{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T19:20:42Z","timestamp":1791832842676,"version":"4.3.4"},"reference-count":101,"publisher":"Springer Science and Business Media LLC","issue":"8019","license":[{"start":{"date-parts":[[2024,6,12]],"date-time":"2024-06-12T00:00:00Z","timestamp":1718150400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,6,12]],"date-time":"2024-06-12T00:00:00Z","timestamp":1718150400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"published-print":{"date-parts":[[2024,7,4]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Malaria-causing protozoa of the genus <jats:italic>Plasmodium<\/jats:italic> have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species<jats:sup>1<\/jats:sup>. Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe<jats:sup>1,2<\/jats:sup>. To address these questions, we generated high-coverage ancient mitochondrial and nuclear\u00a0genome-wide data from <jats:italic>P. falciparum<\/jats:italic>, <jats:italic>P. vivax<\/jats:italic> and <jats:italic>P. malariae<\/jats:italic> from 16 countries spanning around 5,500 years of human history. We identified <jats:italic>P. vivax<\/jats:italic> and <jats:italic>P. falciparum<\/jats:italic> across geographically disparate regions of Eurasia from as early as the fourth and first millennia <jats:sc>bce<\/jats:sc>, respectively; for <jats:italic>P. vivax<\/jats:italic>, this evidence pre-dates textual references by several millennia<jats:sup>3<\/jats:sup>. Genomic analysis supports distinct disease histories for <jats:italic>P. falciparum<\/jats:italic> and <jats:italic>P. vivax<\/jats:italic> in the Americas: similarities between now-eliminated European and peri-contact South American strains indicate that European colonizers were the source of American <jats:italic>P. vivax<\/jats:italic>, whereas the trans-Atlantic slave trade probably introduced <jats:italic>P. falciparum<\/jats:italic> into the Americas. Our data underscore the role of cross-cultural contacts in the dissemination of malaria, laying the biomolecular foundation for future palaeo-epidemiological research into the impact of <jats:italic>Plasmodium<\/jats:italic> parasites on human history. Finally, our unexpected discovery of <jats:italic>P. falciparum<\/jats:italic> in the high-altitude Himalayas provides a rare case study in which individual mobility can be inferred from infection status, adding to our knowledge of cross-cultural connectivity in the region nearly three millennia ago.<\/jats:p>","DOI":"10.1038\/s41586-024-07546-2","type":"journal-article","created":{"date-parts":[[2024,6,12]],"date-time":"2024-06-12T16:02:14Z","timestamp":1718208134000},"page":"125-133","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":49,"title":["Ancient Plasmodium genomes shed light on the history of human malaria"],"prefix":"10.1038","volume":"631","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5484-7974","authenticated-orcid":false,"given":"Megan","family":"Michel","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2975-3869","authenticated-orcid":false,"given":"Eirini","family":"Skourtanioti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Federica","family":"Pierini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evelyn K.","family":"Guevara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angela","family":"M\u00f6tsch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arthur","family":"Kocher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0518-4518","authenticated-orcid":false,"given":"Rodrigo","family":"Barquera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-6087-8031","authenticated-orcid":false,"given":"Raffaela A.","family":"Bianco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9118-2839","authenticated-orcid":false,"given":"Selina","family":"Carlhoff","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorenza","family":"Coppola Bove","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suzanne","family":"Freilich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen","family":"Giffin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8377-468X","authenticated-orcid":false,"given":"Taylor","family":"Hermes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alina","family":"Hi\u00df","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florian","family":"Knolle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth A.","family":"Nelson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3825-8536","authenticated-orcid":false,"given":"Gunnar U.","family":"Neumann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luka","family":"Papac","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2800-0371","authenticated-orcid":false,"given":"Sandra","family":"Penske","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4204-5018","authenticated-orcid":false,"given":"Adam