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    Coupled abiotic-biotic cycling of nitrous oxide in tropical peatlands

    Thompson, R. L. et al. Acceleration of global N2O emissions seen from two decades of atmospheric inversion. Nat. Clim. Change 9, 993–998 (2019).CAS 
    Article 

    Google Scholar 
    Tian, H. et al. A comprehensive quantification of global nitrous oxide sources and sinks. Nature 586, 248–256 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhuang, Q., Lu, Y. & Chen, M. An inventory of global N2O emissions from the soils of natural terrestrial ecosystems. Atm. Environ. 47, 66–75 (2012).CAS 
    Article 

    Google Scholar 
    Huang, J. et al. Estimation of regional emissions of nitrous oxide from 1997 to 2005 using multinetwork measurements, a chemical transport model, and an inverse method. J. Geophys. Res. 113, D17313 (2008).Article 

    Google Scholar 
    D’Amelio, M. T. S., Gatti, L. V., Miller, J. B. & Tans, P. Regional N2O fluxes in Amazonia derived from aircraft vertical profiles. Atmos. Chem. Phys. 9, 8785–8797 (2009).Article 

    Google Scholar 
    Teh, Y. A., Murphy, W. A., Berrio, J.-C., Boom, A. & Page, S. E. Seasonal variability in methane and nitrous oxide fluxes from tropical peatlands in the western Amazon basin. Biogeosciences 14, 3669–3683 (2017).CAS 
    Article 

    Google Scholar 
    Finn, D. R. et al. Methanogens and methanotrophs show nutrient-dependent community assemblage patterns across tropical peatlands of the Pastaza-Marañón Basin, Peruvian Amazonia. Front. Microbiol. 11, 746 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Buessecker, S. et al. Effects of sterilization techniques on chemodenitrification and N2O production in tropical peat soil microcosms. Biogeosciences 16, 4601–4612 (2019).CAS 
    Article 

    Google Scholar 
    Heil, J., Liu, S., Vereecken, H. & Brüggemann, N. Abiotic nitrous oxide production from hydroxylamine in soils and their dependence on soil properties. Soil Biol. Biochem. 84, 107–115 (2015).CAS 
    Article 

    Google Scholar 
    Samarkin, V. A. et al. Abiotic nitrous oxide emission from the hypersaline Don Juan Pond in Antarctica. Nat. Geosci. 3, 341–344 (2010).CAS 
    Article 

    Google Scholar 
    Otte, J. M. et al. N2O formation by nitrite-induced (chemo)denitrification in coastal marine sediment. Sci. Rep. 9, 10691 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Jones, L. C., Peters, B., Pacheco, J. S. L., Casciotti, K. L. & Fendorf, S. Stable isotopes and iron oxide mineral products as markers of chemodenitrification. Environ. Sci. Technol. 49, 3444–3452 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Tolman, W. B. Binding and activation of N2O at transition-metal centers: recent mechanistic insights. Angew. Chem. Int. Ed. 49, 1018–1024 (2010).CAS 
    Article 

    Google Scholar 
    Holtan-Hartwig, L., Dörsch, P. & Bakken, L. R. Low temperature control of soil denitrifying communities: kinetics of N2O production and reduction. Soil Biol. Biochem. 34, 1797–1806 (2002).CAS 
    Article 

    Google Scholar 
    Gorelsky, S. I., Ghosh, S. & Solomon, E. I. Mechanism of N2O reduction by the μ4-S tetranuclear CuZ cluster of nitrous oxide reductase. J. Am. Chem. Soc. https://doi.org/10.1021/ja055856o (2005).Tsai, M.-L. et al. [Cu2O]2+ active site formation in Cu–ZSM-5: geometric and electronic structure requirements for N2O activation. J. Am. Chem. Soc. https://doi.org/10.1021/ja4113808 (2014).Sanford, R. A. et al. Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils. Proc. Natl Acad. Sci. USA 109, 19709–19714 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Jones, C. M. et al. Recently identified microbial guild mediates soil N2O sink capacity. Nat. Clim. Change 4, 801–805 (2014).CAS 
    Article 

    Google Scholar 
    Hallin, S., Philippot, L., Löffler, F. E., Sanford, R. A. & Jones, C. M. Genomics and ecology of novel N2O-reducing microorganisms. Trends Microbiol. 26, 43–55 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Lycus, P. et al. A bet-hedging strategy for denitrifying bacteria curtails their release of N2O. Proc. Natl Acad. Sci. USA 115, 11820–11825 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Burns, L. C., Stevens, R. J. & Laughlin, R. J. Determination of the simultaneous production and consumption of soil nitrite using 15N. Soil Biol. Biochem. 27, 839–844 (1995).CAS 
    Article 

    Google Scholar 
    Burns, L. C., Stevens, R. J. & Laughlin, R. J. Production of nitrite in soil by simultaneous nitrification and denitrification. Soil Biol. Biochem. 28, 609–616 (1996).CAS 
    Article 

    Google Scholar 
    Wullstein, L. H. & Gilmour, C. M. Non-enzymatic formation of nitrogen gas. Nature 210, 1150–1151 (1966).CAS 
    Article 

    Google Scholar 
    Liu, S., Schloter, M., Hu, R., Vereecken, H. & Brüggemann, N. Hydroxylamine contributes more to abiotic N2O production in soils than nitrite. Front. Environ. Sci. https://doi.org/10.3389/fenvs.2019.00047 (2019).Thorn, K. A. & Mikita, M. A. Nitrite fixation by humic substances: nitrogen-15 nuclear magnetic resonance evidence for potential intermediates in chemodenitrification. Soil Sci. Soc. Am. J. 64, 568–582 (2000).CAS 
    Article 

    Google Scholar 
    Thorn, K. A., Younger, S. J. & Cox, L. G. Order of functionality loss during photodegradation of aquatic humic substances. J. Environ. Qual. 39, 1416–1428 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    Klüpfel, L., Piepenbrock, A., Kappler, A. & Sander, M. Humic substances as fully regenerable electron acceptors in recurrently anoxic environments. Nat. Geosci. 7, 195–200 (2014).Article 

    Google Scholar 
    Lovley, D. R. & Blunt-Harris, E. L. Role of humic-bound iron as an electron transfer agent in dissimilatory Fe(III) reduction. Appl. Environ. Microbiol. 65, 4252–4254 (1999).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kappler, A., Benz, M., Schink, B. & Brune, A. Electron shuttling via humic acids in microbial iron(III) reduction in a freshwater sediment. FEMS Microbiol. Ecol. 47, 85–92 (2004).CAS 
    PubMed 
    Article 

    Google Scholar 
    Van Cleemput, O., Patrick, W. H. & McIlhenny, R. C. Nitrite decomposition in flooded soil under different pH and redox potential conditions. Soil Sci. Soc. Am. J. 40, 55–60 (1976).Article 

    Google Scholar 
    Van Cleemput, O. & Baert, L. Nitrite: a key compound in N loss processes under acid conditions? Plant Soil 76, 233–241 (1984).Article 

    Google Scholar 
    Porter, L. K. Gaseous products produced by anaerobic reaction of sodium nitrite with oxime compounds and oximes synthesized from organic matter. Soil Sci. Soc. Am. J. 33, 696–702 (1969).CAS 
    Article 

    Google Scholar 
    Liu, B., Mørkved, P. T., Frostegård, Å. & Bakken, L. R. Denitrification gene pools, transcription and kinetics of NO, N2O and N2 production as affected by soil pH. FEMS Microbiol. Ecol. 72, 407–417 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    Palmer, K., Biasi, C. & Horn, M. A. Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra. ISME J. 6, 1058–1077 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Domeignoz-Horta, L. et al. The diversity of the N2O reducers matters for the N2O:N2 denitrification end-product ratio across an annual and a perennial cropping system. Front. Microbiol. https://doi.org/10.3389/fmicb.2015.00971 (2015).Domeignoz-Horta, L. A. et al. Peaks of in situ N2O emissions are influenced by N2O-producing and reducing microbial communities across arable soils. Glob. Change Biol. 24, 360–370 (2018).Article 

    Google Scholar 
    Onley, J. R., Ahsan, S., Sanford, R. A. & Löffler, F. E. Denitrification by Anaeromyxobacter dehalogenans, a common soil bacterium lacking the nitrite reductase genes nirS and nirK. Appl. Environ. Microbiol. 84, 4 (2018).Article 

    Google Scholar 
    Sanford, R. A., Cole, J. R. & Tiedje, J. M. Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium. Appl. Environ. Microbiol. 68, 893–900 (2002).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Mohr, K. I., Zindler, T., Wink, J., Wilharm, E. & Stadler, M. Myxobacteria in high moor and fen: an astonishing diversity in a neglected extreme habitat. MicrobiologyOpen 6, e00464 (2017).PubMed Central 
    Article 

    Google Scholar 
    Hori, T., Müller, A., Igarashi, Y., Conrad, R. & Friedrich, M. W. Identification of iron-reducing microorganisms in anoxic rice paddy soil by ¹³C-acetate probing. ISME J. 4, 267–278 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    Kawaichi, S. et al. Ardenticatena maritima gen. nov., sp. nov., a ferric iron- and nitrate-reducing bacterium of the phylum ‘Chloroflexi’ isolated from an iron-rich coastal hydrothermal field, and description of Ardenticatenia classis nov. Int. J. Sys. Evol. Microbiol. 63, 2992–3002 (2013).CAS 
    Article 

    Google Scholar 
    Podosokorskaya, O. A. et al. Characterization of Melioribacter roseus gen. nov., sp. nov., a novel facultatively anaerobic thermophilic cellulolytic bacterium from the class Ignavibacteria, and a proposal of a novel bacterial phylum Ignavibacteriae. Environ. Microbiol. 15, 1759–1771 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    Yoon, S. et al. Nitrous oxide reduction kinetics distinguish bacteria harboring clade I nosz from those harboring clade II NosZ. Appl. Environ. Microbiol. 82, 3793–3800 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Maher, B. A. & Taylor, R. M. Formation of ultrafine-grained magnetite in soils. Nature 336, 368–370 (1988).CAS 
    Article 

    Google Scholar 
    Sanchez, P. A. Properties and Management of Soils in the Tropics (Wiley, 1976).White, A. F. et al. Chemical weathering in a tropical watershed, Luquillo Mountains, Puerto Rico: I. Long-term versus short-term weathering fluxes. Geochim. Cosmochim. Acta 62, 209–226 (1998).CAS 
    Article 

    Google Scholar 
    Hall, S. J., Liptzin, D., Buss, H. L., DeAngelis, K. & Silver, W. L. Drivers and patterns of iron redox cycling from surface to bedrock in a deep tropical forest soil: a new conceptual model. Biogeochemistry 130, 177–190 (2016).CAS 
    Article 

    Google Scholar 
    Buchwald, C., Grabb, K., Hansel, C. M. & Wankel, S. D. Constraining the role of iron in environmental nitrogen transformations: dual stable isotope systematics of abiotic NO2− reduction by Fe(II) and its production of N2O. Geochim. Cosmochim. Acta 186, 1–12 (2016).CAS 
    Article 

    Google Scholar 
    Grabb, K. C., Buchwald, C., Hansel, C. M. & Wankel, S. D. A dual nitrite isotopic investigation of chemodenitrification by mineral-associated Fe(II) and its production of nitrous oxide. Geochim. Cosmochim. Acta 196, 388–402 (2017).CAS 
    Article 

    Google Scholar 
    Drewer, J. et al. Linking nitrous oxide and nitric oxide fluxes to microbial communities in tropical forest soils and oil palm plantations in Malaysia in laboratory incubations. Front. For. Glob. Change 3, 4 (2020).Article 

    Google Scholar 
    Yvon-Durocher, G., Jones, J. I., Trimmer, M., Woodward, G. & Montoya, J. M. Warming alters the metabolic balance of ecosystems. Phil. Trans. R. Soc. B 365, 2117–2126 (2010).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Yvon-Durocher, G. et al. Reconciling the temperature dependence of respiration across timescales and ecosystem types. Nature 487, 472–476 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Jauhiainen, J., Kerojoki, O., Silvennoinen, H., Limin, S. & Vasander, H. Heterotrophic respiration in drained tropical peat is greatly affected by temperature – a passive ecosystem cooling experiment. Environ. Res. Lett. 9, 105013 (2014).Article 

    Google Scholar 
    Wang, S., Zhuang, Q., Lähteenoja, O., Draper, F. C. & Cadillo-Quiroz, H. Potential shift from a carbon sink to a source in Amazonian peatlands under a changing climate. Proc. Natl Acad. Sci. USA 115, 12407–12412 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Stumm, W. & Lee, G. F. Oxygenation of ferrous iron. Ind. Eng. Chem. 53, 143–146 (1961).CAS 
    Article 

