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Ancient DNA reveals phenological diversity of Coast Salish herring harvests over multiple centuries

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  • Luck, G. W., Daily, G. C. & Ehrlich, P. R. Population diversity and ecosystem services. Trends Ecol. Evol. 18, 331–336. https://doi.org/10.1016/S0169-5347(03)00100-9 (2003).

    Article 

    Google Scholar 

  • Schindler, D. E. et al. Population diversity and the portfolio effect in an exploited species. Nature 465, 609–612. https://doi.org/10.1038/nature09060 (2010).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Moore, J. W., Yeakel, J. D., Peard, D., Lough, J. & Beere, M. Life-history diversity and its importance to population stability and persistence of a migratory fish: Steelhead in two large North American watersheds. J. Anim. Ecol. 83, 1035–1046. https://doi.org/10.1111/1365-2656.12212 (2014).

    Article 
    PubMed 

    Google Scholar 

  • Barrett, R. D. H. et al. Linking a mutation to survival in wild mice. Science 363, 499. https://doi.org/10.1126/science.aav3824 (2019).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Jones, F. C. et al. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484, 55. https://doi.org/10.1038/nature10944 (2012).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Savage, A. E. & Zamudio, K. R. MHC genotypes associate with resistance to a frog-killing fungus. Proc. Natl. Acad. Sci. 108, 16705. https://doi.org/10.1073/pnas.1106893108 (2011).

    ADS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hofinger, B. J. et al. An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations. Mol. Ecol. 20, 3653–3668. https://doi.org/10.1111/j.1365-294X.2011.05201.x (2011).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Ceballos, G., Ehrlich, P. R. & Dirzo, R. Biological annihilation via the ongoing sixth mass extinction signaled by vertebrate population losses and declines. Proc. Natl. Acad. Sci. 114, E6089. https://doi.org/10.1073/pnas.1704949114 (2017).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hughes, J. B., Daily, G. C. & Ehrlich, P. R. Population diversity: its extent and extinction. Science 278, 689. https://doi.org/10.1126/science.278.5338.689 (1997).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Fernández-Llamazares, Á. et al. Scientists’ warning to humanity on threats to indigenous and local knowledge systems. J. Ethnobiol. 41(144–169), 126 (2021).

    Google Scholar 

  • Womble, J. N., Willson, M. F., Sigler, M. F., Kelly, B. P. & VanBlaricom, G. R. Distribution of Steller sea lions (Eumetopias jubatus) in relation to spring-spawning fish in SE Alaska. Mar. Ecol. Prog. Ser. 294, 271–282 (2005).

    ADS 
    Article 

    Google Scholar 

  • Thomas, G. L. & Thorne, R. E. Night-time predation by Steller sea lions. Nature 411, 1013–1013. https://doi.org/10.1038/35082745 (2001).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Chamberlin, J. W., Beckman, B. R., Greene, C. M., Rice, C. A. & Hall, J. E. How relative size and abundance structures the relationship between size and individual growth in an ontogenetically piscivorous fish. Ecol. Evol. 7, 6981–6995. https://doi.org/10.1002/ece3.3218 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hatch, S. A. Kittiwake diets and chick production signal a 2008 regime shift in the Northeast Pacific. Mar. Ecol. Prog. Ser. 477, 271–284 (2013).

    ADS 
    Article 

    Google Scholar 

  • Schrimpf, M. B., Parrish, J. K. & Pearson, S. F. Trade-offs in prey quality and quantity revealed through the behavioral compensation of breeding seabirds. Mar. Ecol. Prog. Ser. https://doi.org/10.3354/meps09750 (2012).

    Article 

    Google Scholar 

  • Willson, M. F. & Womble, J. N. Vertebrate exploitation of pulsed marine prey: A review and the example of spawning herring. Rev. Fish Biol. Fisheries 16, 183–200. https://doi.org/10.1007/s11160-006-9009-7 (2006).

    Article 

    Google Scholar 

  • Sandell, T., Lindquist, A., Dionne, P. & Lowry, D. 2016 Washington State herring stock status report (Washington Department of Fish and Wildlife, 2019).