B.","family":"Rohrlach","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nada","family":"Salem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lena","family":"Semerau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9357-5238","authenticated-orcid":false,"given":"Vanessa","family":"Villalba-Mouco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabelle","family":"Abadie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7033-4319","authenticated-orcid":false,"given":"Mark","family":"Aldenderfer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica F.","family":"Beckett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Brown","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Franco G. R.","family":"Campus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tsang","family":"Chenghwa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0188-0540","authenticated-orcid":false,"given":"Mar\u00eda","family":"Cruz Berrocal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ladislav","family":"Dama\u0161ek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kellie Sara","family":"Duffett Carlson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rapha\u00ebl","family":"Durand","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4847-8532","authenticated-orcid":false,"given":"Michal","family":"Ern\u00e9e","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristinel","family":"F\u00e2nt\u0103neanu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannah","family":"Frenzel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9390-8111","authenticated-orcid":false,"given":"Gabriel","family":"Garc\u00eda Ati\u00e9nzar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonia","family":"Guill\u00e9n","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1635-9021","authenticated-orcid":false,"given":"Ellen","family":"Hsieh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5978-9064","authenticated-orcid":false,"given":"Maciej","family":"Karwowski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Kelvin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nikki","family":"Kelvin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Khokhlov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca L.","family":"Kinaston","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arkadii","family":"Korolev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-7631-1974","authenticated-orcid":false,"given":"Kim-Louise","family":"Krettek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4915-0179","authenticated-orcid":false,"given":"Mario","family":"K\u00fc\u00dfner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luca","family":"Lai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cory","family":"Look","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7922-4482","authenticated-orcid":false,"given":"Kerttu","family":"Majander","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kirsten","family":"Mandl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vittorio","family":"Mazzarello","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7964-9387","authenticated-orcid":false,"given":"Michael","family":"McCormick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3957-3378","authenticated-orcid":false,"given":"Patxuka","family":"de Miguel Ib\u00e1\u00f1ez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reg","family":"Murphy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-5003-0243","authenticated-orcid":false,"given":"Rita E.","family":"N\u00e9meth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8696-1707","authenticated-orcid":false,"given":"Kerkko","family":"Nordqvist","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7368-2020","authenticated-orcid":false,"given":"Friederike","family":"Novotny","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-1794-5983","authenticated-orcid":false,"given":"Martin","family":"Obenaus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lauro","family":"Olmo-Enciso","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P\u00e4ivi","family":"Onkamo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3629-8251","authenticated-orcid":false,"given":"J\u00f6rg","family":"Orschiedt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valerii","family":"Patrushev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanni","family":"Peltola","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5743-0613","authenticated-orcid":false,"given":"Alejandro","family":"Romero","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Salvatore","family":"Rubino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4117-5248","authenticated-orcid":false,"given":"Antti","family":"Sajantila","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Domingo