    Google Scholar 
    Theis, T. L. & Singer, P. C. Complexation of iron(II) by organic matter and its effect on iron(II) oxygenation. Environ. Sci. Technol. 8, 569–573 (1974).CAS 
    Article 

    Google Scholar 
    Wan, X. et al. Complexation and reduction of iron by phenolic substances: implications for transport of dissolved Fe from peatlands to aquatic ecosystems and global iron cycling. Chem. Geol. 498, 128–138 (2018).CAS 
    Article 

    Google Scholar 
    Daugherty, E. E., Gilbert, B., Nico, P. S. & Borch, T. Complexation and redox buffering of iron(II) by dissolved organic matter. Environ. Sci. Technol. 51, 11096–11104 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Prananto, J. A., Minasny, B., Comeau, L.-P., Rudiyanto, R. & Grace, P. Drainage increases CO2 and N2O emissions from tropical peat soils. Glob. Change Biol. 26, 4583–4600 (2020).Article 

    Google Scholar 
    Stirling, E., Fitzpatrick, R. W. & Mosley, L. Drought effects on wet soils in inland wetlands and peatlands. Earth Sci. Rev. 210, 103387 (2020).CAS 
    Article 

    Google Scholar 
    Hodgkins, S. B. et al. Tropical peatland carbon storage linked to global latitudinal trends in peat recalcitrance. Nat. Commun. 9, 3640 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Gumbricht, T. et al. An expert system model for mapping tropical wetlands and peatlands reveals South America as the largest contributor. Glob. Change Biol. 23, 3581–3599 (2017).Article 

    Google Scholar 
    IPCC Climate Change 2021: The Physical Science Basis (eds Masson-Delmotte, V. et al.) (Cambridge Univ. Press, 2021).Babbin, A. R., Bianchi, D., Jayakumar, A. & Ward, B. B. Rapid nitrous oxide cycling in the suboxic ocean. Science 348, 1127–1129 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Hamilton, S. K. & Ostrom, N. E. Measurement of the stable isotope ratio of dissolved N2 in 15N tracer experiments. Limnol. Oceanogr. Methods 5, 233–240 (2007).CAS 
    Article 

    Google Scholar 
    Ostrom, N. E., Gandhi, H., Trubl, G. & Murray, A. E. Chemodenitrification in the cryoecosystem of Lake Vida, Victoria Valley, Antarctica. Geobiology 14, 575–587 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    Stumm, W. & Morgan, J. J. Aquatic Chemistry 3rd edn (John Wiley & Sons, 1996).Homyak, P. M., Kamiyama, M., Sickman, J. O. & Schimel, J. P. Acidity and organic matter promote abiotic nitric oxide production in drying soils. Glob. Change Biol. 23, 1735–1747 (2017).Article 

    Google Scholar 
    Henry, S., Bru, D., Stres, B., Hallet, S. & Philippot, L. Quantitative detection of the nosZ gene, encoding nitrous oxide reductase, and comparison of the abundances of 16S rRNA, narG, nirK, and nosZ genes in soils. Appl. Environ. Microbiol. 72, 5181–5189 (2006).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Jones, C. M., Graf, D. R., Bru, D., Philippot, L. & Hallin, S. The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink. ISME J. 7, 417–426 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhang, B. et al. A new primer set for clade I nosZ that recovers genes from a broader range of taxa. Biol. Fertil. Soils 57, 523–531 (2021).CAS 
    Article 

    Google Scholar 
    Herbold, C. W. et al. A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes. Front. Microbiol. 6, 8966 (2015).Article 

    Google Scholar 
    Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    Edgar, R. C. UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. Preprint at https://www.biorxiv.org/content/early/2016/10/15/081257 (2016).Wang, Q. et al. Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using Framebot, a new informatics tool. mBio 4, e00592-13 (2013).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Fish, J. A. et al. FunGene: the functional gene pipeline and repository. Front. Microbiol. 4, 291 (2013).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Huson, D. H. et al. MEGAN Community Edition – interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput. Biol. 12, e1004957 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Huson, D. H. et al. MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs. Biol. Direct 13, 6 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ondov, B. D., Bergman, N. H. & Phillippy, A. M. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12, 385 (2011).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar  More

  • in

    Ancient DNA provides insights into 4,000 years of resource economy across Greenland

    Raghavan, M. et al. The genetic prehistory of the New World Arctic. Science 345, 1255832 (2014).Meldgaard, M. Ancient Harp Seal Hunters of Disko Bay (Museum Tusculanum Press, 2004).Grønnow, B. & Jensen, J. F. The Northernmost Ruins of the Globe: Eigil Knuth’s Archaeological Investigations in Peary Land and Adjacent Areas of High Arctic Greenland (Museum Tusculanum Press, 2003).Jensen, J. F. in The Oxford Handbook of the Prehistoric Arctic (eds Friesen, T. M. & Mason, O.) 673–691 (Oxford Univ. Press, 2016). https://doi.org/10.1093/oxfordhb/9780199766956.013.56Buckland, P. C., Ski, A. M. A. Y. E. W., Mcgovern, T. H. & Ogilvie, A. E. J. Bioarchaeological and climatological evidence for the fate of Norse farmers in medieval Greenland. Antiquity 70, 88–96 (1996).Article 

    Google Scholar 
    Gulløv, H. C. Grønlands Forhistorie (Gyldendal, 2004).Friesen, T. M. & Arnold, C. D. The timing of the Thule migration: new dates from the Western Canadian. Soc. Am. Archaeol. 73, 527–538 (2008).
    Google Scholar 
    Moltke, I. et al. Uncovering the genetic history of the present-day Greenlandic population. Am. J. Hum. Genet. 96, 54–69 (2015).CAS 
    Article 

    Google Scholar 
    Gulløv, H. C. From Middle Ages to Colonial Times: Archaeological and Ethnohistorical Studies of the Thule Culture in South West Greenland 1300–1800 AD (Dansk Polar Center, 1997).Gulløv, H. C. et al. Danmark og Kolonierne: Grønland (Gads Forlag, 2017).Ameen, C. et al. Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic. Proc. R. Soc. B 286, 20191929 (2019).Grønnow, B. et al. At the edge: High Arctic Walrus hunters during the Little Ice Age. Antiquity 85, 960–977 (2011).Article 

    Google Scholar 
    Fitzhugh, B. in The Oxford Handbook of the Prehistoric Arctic (eds Friesen, M. & Mason, O.) 253–278 (Oxford Univ. Press, 2016).Lyman, R. L. Vertebrate Taphonomy (Cambridge Univ. Press, 1994).Seersholm, F. V. et al. DNA evidence of bowhead whale exploitation by Greenlandic Paleo-Inuit 4000 years ago. Nat. Commun. 7, 13389 (2016). https://doi.org/10.1038/ncomms13389Betts, M. in The Oxford Handbook of the Prehistoric Arctic (eds Friesen, M. & Mason, O.) 81–108 (Oxford Univ. Press, 2016). https://doi.org/10.1093/oxfordhb/9780199766956.013.8Szpak, P. Fish bone chemistry and ultrastructure: implications for taphonomy and stable isotope analysis. J. Archaeol. Sci. 38, 3358–3372 (2011).Article 

    Google Scholar 
    Murray, D. C. et al. Scrapheap challenge: a novel bulk-bone metabarcoding method to investigate ancient DNA in faunal assemblages. Sci. Rep. 3, 3371 (2013).Article 

    Google Scholar 
    Møhl, J. in From Middle Ages to Colonial Times (ed. Gulløv, H. C.) 495–501 (Kommissionen for videnskabelige undersøgelser i Grønland, 1980).Møhl, U. Animal Bones from Itivnera, West Greenland: A Reindeer Hunting Site of the Sarqaq Culture (C. A. Reitzels Forlag, 1972).Stat, M. et al. Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment. Sci. Rep. 7, 12240 (2017).Article 

    Google Scholar 
    Arneborg, J. et al. Norse Greenland Dietary Economy ca. AD 980–ca. AD 1450: introduction. J. North Atl. S3, 1–39 (2012).
    Google Scholar 
    Whitridge, P. Zen fish: a consideration of the discordance between artifactual and zooarchaeological indicators of Thule Inuit fish use. J. Anthropol. Archaeol. 20, 3–72 (2001).Article 

    Google Scholar 
    Seersholm, F. V. et al. Rapid range shifts and megafaunal extinctions associated with late Pleistocene climate change. Nat. Commun. 11, 2770 (2020).Seersholm, F. V. et al. Ancient DNA preserved in small bone fragments from the P.W. Lund collection. Ecol. Evol. 11, 2064–2071 (2021).Article 

    Google Scholar 
    Wheeler, A. & Jones, A. K. J. Fishes (Cambridge Manuals in Archaeology) (Cambridge Univ. Press, 1989).Gotfredsen, A. B. Former occurrences of geese (Genera Anser and Branta) in ancient West Greenland: morphological and biometric approaches. Acta Zool. 45, 179–204 (2002).
    Google Scholar 
    Gotfredsen, A. B. & Møbjerg, T. Nipisat—A Saqqaq Culture Site in Sissimut, Central West Greenland (Museum Tusculanum Press, 2004).Bockstoce, J. R. On the development of whaling in the western Thule culture. Folk 18, 41–45 (1976).
    Google Scholar 
    Ferguson, S. H., Higdon, J. W., Hall, P. A., Hansen, R. G. & Doniol-Valcroze, T. Developing a precautionary management approach for the eastern Canada–west Greenland population of bowhead whales (Balaena mysticetus). Front. Mar. Sci. 8, 709989 (2021).Eschricht, D. F. Undersögelser over Hvaldyrene (Bianco Lunos Bogtrykkeri, 1846).Mikkelsen, N. et al. European trading, whaling and climate history of west Greenland documented by historical records, drones and marine sediments. Geol. Surv. Den. Greenl. Bull. 41, 67–70 (2018).
    Google Scholar 
    Borge, T., Bachmann, L., Bjørnstad, G. & Wiig, Ø. Genetic variation in Holocene bowhead whales from Svalbard. Mol. Ecol. 16, 2223–2235 (2007).CAS 
    Article 

    Google Scholar 
    LeDuc, R. G. Mitochondrial genetic variation in bowhead whales in the western Arctic. J. Cetacean Res. Manag. 10, 93–97 (2008).
    Google Scholar 
    McLeod, B. A. Examination of ten thousand years of mitochondrial DNA diversity and population demographics in bowhead whales (Balaena mysticetus) of the Central Canadian Arctic. Mar. Mammal. Sci. 28, 426–443 (2012).Article 

    Google Scholar 
    Foote, A. D. et al. Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts. Nat. Commun. 4, 1677 (2013).Article 

    Google Scholar 
    Meldgaard, M. The Greenland Caribou—Zoogeography, Taxonomy, and Population Dynamics (Museum Tusculanum Press, 1986).Meldgaard, M. New perspectives on the zoogeography of the Greenlandic caribou (Rangifer tarandus). In Proc. 4th North American Caribou Workshop (eds Butler, C. & Mahoney, S. P.) 37–63 (Newfoundland and Labrador Wildlife Division, 1991).Solazzo, C., Fitzhugh, W., Kaplan, S., Potter, C. & Dyer, J. M. Molecular markers in keratins from Mysticeti whales for species identification of baleen in museum and archaeological collections. PLoS ONE 12, e0183053 (2017).Article 

    Google Scholar 
    Nowacek, D. P. et al. Buoyant balaenids: the ups and downs of buoyancy in right whales. Proc. R. Soc. B 268, 1811–1816 (2001).CAS 
    Article 

    Google Scholar 
    Hollesen, J. et al. Climate change and the deteriorating archaeological and environmental archives of the Arctic. Antiquity 92, 573–586 (2018).Article 

    Google Scholar 
    Hollesen, J. et al. Predicting the loss of organic archaeological deposits at a regional scale in Greenland. Sci. Rep. 9, 9097 (2019).Matthiesen, H., Høier Eriksen, A. M., Hollesen, J. & Collins, M. Bone degradation at five Arctic archaeological sites: quantifying the importance of burial environment and bone characteristics. J. Archaeol. Sci. 125, 105296 (2021).Seersholm, F. V. et al. Subsistence practices, past biodiversity, and anthropogenic impacts revealed by New Zealand-wide ancient DNA survey. Proc. Natl Acad. Sci. USA https://doi.org/10.1073/pnas.1803573115 (2018).Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–63 (2013).CAS 
    Article 

    Google Scholar 
    Boyer, F. et al. obitools: a unix-inspired software package for DNA metabarcoding. Mol. Ecol. Resour. 16, 176–182 (2016).CAS 
    Article 

    Google Scholar 
    Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).Article 

    Google Scholar 
    Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).CAS 
    Article 

