barton, K. J. Effects of flipper bands on foraging behavior and survival of Adélie penguins (Pygoscelis adeliae). Auk 123, 858–869. https://doi.org/10.1093/auk/123.3.858 (2006).
    Article  Google Scholar 

    26.
    Esler, D., Mulcahy, D. M. & Jarvis, R. L. Testing assumptions for unbiased estimation of survival of radiomarked harlequin ducks. J. Wildl. Manag. 1, 591–598. https://doi.org/10.2307/3803257 (2000).
    Article  Google Scholar 

    27.
    Gibson, D. et al. Effects of radio collars on survival and lekking behavior of male greater sage-grouse. The Condor 115, 769–776. https://doi.org/10.1525/cond.2013.120176 (2013).
    Article  Google Scholar 

    28.
    Ginsberg, J. R. et al. Handling and survivorship of African wild dog (Lycaon pictus) in five ecosystems. Conserv. Biol. 9, 665–674. https://doi.org/10.1046/j.1523-1739.1995.09030665.x (1995).
    Article  Google Scholar 

    29.
    Ponjoan, A. et al. Adverse effects of capture and handling little bustard. J. Wildl. Manag. 72, 315–319. https://doi.org/10.2193/2006-443 (2008).
    Article  Google Scholar 

    30.
    Kukalová, M., Gazárková, A. & Adamík, P. Should I stay or should I go? The influence of handling by researchers on den use in an arboreal nocturnal rodent. Ethology 119, 848–859. https://doi.org/10.1111/eth.12126 (2013).
    Article  Google Scholar 

    31.
    Wingfield, J. C. & Sapolsky, R. M. Reproduction and resistance to stress: when and how. J. Neuroendocrinol. 15, 711–724. https://doi.org/10.1046/j.1365-2826.2003.01033.x (2003).
    CAS  Article  PubMed  Google Scholar 

    32.
    Grissom, N. & Bhatnagar, S. Habituation to repeated stress: get used to it. Neurobiol. Learn. Mem. 92, 215–224. https://doi.org/10.1016/j.nlm.2008.07.001 (2009).
    Article  PubMed  Google Scholar 

    33.
    Lindenmayer, D. B. et al. Value of long-term ecological studies. Austral. Ecol. 37, 745–757. https://doi.org/10.1111/j.1442-9993.2011.02351.x (2012).
    Article  Google Scholar 

    34.
    Schell, C. J., Young, J. K., Lonsdorf, E. V., Santymire, R. M. & Mateo, J. M. Parental habituation to human disturbance over time reduces fear of humans in coyote offspring. Ecol. Evol. 8, 12965–12980. https://doi.org/10.1002/ece3.4741 (2018).
    Article  PubMed  PubMed Central  Google Scholar 

    35.
    Campbell, R. D., Newman, C., Macdonald, D. W. & Rosell, F. Proximate weather patterns and spring green-up phenology effect Eurasian beaver (Castor fiber) body mass and reproductive success: the implications of climate change and topography. Global Change Biol. 19, 1311–1324. https://doi.org/10.1111/gcb.12114 (2013).
    ADS  Article  Google Scholar 

    36.
    Campbell, R. D., Rosell, F., Newman, C. & Macdonald, D. W. Age-related changes in somatic condition and reproduction in the Eurasian beaver: resource history influences onset of reproductive senescence. PLoS ONE 12, e0187484. https://doi.org/10.1371/journal.pone.0187484 (2017).
    CAS  Article  PubMed  PubMed Central  Google Scholar 

    37.
    Parker, H., Zedrosser, A. & Rosell, F. Age-specific reproduction in relation to body size and condition in female Eurasian beavers. J. Zool. 302, 236–243. https://doi.org/10.1111/jzo.12458 (2017).
    Article  Google Scholar 

    38.
    Sun, L. X. & Muller-Schwarze, D. Anal gland secretion codes for relatedness in the beaver Castor canadensis. Ethology 104, 917–927. https://doi.org/10.1111/j.1439-0310.1998.tb00041.x (1998).
    Article  Google Scholar 