C.","family":"Salazar-Garc\u00eda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena","family":"Serrano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7813-7929","authenticated-orcid":false,"given":"Shapulat","family":"Shaydullaev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emanuela","family":"Sias","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mario","family":"\u0160laus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ladislav","family":"Stan\u010do","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Treena","family":"Swanston","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3080-3085","authenticated-orcid":false,"given":"Maria","family":"Teschler-Nicola","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0575-7681","authenticated-orcid":false,"given":"Frederique","family":"Valentin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katrien","family":"Van de Vijver","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1604-5540","authenticated-orcid":false,"given":"Tamara L.","family":"Varney","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3913-4554","authenticated-orcid":false,"given":"Alfonso","family":"Vigil-Escalera Guirado","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher K.","family":"Waters","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9762-2038","authenticated-orcid":false,"given":"Estella","family":"Weiss-Krejci","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eduard","family":"Winter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4485-8570","authenticated-orcid":false,"given":"Thiseas C.","family":"Lamnidis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6242-3058","authenticated-orcid":false,"given":"Kay","family":"Pr\u00fcfer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3861-8677","authenticated-orcid":false,"given":"Kathrin","family":"N\u00e4gele","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3615-3936","authenticated-orcid":false,"given":"Maria","family":"Spyrou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1017-9150","authenticated-orcid":false,"given":"Stephan","family":"Schiffels","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philipp W.","family":"Stockhammer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2475-2007","authenticated-orcid":false,"given":"Wolfgang","family":"Haak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8206-3907","authenticated-orcid":false,"given":"Cosimo","family":"Posth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina","family":"Warinner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kirsten I.","family":"Bos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1176-1166","authenticated-orcid":false,"given":"Alexander","family":"Herbig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9144-3920","authenticated-orcid":false,"given":"Johannes","family":"Krause","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,6,12]]},"reference":[{"key":"7546_CR1","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1128\/CMR.15.4.564-594.2002","volume":"15","author":"R Carter","year":"2002","unstructured":"Carter, R. & Mendis, K. N. Evolutionary and historical aspects of the burden of malaria. Clin. Microbiol. Rev. 15, 564\u2013594 (2002).","journal-title":"Clin. Microbiol. Rev."},{"key":"7546_CR2","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-017-01534-5","volume":"7","author":"P Gelabert","year":"2017","unstructured":"Gelabert, P., Olalde, I., de-Dios, T., Civit, S. & Lalueza-Fox, C. Malaria was a weak selective force in ancient Europeans. Sci. Rep. 7, 1377 (2017).","journal-title":"Sci. Rep."},{"key":"7546_CR3","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1017\/S0025727300007651","volume":"48","author":"R Sallares","year":"2004","unstructured":"Sallares, R., Bouwman, A. & Anderung, C. The spread of malaria to southern europe in antiquity: new approaches to old problems. Med. Hist. 48, 311\u2013328 (2004).","journal-title":"Med. Hist."},{"key":"7546_CR4","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1016\/S0140-6736(18)30324-6","volume":"391","author":"EA Ashley","year":"2018","unstructured":"Ashley, E. A., Pyae Phyo, A. & Woodrow, C. J. Malaria. Lancet 391, 1608\u20131621 (2018).","journal-title":"Lancet"},{"key":"7546_CR5","unstructured":"World Health Organization. World Malaria Report 2021 (World Health Organization, 2021)."},{"key":"7546_CR6","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1086\/432519","volume":"77","author":"DP Kwiatkowski","year":"2005","unstructured":"Kwiatkowski, D. P. How malaria has affected the human genome and what human genetics can teach us about malaria. Am. J. Hum. Genet. 77, 171\u2013192 (2005).","journal-title":"Am. J. Hum. Genet."},{"key":"7546_CR7","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1038\/nature09442","volume":"467","author":"W Liu","year":"2010","unstructured":"Liu, W. et al. Origin of the human malaria parasite Plasmodium falciparum in gorillas. Nature 467, 420\u2013425 (2010).","journal-title":"Nature"},{"key":"7546_CR8","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms11078","volume":"7","author":"SA Sundararaman","year":"2016","unstructured":"Sundararaman, S. A. et al. Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria. Nat. Commun. 7, 11078 (2016).","journal-title":"Nat. Commun."},{"key":"7546_CR9","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.1038\/ng.2373","volume":"44","author":"DE Neafsey","year":"2012","unstructured":"Neafsey, D. E. et al. The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum. Nat. Genet. 44, 1046\u20131050 (2012).","journal-title":"Nat. Genet."},{"key":"7546_CR10","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/j.ijpara.2016.05.008","volume":"47","author":"DE Loy","year":"2017","unstructured":"Loy, D. E. et al. Out of Africa: origins and evolution of the human malaria parasites Plasmodium falciparum and Plasmodium vivax. Int. J. Parasitol. 47, 87\u201397 (2017).","journal-title":"Int. J. Parasitol."},{"key":"7546_CR11","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.1093\/molbev\/msi160","volume":"22","author":"J Mu","year":"2005","unstructured":"Mu, J. et al. Host switch leads to emergence of Plasmodium vivax malaria in humans. Mol. Biol. Evol. 22, 1686\u20131693 (2005).","journal-title":"Mol. Biol. Evol."},{"key":"7546_CR12","doi-asserted-by":"crossref","first-page":"1733","DOI":"10.1093\/molbev\/msi168","volume":"22","author":"S Jongwutiwes","year":"2005","unstructured":"Jongwutiwes, S. et al. Mitochondrial genome sequences support ancient population expansion in Plasmodium vivax. Mol. Biol. Evol. 22, 1733\u20131739 (2005).","journal-title":"Mol. Biol. Evol."},{"key":"7546_CR13","doi-asserted-by":"crossref","first-page":"eabc3713","DOI":"10.1126\/sciadv.abc3713","volume":"7","author":"J Daron","year":"2021","unstructured":"Daron, J. et al. Population genomic evidence of Plasmodium vivax Southeast Asian origin. Sci. Adv. 7, eabc3713 (2021).","journal-title":"Sci. Adv."},{"key":"7546_CR14","first-page":"E8450","volume":"115","author":"DE Loy","year":"2018","unstructured":"Loy, D. E. et al. Evolutionary history of human Plasmodium vivax revealed by genome-wide analyses of related ape parasites. Proc. Natl Acad. Sci. USA 115, E8450\u2013E8459 (2018).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7546_CR15","volume":"5","author":"W Liu","year":"2014","unstructured":"Liu, W. et al. African origin of the malaria parasite Plasmodium vivax. Nat. Commun. 5, 3346 (2014).","journal-title":"Nat. Commun."},{"key":"7546_CR16","doi-asserted-by":"crossref","first-page":"e0007140","DOI":"10.1371\/journal.pntd.0007140","volume":"13","author":"KA Twohig","year":"2019","unstructured":"Twohig, K. A. et al. Growing evidence of Plasmodium vivax across malaria-endemic Africa. PLoS Negl. Trop. Dis. 13, e0007140 (2019).","journal-title":"PLoS Negl. Trop. Dis."},{"key":"7546_CR17","doi-asserted-by":"crossref","first-page":"13973","DOI":"10.1073\/pnas.96.24.13973","volume":"96","author":"PA Zimmerman","year":"1999","unstructured":"Zimmerman, P. A. et al. Emergence of FY*Anull in a Plasmodium vivax-endemic region of Papua New Guinea. Proc. Natl Acad. Sci. USA 96, 13973\u201313977 (1999).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7546_CR18","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1186\/1756-3305-4-92","volume":"4","author":"PW Gething","year":"2011","unstructured":"Gething, P. W. et al. Modelling the global constraints of temperature on transmission of Plasmodium falciparum and P. vivax. Parasit. Vectors 4, 92 (2011).","journal-title":"Parasit. Vectors"},{"key":"7546_CR19","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1111\/ele.12015","volume":"16","author":"EA Mordecai","year":"2013","unstructured":"Mordecai, E. A. et al. Optimal temperature for malaria transmission is dramatically lower than previously predicted. Ecol. Lett. 16, 22\u201330 (2013).","journal-title":"Ecol. Lett."},{"key":"7546_CR20","doi-asserted-by":"crossref","unstructured":"Grauer, A. L. & Roberts, C. A. in Ortner\u2019s Identification of Pathological Conditions in Human Skeletal Remains 3rd edn (ed. Buikstra, J. E.) 441\u2013478 (Academic Press, 2019).","DOI":"10.1016\/B978-0-12-809738-0.00012-0"},{"key":"7546_CR21","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1002\/ajpa.24738","volume":"181","author":"T Wang","year":"2023","unstructured":"Wang, T. et al. Paleoepidemiology of cribra orbitalia: insights from early seventh millennium BP Con Co Ngua, Vietnam. Am. J. Biol. Anthropol. 181, 250\u2013261 (2023).","journal-title":"Am. J. Biol. Anthropol."},{"key":"7546_CR22","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1002\/ajpa.22819","volume":"158","author":"NE Smith-Guzm\u00e1n","year":"2015","unstructured":"Smith-Guzm\u00e1n, N. E. The skeletal manifestation of malaria: an epidemiological approach using documented skeletal collections. Am. J. Phys. Anthropol. 158, 624\u2013635 (2015).","journal-title":"Am. J. Phys. Anthropol."