    Google Scholar 
    Dyke, A., Moore, A. & Robertson, L. Deglaciation of North America (Geological Survey of Canada, 2003).Dyke, A. S. An outline of North American deglaciation with emphasis on central and northern Canada. Dev. Quat. Sci. 2, 373–424 (2004).
    Google Scholar 
    Gansauge, M. & Meyer, M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc. 8, 737–748 (2013).Grealy, A. et al. Eggshell palaeogenomics: palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell. Mol. Phylogenet. Evol. 109, 151–163 (2017).CAS 
    Article 

    Google Scholar 
    Lindgreen, S. AdapterRemoval: easy cleaning of next generation sequencing reads. BMC Res. Notes 5, 337 (2012).Article 

    Google Scholar 
    Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).CAS 
    Article 

    Google Scholar  More

  • in

    Genetic and particle modelling approaches to assessing population connectivity in a deep sea lobster

    Farmery, A. K., Hendrie, G. A., O’Kane, G., McManus, A. & Green, B. S. Sociodemographic variation in consumption patterns of sustainable and nutritious seafood in Australia. Front. Nutr. 5, 118. https://doi.org/10.3389/fnut.2018.00118 (2018).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Guillen, J. et al. Global seafood consumption footprint. Ambio 48, 111–122. https://doi.org/10.1007/s13280-018-1060-9 (2019).Article 
    PubMed 

    Google Scholar 
    Norse, E. A. et al. Sustainability of deep-sea fisheries. Mar. Policy 36, 307–320. https://doi.org/10.1016/j.marpol.2011.06.008 (2012).Article 

    Google Scholar 
    Baco, A. R. et al. A synthesis of genetic connectivity in deep-sea fauna and implications for marine reserve design. Mol. Ecol. 25, 3276–3298. https://doi.org/10.1111/mec.13689 (2016).Article 
    PubMed 

    Google Scholar 
    Victorero, L., Watling, L., Deng Palomares, M. L. & Nouvian, C. Out of sight, but within reach: A global history of bottom-trawled deep-sea fisheries from > 400 m depth. Front. Mar. Sci. 5, 98. https://doi.org/10.3389/fmars.2018.00098 (2018).Article 

    Google Scholar 
    Cowen, R. K. & Sponaugle, S. Larval dispersal and marine population connectivity. Ann. Rev. Mar. Sci. 1, 443–466. https://doi.org/10.1146/annurev.marine.010908.163757 (2009).Article 
    PubMed 

    Google Scholar 
    Taylor, M. L. & Roterman, C. N. Invertebrate population genetics across Earth’s largest habitat: The deep-sea floor. Mol. Ecol. 26, 4872–4896. https://doi.org/10.1111/mec.14237 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    Allendorf, F. W., England, P. R., Luikart, G., Ritchie, P. A. & Ryman, N. Genetic effects of harvest on wild animal populations. Trends Ecol. Evol. 23, 327–337. https://doi.org/10.1016/j.tree.2008.02.008 (2008).Article 
    PubMed 

    Google Scholar 
    Carreras, C. et al. Population genomics of an endemic Mediterranean fish: Differentiation by fine scale dispersal and adaptation. Sci. Rep. 7, 43417. https://doi.org/10.1038/srep43417 (2017).ADS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Coleman, F. C. & Williams, S. L. Overexploiting marine ecosystem engineers: Potential consequences for biodiversity. Trends Ecol. Evol. 17, 40–44. https://doi.org/10.1016/S0169-5347(01)02330-8 (2002).Article 

    Google Scholar 
    Neubauer, P., Jensen, O. P., Hutchings, J. A. & Baum, J. K. Resilience and recovery of overexploited marine populations. Science 340, 347–349. https://doi.org/10.1126/science.1230441 (2013).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Ovenden, J. R., Berry, O., Welch, D. J., Buckworth, R. C. & Dichmont, C. M. Ocean’s eleven: A critical evaluation of the role of population, evolutionary and molecular genetics in the management of wild fisheries. Fish Fish. 16, 125–159. https://doi.org/10.1111/faf.12052 (2015).Article 

    Google Scholar 
    Pinsky, M. L. & Palumbi, S. R. Meta-analysis reveals lower genetic diversity in overfished populations. Mol. Ecol. 23, 29–39. https://doi.org/10.1111/mec.12509 (2014).Article 
    PubMed 

    Google Scholar 
    Sundqvist, L., Keenan, K., Zackrisson, M., Prodöhl, P. & Kleinhans, D. Directional genetic differentiation and relative migration. Ecol. Evol. 6, 3461–3475. https://doi.org/10.1002/ece3.2096 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Waples, R. S. et al. Guidelines for genetic data analysis. J. Cetac. Res. Manag. 18, 33–80 (2018).ADS 

    Google Scholar 
    Hauser, L., Adcock, G. J., Smith, P. J., Bernal Ramírez, J. H. & Carvalho, G. R. Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). Proc. Natl. Acad. Sci. 99, 11742–11747. https://doi.org/10.1073/pnas.172242899 (2002).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Laikre, L., Palm, S. & Ryman, N. Genetic population structure of fishes: Implications for coastal zone management. AMBIO A J. Hum. Environ. 34, 111–119. https://doi.org/10.1579/0044-7447-34.2.111 (2005).Article 

    Google Scholar 
    Gaggiotti, O. E. Population genetic models of source–sink metapopulations. Theor. Popul. Biol. 50, 178–208. https://doi.org/10.1006/tpbi.1996.0028 (1996).CAS 
    Article 
    PubMed 
    MATH 

    Google Scholar 
    Hughes, A. R., Inouye, B. D., Johnson, M. T. J., Underwood, N. & Vellend, M. Ecological consequences of genetic diversity. Ecol. Lett. 11, 609–623. https://doi.org/10.1111/j.1461-0248.2008.01179.x (2008).Article 
    PubMed 

    Google Scholar 
    Bracco, A., Liu, G., Galaska, M. P., Quattrini, A. M. & Herrera, S. Integrating physical circulation models and genetic approaches to investigate population connectivity in deep-sea corals. J. Mar. Syst. 198, 103189. https://doi.org/10.1016/j.jmarsys.2019.103189 (2019).Article 

    Google Scholar 
    Liu, S.-Y.V., Hsin, Y.-C. & Cheng, Y.-R. Using particle tracking and genetic approaches to infer population connectivity in the deep-sea scleractinian coral Deltocyathus magnificus in the South China sea. Deep Sea Res. Part I 161, 103297. https://doi.org/10.1016/j.dsr.2020.103297 (2020).Article 

    Google Scholar 
    Dambach, J., Raupach, M. J., Leese, F., Schwarzer, J. & Engler, J. O. Ocean currents determine functional connectivity in an Antarctic deep-sea shrimp. Mar. Ecol. 37, 1336–1344. https://doi.org/10.1111/maec.12343 (2016).ADS 
    CAS 
    Article 

    Google Scholar 
    Selkoe, K. A., Henzler, C. M. & Gaines, S. D. Seascape genetics and the spatial ecology of marine populations. Fish Fish. 9, 363–377. https://doi.org/10.1111/j.1467-2979.2008.00300.x (2008).Article 

    Google Scholar 
    Yan, R.-J., Schnabel, K. E., Rowden, A. A., Guo, X.-Z. & Gardner, J. P. A. Population structure and genetic connectivity of squat lobsters (Munida Leach, 1820) associated with vulnerable marine ecosystems in the southwest Pacific Ocean. Front. Mar. Sci. https://doi.org/10.3389/fmars.2019.00791 (2020).Article 

    Google Scholar 
    Breusing, C. et al. Biophysical and population genetic models predict the presence of “phantom” stepping stones connecting Mid-Atlantic Ridge vent ecosystems. Curr. Biol. 26, 2257–2267. https://doi.org/10.1016/j.cub.2016.06.062 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    Fisheries New Zealand. Fisheries Assessment: Scampi (SCI). https://fs.fish.govt.nz/Page.aspx?pk=113&dk=24443 (2017).Botsford, L. W. et al. Connectivity, sustainability, and yield: Bridging the gap between conventional fisheries management and marine protected areas. Rev. Fish Biol. Fish. 19, 69–95. https://doi.org/10.1007/s11160-008-9092-z (2009).Article 

    Google Scholar 
    NIWA. Annual Distribution of Scampi. Ministry for Primary Industries, New Zealand. https://mpi.maps.arcgis.com/home/item.html?id=97da6c1a912b45a8855bf741211f5911 (2016).Heasman, K. G. & Jeffs, A. G. Fecundity and potential juvenile production for aquaculture of the New Zealand scampi, Metanephrops challengeri (Balss, 1914) (Decapoda: Nephropidae). Aquaculture 511, 634184. https://doi.org/10.1016/j.aquaculture.2019.05.069 (2019).Article 

    Google Scholar 
    Smith, P. J. Allozyme variation in scampi (Metanephrops challengeri) fisheries around New Zealand. NZ J. Mar. Freshw. Res. 33, 491–497. https://doi.org/10.1080/00288330.1999.9516894 (1999).Article 

    Google Scholar 
    Berry, P. The biology of Nephrops andamanicus Wood-Mason (Decapoda, Reptantia). Report No. 22, 1–55 (South African Association for Marine Biological Research, Oceanographic Research Institute, Durban, South Africa, 1969).Major, R. N. & Jeffs, A. G. Orientation and food search behaviour of a deep sea lobster in turbulent versus laminar odour plumes. Helgol. Mar. Res. 71, 9. https://doi.org/10.1186/s10152-017-0489-8 (2017).Article 

    Google Scholar 
    Tuck, I. D., Parsons, D. M., Hartill, B. W. & Chiswell, S. M. Scampi (Metanephrops challengeri) emergence patterns and catchability. ICES J. Mar. Sci. 72, i199–i210. https://doi.org/10.1093/icesjms/fsu244 (2015).Article 

    Google Scholar 
    Chiswell, S. M. & Booth, J. D. Sources and sinks of larval settlement in Jasus edwardsii around New Zealand: Where do larvae come from and where do they go?. Mar. Ecol. Prog. Ser. 354, 201–217. https://doi.org/10.3354/meps07217 (2008).ADS 
    Article 

    Google Scholar 
    Silva, C. N. S., Macdonald, H. S., Hadfield, M. G., Cryer, M. & Gardner, J. P. A. Ocean currents predict fine-scale genetic structure and source-sink dynamics in a marine invertebrate coastal fishery. ICES J. Mar. Sci. 76, 1007–1018. https://doi.org/10.1093/icesjms/fsy201 (2019).Article 

    Google Scholar 
    Singh, S. P., Groeneveld, J. C., Hart-Davis, M. G., Backeberg, B. C. & Willows-Munro, S. Seascape genetics of the spiny lobster Panulirus homarus in the Western Indian Ocean: Understanding how oceanographic features shape the genetic structure of species with high larval dispersal potential. Ecol. Evol. 8, 12221–12237. https://doi.org/10.1002/ece3.4684 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Singh, S. P., Groeneveld, J. C. & Willows-Munro, S. Between the current and the coast: Genetic connectivity in the spiny lobster Panulirus homarus rubellus, despite potential barriers to gene flow. Mar. Biol. 166, 36. https://doi.org/10.1007/s00227-019-3486-4 (2019).Article 

    Google Scholar 
    Thomas, L. & Bell, J. J. Testing the consistency of connectivity patterns for a widely dispersing marine species. Heredity 111, 345–354. https://doi.org/10.1038/hdy.2013.58 (2013).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Baeza, J. A., Holstein, D., Umaña-Castro, R. & Mejía-Ortíz, L. M. Population genetics and biophysical modeling inform metapopulation connectivity of the Caribbean king crab Maguimithrax spinosissimus. Mar. Ecol. Prog. Ser. 610, 83–97 (2019).ADS 
    CAS 
    Article 

    Google Scholar 
    Hedgecock, D., Barber, P. H. & Edmands, S. Genetic approaches to measuring connectivity. Oceanography 20, 70–79 (2007).Article 

    Google Scholar 
    Jahnke, M. & Jonsson, P. R. Biophysical models of dispersal contribute to seascape genetic analyses. Philos. Trans. R. Soc. B Biol. Sci. 377, 20210024. https://doi.org/10.1098/rstb.2021.0024 (2022).Article 

    Google Scholar 
    Sebastian, W. et al. Genomic investigations provide insights into the mechanisms of resilience to heterogeneous habitats of the Indian Ocean in a pelagic fish. Sci. Rep. 11, 20690. https://doi.org/10.1038/s41598-021-00129-5 (2021).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lal, M. M., Southgate, P. C., Jerry, D. R., Bosserelle, C. & Zenger, K. R. A parallel population genomic and hydrodynamic approach to fishery management of highly-dispersive marine invertebrates: The case of the Fijian black-lip pearl oyster Pinctada margaritifera. PLoS ONE 11, e0161390. https://doi.org/10.1371/journal.pone.0161390 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Xu, T. et al. Hidden historical habitat-linked population divergence and contemporary gene flow of a deep-sea patellogastropod limpet. Mol. Biol. Evol. 38, 5640–5654. https://doi.org/10.1093/molbev/msab278 (2021).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    de Souza, J. M. A. C. et al. Moana Ocean Hindcast—A 25+ years simulation for New Zealand Waters using the ROMS v3.9 model. EGUsphere https://doi.org/10.5194/egusphere-2022-41 (2022).Norrie, C., Dunphy, B., Roughan, M., Weppe, S. & Lundquist, C. Spill-over from aquaculture may provide a larval subsidy for the restoration of mussel reefs. Aquac. Environ. Interact. 12, 231–249 (2020).Article 