  • Petrou, E. L. et al. Functional genetic diversity in an exploited marine species and its relevance to fisheries management. Proc. R. Soc. B Biol. Sci. 288, 20202398. https://doi.org/10.1098/rspb.2020.2398 (2021).

    CAS 
    Article 

    Google Scholar 

  • Chamberlin, J. et al. Phenological diversity of a prey species supports life-stage specific foraging opportunity for a mobile consumer. ICES J. Mar. Sci. 78, 3089–3100. https://doi.org/10.1093/icesjms/fsab176 (2021).

    Article 

    Google Scholar 

  • Lok, E. K. et al. Spatiotemporal associations between Pacific herring spawn and surf scoter spring migration: Evaluating a silver wave hypothesis. Mar. Ecol. Prog. Ser. 457, 139–150 (2012).

    ADS 
    Article 

    Google Scholar 

  • Armstrong, J. B., Takimoto, G., Schindler, D. E., Hayes, M. M. & Kauffman, M. J. Resource waves: Phenological diversity enhances foraging opportunities for mobile consumers. Ecology 97, 1099–1112. https://doi.org/10.1890/15-0554.1 (2016).

    Article 
    PubMed 

    Google Scholar 

  • McKechnie, I. et al. Archaeological data provide alternative hypotheses on Pacific herring (Clupea pallasii) distribution, abundance, and variability. Proc. Natl. Acad. Sci. https://doi.org/10.1073/pnas.1316072111 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Moss, M. L., Rodrigues, A. T., Speller, C. F. & Yang, D. Y. The historical ecology of Pacific herring: Tracing Alaska Native use of a forage fish. J. Archaeol. Sci. Rep. https://doi.org/10.1016/j.jasrep.2015.10.005 (2016).

    Article 

    Google Scholar 

  • Kopperl, R. E. Herring use in southern Puget Sound: Analysis of fish remains at 45-KI-437. Northwest Anthropol. Res. Notes 35, 1–20 (2001).

    Google Scholar 

  • McKechnie, I. & Moss, M. L. Meta-analysis in zooarchaeology expands perspectives on Indigenous fisheries of the Northwest Coast of North America. J. Archaeol. Sci. Rep. 8, 470–485. https://doi.org/10.1016/j.jasrep.2016.04.006 (2016).

    Article 

    Google Scholar 

  • Caldwell, M. E. et al. A bird’s eye view of northern Coast Salish intertidal resource management features, southern British Columbia, Canada. J. Isl. Coast. Archaeol. 7, 219–233. https://doi.org/10.1080/15564894.2011.586089 (2012).

    Article 

    Google Scholar 

  • Eells, M. & Castile, G. P. The Indians of Puget Sound: The Notebooks of Myron Eells (University of Washington Press, 1985).

    Google Scholar 

  • Smith, M. W. The Puyallup-Nisqually (Columbia University Press, 1940).

    Book 

    Google Scholar 

  • Thornton, T. F. & Moss, M. L. Herring and People in the North Pacific: Sustaining a Keystone Species (University of Washington Press, 2021).

    Google Scholar 

  • Powell, M. Divided waters: Heiltsuk spatial management of herring fisheries and the politics of native sovereignty. West. Hist. Q. 43, 463–484. https://doi.org/10.2307/westhistquar.43.4.0463 (2012).

    Article 

    Google Scholar 

  • Gauvreau, A. M., Lepofsky, D., Rutherford, M. & Reid, M. “Everything revolves around the herring”: The Heiltsuk–herring relationship through time. Ecol. Soc. https://doi.org/10.5751/ES-09201-220210 (2017).

    Article 

    Google Scholar 

  • von der Porten, S., Lepofsky, D., McGregor, D. & Silver, J. Recommendations for marine herring policy change in Canada: Aligning with Indigenous legal and inherent rights. Mar. Policy 74, 68–76. https://doi.org/10.1016/j.marpol.2016.09.007 (2016).

    Article 

    Google Scholar 

  • Hammond, J. Fish in puget sound. Am. Angler 25, 392–393 (1886).

    Google Scholar 

  • Bargmann, G. Forage fish management plan (Washington Department of Fish and Wildlife, 1998).

