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Picuris Pueblo oral history and genomics reveal continuity in US Southwest

  • Claw, K. G. et al. Chaco Canyon dig unearths ethical concerns. Hum. Biol. 89, 177 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bardill, J. et al. Advancing the ethics of paleogenomics. Science 360, 384–385 (2018).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Garrison, N. A. et al. Genomic research through an indigenous lens: understanding the expectations. Ann. Rev. Genom. Hum. Genet. 20, 495–517 (2019).

    Article 
    CAS 

    Google Scholar
     

  • Tsosie, K. S. et al. Ancient-DNA researchers write their own rules. Nature 600, 37–37 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Rasmussen, M. et al. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506, 225–229 (2014).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rasmussen, M. et al. The ancestry and affiliations of Kennewick Man. Nature 523, 455–458 (2015).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Moreno-Mayar, J. V. et al. Early human dispersals within the Americas. Science 362, eaav2621 (2018).

    Article 
    ADS 
    PubMed 

    Google Scholar
     

  • Severson, A. L. et al. Ancient and modern genomics of the Ohlone Indigenous population of California. Proc. Natl Acad. Sci. USA 119, e2111533119 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • First Rider, D. et al. Genomic analyses correspond with deep persistence of peoples of Blackfoot Confederacy from glacial times. Sci. Adv. 10, eadl6595 (2024).

    Article 
    PubMed 

    Google Scholar
     

  • Kennett, D. J. et al. Archaeogenomic evidence reveals prehistoric matrilineal dynasty. Nat. Commun. 8, 14115 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Colton, H. S. The rise and fall of the prehistoric population of Northern Arizona. Science 84, 337–343 (1936).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Diamond, J. Collapse: How Societies Choose to Fail or Succeed (Penguin, 2005).

  • Diamond, J. Two views of collapse. Nature 463, 880–881 (2010).

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Derry, D. E. Later Athapaskan prehistory: a migration hypothesis. Western Can. J. Anthropol. 5, 134–137 (1975).


    Google Scholar
     

  • Seymour, D. J. Gateways for Athabascan migration to the American Southwest. Plains Anthropol. 57, 149–161 (2012).

    Article 

    Google Scholar
     

  • Ives, J. W. A Theory of Northern Athapaskan Prehistory (Routledge, 2019).

  • World Heritage in the United States. National Park Service www.nps.gov/subjects/internationalcooperation/worldheritage.htm (2024).

  • Kantner, J. Ancient Puebloan Southwest (Cambridge Univ. Press, 2004).

  • Lekson, S. H. The Architecture of Chaco Canyon, New Mexico (Univ. Utah Press, 2007).

  • Lekson, S. H. & Cameron, C. M. The abandonment of Chaco Canyon, the Mesa Verde Migrations, and the reorganization of the Pueblo World. J. Anthropol. Archaeol. 14, 184–202 (1995).

    Article 

    Google Scholar
     

  • Lentz, D. L. et al. Ecosystem impacts by the Ancestral Puebloans of Chaco Canyon, New Mexico, USA. PLoS ONE 16, e0258369 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ortiz, A. The Tewa World: Space, Time, Being, and Becoming in a Pueblo Society (Univ. Chicago Press, 1969).

  • Sando, J. S. Nee Hemish, a History of Jemez Pueblo (Univ. New Mexico Press, 1982).

  • Sando, J. S. Pueblo Nations: Eight Centuries of Pueblo Indian History (Clear Light, 1992).

  • Naranjo, T. Thoughts on migration by Santa Clara Pueblo. J. Anthropol. Archaeol. 14, 247–250 (1995).

    Article 

    Google Scholar
     

  • Colwell-Chanthaphonh, C. Native American perspectives of the past in the San Pedro Valley of Southeastern Arizona. KIVA 69, 5–29 (2003).

    Article 

    Google Scholar
     

  • Sekaquaptewa, E. & Washburn, D. They go along singing: reconstructing the Hopi past from ritual metaphors in song and image. Am. Antiq. 69, 457–486 (2004).