    Google Scholar 
    Larsson, J. et al. Regional genetic differentiation in the blue mussel from the Baltic Sea area. Estuar. Coast. Shelf Sci. 195, 98–109. https://doi.org/10.1016/j.ecss.2016.06.016 (2017).ADS 
    Article 

    Google Scholar 
    Nicolle, A. et al. Modelling larval dispersal of Pecten maximus in the English Channel: A tool for the spatial management of the stocks. ICES J. Mar. Sci. 74, 1812–1825. https://doi.org/10.1093/icesjms/fsw207 (2017).Article 

    Google Scholar 
    Hold, N. et al. Using biophysical modelling and population genetics for conservation and management of an exploited species, Pecten maximus L. Fish. Oceanogr. 30, 740–756. https://doi.org/10.1111/fog.12556 (2021).Article 

    Google Scholar 
    Truelove, N. K. et al. Biophysical connectivity explains population genetic structure in a highly dispersive marine species. Coral Reefs 36, 233–244. https://doi.org/10.1007/s00338-016-1516-y (2017).ADS 
    Article 

    Google Scholar 
    Busch, K. et al. Population connectivity of fan-shaped sponge holobionts in the deep Cantabrian Sea. Deep Sea Res. Part I 167, 103427. https://doi.org/10.1016/j.dsr.2020.103427 (2021).Article 

    Google Scholar 
    Ross, P. M., Hogg, I. D., Pilditch, C. A. & Lundquist, C. J. Phylogeography of New Zealand’s coastal benthos. NZ J. Mar. Freshw. Res. 43, 1009–1027. https://doi.org/10.1080/00288330.2009.9626525 (2009).Article 

    Google Scholar 
    Tuck, I. D. Characterisation and a length-based assessment model for scampi (Metanephrops challengeri) at the Auckland Islands (SCI 6A). Report No. 2015/21, 160 (Ministry for Primary Industries, Wellington, 2015).Verry, A. J. F., Walton, K., Tuck, I. D. & Ritchie, P. A. Genetic structure and recent population expansion in the commercially harvested deepsea decapod, Metanephrops challengeri (Crustacea: Decapoda). NZ J. Mar. Freshw. Res. 54, 251–270. https://doi.org/10.1080/00288330.2019.1707696 (2020).CAS 
    Article 

    Google Scholar 
    Selkoe, K. A. et al. A decade of seascape genetics: Contributions to basic and applied marine connectivity. Mar. Ecol. Prog. Ser. 554, 1–19. https://doi.org/10.3354/meps11792 (2016).ADS 
    Article 

    Google Scholar 
    Hare, M. P. et al. Understanding and estimating effective population size for practical application in marine species management. Conserv. Biol. 25, 438–449. https://doi.org/10.1111/j.1523-1739.2010.01637.x (2011).Article 
    PubMed 

    Google Scholar 
    Ashry, N. A. Plant biodiversity and biotechnology. In From Plant Genomics to Plant Biotechnology (eds Poltronieri, P. et al.) 205–222 (Woodhead Publishing, 2013).Chapter 

    Google Scholar 
    Sgrò, C. M., Lowe, A. J. & Hoffmann, A. A. Building evolutionary resilience for conserving biodiversity under climate change. Evol. Appl. 4, 326–337. https://doi.org/10.1111/j.1752-4571.2010.00157.x (2011).Article 
    PubMed 

    Google Scholar 
    Kerr, L. A., Cadrin, S. X. & Secor, D. H. Simulation modelling as a tool for examining the consequences of spatial structure and connectivity on local and regional population dynamics. ICES J. Mar. Sci. 67, 1631–1639. https://doi.org/10.1093/icesjms/fsq053 (2010).Article 

    Google Scholar 
    Carroll, E. L. et al. Perturbation drives changing metapopulation dynamics in a top marine predator. Proc. R. Soc. B Biol. Sci. 287, 20200318. https://doi.org/10.1098/rspb.2020.0318 (2020).Article 

    Google Scholar 
    Chiswell, S. M., Bostock, H. C., Sutton, P. J. H. & Williams, M. J. M. Physical oceanography of the deep seas around New Zealand: A review. NZ J. Mar. Freshw. Res. 49, 286–317. https://doi.org/10.1080/00288330.2014.992918 (2015).Article 

    Google Scholar 
    Chiswell, S. M. & Roemmich, D. The East Cape Current and two eddies: A mechanism for larval retention?. NZ J. Mar. Freshw. Res. 32, 385–397. https://doi.org/10.1080/00288330.1998.9516833 (1998).Article 

    Google Scholar 
    Condie, S. & Condie, R. Retention of plankton within ocean eddies. Glob. Ecol. Biogeogr. 25, 1264–1277. https://doi.org/10.1111/geb.12485 (2016).Article 

    Google Scholar 
    Lesser, J. H. R. Phyllosoma larvae of Jasus edwardsii (Hutton) (Crustacea: Decapoda: Palinuridae) and their distribution off the east coast of the North Island, New Zealand. NZ J. Mar. Freshw. Res. 12, 357–370. https://doi.org/10.1080/00288330.1978.9515763 (1978).Article 

    Google Scholar 
    Kawecki, T. J. Ecological and evolutionary consequences of source-sink population dynamics. In Ecology, Genetics and Evolution of Metapopulations (eds Hanski, I. & Gaggiotti, O. E.) 387–414 (Academic Press, 2004).Chapter 

    Google Scholar 
    Figueira, W. F. & Crowder, L. B. Defining patch contribution in source-sink metapopulations: the importance of including dispersal and its relevance to marine systems. Popul. Ecol. 48, 215–224. https://doi.org/10.1007/s10144-006-0265-0 (2006).Article 

    Google Scholar 
    Heinrichs, J. A. et al. Recent advances and current challenges in applying source-sink theory to species conservation. Curr. Landsc. Ecol. Rep. 4, 51–60. https://doi.org/10.1007/s40823-019-00039-3 (2019).Article 

    Google Scholar 
    Hastings, A. & Botsford, L. W. Persistence of spatial populations depends on returning home. Proc. Natl. Acad. Sci. 103, 6067–6072. https://doi.org/10.1073/pnas.0506651103 (2006).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Heinrichs, J. A., Lawler, J. J. & Schumaker, N. H. Intrinsic and extrinsic drivers of source-sink dynamics. Ecol. Evol. 6, 892–904. https://doi.org/10.1002/ece3.2029 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gilroy, J. J. & Edwards, D. P. Source-sink dynamics: A neglected problem for landscape-scale biodiversity conservation in the Tropics. Curr. Landsc. Ecol. Rep. 2, 51–60. https://doi.org/10.1007/s40823-017-0023-3 (2017).Article 

    Google Scholar 
    Lal, M. M., Bosserelle, C., Kishore, P. & Southgate, P. C. Understanding marine larval dispersal in a broadcast-spawning invertebrate: A dispersal modelling approach for optimising spat collection of the Fijian black-lip pearl oyster Pinctada margaritifera. PLoS ONE 15, e0234605. https://doi.org/10.1371/journal.pone.0234605 (2020).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chassé, J. & Miller, R. J. Lobster larval transport in the southern Gulf of St. Lawrence. Fish. Oceanogr. 19, 319–338. https://doi.org/10.1111/j.1365-2419.2010.00548.x (2010).Article 

    Google Scholar 
    Lindegren, M., Andersen, K. H., Casini, M. & Neuenfeldt, S. A metacommunity perspective on source–sink dynamics and management: the Baltic Sea as a case study. Ecol. Appl. 24, 1820–1832. https://doi.org/10.1890/13-0566.1 (2014).Article 
    PubMed 

    Google Scholar 
    Tuck, I. D. et al. Estimating the abundance of scampi in SCI 6A (Auckland Islands) in 2013. Report No. 2015/10, 48 (Ministry for Primary Industries, 2015).Brierley, A. S. & Kingsford, M. J. Impacts of climate change on marine organisms and ecosystems. Curr. Biol. 19, R602–R614. https://doi.org/10.1016/j.cub.2009.05.046 (2009).CAS 
    Article 
    PubMed 

    Google Scholar 
    Caesar, L., Rahmstorf, S., Robinson, A., Feulner, G. & Saba, V. Observed fingerprint of a weakening Atlantic Ocean overturning circulation. Nature 556, 191–196. https://doi.org/10.1038/s41586-018-0006-5 (2018).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Thornalley, D. J. R. et al. Anomalously weak Labrador Sea convection and Atlantic overturning during the past 150 years. Nature 556, 227–230. https://doi.org/10.1038/s41586-018-0007-4 (2018).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    van Gennip, S. J. et al. Going with the flow: The role of ocean circulation in global marine ecosystems under a changing climate. Glob. Change Biol. 23, 2602–2617. https://doi.org/10.1111/gcb.13586 (2017).ADS 
    Article 

    Google Scholar 
    Bashevkin, S. M. et al. Larval dispersal in a changing ocean with an emphasis on upwelling regions. Ecosphere 11, e03015. https://doi.org/10.1002/ecs2.3015 (2020).Article 

    Google Scholar 
    Gerber, L. R., Mancha-Cisneros, M. D. M., O’Connor, M. I. & Selig, E. R. Climate change impacts on connectivity in the ocean: Implications for conservation. Ecosphere 5, 1–18. https://doi.org/10.1890/es13-00336.1 (2014).Article 

    Google Scholar 
    Hoegh-Gulderg, O. & Pearse, J. Temperature, food availability, and the development of marine invertebrate larvae. Am. Zool. 35, 415–425. https://doi.org/10.1093/icb/35.4.415 (1995).Article 

    Google Scholar 
    O’Connor, M. I. et al. Temperature control of larval dispersal and the implications for marine ecology, evolution, and conservation. Proc. Natl. Acad. Sci. USA 104, 1266–1271. https://doi.org/10.1073/pnas.0603422104 (2007).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Cetina-Heredia, P., Roughan, M., van Sebille, E., Feng, M. & Coleman, M. A. Strengthened currents override the effect of warming on lobster larval dispersal and survival. Glob. Change Biol. 21, 4377–4386. https://doi.org/10.1111/gcb.13063 (2015).ADS 
    Article 

    Google Scholar 
    Borja, A. et al. Past and future grand challenges in marine ecosystem ecology. Front. Mar. Sci. https://doi.org/10.3389/fmars.2020.00362 (2020).Article 

    Google Scholar 
    Ogilvie, S. et al. Mātauranga Māori driving innovation in the New Zealand scampi fishery. NZ J. Mar. Freshw. Res. 52, 590–602. https://doi.org/10.1080/00288330.2018.1532441 (2018).Article 

    Google Scholar 
    Andrews, S. FastQC: A quality control tool for high throughput sequence data v. 0.11.7 (Babraham Bioinformatics, 2010). http://www.bioinformatics.babraham.ac.uk/projects/fastqc.Rochette, N. C., Rivera-Colón, A. G. & Catchen, J. M. Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Mol. Ecol. 28, 4737–4754. https://doi.org/10.1111/mec.15253 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158. https://doi.org/10.1093/bioinformatics/btr330 (2011).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing v. 4.1.0 (R Studio v1.4.1106) (R Foundation for Statistical Computing, Vienna, Austria, 2021). https://www.R-project.org/.Díaz-Arce, N. & Rodríguez-Ezpeleta, N. Selecting RAD-seq data analysis parameters for population genetics: The more the better?. Front. Genet. 10, 533. https://doi.org/10.3389/fgene.2019.00533 (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Potapov, V. & Ong, J. L. Examining sources of error in PCR by single-molecule sequencing. PLoS ONE 12, e0169774. https://doi.org/10.1371/journal.pone.0169774 (2017).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Goudet, J. & Jombart, T. hierfstat: Estimation and Tests of Hierarchical F-Statistics v. 0.04-22 (Comprehensive R Archive Network (CRAN), 2015). https://CRAN.R-project.org/package=hierfstat.Nei, M. Molecular Evolutionary Genetics (Columbia University Press, 1987).Book 

    Google Scholar 
    Nei, M. & Chesser, R. K. Estimation of fixation indices and gene diversities. Ann. Hum. Genet. 47, 253–259. https://doi.org/10.1111/j.1469-1809.1983.tb00993.x (1983).CAS 
    Article 
    PubMed 
    MATH 