    39.
    Rosell, F., Bergan, P. & Parker, H. Scent-marking in the Eurasian beaver (Castor fiber) as a means of territory defense. J. Chem. Ecol. 24, 207–219. https://doi.org/10.1023/A:1022524223435 (1998).
    CAS  Article  Google Scholar 

    40.
    Mayer, M., Frank, S. C., Zedrosser, A. & Rosell, F. Causes and consequences of inverse density-dependent territorial behaviour and aggression in a monogamous mammal. J. Anim. Ecol. 89, 577–588. https://doi.org/10.1111/1365-2656.13100 (2019).
    Article  PubMed  Google Scholar 

    41.
    Hohwieler, K., Rosell, F. & Mayer, M. Scent-marking behavior by subordinate Eurasian beavers. Ethology 124, 591–599. https://doi.org/10.1111/eth.12762 (2018).
    Article  Google Scholar 

    42.
    Steyaert, S. M. J. G., Zedrosser, A. & Rosell, F. Socio-ecological features other than sex affect habitat selection in the socially obligate monogamous Eurasian beaver. Oecologia 179, 1023–1032. https://doi.org/10.1007/s00442-015-3388-1 (2015).
    ADS  Article  PubMed  PubMed Central  Google Scholar 

    43.
    Gallant, D., Bérubé, C. H., Tremblay, E. & Vasseur, L. An extensive study of the foraging ecology of beavers (Castor canadensis) in relation to habitat quality. Can. J. Zool. 82, 922–933. https://doi.org/10.1139/z04-067 (2004).
    Article  Google Scholar 

    44.
    Haarberg, O. & Rosell, F. Selective foraging on woody plant species by the Eurasian beaver (Castor fiber) in Telemark Norway. J. Zool. 270, 201–208. https://doi.org/10.1111/j.1469-7998.2006.00142.x (2006).
    Article  Google Scholar 

    45.
    Pinto, B., Santos, M. J. & Rosell, F. Habitat selection of the Eurasian beaver (Castor fiber) near its carrying capacity: an example from Norway. Can. J. Zool. 87, 317–325. https://doi.org/10.1139/Z09-015 (2009).
    Article  Google Scholar 

    46.
    Sharpe, F. & Rosell, F. Time budgets and sex differences in the Eurasian beaver. Anim. Behav. 66, 1059–1067. https://doi.org/10.1006/anbe.2003.2274 (2003).
    Article  Google Scholar 

    47.
    Graf, P. M., Mayer, M., Zedrosser, A., Hacklander, K. & Rosell, F. Territory size and age explain movement patterns in the Eurasian beaver. Mamm. Biol. 81, 587–594. https://doi.org/10.1016/j.mambio.2016.07.046 (2016).
    Article  Google Scholar 

    48.
    Gallant, D. et al. Linking time budgets to habitat quality suggests that beavers (Castor canadensis) are energy maximizers. Can. J. Zool. 94, 671–676. https://doi.org/10.1139/cjz-2016-0016 (2016).
    ADS  Article  Google Scholar 

    49.
    Graf, P. M., Hochreiter, J., Hacklander, K., Wilson, R. P. & Rosell, F. Short-term effects of tagging on activity and movement patterns of Eurasian beavers (Castor fiber). Eur. J. Wildl. Res. 62, 725–736. https://doi.org/10.1007/s10344-016-1051-8 (2016).
    Article  Google Scholar 

    50.
    Deguchi, T., Suryan, R. M. & Ozaki, K. Muscle damage and behavioral consequences from prolonged handling of albatross chicks for transmitter attachment. J. Wildl. Manag. 78, 1302–1309. https://doi.org/10.1002/jwmg.765 (2014).
    Article  Google Scholar 

    51.
    Grisham, B. A. et al. Evaluation of capture techniques on Lesser Prairie-Chicken trap injury and survival. J. Fish Wildl. Manag. 6, 318–326. https://doi.org/10.3996/032015-JFWM-022 (2015).
    Article  Google Scholar 

    52.
    Laurenson, M. K. & Caro, T. Monitoring the effects of non-trivial handling in free-living cheetahs. Anim. Behav. 47, 547–557. https://doi.org/10.1006/anbe.1994.1078 (1994).
    Article  Google Scholar 