    Article 

    Google Scholar
     

  • Colwell-Chanthaphonh, C. & Ferguson, T. J. Memory pieces and footprints: multivocality and the meanings of ancient times and ancestral places among the Zuni and Hopi. Am. Anthropol. 108, 148–162 (2006).

    Article 

    Google Scholar
     

  • Bernardini, W. Identity as history: Hopi clans and the curation of oral tradition. J. Anthropol. Res. 64, 483–509 (2008).

    Article 

    Google Scholar
     

  • Hays-Gilpin, K. & Lomatewama, R. Some contemporary pueblo perspectives on archaeology in the Pueblo world. KIVA 78, 229–246 (2013).

    Article 

    Google Scholar
     

  • Schaafsma, P. The Cave in the Kiva: the Kiva Niche and painted walls in the Rio Grande Valley. Am. Antiq. 74, 664–690 (2009).

    Article 

    Google Scholar
     

  • Washburn, D. K., Crowe, D. W. & Ahlstrom, R. V. N. A symmetry analysis of design structure: 1,000 years of continuity and change in Puebloan ceramic design. Am. Antiq. 75, 743–772 (2010).

    Article 

    Google Scholar
     

  • Fowles, S. M. An Archaeology of Doings: Secularism and the Study of Pueblo Religion (School for Advanced Research Press, 2013).

  • Dick, H. W. Picuris Pueblo Excavations, November 1964 Document No. PB 177047 (Department of the Interior, National Park Service, National Technical Service Information, 1965).

  • Colwell, C. in The Oxford Handbook of Southwest Archaeology (eds Mills, B. & Fowles, S. M.) (Oxford Univ. Press, 2017).

  • Young, M. J. Signs from the Ancestors: Zuni Cultural Symbolism and Perceptions of Rock Art (Univ. Pennsylvania Press, 1990).

  • Swanton, J. R. & Dixon, R. B. Primitive American history. Am. Anthropol. 16, 376–412 (1914).

    Article 

    Google Scholar
     

  • Lowie, R. H. Oral tradition and history. Am. Anthropol. 17, 597–599 (1915).

    Article 

    Google Scholar
     

  • Mason, R. J. Archaeology and Native North American oral traditions. Am. Antiq. 65, 239–266 (2000).

    Article 

    Google Scholar
     

  • Whiteley, P. M. Archaeology and oral tradition: the scientific importance of dialogue. Am. Antiq. 67, 405–415 (2002).

    Article 

    Google Scholar
     

  • Schaafsma, C. F. Truth dwells in the deeps: Southwestern oral traditions and archaeological interpretations. J. Southwest 46, 621–642 (2004).


    Google Scholar
     

  • Wiget, A. O. Truth and the Hopi: an historiographic study of documented oral tradition concerning the coming of the Spanish. Ethnohistory 29, 181–199 (1982).

    Article 

    Google Scholar
     

  • Colwell-Chanthaphonh, C. Western Apache oral histories and traditions of the Camp Grant Massacre. American Indian Quarterly 27, 639–666 (2003).

    Article 

    Google Scholar
     

  • Echo-Hawk, R. C. Ancient history in the New World: integrating oral traditions and the archaeological record in deep time. Am. Antiq. 65, 267–290 (2000).

    Article 

    Google Scholar
     

  • Rohland, N., Glocke, I., Aximu-Petri, A. & Meyer, M. Extraction of highly degraded DNA from ancient bones, teeth and sediments for high-throughput sequencing. Nat. Protoc. 13, 2447–2461 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Damgaard, P. B. et al. Improving access to endogenous DNA in ancient bones and teeth. Sci. Rep. 5, 11184 (2015).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. https://doi.org/10.1101/pdb.prot5448 (2010).

  • Margaryan, A. et al. Population genomics of the Viking world. Nature 585, 390–396 (2020).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Gansauge, M.-T., Aximu-Petri, A., Nagel, S. & Meyer, M. Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA. Nat. Protoc. 15, 2279–2300 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Briggs, A. W. et al. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87 (2010).