    Google Scholar 
    Archer, F. I., Adams, P. E. & Schneiders, B. B. stratag: An R package for manipulating, summarizing and analysing population genetic data. Mol. Ecol. Resour. 17, 5–11. https://doi.org/10.1111/1755-0998.12559 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    Kamvar, Z. N., Tabima, J. F. & Grünwald, N. J. Poppr: An R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2, e281. https://doi.org/10.7717/peerj.281 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kamvar, Z. N., Brooks, J. C. & Grünwald, N. J. Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Front. Genet. 6, 208. https://doi.org/10.3389/fgene.2015.00208 (2015).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Jombart, T. adegenet: A R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405. https://doi.org/10.1093/bioinformatics/btn129 (2008).CAS 
    Article 
    PubMed 

    Google Scholar 
    Jombart, T. & Ahmed, I. adegenet 1.3–1: New tools for the analysis of genome-wide SNP data. Bioinformatics 27, 3070–3071. https://doi.org/10.1093/bioinformatics/btr521 (2011).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Miller, J. M., Cullingham, C. I. & Peery, R. M. The influence of a priori grouping on inference of genetic clusters: Simulation study and literature review of the DAPC method. Heredity 125, 269–280. https://doi.org/10.1038/s41437-020-0348-2 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Keenan, K., McGinnity, P., Cross, T. F., Crozier, W. W. & Prodöhl, P. A. diveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors. Methods Ecol. Evol. 4, 782–788. https://doi.org/10.1111/2041-210x.12067 (2013).Article 

    Google Scholar 
    Nei, M. Analysis of gene diversity in subdivided populations. Proc. Natl. Acad. Sci. 70, 3321–3323. https://doi.org/10.1073/pnas.70.12.3321 (1973).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 
    MATH 

    Google Scholar 
    Dagestad, K. F., Röhrs, J., Breivik, Ø. & Ådlandsvik, B. OpenDrift v1.0: A generic framework for trajectory modelling. Geosci. Model Dev. 11, 1405–1420. https://doi.org/10.5194/gmd-11-1405-2018 (2018).ADS 
    Article 

    Google Scholar 
    Jeffs, A., Daniels, C. & Heasman, K. In Fisheries and Aquaculture: Natural History of Crustacea, Vol. 9 (eds Lovrich, G. & Thiel, M.) 285–311 (Oxford University Press, 2020).Lundquist, C. J., Oldman, J. W. & Lewis, M. J. Predicting suitability of cockle Austrovenus stutchburyi restoration sites using hydrodynamic models of larval dispersal. NZ J. Mar. Freshw. Res. 43, 735–748. https://doi.org/10.1080/00288330909510038 (2009).Article 

    Google Scholar 
    Lundquist, C. J., Thrush, S. F., Oldman, J. W. & Senior, A. K. Limited transport and recolonization potential in shallow tidal estuaries. Limnol. Oceanogr. 49, 386–395. https://doi.org/10.4319/lo.2004.49.2.0386 (2004).ADS 
    Article 

    Google Scholar 
    Okubo, A. & Ebbesmeyer, C. C. Determination of vorticity, divergence, and deformation rates from analysis of drogue observations. Deep-Sea Res. Oceanogr. Abstr. 23, 349–352. https://doi.org/10.1016/0011-7471(76)90875-5 (1976).ADS 
    Article 

    Google Scholar 
    Pierce, D. ncdf4: Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files v. 1.17 (Comprehensive R Archive Network (CRAN), 2019). https://CRAN.R-project.org/package=ncdf4.Coelho, S. C. C., Gherardi, D. F. M., Gouveia, M. B. & Kitahara, M. V. Western boundary currents drive sun-coral (Tubastraea spp.) coastal invasion from oil platforms. Sci. Rep. 12, 5286. https://doi.org/10.1038/s41598-022-09269-8 (2022).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Demmer, J. et al. The role of wind in controlling the connectivity of blue mussels (Mytilus edulis L.) populations. Mov. Ecol. 10, 3. https://doi.org/10.1186/s40462-022-00301-0 (2022).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Atalah, J., South, P. M., Briscoe, D. K. & Vennell, R. Inferring parental areas of juvenile mussels using hydrodynamic modelling. Aquaculture 555, 738227. https://doi.org/10.1016/j.aquaculture.2022.738227 (2022).Article 

    Google Scholar 
    McGeady, R., Lordan, C. & Power, A. M. Long-term interannual variability in larval dispersal and connectivity of the Norway lobster (Nephrops norvegicus) around Ireland: When supply-side matters. Fish. Oceanogr. 31, 255–270. https://doi.org/10.1111/fog.12576 (2022).Article 

    Google Scholar 
    Pante, E. & Simon-Bouhet, B. marmap: A package for importing, plotting and analyzing bathymetric and topographic data in R. PLoS ONE 8, e73051. https://doi.org/10.1371/journal.pone.0073051 (2013).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).MATH 

    Google Scholar 
    Becker, R. A., Wilks, A. R. & Brownrigg, R. mapdata: Extra Map Databases v. 2.3.0 (Comprehensive R Archive Network (CRAN), 2018). https://CRAN.R-project.org/package=mapdata.McIlroy, D., Brownrigg, R., Minka, T. P. & Bivan, R. mapproj: Map Projections v. 1.2.7 (Comprehensive R Archive Network (CRAN), 2020). https://CRAN.R-project.org/package=mapproj.South, A. rnaturalearth: World Map Data from Natural Earth v. 0.1.0 (Comprehensive R Archive Network (CRAN), 2017). https://CRAN.R-project.org/package=rnaturalearth. More

  • in

    A pachyderm perfume: odour encodes identity and group membership in African elephants

    Wyatt, T. Pheromones and Animal Behavior: Communication by Smell and Taste (Cambridge University Press, 2003).Book 

    Google Scholar 
    Wyatt, T. D. Fifty years of pheromones. Nature 457, 262–263 (2009).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Burgener, N., Dehnhard, M., Hofer, H. & East, M. Does anal gland scent signal identity in the spotted hyena?. Anim. Behav. 77, 707–715 (2009).Article 

    Google Scholar 
    Kent, L. & Tang-Martínez, Z. Evidence of individual odors and individual discrimination in the raccoon, Procyon lotor. J. Mamm. 95, 1254–1262 (2014).Article 

    Google Scholar 
    Klücklich, M., Weiß, B. M., Birkemere, C., Einspanier, A. & Widdig, A. Chemical cues of female fertility states in a non-human primate. Sci. Rep. 9, 9–12 (2019).
    Google Scholar 
    Setchell, J. M. et al. Chemical composition of scent-gland secretions in an Old World monkey (Mandrillus sphinx): Influence of sex, male status, and individual identity. Chem. Sens. 35, 205–220 (2010).CAS 
    Article 

    Google Scholar 
    Marneweck, C., Jurgens, A. & Shrader, A. M. Dung odours signal sex, age, territorial and oestrous state in white rhinos. Proc. R. Soc. B 284, 20162376 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Heth, G., Todrank, J., Busquet, N. & Baudoin, C. Genetic relatedness assessment through individual odour similarities (G-ratios) in mice. Biol. J. Lin. Soc. 78, 595–603 (2003).Article 

    Google Scholar 
    Heth, G., Todrank, J., Begall, S., Wegner, R. & Burda, H. Genetic relatedness discrimination in eusocial Cryptomys anselli mole-rats, Bathyergidae, Rodentia. Folia Zool. 53, 269–278 (2004).
    Google Scholar 
    Busquet, N. & Baudoin, C. Odour similarities as a basis for discriminating degrees of kinship in rodents: Evidence from Mus spicilegus. Anim. Behav. 70, 997–1002 (2005).Article 

    Google Scholar 
    Stoffel, M. A. et al. Chemical fingerprints encode mother–offspring similarity, colony membership, relatedness, and genetic quality in fur seals. PNAS 112(36), E5005–E5012 (2015).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Charpentier, M., Boulet, M. & Drea, C. Smelling right: The scent of male lemurs advertises genetic quality and relatedness. Mol. Ecol. 17, 3225–3233 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Boulet, M., Charpentier, M. J. E. & Drea, C. M. Decoding an olfactory mechanism of kin recognition and inbreeding avoidance in primates. BMC Evol. Biol. 9, 281 (2009).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kean, E. F., Bruford, M., Russo, I. R., Müller, C. & Chadwick, E. Odour dialects among wild mammals. Sci. Rep. 7, 13593 (2017).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wedekind, C., Seebeck, T., Bettens, F. & Paepke, A. J. MHC-dependent mate preferences in humans. Proc. Biol. Sci. 260, 245–249 (1995).CAS 
    PubMed 
    Article 

    Google Scholar 
    Penn, D. & Potts, W. K. Untrained mice discriminate MHC-determined odors. Phys. Behav. 64(3), 235–243 (1998).CAS 
    Article 

    Google Scholar 
    Sun, L. & Müller-Schwarze, D. Anal gland secretion codes for family membership in beaver. Behav. Ecol. Sociobiol. 44(3), 199–208 (1998).Article 

    Google Scholar 
    Bloss, J., Acree, T. E., Bloss, J. M., Hood, W. R. & Kunz, T. H. Potential use of chemical cues for colony-mate recognition in the big brown bat, Eptesicus fuscus. J. Chem. Ecol. 28(4), 819–834 (2002).CAS 
    PubMed 
    Article 

    Google Scholar 
    Weiß, B. M. et al. A non-invasive method for sampling the body odour of mammals. Methods Ecol. Evol. 9, 420–429 (2018).Article 

    Google Scholar 
    O’Riain, M. J. & Jarvis, J. U. M. Colony member recognition and xenophobia in the naked mole-rat. Anim. Behav. 53, 487–498 (1997).Article 

    Google Scholar 
    Henkel, S. & Setchell, J. Group and kin recognition via olfactory cues in chimpanzees (Pan troglodytes). Proc. R. Soc. B. 285, 20181527 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Henkel, S., Lambides, A. R., Berger, A., Thomsen, R. & Widdig, A. Rhesus macaques (Macaca mulatta) recognize group membership via olfactory cues alone. Behav. Ecol. Sociobiol. 69, 2019–2034 (2015).Article 

    Google Scholar 
    Tzur, S., Todrank, J., Jürgens, A., Nevo, E. & Heth, G. Odour–genes covariance within a natural population of subterranean Spalax galili blind mole rats. Biol. J. Lin. Soc. 96, 483–490 (2009).Article 

    Google Scholar 
    Leclaire, S., Jacob, S., Greene, L. K., Dubay, G. R. & Drea, C. M. Social odours covary with bacterial community in the anal secretions of wild meerkats. Sci. Rep. 7, 1–13 (2017).CAS 
    Article 

    Google Scholar 
    Archie, E. & Theis, K. Animal behavior meets microbial ecology. Anim. Behav. 82, 425–436 (2011).Article 

    Google Scholar 
    Sukumar, R. The Living Elephants: Evolutionary Ecology, Behavior and Conservation (Oxford University Press, 2003).
    Google Scholar 
    Jachowski, D. The Amboseli Elephants: A long-term perspective on a long-lived mammal by C. J. Moss; H. Croze; P. C. Lee. J. Mammal. 93, 294–295 (2012).Article 

    Google Scholar 
    Slotow, R., van Dyk, G., Poole, J., Page, B. & Klocke, A. Older bull elephants control young males. Nature 408, 425–426 (2000).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Niimura, Y., Matsui, A. & Touhara, K. Extreme expansion of the olfactory receptor gene repertoire in African elephants and evolutionary dynamics of orthologous gene groups in 13 placental mammals. Genome Res. 24, 1485–1496 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Goodwin, T. E., Broederdorf, L. J. & Burkert, B. A. Chemical signals of elephant musth: Temporal aspects of microbially-mediated modifications. J. Chem. Ecol. 38, 81–87 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Schulte, B. A. & Rasmussen, L. E. L. Musth, sexual selection, testosterone and metabolites. In Advances in Chemical Communication in Vertebrates (eds Johnston, R. E. et al.) 383–397 (Plenum Press, New York, 1999).
    Google Scholar 
    Rasmussen, L. E. L. Chemical communication: An integral part of functional Asian elephant (Elephas maximus) society. Ecoscience 5, 410–426 (1998).Article 

    Google Scholar 
    Rasmussen, L. E. L. & Krishnamurthy, V. How chemical signals integrate Asian elephant society: The known and the unknown. Zool. Biol. 19, 405–423 (2000).CAS 
    Article 

    Google Scholar 
    Greenwood, D. R., Comesky, D., Hunt, M. B. & Rasmussen, L. E. L. Chirality in elephant pheromones. Nature 438, 1097–1098 (2005).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Clutton-Brock, T. H. & Huchard, E. Social competition and selection in males and females. Phil. Trans. R. Soc. 368, 20130074 (2013).CAS 
    Article 