    53.
    Jakob, E. M., Marshall, S. D. & Uetz, G. W. Estimating fitness: a comparison of body condition indices. Oikos 77, 61–67. https://doi.org/10.2307/3545585 (1996).
    Article  Google Scholar 

    54.
    Millar, J. S. & Hickling, G. J. Fasting endurance and the evolution of mammalian body size. Funct. Ecol. 4, 5–12. https://doi.org/10.2307/2389646 (1990).
    Article  Google Scholar 

    55.
    Guinet, C., Roux, J. P., Bonnet, M. & Mison, V. Effect of body size, body mass, and body condition on reproduction of female South African fur seals (Arctocephalus pusillus) in Namibia. Can. J. Zool. 76, 1418–1424. https://doi.org/10.1139/z98-082 (1998).
    Article  Google Scholar 

    56.
    Smith, D. W. & Jenkins, S. H. Seasonal change in body mass and size of tail of northern beavers. J. Mammal. 78, 869–876. https://doi.org/10.2307/1382945 (1997).
    Article  Google Scholar 

    57.
    Magurran, A. E. & Garcia, C. M. Sex differences in behaviour as an indirect consequence of mating system. J. Fish Biol. 57, 839–857. https://doi.org/10.1111/j.1095-8649.2000.tb02196.x (2000).
    Article  Google Scholar 

    58.
    Drickamer, L. C., Vandenbergh, J. G. & Colby, D. R. Predictors of dominance in the male golden hamster (Mesocricetus auratus). Anim. Behav. 21, 557–563. https://doi.org/10.1016/s0003-3472(73)80016-8 (1973).
    CAS  Article  PubMed  Google Scholar 

    59.
    Bernstein, I. S. Dominance: the baby and the bathwater. Behav. Brain Sci. 4, 419–429. https://doi.org/10.1017/S0140525X00009614 (1981).
    Article  Google Scholar 

    60.
    Taillon, J. & Côté, S. D. The role of previous social encounters and body mass in determining social rank: an experiment with white-tailed deer. Anim. Behav. 72, 1103–1110. https://doi.org/10.1016/j.anbehav.2006.03.016 (2006).
    Article  Google Scholar 

    61.
    Marolf, B., McElligott, A. G. & Müller, A. E. Female social dominance in two Eulemur species with different social organizations. Zoo. Biol. 26, 201–214. https://doi.org/10.1002/zoo.20135 (2007).
    Article  PubMed  Google Scholar 

    62.
    Huang, B., Wey, T. W. & Blumstein, D. T. Correlates and consequences of dominance in a social rodent. Ethology 117, 573–585 (2011).
    Article  Google Scholar 

    63.
    Righton, D., Miller, M. & Ormond, R. Correlates of territory size in the butterflyfish Chaetodon austriacus (Rüppell). J. Exp. Mar. Biol. Ecol. 226, 183–193. https://doi.org/10.1016/s0022-0981(97)00235-9 (1998).
    Article  Google Scholar 

    64.
    Bobek, B. Summer food as the factor limiting roe deer population size. Nature 268, 47. https://doi.org/10.1038/268047a0 (1977).
    ADS  Article  Google Scholar 

    65.
    Myers, J. P., Connors, P. G. & Pitelka, F. A. Territory size in wintering sanderlings: the effects of prey abundance and intruder density. Auk 96, 551–561. https://doi.org/10.1093/auk/96.3.551 (1979).
    Article  Google Scholar 

    66.
    Gass, C. L., Angehr, G. & Centa, J. Regulation of food supply by feeding territoriality in the rufous hummingbird. Can. J. Zool. 54, 2046–2054. https://doi.org/10.1139/z76-238 (1976).
    Article  Google Scholar 

    67.
    Adams, E. S. Approaches to the study of territory size and shape. Annu. Rev. Ecol. Syst. 32, 277–303. https://doi.org/10.1146/annurev.ecolsys.32.081501.114034 (2001).
    Article  Google Scholar 

    68.
    Kelly, K. G., Diamond, A. W., Holberton, R. L. & Bowser, A. K. Researcher handling of incubating Atlantic Puffins Fratercula arctica has no effect on reproductive success. Mar. Ornithol. 43, 77–82 (2015).
    Google Scholar 