    Article 
    PubMed 

    Google Scholar
     

  • Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA 104, 14616–14621 (2007).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fu, Q. et al. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23, 553–559 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinf. 15, 356 (2014).

    Article 

    Google Scholar
     

  • Moreno-Mayar, J. V. et al. A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data. Bioinformatics 36, 828–841 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rubinacci, S., Ribeiro, D. M., Hofmeister, R. J. & Delaneau, O. Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nat. Genet. 53, 120–126 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sousa da Mota, B. et al. Imputation of ancient human genomes. Nat. Commun. 14, 3660 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Allentoft, M. E. et al. Population genomics of post-glacial western Eurasia. Nature 625, 301–311 (2024).

  • Reich, D. et al. Reconstructing Native American population history. Nature 488, 370–374 (2012).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Raghavan, M. et al. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 349, aab3884 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Browning, S. R. & Browning, B. L. Identity by descent between distant relatives: detection and applications. Ann. Rev. Genet. 46, 617–633 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jobling, M. A. & Tyler-Smith, C. Human Y-chromosome variation in the genome-sequencing era. Nat. Rev. Genet. 18, 485–497 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kivisild, T. Maternal ancestry and population history from whole mitochondrial genomes. Investig. Genet. 6, 3 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Willerslev, E. & Meltzer, D. J. Peopling of the Americas as inferred from ancient genomics. Nature 594, 356–364 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Moreno-Mayar, J. V. et al. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature 553, 203–207 (2018).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Scheib, C. L. et al. Ancient human parallel lineages within North America contributed to a coastal expansion. Science 360, 1024–1027 (2018).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Posth, C. et al. Reconstructing the deep population history of Central and South America. Cell 175, 1185–1197.e22 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Castro e Silva, M. A., Ferraz, T., Bortolini, M. C., Comas, D. & Hünemeier, T. Deep genetic affinity between coastal Pacific and Amazonian natives evidenced by Australasian ancestry. Proc. Natl Acad. Sci. USA 118, e2025739118 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nakatsuka, N. et al. Genetic continuity and change among the Indigenous peoples of California. Nature 624, 122–129 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Villa-Islas, V. et al. Demographic history and genetic structure in pre-Hispanic Central Mexico. Science 380, eadd6142 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Browning, S. R. & Browning, B. L. Accurate non-parametric estimation of recent effective population size from segments of identity by descent. Am. J. Hum. Genet. 97, 404–418 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tournebize, R., Chu, G. & Moorjani, P. Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals. PLoS Genet. 18, e1010243 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fournier, R., Tsangalidou, Z., Reich, D. & Palamara, P. F. Haplotype-based inference of recent effective population size in modern and ancient DNA samples. Nat. Commun. 14, 7945 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ortiz, A. Handbook of North American Indians Vol. 9 Southwest (Smithsonian Institution, 1979).

  • Adler, M. A. & Dick, H. W. Picuris Pueblo through Time: Eight Centuries of Change in a Northern Rio Grande Pueblo (William P. Clements Center for Southwest Studies, 1999).

  • Schroeder, A. H. A Brief History of Picuris Pueblo: A Tiwa Indian Group in North Central New Mexico (Alamosa, 1974).

  • Felsenstein, J. Inbreeding and variance effective numbers in populations with overlapping generations. Genetics 68, 581–597 (1971).

    Article 
    MathSciNet 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Frankham, R. Effective population size/adult population size ratios in wildlife: a review. Genet. Res. 66, 95–107 (1995).

    Article 

    Google Scholar
     

  • Mithun, M. The Languages of Native North America (Cambridge Univ. Press, 2001).

  • Sundberg, L. D. Dinétah: An Early History of the Navajo People (Sunstone, 1995).

  • Magne, M. P. R. & Matson, R. G. Moving on: expanding perspectives on Athapaskan migration. Can. J. Archaeol. 34, 212–239 (2010).