},{"key":"7546_CR23","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1016\/j.jaa.2018.01.004","volume":"49","author":"S Marciniak","year":"2018","unstructured":"Marciniak, S., Herring, D. A., Sperduti, A., Poinar, H. N. & Prowse, T. L. A multi-faceted anthropological and genomic approach to framing Plasmodium falciparum malaria in Imperial period central-southern Italy (1st\u20134th c. CE). J. Anthropol. Archaeol. 49, 210\u2013224 (2018).","journal-title":"J. Anthropol. Archaeol."},{"key":"7546_CR24","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1002\/ajpa.23258","volume":"164","author":"F Rivera","year":"2017","unstructured":"Rivera, F. & Miraz\u00f3n Lahr, M. New evidence suggesting a dissociated etiology for cribra orbitalia and porotic hyperostosis. Am. J. Phys. Anthropol. 164, 76\u201396 (2017).","journal-title":"Am. J. Phys. Anthropol."},{"key":"7546_CR25","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1002\/ajpa.21031","volume":"139","author":"PL Walker","year":"2009","unstructured":"Walker, P. L., Bathurst, R. R., Richman, R., Gjerdrum, T. & Andrushko, V. A. The causes of porotic hyperostosis and cribra orbitalia: a reappraisal of the iron-deficiency-anemia hypothesis. Am. J. Phys. Anthropol. 139, 109\u2013125 (2009).","journal-title":"Am. J. Phys. Anthropol."},{"key":"7546_CR26","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1111\/emed.12212","volume":"25","author":"TP Newfield","year":"2017","unstructured":"Newfield, T. P. Malaria and malaria-like disease in the early Middle Ages. Early Mediev. Eur. 25, 251\u2013300 (2017).","journal-title":"Early Mediev. Eur."},{"key":"7546_CR27","volume":"8","author":"PT Rodrigues","year":"2018","unstructured":"Rodrigues, P. T. et al. Human migration and the spread of malaria parasites to the New World. Sci. Rep. 8, 1993 (2018).","journal-title":"Sci. Rep."},{"key":"7546_CR28","doi-asserted-by":"crossref","first-page":"2050","DOI":"10.1093\/molbev\/mst104","volume":"30","author":"JE Taylor","year":"2013","unstructured":"Taylor, J. E. et al. The evolutionary history of Plasmodium vivax as inferred from mitochondrial genomes: parasite genetic diversity in the Americas. Mol. Biol. Evol. 30, 2050\u20132064 (2013).","journal-title":"Mol. Biol. Evol."},{"key":"7546_CR29","doi-asserted-by":"crossref","first-page":"e29137","DOI":"10.1371\/journal.pone.0029137","volume":"6","author":"R Culleton","year":"2011","unstructured":"Culleton, R. et al. The origins of African Plasmodium vivax; insights from mitochondrial genome sequencing. PLoS One 6, e29137 (2011).","journal-title":"PLoS One"},{"key":"7546_CR30","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1093\/molbev\/msz264","volume":"37","author":"L van Dorp","year":"2020","unstructured":"van Dorp, L. et al. Plasmodium vivax malaria viewed through the lens of an eradicated European strain. Mol. Biol. Evol. 37, 773\u2013785 (2020).","journal-title":"Mol. Biol. Evol."},{"key":"7546_CR31","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1038\/hdy.2011.16","volume":"107","author":"PW Hedrick","year":"2011","unstructured":"Hedrick, P. W. Population genetics of malaria resistance in humans. Heredity 107, 283\u2013304 (2011).","journal-title":"Heredity"},{"key":"7546_CR32","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/s41576-019-0119-1","volume":"20","author":"MA Spyrou","year":"2019","unstructured":"Spyrou, M. A., Bos, K. I., Herbig, A. & Krause, J. Ancient pathogen genomics as an emerging tool for infectious disease research. Nat. Rev. Genet. 20, 323\u2013340 (2019).","journal-title":"Nat. Rev. Genet."},{"key":"7546_CR33","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1016\/j.ijpp.2023.03.002","volume":"41","author":"R Schats","year":"2023","unstructured":"Schats, R. Developing an archaeology of malaria. A critical review of current approaches and a discussion on ways forward. Int. J. Paleopathol. 41, 32\u201342 (2023).","journal-title":"Int. J. Paleopathol."},{"key":"7546_CR34","first-page":"e000289","volume":"5","author":"T de-Dios","year":"2019","unstructured":"de-Dios, T. et al. Genetic affinities of an eradicated European Plasmodium falciparum strain. Microb. Genom. 5, e000289 (2019).","journal-title":"Microb. Genom."},{"key":"7546_CR35","doi-asserted-by":"crossref","first-page":"11495","DOI":"10.1073\/pnas.1611017113","volume":"113","author":"P Gelabert","year":"2016","unstructured":"Gelabert, P. et al. Mitochondrial DNA from the eradicated European Plasmodium vivax and P. falciparum from 70-year-old slides from the Ebro Delta in Spain. Proc. Natl Acad. Sci. USA 113, 11495\u201311500 (2016).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7546_CR36","doi-asserted-by":"crossref","first-page":"R1220","DOI":"10.1016\/j.cub.2016.10.016","volume":"26","author":"S Marciniak","year":"2016","unstructured":"Marciniak, S. et al. Plasmodium falciparum malaria in 1st \u20132nd century CE southern Italy. Curr. Biol. 26, R1220\u2013R1222 (2016).","journal-title":"Curr. Biol."