    69.
    Ramsay, M. A. & Stirling, I. Long-term effects of drugging and handling free-ranging polar bears. J. Wildl. Manag. 1, 619–626. https://doi.org/10.2307/3800972 (1986).
    CAS  Article  Google Scholar 

    70.
    Serventy, D. L. & Curry, P. J. Observations on colony size, breeding success, recruitment and inter-colony dispersal in a Tasmanian colony of Short-tailed Shearwaters Puffinus tenuirostris over a 30-year peroid. EMU 84, 71–79. https://doi.org/10.1071/MU9840071 (1984).
    Article  Google Scholar 

    71.
    Schradin, C. & Hayes, L. D. A synopsis of long-term field studies of mammals: achievements, future directions, and some advice. J. Mammal. 98, 670–677. https://doi.org/10.1093/jmammal/gyx031 (2017).
    Article  Google Scholar 

    72.
    Blumstein, D. T. Habituation and sensitization: new thoughts about old ideas. Anim. Behav. 120, 255–262. https://doi.org/10.1016/j.anbehav.2016.05.012 (2016).
    Article  Google Scholar 

    73.
    Baudains, T. P. & Lloyd, P. Habituation and habitat changes can moderate the impacts of human disturbance on shorebird breeding performance. Anim. Conserv. 10, 400–407. https://doi.org/10.1111/j.1469-1795.2007.00126.x (2007).
    Article  Google Scholar 

    74.
    Vincze, E. et al. Habituation to human disturbance is faster in urban than rural house sparrows. Behav. Ecol. 27, 1304–1313. https://doi.org/10.1093/beheco/arw047 (2016).
    Article  Google Scholar 

    75.
    Van Oers, K. & Carere, C. Long-term effects of repeated handling and bleeding in wild caught great tits Parus major. J. Ornithol. 148, 185–190. https://doi.org/10.1007/s10336-007-0200-y (2007).
    Article  Google Scholar 

    76.
    Ordiz, A. et al. Habituation, sensitization, or consistent behavioral responses? Brown bear responses after repeated approaches by humans on foot. Biol. Conserv. 232, 228–237. https://doi.org/10.1016/j.biocon.2019.01.016 (2019).
    Article  Google Scholar 

    77.
    Seress, G. et al. Effects of capture and video-recording on the behavior and breeding success of Great Tits in urban and forest habitats. J. Field Ornithol. 88, 299–312. https://doi.org/10.1111/jofo.12205 (2017).
    Article  Google Scholar 

    78.
    Ellenberg, U., Mattern, T., Houston, D. M., Davis, L. S. & Seddon, P. J. Previous experiences with humans affect responses of Snares Penguins to experimental disturbance. J. Ornithol. 153, 621–631. https://doi.org/10.1007/s10336-011-0780-4 (2012).
    Article  Google Scholar 

    79.
    Ditmer, M. A. et al. Bears habituate to the repeated exposure of a novel stimulus, unmanned aircraft systems. Conserv. Physiol. 7, 67. https://doi.org/10.1093/conphys/coy067 (2019).
    Article  Google Scholar 

    80.
    Rabdeau, J., Badenhausser, I., Moreau, J., Bretagnolle, V. & Monceau, K. To change or not to change experimenters: caveats for repeated behavioural and physiological measures in Montagu’s harrier. J. Avian Biol. 50, 1. https://doi.org/10.1111/jav.02160 (2019).
    Article  Google Scholar 

    81.
    Rode, K. D. et al. Effects of capturing and collaring on polar bears: findings from long-term research on the southern Beaufort Sea population. Wildl. Res. 41, 311–322. https://doi.org/10.1071/WR13225 (2014).
    Article  Google Scholar 

    82.
    Larsen, K. W. & Boutin, S. Movements, survival, and settlement of red squirrel (Tamiasciurus hudsonicus) offspring. Ecology 75, 214–223. https://doi.org/10.2307/1939395 (1994).
    Article  Google Scholar 

    83.
    Mayer, M., Zedrosser, A. & Rosell, F. Couch potatoes do better: Delayed dispersal and territory size affect the duration of territory occupancy in a monogamous mammal. Ecol. Evol. 7, 4347–4356. https://doi.org/10.1002/ece3.2988 (2017).
    Article  PubMed  PubMed Central  Google Scholar 