    Google Scholar 
    Wittemyer, G. & Getz, W. M. Hierarchical dominance structure and social organization in African elephants Loxodonta africana. Anim. Behav. 73, 671–681 (2007).Article 

    Google Scholar 
    Moss, C. Elephant memories (William Morrow, 1988).
    Google Scholar 
    Buss, I. O., Rasmussen, L. E. L. & Smuts, G. L. Role of stress and individual recognition in the function of the African elephants’ temporal gland. Mammalia 40(3), 437–451 (1976).Article 

    Google Scholar 
    Wittemyer, G., Douglas-Hamilton, I. & Getz, W. M. The socioecology of elephants: Analysis of the processes creating multi-tiered social structures. Anim. Behav. 69(6), 1357–1371 (2005).Article 

    Google Scholar 
    Bates, L. A. et al. African elephants have expectations about the locations of out-of-sight family members. Biol. Lett. 4(1), 34–36 (2008).PubMed 
    Article 

    Google Scholar 
    Bates, L. A. et al. Elephants classify human ethnic groups by odor and garment color. Curr. Biol 17(22), 1938–1942 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    Plotnik, J. M. et al. Elephants have a nose for quantity. PNAS 116(25), 12566–12571 (2019).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    de Silva, S., Schmid, V. & Wittemyer, G. Fission–fusion processes weaken dominance networks of female Asian elephants in a productive habitat. Behav. Ecol. https://doi.org/10.1093/beheco/arw153 (2016).Article 

    Google Scholar 
    Archie, E. A., Moss, C. J. & Alberts, S. C. The ties that bind: Genetic relatedness predicts the fission and fusion of social groups in wild African elephants. Proc. R. Soc. Lond. 273, 513–522 (2006).CAS 

    Google Scholar 
    Allen, C. R. B., Brent, L. J. N., Motsentwa, T., Weiss, M. N. & Croft, D. P. Importance of old bulls: Leaders and followers in collective movements of all-male groups in African savannah elephants (Loxodonta africana). Sci. Rep. https://doi.org/10.1038/s41598-020-70682-y (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Goodwin, T. et al. The Role of Bacteria in Chemical Signals of Elephant Musth. In Chemical Signals in Vertebrates Vol. 13 (eds Schulte, B. et al.) (Springer, 2016).
    Google Scholar 
    Wittemyer, G. et al. Where sociality and relatedness diverge: The genetic basis for hierarchical social organization in African elephants. Proc. Biol. Sci. 7(276), 3513–3521 (2009).
    Google Scholar 
    Stoeger, A. & Baotic, A. Information content and acoustic structure of male African elephant social rumbles. Sci. Rep. 6, 27585 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    McComb, K., Reby, D., Baker, L., Moss, C. & Sayialel, S. Long-distance communication of social identity in African elephants. Anim. Behav. 65, 317–329 (2003).Article 

    Google Scholar 
    Archie, E. A. et al. Behavioural inbreeding avoidance in wild African elephants. Molec. Ecol 16, 4138–4148 (2007).CAS 
    Article 

    Google Scholar 
    von Dürckheim, K. Olfaction and scent discrimination in African elephants. PhD thesis, Stellenbosch University, South Africa (2021).Goodwin, T. E. et al. African elephant sesquiterpenes. II. Identification and synthesis of new derivatives of 2,3-dihydrofarnesol. J. Nat. Prod. 65, 1319–1322 (2002).CAS 
    PubMed 
    Article 

    Google Scholar 
    Goodwin, T. E. et al. Chemical analysis of African elephant urine: A search for putative pheromones. In Chemical Signals in Vertebrates 10 (eds Mason, R. T. et al.) 128–139 (Springer Press, 2005).Chapter 

    Google Scholar 
    Goodwin, T. E. et al. Insect pheromones and precursors in female African elephant urine. J. Chem. Ecol. 32, 1849–1853 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    Burger, B. V. Mammalian semiochemicals. In The chemistry of Pheromones and Other Semiochemicals II. Topics in Current Chemistry Vol. 240 (ed. Schulz, S.) 231–278 (Springer, 2005).
    Google Scholar 
    Charpentier, M. J. E., Barthes, N., Proffit, M., Bessière, J. M. & Grison, C. Critical thinking in the chemical ecology of mammalian communication: Roadmap for future studies. Funct. Ecol. 26, 769–774 (2012).Article 

    Google Scholar 
    Apps, P., Weldon, P. & Kramer, M. Chemical signals in terrestrial vertebrates: Search for design features. Nat. Prod. Rep. 32, 1131–1153 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Burgener, N., East, M., Hofer, H. & Dehnhard, M. Do spotted hyena scent marks code for clan membership? In Chemical Signals in Vertebrates XI (eds Hurst, J. L. et al.) 169–178 (Springer, 2008).Chapter 

    Google Scholar 
    Lukas, D. & Clutton-Brock, T. Social complexity and kinship in animal societies. Ecol. Lett. 21, 1129–1134. https://doi.org/10.1111/ele.13079 (2018).Article 
    PubMed 

    Google Scholar 
    Meyer, J. M., Goodwin, T. E. & Schulte, B. A. Intrasexual chemical communication and social responses of captive female African elephants, Loxodonta africana. Anim. Behav. 76, 163–174 (2008).Article 

    Google Scholar 
    Soltis, J., Leong, K. & Savage, A. African elephant vocal communication II: Rumble variation reflects the individual identity and emotional state of callers. Anim. Behav. 70(3), 589–599 (2005).Article 

    Google Scholar 
    Scordato, E. S. & Drea, C. M. Scents and sensibility: Information content of olfactory signals in the ringtailed lemur, Lemur catta. Anim. Behav. 73, 301–314 (2007).Article 

    Google Scholar 
    Palagi, E. & Dapporto, L. Beyond odor discrimination: Demonstrating individual recognition by scent in Lemur catta. Chem. Sens. 31, 437–443 (2006).Article 

    Google Scholar 
    Johnston, R. E., Derzie, A., Chiang, G., Jernigan, P. & Lee, H. C. Individual scent signatures in golden hamsters: Evidence for specialization of function. Anim. Behav. 45, 1061–1070 (1993).Article 

    Google Scholar 
    Coffin, H., Watters, J. & Mateo, J. Odor-based recognition of familiar and related conspecifics: A first test conducted on captive Humboldt Penguins (Spheniscus humboldti). PLoS ONE 6, e25002 (2011).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Leclaire, S. et al. An individual and a sex odor signature in kittiwakes? Study of the semiochemical composition of preen secretion and preen down feathers. Naturwissenschaften 98, 615–624 (2011).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    von Dürckheim, K. et al. African elephants (Loxodonta africana) display remarkable olfactory acuity in human scent matching to sample performance. Appl. Anim. Behav. 200, 123–129 (2018).Article 

    Google Scholar 
    Bates, L. A., Poole, J. H. & Byrne, R. W. Elephant cognition. Curr. Biol. 18, 544–546. https://doi.org/10.1016/j.cub.2008.04.019 (2008).CAS 
    Article 

    Google Scholar 
    Kean, E., Müller, C. & Chadwick, E. Otter scent signals age, sex, and reproductive status. Chem. Sens. 36, 555–564 (2011).CAS 
    Article 

    Google Scholar 
    Kioko, J., Taylor, K., Milne, H. J., Hayes, K. Z. & Kiffner, C. Temporal gland secretion in African elephants (Loxodonta africana). Mamm. Biol. 82, 34–44 (2017).Article 

    Google Scholar 
    Macdonald, E., Fernandez-Duque, E., Sian, E. & Hagey, L. Sex, age, and family differences in the chemical composition of owl monkey (Aotus nancymaae) subcaudal scent secretions. Am. J. Primatol. 70, 12–18 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhang, J. et al. Potential chemosignals in the anogenital gland secretion of giant pandas, Ailuropoda melanoleuca, associated with sex and individual identity. J. Chem. Ecol. 34, 398–407 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Theis, K. R. et al. Symbiotic bacteria appear to mediate hyena social odors. Proc. Natl. Acad. Sci. 110(49), 19832–19837 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Merritt, G. C., Goodrich, B. S., Hesterman, E. R. & Myktowycz, R. Microflora and volatile fatty acids present in the inguinal pouches of the wild rabbit, Oryctolagus cuniculus in Australia. J. Chem. Ecol. 8, 217–1225 (1982).Article 

    Google Scholar 
    Müller-Schwarze, D. & Heckman, S. The social role of scent in beaver (Castor canadensis). J. Chem. Ecol. 6, 81–95 (1980).Article 

    Google Scholar 
    Albone, E. S., Eglinton, G., Walker, J. M. & Ware, G. C. Anal sac secretion of red fox (Vulpes vulpes), its chemistry and microbiology: Comparison with anal sac secretion of lion (Panthera leo). Life Sci. 14, 387–400 (1974).CAS 
    PubMed 
    Article 

    Google Scholar 
    Gorman, M. L. A mechanism for individual recognition by odour in Herpestes auropunctatus (Carnivora: Viverridae). Anim. Behav. 24, 141–145 (1976).Article 

    Google Scholar 
    Theis, K. R., Schmidt, M. S. & Holekamp, K. E. Evidence for a bacterial mechanism for group-specific social odors among hyenas. Sci. Rep. 2, 615 (2012).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Theis, K. R., Heckla, A. L., Verge, J. R. & Holekamp, K. E. The ontogeny of pasting behavior in free-living spotted hyenas, Crocuta crocuta. In Chemical Signals in Vertebrates Vol. 11 (eds Hurst, J. L. et al.) 179–188 (Springer, 2008).
    Google Scholar 
    Chiyo, P. I. et al. The influence of social structure, habitat, and host traits on the transmission of Escherichia coli in wild elephants. PLoS ONE 9(4), e93408 (2014).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Archie, E. A., Moss, C. J. & Alberts, S. C. Characterization of tetranucleotide microsatellite loci in the African Savannah elephant (Loxodonta africana africana). Mol. Ecol. Notes. 3, 244–246 (2003).CAS 
    Article 

    Google Scholar 
    Comstock, K. E., Wasser, S. K. & Ostrander, E. A. Polymorphic microsatellite DNA loci identified in the African elephant (Loxodonta africana). Mol. Ecol. 9, 1004–1006 (2000).CAS 
    PubMed 
    Article 

    Google Scholar 
    Eggert, L. S., Eggert, J. A. & Woodruff, D. S. Estimating population sizes for elusive animals: The forest elephants of Kakum National Park, Ghana. Mol. Ecol. 12, 1389–1402 (2003).CAS 
    PubMed 
    Article 

    Google Scholar 
    Toonen, R. J. & Hughes, S. Increased throughput for fragment analysis on an ABI PRISM 377 automated sequencer using a membrane comb and STRand software. Biotechniques 6, 1320–1324 (2001).
    Google Scholar 
    Belkhir, K., Castric, V. & Bonhomme, F. IDENTIX, a software to test for relatedness in a population using permutation methods. Mol. Ecol. Notes 2, 611–614 (2002).Article 

    Google Scholar 
    Queller, D. & Goodnight, K. Estimating relatedness using genetic markers. Evolution 43(2), 258–275 (1989).PubMed 
    Article 

    Google Scholar 
    Marshall, T. C., Slate, J., Kruuk, L. E. B. & Pemberton, J. M. Statistical confidence for likelihood-based paternity inference in natural populations. Mol. Ecol. 7, 639–655 (1998).CAS 
    PubMed 
    Article 

    Google Scholar 
    Ottensmann, M., Stoffel, M. A., Nichols, H. J. & Hoffman, J. I. GCalignR: An R Package for aligning gas-chromatography data for ecological and evolutionary studies. PLoS ONE 13(6), e0198311 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Morelli, T. et al. Relatedness communicated in lemur scent. Naturwissenschaften 100, 769–777 (2013).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Oksanen, J., Blanchet, F., Guillaume. F., Kindt, R., Legendre, P., Minchin, P., O’Hara, R.B., Simpson, G., Solymos, P., Stevens, M.H.H., Wagner, H. Vegan: community ecology package. R package vegan, vers. 2.2-1. (2015). More

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    Saving the Amazon: how science is helping Indigenous people protect their homelands

    One thing that the team at Los Amigos did not do is peer deeper into the reserve to try to determine where the Mashco Piro are camped out. Gutiérrez says the decision on whether to establish some kind of monitoring system for isolated communities rests with governments and Indigenous groups, but few doubt that it is possible.
    Some researchers worry about the implications of this kind of work. Greg Asner, an ecologist at Arizona State University in Tempe, regularly captured evidence of encampments of isolated groups more than a decade ago, when his team was surveying the Peruvian Amazon in a plane equipped with a powerful laser-based system that provides 3D images of the forest. He flagged the images to his sources at Peru’s environment ministry, but never saw the groups themselves as a legitimate research topic. Even today, he doesn’t see the value in actively tracking them.
    “It’s creepy, like describing the home range of jaguars, but human rights are different than jaguar rights,” says Asner. “If we know they are in there, why do we need to know exactly where they are sleeping at night?”
    Despite the ethical worries about monitoring, some Indigenous leaders are open to the idea. Knowing where isolated groups are could help surrounding Indigenous communities to prevent unintended and dangerous contact, but “it is the Indigenous organizations that should implement and execute any system of control and surveillance of the Indigenous peoples in isolation,” says Julio Cusurichi, president of FENAMAD, which has worked with the Peruvian government to prevent contact and conflict since the Mashco Piro began to emerge.
    FENAMAD was also instrumental in pushing for the creation of the Madre de Dios reserve in 2002. Twenty years later, however, the reserve’s borders have yet to be finalized, and the Indigenous organization is still pushing to expand the eastern boundary to cover areas where the Mashco Piro are known to roam. The problem is that these same areas are currently occupied by logging concessions, which would be costly for the government to cancel.