},{"key":"7546_CR37","doi-asserted-by":"crossref","first-page":"136","DOI":"10.12688\/wellcomeopenres.17795.1","volume":"7","author":"MalariaGEN","year":"2022","unstructured":"MalariaGEN et al. An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples [version 1; peer review: 2 approved]. Wellcome Open Res. 7, 136 (2022).","journal-title":"Wellcome Open Res."},{"key":"7546_CR38","doi-asserted-by":"crossref","first-page":"42","DOI":"10.12688\/wellcomeopenres.16168.1","volume":"6","author":"MalariaGEN","year":"2021","unstructured":"MalariaGEN et al. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples [version 2; peer review: 2 approved]. Wellcome Open Res. 6, 42 (2021).","journal-title":"Wellcome Open Res."},{"key":"7546_CR39","first-page":"51","volume":"136","author":"A Simons","year":"1994","unstructured":"Simons, A., Sch\u00f6n, W. & Shrestha, S. S. Preliminary report on the 1992 campaign of the team of the Institute of Prehistory, University of Cologne. Ancient Nepal 136, 51\u201375 (1994).","journal-title":"Ancient Nepal"},{"key":"7546_CR40","unstructured":"Ramsl, P. C. in Iron Age Connectivity in the Carpathian Basin. Proc. Int. Colloquium from T\u00e2rgu Mure\u0219 (eds Berecki, S. et al.) 39\u201350 (MEGA, 2018)."},{"key":"7546_CR41","unstructured":"Collis, J. in The European Iron Age Ch. 5 (Routledge, 1997)."},{"key":"7546_CR42","doi-asserted-by":"crossref","first-page":"eabi7038","DOI":"10.1126\/sciadv.abi7038","volume":"7","author":"V Villalba-Mouco","year":"2021","unstructured":"Villalba-Mouco, V. et al. Genomic transformation and social organization during the Copper Age\u2013Bronze Age transition in southern Iberia. Sci. Adv. 7, eabi7038 (2021).","journal-title":"Sci. Adv."},{"key":"7546_CR43","first-page":"288","volume":"3","author":"\u041d\u0412 \u041e\u0432\u0447\u0438\u043d\u043d\u0438\u043a\u043e\u0432\u0430","year":"1998","unstructured":"\u041e\u0432\u0447\u0438\u043d\u043d\u0438\u043a\u043e\u0432\u0430, \u041d. \u0412. & \u0425\u043e\u0445\u043b\u043e\u0432, \u0410. \u0410. \u0418\u0441\u0441\u043b\u0435\u0434\u043e\u0432\u0430\u043d\u0438\u0435 \u0433\u0440\u0443\u043d\u0442\u043e\u0432\u043e\u0433\u043e \u043c\u043e\u0433\u0438\u043b\u044c\u043d\u0438\u043a\u0430 \u0443 \u0441. \u0413\u0443\u043d\u0434\u043e\u0440\u043e\u0432\u043a\u0430 \u0432 \u043b\u0435\u0441\u043e\u0441\u0442\u0435\u043f\u043d\u043e\u043c \u041f\u043e\u0432\u043e\u043b\u0436\u044c\u0435. \u0422\u0432\u0435\u0440\u0441\u043a\u043e\u0439 \u0430\u0440\u0445\u0435\u043e\u043b\u043e\u0433\u0438\u0447\u0435\u0441\u043a\u0438\u0439 \u0441\u0431\u043e\u0440\u043d\u0438\u043a 3, 288\u2013299 (1998).","journal-title":"\u0422\u0432\u0435\u0440\u0441\u043a\u043e\u0439 \u0430\u0440\u0445\u0435\u043e\u043b\u043e\u0433\u0438\u0447\u0435\u0441\u043a\u0438\u0439 \u0441\u0431\u043e\u0440\u043d\u0438\u043a"},{"key":"7546_CR44","doi-asserted-by":"crossref","first-page":"79","DOI":"10.4269\/ajtmh.2007.77.79","volume":"77","author":"RN Price","year":"2007","unstructured":"Price, R. N. et al. Vivax malaria: neglected and not benign. Am. J. Trop. Med. Hyg. 77, 79\u201387 (2007).","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"7546_CR45","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.molbiopara.2016.07.005","volume":"210","author":"S Kumar","year":"2016","unstructured":"Kumar, S. et al. Distinct genomic architecture of Plasmodium falciparum populations from South Asia. Mol. Biochem. Parasitol. 210, 1\u20134 (2016).","journal-title":"Mol. Biochem. Parasitol."},{"key":"7546_CR46","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1073\/pnas.1119058109","volume":"109","author":"E Yalcindag","year":"2012","unstructured":"Yalcindag, E. et al. Multiple independent introductions of Plasmodium falciparum in South America. Proc. Natl Acad. Sci. USA 109, 511\u2013516 (2012).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7546_CR47","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1126\/science.1244325","volume":"343","author":"AS Siraj","year":"2014","unstructured":"Siraj, A. S. et al. Altitudinal changes in malaria incidence in highlands of Ethiopia and Colombia. Science 343, 1154\u20131158 (2014).","journal-title":"Science"},{"key":"7546_CR48","first-page":"293","volume":"1","author":"M Aldenderfer","year":"2013","unstructured":"Aldenderfer, M. Variation in mortuary practice on the early Tibetan plateau and the high Himalayas. J. Int. Ass. Bon Res. 1, 293\u2013318 (2013).","journal-title":"J. Int. Ass. Bon Res."},{"key":"7546_CR49","unstructured":"Tiwari, D. N. Cave burials from western Nepal, Mustang. Ancient Nepal 85, 1\u201312 (1984\u20131985)."},{"key":"7546_CR50","volume":"13","author":"C-C Liu","year":"2022","unstructured":"Liu, C.-C. et al. Ancient genomes from the Himalayas illuminate the genetic history of Tibetans and their Tibeto-Burman speaking neighbors. Nat. Commun. 13, 1203 (2022).","journal-title":"Nat. Commun."