  • Stick, K. C. & Lindquist, A. 2008 Washington State herring stock status report (Washington Department of Fish and Wildlife, 2009).

  • Erlandson, J. M. & Rick, T. C. Archaeology meets marine ecology: The antiquity of maritime cultures and human impacts on marine fisheries and ecosystems. Ann. Rev. Mar. Sci. 2, 231–251. https://doi.org/10.1146/annurev.marine.010908.163749 (2009).

    Article 

    Google Scholar 

  • Hadly, E. A. & Barnosky, A. D. in Conservation Paleobiology: Using the Past to Manage for the Future Vol. 15 (eds Dietl, G. P. & Flessa, K. W.) 39–59 (Paleontological Society Papers, 2009).

  • Wolverton, S. & Lyman, R. L. in Conservation Biology and Applied Zooarchaeology (eds Wolverton, S. & Lyman, R. L.) 1–22 (University of Arizona Press, 2012).

  • Rogers, L. A. et al. Centennial-scale fluctuations and regional complexity characterize Pacific salmon population dynamics over the past five centuries. Proc. Natl. Acad. Sci. 110, 1750. https://doi.org/10.1073/pnas.1212858110 (2013).

    ADS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wright, C. A., Dallimore, A., Thomson, R. E., Patterson, R. T. & Ware, D. M. Late Holocene paleofish populations in Effingham Inlet, British Columbia, Canada. Palaeogeogr. Palaeoclimatol. Palaeoecol. 224, 367–384. https://doi.org/10.1016/j.palaeo.2005.03.041 (2005).

    Article 

    Google Scholar 

  • Thompson, T. Q. et al. Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations. Proc. Natl. Acad. Sci. 116, 177. https://doi.org/10.1073/pnas.1811559115 (2019).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Halffman, C. M. et al. Early human use of anadromous salmon in North America at 11,500 y ago. Proc. Natl. Acad. Sci. 112, 12344–12348. https://doi.org/10.1073/pnas.1509747112 (2015).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Quinn, T. An environmental and historical overview of the Puget Sound ecosystem (U.S. Geological Survey, 2010).

  • Kopperl, R. E., Taylor, A. K., Miss, C. J., Ames, K. M. & Hodges, C. M. The Bear Creek Site (45KI839), a Late Pleistocene-Holocene transition occupation in the Puget Sound lowland, King County, Washington. PaleoAmerica 1, 116–120. https://doi.org/10.1179/2055556314Z.0000000004 (2015).

    Article 

    Google Scholar 

  • Gunther, E. Klallam Ethnography (University of Washington Press, 1927).

    Google Scholar 

  • Elmendorf, W. W. & Kroeber, A. L. The Structure of Twana Culture (Washington State University Press, 1992).

    Google Scholar 

  • The Suquamish Tribe. Fish consumption survey of the Suquamish Indian tribe of the Port Madison Indian Reservation, Puget Sound Region (Suquamish, WA, 2000).

  • Suttles, W. P. The Economic Life of the Coast Salish of Haro and Rosario Straits (Garland Publishing, 1974).

    Google Scholar 

  • Lane, B. The Indian herring fishery from the earliest times to the mid-nineteenth century (United States Depatment of the Interior, 1974).

  • Stein, J. K. in Vashon Island Archaeology: A View from Burton Acres Shell Midden (eds Stein, J. K. & Phillips, L. S.) 5–16 (Burke Musseum, 2002).

  • Lewarch, D. E. et al. Data recovery excavations at the Bay Street Shell Midden (45KP115), Kitsap County, Washington (Larson Anthropological Archaeological Services Limited, 2002).

  • De Danaan, L. in Vashon Island Archaeology: A View from Burton Acres Shell Midden (eds Stein, J. K. & Phillips, L. S.) 17–31 (Burke Museum, 2002).

  • Stein, J. K. in Vashon Island Archaeology: A View from Burton Acres Shell Midden (eds Stein, J. K. & Phillips, L. S.) 47–64 (Burke Musseum, 2002).