    Google Scholar
     

  • Hall, E. T. Jr. Southwestern dated ruins, IV. Tree-Ring Bull. 17, 26–28 (1951).


    Google Scholar
     

  • Habicht-Mauche, J. A. Coronado’s Querechos and Teyas in the archaeological record of the Texas Panhandle. Plains Anthropologist 37, 247–259 (1992).

    Article 

    Google Scholar
     

  • Luckman, B. H. The Little Ice Age in the Canadian Rockies. Geomorphology 32, 357–384 (2000).

    Article 
    ADS 

    Google Scholar
     

  • Mann, M. E. et al. Global signatures and dynamical origins of the Little Ice Age and Medieval climate anomaly. Science 326, 1256–1260 (2009).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Harney, É., Patterson, N., Reich, D. & Wakeley, J. Assessing the performance of qpAdm: a statistical tool for studying population admixture. Genetics 217, iyaa045 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hodge, F. W. Pueblo Indian clans. Am. Anthropol. 9, 345–352 (1896).

    Article 

    Google Scholar
     

  • Carr, M., Spencer, K. & Woolley, D. Navaho clans and marriage at Pueblo Alto. Am. Anthropol. 41, 245–257 (1939).

    Article 

    Google Scholar
     

  • Reichard, G. A. Social Life of the Navajo Indians: With Some Attention to Minor Ceremonies (Columbia Univ. Press, 1969).

  • De Reuse, W. J. in Studies in Language Companion Series Vol. 185 (eds Dakin, K. et al.) 301–318 (John Benjamins Publishing Company, 2017).

  • de la Fuente, C. et al. Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia. Proc. Natl Acad. Sci. USA 115, E4006–E4012 (2018).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schroeder, H. et al. Origins and genetic legacies of the Caribbean Taino. Proc. Natl Acad. Sci. USA 115, 2341–2346 (2018).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Capodiferro, M. R. et al. Archaeogenomic distinctiveness of the Isthmo-Colombian area. Cell 184, 1706–1723.e24 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Barquera, R. et al. Ancient genomes reveal insights into ritual life at Chichén Itzá. Nature https://doi.org/10.1038/s41586-024-07509-7 (2024).

  • Summer internship for INdigenous peoples in Genomics (SING) Consortium et al. A framework for enhancing ethical genomic research with Indigenous communities. Nat. Commun. 9, 2957 (2018).

    Article 
    ADS 

    Google Scholar
     

  • Kowal, E. et al. Community partnerships are fundamental to ethical ancient DNA research. Hum. Genet. Genom. Adv. 4, 100161 (2023).

    Article 
    CAS 

    Google Scholar
     

  • Earth Resources Observation and Science (EROS) Center. USGS EROS Archive—Digital Elevation—Shuttle Radar Topography Mission (SRTM) Void Filled. USGS https://doi.org/10.5066/F7F76B1X (2018).

  • Ramsey, C. B. Bayesian analysis of radiocarbon dates. Radiocarbon 51, 337–360 (2009).

    Article 
    CAS 

    Google Scholar
     

  • Reimer, P. J. et al. The IntCal20 Northern Hemisphere radiocarbon age calibration curve (0–55 cal kBP). Radiocarbon 62, 725–757 (2020).

    Article 
    CAS 

    Google Scholar
     

  • Schubert, M., Lindgreen, S. & Orlando, L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res. Notes 9, 88 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Weissensteiner, H. et al. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 44, W58–W63 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Katoh, K. & Standley, D. M. MAFFT Multiple Sequence Alignment Software Version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. & Stamatakis, A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35, 4453–4455 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bouckaert, R. et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 10, e1003537 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Poznik, G. D. et al. Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science 341, 562–565 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pinotti, T. et al. Y Chromosome sequences reveal a short Beringian standstill, rapid expansion, and early population structure Native American Founders. Curr. Biol. 29, 149–157.e3 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Popović, D. et al. Ancient genomes reveal long-range influence of the pre-Columbian culture and site of Tiwanaku. Sci. Adv. 7, eabg7261 (2021).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Campelo dos Santos, A. L. et al. Genomic evidence for ancient human migration routes along South America’s Atlantic coast. Proc. R. Soc. B: Biol. Sci. 289, 20221078 (2022).