    Julio Cusurichi, president of the Native Federation of the Madre de Dios River and Tributaries (FENAMAD).

    Julio Cusurichi, president of the Native Federation of the Madre de Dios River and Tributaries (FENAMAD).

    For Cusurichi, the killing of the logger in August is yet another reminder of the precarious situation along the border of the reserve and the risks to both outsiders and the Mashco Piro. Too often, he contends, the government is more concerned with protecting economic interests than the rights of isolated peoples.
    Tauli-Corpuz, the former UN rapporteur, has little doubt that scientists mean well, but she worries about any efforts to document the precise location of isolated groups. “If this information falls into the wrong hands, these people will be disturbed in ways they could never imagine,” she says.
    Officials from the culture ministry acknowledged these dangers in discussions with Nature, and said they were looking at potential regulations to control the flow of information and restrict who can peer into the reserves.
    Although Forsyth says the ministry is full of people who want to do the right thing, he is wary of assuming that government officials always mean well. In Brazil, critics have accused President Bolsonaro, a right-wing populist, of sidelining scientists at FUNAI and attempting to appoint a former Christian missionary to head the division that handles isolated peoples. In the Madre de Dios region, the former governor, Luis Hidalgo Okimura, disappeared in February just before he was to be jailed in connection with an investigation into an illegal logging ring.
    “In some cases, the government may not be trustworthy,” Forsyth warns. He places more faith in Indigenous organizations and their advocates. “Giving them access to whatever information they would like or can’t generate themselves ought to be the priority.” More

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    Asteroid smash and poaching decline

    As the Italian probe LICIACube whizzed past asteroids Didymos (bottom) and Dimorphos (top), it captured a debris plume spraying out from the DART spacecraft as it smashed into Dimorphos.Credit: ASI/NASA

    Astronomers see fireworks as spacecraft ploughs into asteroidTelescopes in space and across Earth captured the spectacular aftermath of NASA’s Double Asteroid Redirection Test (DART) spacecraft crashing into the asteroid Dimorphos on 26 September.The goal was to knock the harmless space rock into a slightly different orbit to test whether humanity could do such a thing if a dangerous asteroid were ever detected heading for Earth. The smash-up was “the first human experiment to deflect a celestial body”, says Thomas Zurbuchen, NASA’s associate administrator for science, and “an enormous success”.A ringside view came from LICIACube, a tiny Italian spacecraft that flew along with DART and photographed the impact, which took place 11 million kilometres from Earth. LICIACube’s first images, released by the Italian Space Agency on 27 September, show a large fireworks-like plume of rocks and other debris coming off Dimorphos (pictured, top) after DART had ploughed into it.It will take days to weeks before mission scientists can confirm whether the test worked, and did in fact cut the time it takes Dimorphos to orbit its partner asteroid, Didymos (pictured, bottom), by 10–15 minutes.

    The shell of the endangered hawksbill sea turtle (pictured) is prized for trinkets and jewellery.Credit: Reinhard Dirscherl/SPL

    Sea turtles swim more freely as poaching declinesPoaching is less of a threat to the survival of sea turtles than it once was, an analysis suggests (J. F. Senko et al. Glob. Change Biol. https://doi.org/gqrzzn; 2022). Illegal sea-turtle catch has dropped sharply since 2000, and most current exploitation occurs in areas with relatively healthy turtle populations.The analysis is the first worldwide estimate of the number of adult sea turtles that are moved on the black market. The authors surveyed sea-turtle specialists and sifted through documents to derive an estimate that around 1.1 million sea turtles were illegally harvested between 1990 and 2020. Nearly 90% of them were funnelled into China and Japan. Of the species that could be identified, the critically endangered hawksbill turtle (Eretmochelys imbricata; pictured), prized for its beautiful shell, was among the most frequently exploited.But the team also found that the illegal catch from 2010 to 2020 was nearly 30% lower than in the previous decade. “The silver lining is that, despite the seemingly large illegal take, exploitation is not having a negative impact on sea-turtle populations on a global scale,” says co-author Jesse Senko, a marine-conservation scientist at Arizona State University in Tempe. More

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    Author Correction: Causal networks of phytoplankton diversity and biomass are modulated by environmental context

    National Center for Theoretical Sciences, Taipei, 10617, TaiwanChun-Wei Chang & Chih-hao HsiehResearch Center for Environmental Changes, Academia Sinica, Taipei, 11529, TaiwanChun-Wei Chang, Fuh-Kwo Shiah & Chih-hao HsiehFaculty of Advanced Science and Technology, Ryukoku University, Otsu, Shiga, 520-2194, JapanTakeshi MikiInstitute of Oceanography, National Taiwan University, Taipei, 10617, TaiwanTakeshi Miki, Fuh-Kwo Shiah & Chih-hao HsiehCenter for Biodiversity Science, Ryukoku University, Otsu, Shiga, 520-2194, JapanTakeshi MikiHealth Science Center Libraries, University of Florida, Gainesville, FL, 32611, USAHao YeUniv. Lille, CNRS, Univ, Littoral Côte D’Opale, IRD, UMR 8187, LOG— Laboratoire D’Océanologie et de Géosciences, Station Marine de Wimereux, F- 59000, Lille, FranceSami SouissiLeibniz Institute of Freshwater Ecology and Inland Fisheries, IGB, 12587, Berlin, GermanyRita AdrianFreie Universität Berlin, Department of Biology, Chemistry and Pharmacy, 14195, Berlin, GermanyRita AdrianNational Research Institute for Agriculture, Food and Environment (INRAE), CARRTEL, Université Savoie Mont Blanc, 74200, Thonon les Bains, FranceOrlane AnnevilleCentre for Limnology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5D, 51014, Tartu, EstoniaHelen Agasild & Peeter NõgesDepartment of Ecosystem Studies, School of Environmental Science, The University of Shiga Prefecture, Hikone, 522-8533, Shiga, JapanSyuhei Ban & Xin LiuKinneret Limnological Laboratory, Israel Oceanographic & Limnological Research, P.O. Box 447, 14950, Migdal, IsraelYaron Be’eri-Shlevin, Gideon Gal & Tamar ZoharyBiodiversity Research Center, Academia Sinica, Taipei, 11529, TaiwanYin-Ru Chiang & Jiunn-Tzong WuUK Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, Lancashire, LA1 4AP, UKHeidrun Feuchtmayr & Stephen J. ThackerayLake Biwa Environmental Research Institute, Otsu, 520-0022, JapanSatoshi Ichise & Michio KumagaiFaculty of Environment and Information Sciences, Yokohama National University, Yokohama, 240-8502, Kanagawa, JapanMaiko KagamiDepartment of Environmental Science, Faculty of Science, Toho University, Funabashi, Chiba, 274-8510, JapanMaiko KagamiResearch Center for Lake Biwa & Environmental Innovation, Ritsumeikan University, Kusatsu, 525-0058, Shiga, JapanMichio KumagaiBiodiversity Division, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, JapanShin-Ichiro S. MatsuzakiCNR Water Research Institute (IRSA), L.go Tonolli 50, 28922, Verbania, Pallanza, ItalyMarina M. Manca, Roberta Piscia & Michela RogoraPlymouth Marine Laboratory, Prospect Place, West Hoe, Plymouth, PL1 3DH, UKClaire E. WiddicombeInstitute of Ecology and Evolutionary Biology, Department of Life Science, National Taiwan University, Taipei, 10617, TaiwanChih-hao Hsieh More

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    The impact of restoration methods for Solidago-invaded land on soil invertebrates

    Bauer, T., Bäte, D. A., Kempfer, F. & Schirmel, J. Differing impacts of two major plant invaders on urban plant-dwelling spiders (Araneae) during flowering season. Biol. Invasions 23(5), 1473–1485. https://doi.org/10.1007/s10530-020-02452-w (2021).Article 

    Google Scholar 
    Ustinova, E. N., Schepetov, D. M., Lysenkov, S. N. & Tiunov, A. V. Soil arthropod communities are not affected by invasive Solidago gigantea Aiton (Asteraceae), based on morphology and metabarcoding analyses. Soil Biol. Biochem. 159, 108288. https://doi.org/10.1016/j.soilbio.2021.108288 (2021).CAS 
    Article 

    Google Scholar 
    Tanner, R. A. et al. Impacts of an Invasive Non-Native Annual Weed, Impatiens glandulifera, on Above- and Below-Ground Invertebrate Communities in the United Kingdom. PLoS ONE 8(6), e67271. https://doi.org/10.1371/journal.pone.0067271 (2013).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wei, Q. et al. The diversity of soil mesofauna decline after bamboo invasion in subtropical China. Sci. Total Environ. 789, 147982. https://doi.org/10.1016/j.scitotenv.2021.147982 (2021).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Szymura, M. & Szymura, T. H. Growth, phenology, and biomass allocation of alien Solidago species in central Europe. Plant Species Biol. 30(4), 245–256. https://doi.org/10.1111/1442-1984.12059 (2015).Article 

    Google Scholar 
    Bobuľská, L., Demková, L., Čerevková, A. & Renčo, M. Invasive goldenrod (Solidago gigantea) influences soil microbial activities in forest and grassland ecosystems in central Europe. Diversity 11(8), 134. https://doi.org/10.3390/d11080134 (2019).CAS 
    Article 

    Google Scholar 
    Sterzyńska, M., Shrubovych, J. & Nicia, P. Impact of plant invasion (Solidago gigantea L.) on soil mesofauna in a riparian wet meadows. Pedobiologia 64, 1–7. https://doi.org/10.1016/j.pedobi.2017.07.004 (2017).Article 

    Google Scholar 
    Zubek, S. et al. Solidago canadensis invasion in abandoned arable fields induces minor changes in soil properties and does not affect the performance of subsequent crops. Land Degrad. Dev. 31(3), 1–12. https://doi.org/10.1002/ldr.3452 (2019).Article 

    Google Scholar 
    Čerevková, A., Miklisová, D., Bobul’ská, L. & Renčo, M. Impact of the invasive plant Solidago gigantea on soil nematodes in a semi-natural grassland and a temperate broadleaved mixed forest. J. Helminthol. 94, 1–14. https://doi.org/10.1017/S0022149X19000324 (2020).Article 

    Google Scholar 
    de Groot, M., Kleijn, D. & Jogan, N. Species groups occupying different trophic levels respond differently to the invasion of semi-natural vegetation by Solidago canadensis. Biol. Conserv. 136(4), 612–617. https://doi.org/10.1016/j.biocon.2007.01.005 (2007).Article 

    Google Scholar 
    Baranová, B., Manko, P. & Jászay, T. Differences in surface-dwelling beetles of grasslands invaded and non-invaded by goldenrods (Solidago canadensis, S. gigantea) with special reference to Carabidae. J. Insect. Conserv. 18(4), 623–635. https://doi.org/10.1007/s10841-014-9666-0 (2014).Article 

    Google Scholar 
    Lenda, M., Witek, M., Skórka, P., Moroń, D. & Woyciechowski, M. Invasive alien plants affect grassland ant communities, colony size and foraging behaviour. Biol. Invasions 15(11), 2403–2414. https://doi.org/10.1007/s10530-013-0461-8 (2013).Article 

    Google Scholar 
    Kajzer-Bonk, J., Szpiłyk, D. & Woyciechowski, M. Invasive goldenrods affect abundance and diversity of grassland ant communities (Hymenoptera: Formicidae). J. Insect Conserv. 20(1), 99–105. https://doi.org/10.1007/s10841-016-9843-4 (2016).Article 

    Google Scholar 
    Trigos-Peral, G. et al. Ant communities and Solidago plant invasion: Environmental properties and food sources. Entomol. Sci. 21(3), 270–278. https://doi.org/10.1111/ens.12304 (2018).Article 

    Google Scholar 
    Fenesi, A. et al. Solidago canadensis impacts on native plant and pollinator communities in different-aged old fields. Basic Appl. Ecol. 16(4), 335–346. https://doi.org/10.1016/j.baae.2015.03.003 (2015).Article 