  • Yang, D. Y. & Watt, K. Contamination controls when preparing archaeological remains for ancient DNA analysis. J. Archaeol. Sci. 32, 331–336. https://doi.org/10.1016/j.jas.2004.09.008 (2005).

    Article 

    Google Scholar 

  • Yang, D. Y., Liu, L., Chen, X. & Speller, C. F. Wild or domesticated: DNA analysis of ancient water buffalo remains from north China. J. Archaeol. Sci. 35, 2778–2785. https://doi.org/10.1016/j.jas.2008.05.010 (2008).

    Article 

    Google Scholar 

  • Maddox, D. M. et al. A mutation in Syne2 causes early retinal defects in photoreceptors, secondary neurons, and Müller Glia. Invest. Ophthalmol. Vis. Sci. 56, 3776–3787. https://doi.org/10.1167/iovs.14-16047 (2015).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Han, F. et al. Ecological adaptation in Atlantic herring is associated with large shifts in allele frequencies at hundreds of loci. Elife 9, e61076. https://doi.org/10.7554/eLife.61076 (2020).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Smith, M. J. et al. Multiplex preamplification PCR and microsatellite validation enables accurate single nucleotide polymorphism genotyping of historical fish scales. Mol. Ecol. Resour. 11, 268–277. https://doi.org/10.1111/j.1755-0998.2010.02965.x (2011).

    Article 
    PubMed 

    Google Scholar 

  • Speller, C. F. et al. High potential for using DNA from ancient herring bones to inform modern fisheries management and conservation. PLoS ONE 7, e51122. https://doi.org/10.1371/journal.pone.0051122 (2012).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Weir, B. & Cockerham, C. Estimating F-Statistics for the analysis of population structure. Evolution 38, 1358–1370 (1984).

    CAS 
    PubMed 

    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 

  • Jombart, T. adegenet: A R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405 (2008).

    CAS 
    Article 

    Google Scholar 

  • Rousset, F. Genepop’007: A complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Resour. 8, 103–106. https://doi.org/10.1111/j.1471-8286.2007.01931.x (2008).

    Article 
    PubMed 

    Google Scholar 

  • Moran, B. M. & Anderson, E. C. Bayesian inference from the conditional genetic stock identification model. Can. J. Fish. Aquat. Sci. 76, 551–560. https://doi.org/10.1139/cjfas-2018-0016 (2018).

    Article 

    Google Scholar 

  • Moss, M. L. Understanding variability in Northwest Coast faunal assemblages: Beyond economic intensification and cultural complexity. J. Isl. Coast. Archaeol. 7, 1–22. https://doi.org/10.1080/15564894.2011.586090 (2012).

    Article 

    Google Scholar 

  • Greene, C., Kuehne, L., Rice, C., Fresh, K. & Penttila, D. Forty years of change in forage fish and jellyfish abundance across greater Puget Sound, Washington (USA): Anthropogenic and climate associations. Mar. Ecol. Prog. Ser. 525, 153–170 (2015).

    ADS 
    Article 

    Google Scholar 

  • Rice, C. A., Duda, J. J., Greene, C. M. & Karr, J. R. Geographic patterns of fishes and jellyfish in Puget Sound surface waters. Mar. Coast. Fish. 4, 117–128. https://doi.org/10.1080/19425120.2012.680403 (2012).

    Article 

    Google Scholar 

  • Haegele, C. W. & Schweigert, J. F. Distribution and characteristics of herring spawning grounds and description of spawning behavior. Can. J. Fish. Aquat. Sci. 42, s39–s55. https://doi.org/10.1139/f85-261 (1985).

    Article 

    Google Scholar 

  • Gao, Y. W., Joner, S. H. & Bargmann, G. G. Stable isotopic composition of otoliths in identification of spawning stocks of Pacific herring (Clupea pallasi) in Puget Sound. Can. J. Fish. Aquat. Sci. 58, 2113–2120. https://doi.org/10.1139/f01-146 (2001).