    84.
    Mayer, M., Zedrosser, A. & Rosell, F. Extra-territorial movements differ between territory holders and subordinates in a large, monogamous rodent. Sci. Rep. 7, 15261. https://doi.org/10.1038/s41598-017-15540-0 (2017).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    85.
    Rosell, F., Johansen, G. & Parker, H. Eurasian beavers (Castor fiber) behavioral response to simulated territorial intruders. Can. J. Zool. 78, 931–935. https://doi.org/10.1139/cjz-78-6-931 (2000).
    Article  Google Scholar 

    86.
    Rosell, F. & Bjorkoyli, T. A test of the dear enemy phenomenon in the Eurasian beaver. Anim. Behav. 63, 1073–1078. https://doi.org/10.1006/anbe.2002.3010 (2002).
    Article  Google Scholar 

    87.
    Tinnesand, H. V., Jojola, S., Zedrosser, A. & Rosell, F. The smell of desperadoes? Beavers distinguish between dominant and subordinate intruders. Behav. Ecol. Sociobiol. 67, 895–904. https://doi.org/10.1007/s00265-013-1512-y (2013).
    Article  Google Scholar 

    88.
    Fretwell, S. D. Populations in a seasonal environment. (Princeton University Press, 1972).

    89.
    Rosell, F., Parker, H. & Steifetten, O. Use of dawn and dusk sight observations to determine colony size and family composition in Eurasian beaver Castor fiber. Acta Theriol. 51, 107–112. https://doi.org/10.1007/Bf03192662 (2006).
    Article  Google Scholar 

    90.
    Shier, D. M. & Swaisgood, R. R. Fitness costs of neighborhood disruption in translocations of a solitary mammal. Conserv. Biol. 26, 116–123. https://doi.org/10.1111/j.1523-1739.2011.01748.x (2012).
    Article  PubMed  Google Scholar 

    91.
    Shier, D. M. Effect of family support on the success of translocated black-tailed prairie dogs. Conserv. Biol. 20, 1780–1790. https://doi.org/10.1111/j.1523-1739.2006.00512.x (2006).
    CAS  Article  PubMed  Google Scholar 

    92.
    Gaillard, J. M., Allainé, D., Pontier, D., Yoccoz, N. G. & Promislow, D. E. L. Senescence in natural populations of mammals: a reanalysis. Evolution 48, 509–516. https://doi.org/10.1111/j.1558-5646.1994.tb01329.x (1994).
    Article  PubMed  Google Scholar 

    93.
    Lindenmayer, D. B. & Likens, G. E. Adaptive monitoring: a new paradigm for long-term research and monitoring. Trends Ecol. Evol. 24, 482–486. https://doi.org/10.1016/j.tree.2009.03.005 (2009).
    Article  PubMed  Google Scholar 

    94.
    Campbell, R. D., Rosell, F., Nolet, B. A. & Dijkstra, V. A. A. Territory and group sizes in Eurasian beavers (Castor fiber): echoes of settlement and reproduction?. Behav. Ecol. Sociobiol. 58, 597–607. https://doi.org/10.1007/s00265-005-0942-6 (2005).
    Article  Google Scholar 

    95.
    Sun, L., Müller-Schwarze, D. & Schulte, B. A. Dispersal pattern and effective population size of the beaver. Can. J. Zool. 78, 393–398. https://doi.org/10.1139/z99-226 (2000).
    Article  Google Scholar 

    96.
    Campbell, R. D., Nouvellet, P., Newman, C., Macdonald, D. W. & Rosell, F. The influence of mean climate trends and climate variance on beaver survival and recruitment dynamics. Global Change Biol. 18, 2730–2742. https://doi.org/10.1111/j.1365-2486.2012.02739.x (2012).
    ADS  Article  Google Scholar 

    97.
    Rosell, F. & Hovde, B. Methods of aquatic and terrestrial netting to capture Eurasian beavers. Wildl. Soc. Bull. 29, 269–274 (2001).
    Google Scholar 