    Google Scholar 
    Sheley, R. L., Mangold, J. M. & Anderson, J. L. Potential for successional theory to guide restoration of invasive-plant-dominated rangeland. Ecol. Monogr. 76(3), 365–379. https://doi.org/10.1890/0012-9615(2006)076[0365:PFSTTG]2.0.CO;2 (2006).Article 

    Google Scholar 
    Byun, C., de Blois, S. & Brisson, J. Management of invasive plants through ecological resistance. Biol. Invasions 20(1), 13–27. https://doi.org/10.1007/s10530-017-1529-7 (2018).Article 

    Google Scholar 
    Weidlich, E. W. A., Flórido, F. G., Sorrini, T. B. & Brancalion, P. H. S. Controlling invasive plant species in ecological restoration: A global review. J. Appl. Ecol. 57(9), 1806–1817. https://doi.org/10.1111/1365-2664.13656 (2020).Article 

    Google Scholar 
    Zaller, J. G. et al. Effects of glyphosate-based herbicides and their active ingredients on earthworms, water infiltration and glyphosate leaching are influenced by soil properties. Environ. Sci. Eur. 33(1), 1–16. https://doi.org/10.1186/s12302-021-00492-0 (2021).CAS 
    Article 

    Google Scholar 
    Szymura, M., Świerszcz, S. & Szymura, T. H. Restoration of ecologically valuable grassland on sites degraded by invasive Solidago: Lessons from a six year experiment. Land Degrad. Dev. https://doi.org/10.1002/ldr.4278 (2022).Article 

    Google Scholar 
    Świerszcz, S., Szymura, M., Wolski, K. & Szymura, T. H. Comparison of methods for restoring meadows invaded by Solidago species. Pol. J. Environ. Stud. 26(3), 1251–1258. https://doi.org/10.15244/pjoes/67338 (2017).Article 

    Google Scholar 
    Nagy, D. U. et al. The more we do, the less we gain? Balancing effort and efficacy in managing the Solidago gigantea invasion. Weed Res. 60(3), 232–240. https://doi.org/10.1111/wre.12417 (2020).Article 

    Google Scholar 
    Bardgett, R. D. & van der Putten, W. H. Belowground biodiversity and ecosystem functioning. Nature 515, 505–511. https://doi.org/10.1038/nature13855 (2014).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Bardgett, R. D. & Wardle, D. A. Aboveground-Belowground Linkages: Biotic Interactions, Ecosystem Processes, and Global Change (Oxford University Press, Oxford, 2010).
    Google Scholar 
    Gruss, I. et al. Microarthropods and vegetation as biological indicators of soil quality studied in poor sandy sites at former military facilities. Land Degrad. Dev. 33(2), 358–367. https://doi.org/10.1002/ldr.4157 (2022).Article 

    Google Scholar 
    Sabais, A. C. W., Scheu, S. & Eisenhauer, N. Plant species richness drives the density and diversity of Collembola in temperate grassland. Acta Oecol. 37(3), 195–202. https://doi.org/10.1016/j.actao.2011.02.002 (2011).ADS 
    Article 

    Google Scholar 
    Kardol, P. & Wardle, D. A. How understanding aboveground-belowground linkages can assist restoration ecology. Trends Ecol. Evol. 25(11), 670–679. https://doi.org/10.1016/j.tree.2010.09.001 (2010).Article 
    PubMed 

    Google Scholar 
    Eviner, V. T. & Hawkes, C. V. Embracing variability in the application of plant-soil interactions to the restoration of communities and ecosystems. Restor. Ecol. 16(4), 713–729. https://doi.org/10.1111/j.1526-100X.2008.00482.x (2008).Article 

    Google Scholar 
    Zhao, J., Chen, J., Wu, H., Li, L. & Pan, F. Effects of mowing frequency on soil nematode diversity and community structure in a chinese meadow steppe. Sustainability 13, 5555. https://doi.org/10.3390/su13105555 (2021).Article 

    Google Scholar 
    Hyvönen, T. et al. Aboveground and belowground biodiversity responses to seed mixtures and mowing in a long-term set-aside experiment. Agric. Ecosyst. Environ. https://doi.org/10.1016/j.agee.2021.107656 (2021).Article 

    Google Scholar 
    Gilmullina, A., Rumpel, C., Blagodatskaya, E. & Chabbi, A. Management of grasslands by mowing versus grazing – impacts on soil organic matter quality and microbial functioning. Appl. Soil Ecol. https://doi.org/10.1016/j.apsoil.2020.103701 (2020).Article 

    Google Scholar 
    Kladivko, E. J. Tillage systems and soil ecology. Soil Tillage Res. 61(1–2), 61–76. https://doi.org/10.1016/S0167-1987(01)00179-9 (2001).Article 

    Google Scholar 
    Bispo, A. et al. Indicators for monitoring soil biodiversity. Integr. Environ. Assess. Manag. 5(4), 717–719 (2009).CAS 
    Article 

    Google Scholar 
    Santorufo, L., van Gestel, C. A. M., Rocco, A. & Maisto, G. Soil invertebrates as bioindicators of urban soil quality. Environ. Pollut. 161, 57–63. https://doi.org/10.1016/j.envpol.2011.09.042 (2012).CAS 
    Article 
    PubMed 

    Google Scholar 
    Boyce R. L. Life Under Your Feet: Measuring soil invertebrate diversity. Teaching Issues and Experiments in Ecology, Ecological Society of America, 3: Experiment #1. https://tiee.esa.org/vol/v3/experiments/soil/downloads.html (2005).Shannon, C. E. A mathematical theory of communication. Bell Syst. Tech. J. 27, 379–656 (1948).MathSciNet 
    Article 

    Google Scholar 
    Pielou, E. C. The measurement of diversity in different types of biological collections. J. Theor. Biol. 13, 131–144. https://doi.org/10.1016/0022-5193(66)90013-0 (1966).ADS 
    Article 

    Google Scholar 
    Margalef, R. Information theory in ecology. Gen. Syst. 3, 36–71 (1958).
    Google Scholar 
    Jones, H. P. Impact of ecological restoration on ecosystem services. In Encyclopedia of Biodiversity (ed. Levin, S. A.) 199–208 (Academic Press, New York, 2013).Chapter 

    Google Scholar 
    Menta, C. Soil fauna diversity – function, soil degradation, biological indices, soil restoration. In Biodiversity Conservation and Utilization in a Diverse World (ed. Lameed, G. A.) (IntechOpen, London, 2012).
    Google Scholar 
    Hoffland, E., Kuyper, T. W., Comans, R. N. & Creamer, R. E. Eco-functionality of organic matter in soils. Plant Soil 455(1), 1–22. https://doi.org/10.1007/s11104-020-04651-9 (2020).CAS 
    Article 

    Google Scholar 
    Huera-Lucero, T., Labrador-Moreno, J., Blanco-Salas, J. & Ruiz-Téllez, T. A framework to incorporate biological soil quality indicators into assessing the sustainability of territories in the Ecuadorian Amazon. Sustainability 12(7), 3007. https://doi.org/10.3390/su12073007 (2020).Article 

    Google Scholar 
    van Eekeren, N. et al. Microarthropod communities and their ecosystem services restore when permanent grassland with mowing or low-intensity grazing is installed. Agric. Ecosyst. Environ. 323, 107682. https://doi.org/10.1016/j.agee.2021.107682 (2022).Article 

    Google Scholar 
    Humbert, J. Y., Ghazoul, J., Sauter, G. J. & Walter, T. Impact of different meadow mowing techniques on field invertebrates. J. Appl. Entomol. 134(7), 592–599. https://doi.org/10.1111/j.1439-0418.2009.01503.x (2010).Article 

    Google Scholar 
    Steidle, J. L. M., Kimmich, T., Csader, M. & Betz, O. Negative impact of roadside mowing on arthropod fauna and its reduction with ‘arthropod-friendly’ mowing technique. J. Appl. Entomol. https://doi.org/10.1111/jen.12976 (2022).Article 

    Google Scholar 
    Briones, M. J. Soil fauna and soil functions: a jigsaw puzzle. Front. Environ. Sci. 2, 7. https://doi.org/10.3389/fenvs.2014.00007 (2014).Article 

    Google Scholar 
    Shao, C., Chen, J., Li, L. & Zhang, L. Ecosystem responses to mowing manipulations in an arid Inner Mongolia steppe: An energy perspective. J. Arid Environ. 82, 1–10. https://doi.org/10.1016/j.jaridenv.2012.02.019 (2012).ADS 
    Article 

    Google Scholar 
    de Almeida, T., Forey, E. & Chauvat, M. Alien invasive plant effect on soil fauna is habitat dependent. Diversity 14(2), 61. https://doi.org/10.3390/d14020061 (2022).CAS 
    Article 

    Google Scholar 
    Wissuwa, J., Salamon, J. A. & Frank, T. Effects of habitat age and plant species on predatory mites (Acari, Mesostigmata) in grassy arable fallows in Eastern Austria. Soil Biol. Biochem. 50, 96–107. https://doi.org/10.1016/j.soilbio.2012.02.025 (2012).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Petersen, H. Collembolan communities in shrublands along climatic gradients in Europe and the effects of experimental warming and drought on population density, biomass and diversity. Soil Org. 83(3), 463–488 (2011).
    Google Scholar 
    Eisenhauer, N. et al. Plant community impacts on the structure of earthworm communities depend on season and change with time. Soil Biol. Biochem. 41(12), 2430–2443. https://doi.org/10.1016/j.soilbio.2009.09.001 (2009).CAS 
    Article 

    Google Scholar 
    Eisenhauer, N. et al. Plant diversity surpasses plant functional groups and plant productivity as driver of soil biota in the long term. PLoS ONE 6(1), 15–18. https://doi.org/10.1371/journal.pone.0016055 (2011).CAS 
    Article 

    Google Scholar 
    Gao, D., Wang, X., Fu, S. & Zhao, J. Legume plants enhance the resistance of soil to ecosystem disturbance. Front. Plant Sci. 8, 1295. https://doi.org/10.3389/fpls.2017.01295 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Yang, G., Roy, J., Veresoglou, S. D. & Rillig, M. C. Soil biodiversity enhances the persistence of legumes under climate change. New Phytol. 229(5), 2945–2956. https://doi.org/10.1111/nph.17065 (2021).CAS 
    Article 
    PubMed 

    Google Scholar 
    Zhao, J., Zeng, Z., He, X., Chen, H. & Wang, K. Effects of monoculture and mixed culture of grass and legume forage species on soil microbial community structure under different levels of nitrogen fertilization. Eur. J. Soil Biol. 68, 61–68. https://doi.org/10.1016/j.ejsobi.2015.03.008 (2015).CAS 
    Article 

    Google Scholar 
    Zhao, J., Wang, X., Wang, X. & Fu, S. Legume-soil interactions: legume addition enhances the complexity of the soil food web. Plant Soil 385(1), 273–286. https://doi.org/10.1007/s11104-014-2234-2 (2014).CAS 
    Article 

    Google Scholar 
    Bonkowski, M., Villenave, C. & Griffiths, B. Rhizosphere fauna: the functional and structural diversity of intimate interactions of soil fauna with plant roots. Plant Soil 321, 213–233. https://doi.org/10.1007/s11104-009-0013-2 (2009).CAS 
    Article 

    Google Scholar 
    Hector, A., Dobson, K., Minns, A., Bazeley-White, E. & Hartley Lawton, J. Community diversity and invasion resistance: an experimental test in a grassland ecosystem and a review of comparable studies. Ecol. Res. 16(5), 819–83. https://doi.org/10.1046/j.1440-1703.2001.00443.x (2001).Article 

    Google Scholar 
    Gastine, A., Scherer-Lorenzen, M. & Leadley, P. W. No consistent effects of plant diversity on root biomass, soil biota and soil abiotic conditions in temperate grassland communities. Appl. Ecol. 24, 101–111. https://doi.org/10.1016/S0929-1393(02)00137-3 (2003).Article 

    Google Scholar 
    Scherber, C. et al. Effects of plant diversity on invertebrate herbivory in experimental grassland. Oecologia 147(3), 489–500. https://doi.org/10.1007/s00442-005-0281-3 (2006).ADS 
    Article 
    PubMed 

    Google Scholar 
    Viketoft, M., Palmborg, C., Sohlenius, B., Huss-Danell, K. & Bengtsson, J. Plant species effects on soil nematode communities in experimental grasslands. Appl. Soil Ecol. 30(2), 90–103. https://doi.org/10.1016/j.apsoil.2005.02.007 (2005).Article 

    Google Scholar 
    Viketoft, M. et al. Long-term effects of plant diversity and composition on soil nematode communities in model grasslands. Ecology 90(1), 90–99. https://doi.org/10.1890/08-0382.1 (2009).Article 
    PubMed 

    Google Scholar  More