    Article 

    Google Scholar 

  • West, J. E., O’Neill, S. M. & Ylitalo, G. M. Spatial extent, magnitude, and patterns of persistent organochlorine pollutants in Pacific herring (Clupea pallasi) populations in the Puget Sound (USA) and Strait of Georgia (Canada). Sci. Total Environ. 394, 369–378. https://doi.org/10.1016/j.scitotenv.2007.12.027 (2008).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Moss, M. L. The nutritional value of Pacific herring: An ancient cultural keystone species on the Northwest Coast of North America. J. Archaeol. Sci. Rep. 5, 649–655. https://doi.org/10.1016/j.jasrep.2015.08.041 (2016).

    Article 

    Google Scholar 

  • Brown, F. & Brown, Y. K. Staying the course, staying alive- Coastal First Nations fundamental truths: Biodiversity, stewardship and sustainability 82 (2009).

  • Dugmore, A. J. et al. Cultural adaptation, compounding vulnerabilities and conjunctures in Norse Greenland. Proc. Natl. Acad. Sci. 109, 3658. https://doi.org/10.1073/pnas.1115292109 (2012).

    ADS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nunn, P. D. et al. Times of plenty, times of less: Last-millennium societal disruption in the Pacific Basin. Hum. Ecol. 35, 385–401. https://doi.org/10.1007/s10745-006-9090-5 (2007).

    Article 

    Google Scholar 

  • Rose, K. A., Megrey, B. A., Hay, D., Werner, F. & Schweigert, J. Climate regime effects on Pacific herring growth using coupled nutrient-phytoplankton-zooplankton and bioenergetics models. Trans. Am. Fish. Soc. 137, 278–297. https://doi.org/10.1577/T05-152.1 (2008).

    Article 

    Google Scholar 

  • Rosenthal, Y., Linsley, B. K. & Oppo, D. W. Pacific ocean heat content during the past 10,000 years. Science 342, 617. https://doi.org/10.1126/science.1240837 (2013).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Hopt, J. & Grier, C. Continuity amidst change: Village organization and fishing subsistence at the Dionisio Point locality in coastal southern British Columbia. J. Isl. Coast. Archaeol. 13, 21–42. https://doi.org/10.1080/15564894.2016.1257526 (2018).

    Article 

    Google Scholar 

  • Butler, V. L., Campbell, S. K., Bovy, K. M. & Etnier, M. A. Exploring ecodynamics of coastal foragers using integrated faunal records from Čḯxwicən village (Strait of Juan de Fuca, Washington, U.S.A.). J. Archaeol. Sci. Rep. 23, 1143–1167. https://doi.org/10.1016/j.jasrep.2018.09.031 (2019).

    Article 

    Google Scholar 

  • Lamichhaney, S. et al. Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean. Proc. Natl. Acad. Sci. 114, E3452–E3461 (2017).

    CAS 
    Article 

    Google Scholar 

  • Carpenter, M. L. et al. Pulling out the 1%: Whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. Am. J. Hum. Genet. 93, 852–864. https://doi.org/10.1016/j.ajhg.2013.10.002 (2013).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Oosting, T. et al. Unlocking the potential of ancient fish DNA in the genomic era. Evol. Appl. 12, 1513–1522. https://doi.org/10.1111/eva.12811 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Abrahms, B. et al. Emerging perspectives on resource tracking and animal movement ecology. Trends Ecol. Evol. 36, 308–320. https://doi.org/10.1016/j.tree.2020.10.018 (2021).

    Article 
    PubMed 

    Google Scholar 

  • Bronk Ramsey, C. Bayesian analysis of radiocarbon dates. Radiocarbon 51, 337–360. https://doi.org/10.1017/S0033822200033865 (2009).

    Article 

    Google Scholar 

  • Reimer, P. J. et al. The IntCal20 Northern Hemisphere radiocarbon age calibration curve (0–55 cal kBP). Radiocarbon 62, 725–757. https://doi.org/10.1017/RDC.2020.41 (2020).

    CAS 
    Article 

    Google Scholar 

  • Deo, J. N., Stone, J. O. & Stein, J. K. Building confidence in shell: Variations in the marine radiocarbon reservoir correction for the Northwest Coast over the past 3,000 years. Am. Antiq. 69, 771–786. https://doi.org/10.2307/4128449 (2004).

    Article 

    Google Scholar 


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