    98.
    Rosell, F. & Sun, L. Use of anal gland secretion to distinguish the two beaver species Castor canadensis and C. fiber. Wildl. Biol. 5, 119–123. https://doi.org/10.2981/wlb.1999.015 (1999).
    Article  Google Scholar 

    99.
    Rosell, F., Zedrosser, A. & Parker, H. Correlates of body measurements and age in Eurasian beaver from Norway. Eur. J. Wildl. Res. 56, 43–48. https://doi.org/10.1007/s10344-009-0289-9 (2010).
    Article  Google Scholar 

    100.
    Mayer, M., Künzel, F., Zedrosser, A. & Rosell, F. The 7-year itch: non-adaptive mate change in the Eurasian beaver. Behav. Ecol. Sociobiol. 71, 1. https://doi.org/10.1007/s00265-016-2259-z (2017).
    Article  Google Scholar 

    101.
    Buchanan, K. et al. Guidelines for the treatment of animals in behavioural research and teaching. Anim. Behav. 83, 301–309. https://doi.org/10.1016/j.anbehav.2011.10.031 (2012).
    Article  Google Scholar 

    102.
    Aleksiuk, M. The function of the tail as a fat storage depot in the beaver (Castor canadensis). J. Mammal. 51, 145–148. https://doi.org/10.2307/1378541 (1970).
    CAS  Article  PubMed  Google Scholar 

    103.
    Parker, H., Rosell, F. & Mysterud, A. Harvesting of males delays female breeding in a socially monogamous mammal; the beaver. Biol. Lett. 3, 107–109. https://doi.org/10.1098/rsbl.2006.0563 (2007).
    Article  Google Scholar 

    104.
    Fouchet, D., Santin-Janin, H., Sauvage, F., Yoccoz, N. G. & Pontier, D. An R package for analysing survival using continuous-time open capture–recapture models. Methods Ecol. Evol. 7, 518–528. https://doi.org/10.1111/2041-210x.12497 (2016).
    Article  Google Scholar 

    105.
    Borchers, D., Distiller, G., Foster, R., Harmsen, B. & Milazzo, L. Continuous-time spatially explicit capture–recapture models, with an application to a jaguar camera-trap survey. Methods Ecol. Evol. 5, 656–665. https://doi.org/10.1111/2041-210X.12196 (2014).
    Article  Google Scholar 

    106.
    Lebreton, J.-D., Burnham, K. P., Clobert, J. & Anderson, D. R. Modeling survival and testing biological hypotheses using marked animals: a unified approach with case studies. Ecol. Monogr. 62, 67–118. https://doi.org/10.2307/2937171 (1992).
    Article  Google Scholar 

    107.
    Bonnet, X., Naulleau, G. & Shine, R. The dangers of leaving home: dispersal and mortality in snakes. Biol. Conserv. 89, 39–50. https://doi.org/10.1016/S0006-3207(98)00140-2 (1999).
    Article  Google Scholar 

    108.
    Lucas, J. R., Waser, P. M. & Creel, S. R. Death and disappearance: estimating mortality risks associated with philopatry and dispersal. Behav. Ecol. 5, 135–141. https://doi.org/10.1093/beheco/5.2.135 (1994).
    Article  Google Scholar 

    109.
    Zuur, A. F., Ieno, E. N., Walker, N. J., Saveliev, A. A. & Smith, G. M. Mixed effects models and extensions in ecology with R. (Springer, Berlin, 2009).

    110.
    Burnham, K. P. & Anderson, D. R. Model selection and multimodel inference: a practical information-theoretic approach. (Springer, Berlin, 2002).

    111.
    Magnusson, A. et al. Package ‘glmmTMB’. R Package (2017).

    112.
    Barton, K. R-package ‘MuMIn’ (2018).

    113.
    Arnold, T. W. Uninformative parameters and model selection using Akaike’s information criterion. J. Wildl. Manage 74, 1175–1178. https://doi.org/10.1111/j.1937-2817.2010.tb01236.x (2010).
    Article  Google Scholar 

    114.
    Hartig, F. DHARMa: residual diagnostics for hierarchical (multi-level/mixed) regression models. R package (2017).

    115.
    Team, R. C. R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Austria, 2015. (2018). More