    Article 

    Google Scholar
     

  • Rasmussen, M. et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757–762 (2010).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bongers, J. L. et al. Integration of ancient DNA with transdisciplinary dataset finds strong support for Inca resettlement in the south Peruvian coast. Proc. Natl Acad. Sci. USA 117, 18359–18368 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lindo, J. et al. The genetic prehistory of the Andean highlands 7000 years BP through European Contact. Sci. Adv. 4, eaau4921 (2018).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Raghavan, M. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014).

    Article 
    ADS 
    PubMed 

    Google Scholar
     

  • Sikora, M. et al. The population history of northeastern Siberia since the Pleistocene. Nature 570, 182–188 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Flegontov, P. et al. Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America. Nature 570, 236–240 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mallick, S. et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538, 201–206 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bergström, A. et al. Insights into human genetic variation and population history from 929 diverse genomes. Science 367, eaay5012 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Raghavan, M. et al. The genetic prehistory of the New World Arctic. Science 345, 1255832 (2014).

    Article 
    PubMed 

    Google Scholar
     

  • Joseph, S. K. et al. Genomic evidence for adaptation to tuberculosis in the Andes before European contact. iScience 26, 106034 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Byrska-Bishop, M. et al. High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios. Cell 185, 3426–3440.e19 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nakatsuka, N. et al. Ancient genomes in South Patagonia reveal population movements associated with technological shifts and geography. Nat. Commun. 11, 3868 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fernandes, D. M. et al. A genetic history of the pre-contact Caribbean. Nature 590, 103–110 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Nägele, K. et al. Genomic insights into the early peopling of the Caribbean. Science 369, 456–460 (2020).

    Article 
    ADS 
    PubMed 

    Google Scholar
     

  • Tiesler, V. et al. Life and death in early colonial Campeche: new insights from ancient DNA. Antiquity 96, 937–954 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nakatsuka, N. et al. A Paleogenomic reconstruction of the deep population history of the Andes. Cell 181, 1131–1145.e21 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kennett, D. J. et al. South-to-north migration preceded the advent of intensive farming in the Maya region. Nat. Commun. 13, 1530 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gnecchi-Ruscone, G. A. et al. Dissecting the pre-Columbian genomic ancestry of Native Americans along the Andes–Amazonia divide. Mol. Biol. Evol. 36, 1254–1269 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Verdu, P. et al. Patterns of admixture and population structure in native populations of Northwest North America. PLoS Genet. 10, e1004530 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Borda, V. et al. The genetic structure and adaptation of Andean highlanders and Amazonians are influenced by the interplay between geography and culture. Proc. Natl Acad. Sci. USA 117, 32557–32565 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. H. Genet. 81, 559–575 (2007).

    Article 
    CAS 

    Google Scholar
     

  • Maples, B. K., Gravel, S., Kenny, E. E. & Bustamante, C. D. RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference. Am. J. Human Genet. 93, 278–288 (2013).

    Article 
    CAS 

    Google Scholar
     

  • Moreno-Mayar, J. V. FrAnTK: a Frequency-based Analysis ToolKit for efficient exploration of allele sharing patterns in present-day and ancient genomic datasets. G3 https://doi.org/10.1093/g3journal/jkab357 (2021).

  • Maier, R. et al. On the limits of fitting complex models of population history to f-statistics. eLife 12, e85492 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Browning, B. L. & Browning, S. R. Detecting identity by descent and estimating genotype error rates in sequence data. Am. J. Hum. Genet. 93, 840–851 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chintalapati, M., Patterson, N. & Moorjani, P. The spatiotemporal patterns of major human admixture events during the European Holocene. eLife 11, e77625 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

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