},{"key":"7546_CR51","volume":"13","author":"M Dhimal","year":"2014","unstructured":"Dhimal, M. et al. Spatio-temporal distribution of malaria and its association with climatic factors and vector-control interventions in two high-risk districts of Nepal. Malar. J. 13, 457 (2014).","journal-title":"Malar. J."},{"key":"7546_CR52","doi-asserted-by":"crossref","unstructured":"Church, W. B. & von Hagen, A. C. in Handbook of South American Archaeology (eds Silverman, H. & Isbell, W. H.) 903\u2013926 (Springer, 2008).","DOI":"10.1007\/978-0-387-74907-5_45"},{"key":"7546_CR53","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.quascirev.2018.12.004","volume":"207","author":"A Koch","year":"2019","unstructured":"Koch, A., Brierley, C., Maslin, M. M. & Lewis, S. L. Earth system impacts of the European arrival and Great Dying in the Americas after 1492. Quat. Sci. Rev. 207, 13\u201336 (2019).","journal-title":"Quat. Sci. Rev."},{"key":"7546_CR54","unstructured":"Alchon, S. A. C. in A Pest in the Land: New World Epidemics in a Global Perspective 60\u201382 (Univ. New Mexico Press, 2003)."},{"key":"7546_CR55","doi-asserted-by":"crossref","first-page":"e0244497","DOI":"10.1371\/journal.pone.0244497","volume":"15","author":"EK Guevara","year":"2020","unstructured":"Guevara, E. K. et al. Genetic assessment reveals no population substructure and divergent regional and sex-specific histories in the Chachapoyas from northeast Peru. PLoS One 15, e0244497 (2020).","journal-title":"PLoS One"},{"key":"7546_CR56","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1016\/j.jasrep.2018.05.007","volume":"20","author":"K Van de Vijver","year":"2018","unstructured":"Van de Vijver, K. Past life and death in a Flemish town. An archaeo-anthropological study of burials from the medieval and post-medieval St. Rombout\u2019s cemetery in Mechelen, Belgium (10th\u201318th centuries CE). J. Archaeol. Sci. Reports 20, 524\u2013555 (2018).","journal-title":"J. Archaeol. Sci. Reports"},{"key":"7546_CR57","unstructured":"Van de Vijver, K., Kinnaer, F. & Depuydt, S. in The Urban Graveyard: Archaeological Perspectives (eds van Oosten, R. et al.) 239\u2013287 (Sidestone Press, 2018)."},{"key":"7546_CR58","doi-asserted-by":"crossref","first-page":"255","DOI":"10.5744\/bi.2018.1027","volume":"2","author":"K Van de Vijver","year":"2018","unstructured":"Van de Vijver, K. Unraveling the motives behind multiple burial in St. Rombout\u2019s cemetery in Mechelen, Belgium, tenth\u2013eighteenth centuries A.D. Bioarchaeol. Int. 2, 255\u2013282 (2018).","journal-title":"Bioarchaeol. Int."},{"key":"7546_CR59","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1038\/s41586-022-05247-2","volume":"610","author":"J Gretzinger","year":"2022","unstructured":"Gretzinger, J. et al. The Anglo-Saxon migration and the formation of the early English gene pool. Nature 610, 112\u2013119 (2022).","journal-title":"Nature"},{"key":"7546_CR60","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/j.pt.2004.03.006","volume":"20","author":"M Mayxay","year":"2004","unstructured":"Mayxay, M., Pukrittayakamee, S., Newton, P. N. & White, N. J. Mixed-species malaria infections in humans. Trends Parasitol. 20, 233\u2013240 (2004).","journal-title":"Trends Parasitol."},{"key":"7546_CR61","unstructured":"Parker, G. The Army of Flanders and the Spanish Road, 1567\u20131659: The Logistics of Spanish Victory and Defeat in the Low Countries\u2019 Wars. (Cambridge Univ. Press, 1972)."},{"key":"7546_CR62","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1016\/j.cmi.2016.04.023","volume":"22","author":"ET Piperaki","year":"2016","unstructured":"Piperaki, E. T. & Daikos, G. L. Malaria in Europe: emerging threat or minor nuisance? Clin. Microbiol. Infect. 22, 487\u2013493 (2016).","journal-title":"Clin. Microbiol. Infect."},{"key":"7546_CR63","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-019-1903-0","volume":"20","author":"R H\u00fcbler","year":"2019","unstructured":"H\u00fcbler, R. et al. HOPS: automated detection and authentication of pathogen DNA in archaeological remains. Genome Biol. 20, 280 (2019).","journal-title":"Genome Biol."},{"key":"7546_CR64","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform. Bioinformatics 25, 1754\u20131760 (2009).","journal-title":"Bioinformatics"},{"key":"7546_CR65","doi-asserted-by":"crossref","first-page":"e141","DOI":"10.1093\/nar\/gku699","volume":"42","author":"G Renaud","year":"2014","unstructured":"Renaud, G., Stenzel, U. & Kelso, J. leeHom: adaptor trimming and merging for Illumina sequencing reads. Nucleic Acids Res. 42, e141 (2014).","journal-title":"Nucleic Acids Res."},{"key":"7546_CR66","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The Sequence Alignment\/Map format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"7546_CR67","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1093\/bioinformatics\/btr026","volume":"27","author":"R Schmieder","year":"2011","unstructured":"Schmieder, R. & Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863\u2013864 (2011).","journal-title":"Bioinformatics"},{"key":"7546_CR68","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1038\/s41559-017-0446-6","volume":"2","author":"\u00c5J V\u00e5gene","year":"2018","unstructured":"V\u00e5gene, \u00c5. J. et al. Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nat. Ecol. Evol. 2, 520\u2013528 (2018).","journal-title":"Nat. Ecol. Evol."},{"key":"7546_CR69","doi-asserted-by":"crossref","first-page":"e1004957","DOI":"10.1371\/journal.pcbi.1004957","volume":"12","author":"DH Huson","year":"2016","unstructured":"Huson, D. H. et al. MEGAN Community Edition - interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput. Biol. 12, e1004957 (2016).","journal-title":"PLoS Comput. Biol."},{"key":"7546_CR70","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms5052","volume":"5","author":"MD Preston","year":"2014","unstructured":"Preston, M. D. et al. A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains. Nat. Commun. 5, 4052 (2014).","journal-title":"Nat. Commun."},{"key":"7546_CR71","doi-asserted-by":"crossref","first-page":"1028","DOI":"10.1089\/cmb.2006.13.1028","volume":"13","author":"A Morgulis","year":"2006","unstructured":"Morgulis, A., Gertz, E. M., Sch\u00e4ffer, A. A. & Agarwala, R. A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J. Comput. Biol. 13, 1028\u20131040 (2006).","journal-title":"J. Comput. Biol."},{"key":"7546_CR72","doi-asserted-by":"crossref","first-page":"2223","DOI":"10.1073\/pnas.1221359110","volume":"110","author":"Q Fu","year":"2013","unstructured":"Fu, Q. et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl Acad. Sci. USA 110, 2223\u20132227 (2013).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7546_CR73","doi-asserted-by":"crossref","first-page":"e0129102","DOI":"10.1371\/journal.pone.0129102","volume":"10","author":"R Pinhasi","year":"2015","unstructured":"Pinhasi, R. et al. Optimal ancient DNA yields from the inner ear part of the human petrous bone. PLoS ONE 10, e0129102 (2015).","journal-title":"PLoS ONE"},{"key":"7546_CR74","doi-asserted-by":"crossref","first-page":"15758","DOI":"10.1073\/pnas.1314445110","volume":"110","author":"J Dabney","year":"2013","unstructured":"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\u201315763 (2013).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7546_CR75","doi-asserted-by":"crossref","first-page":"2447","DOI":"10.1038\/s41596-018-0050-5","volume":"13","author":"N Rohland","year":"2018","unstructured":"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\u20132461 (2018).","journal-title":"Nat. Protoc."},{"key":"7546_CR76","doi-asserted-by":"crossref","first-page":"20130624","DOI":"10.1098\/rstb.2013.0624","volume":"370","author":"N Rohland","year":"2015","unstructured":"Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil\u2013DNA\u2013glycosylase treatment for screening of ancient DNA. Philos. Trans. R. Soc. Lond. B Biol. Sci. 370, 20130624 (2015).","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"7546_CR77","doi-asserted-by":"publisher","unstructured":"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).","DOI":"10.1101\/pdb.prot5448"},{"key":"7546_CR78","doi-asserted-by":"crossref","first-page":"e79","DOI":"10.1093\/nar\/gkw835","volume":"45","author":"M-T Gansauge","year":"2017","unstructured":"Gansauge, M.-T. et al. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Res. 45, e79 (2017).","journal-title":"Nucleic Acids Res."},{"key":"7546_CR79","doi-asserted-by":"crossref","first-page":"2279","DOI":"10.1038\/s41596-020-0338-0","volume":"15","author":"M-T Gansauge","year":"2020","unstructured":"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\u20132300 (2020).","journal-title":"Nat. Protoc."},{"key":"7546_CR80","doi-asserted-by":"crossref","first-page":"4742","DOI":"10.1093\/nar\/23.22.4742","volume":"23","author":"MM DeAngelis","year":"1995","unstructured":"DeAngelis, M. M., Wang, D. G. & Hawkins, T. L. Solid-phase reversible immobilization for the isolation of PCR products. Nucleic Acids Res. 23, 4742\u20134743 (1995).","journal-title":"Nucleic Acids Res."},{"key":"7546_CR81","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/nature16152","volume":"528","author":"I Mathieson","year":"2015","unstructured":"Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499\u2013503 (2015).","journal-title":"Nature"},{"key":"7546_CR82","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature14317","volume":"522","author":"W Haak","year":"2015","unstructured":"Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207\u2013211 (2015).","journal-title":"Nature"},{"key":"7546_CR83","doi-asserted-by":"crossref","first-page":"e10947","DOI":"10.7717\/peerj.10947","volume":"9","author":"JA Fellows Yates","year":"2021","unstructured":"Fellows Yates, J. A. et al. Reproducible, portable, and efficient ancient genome reconstruction with nf-core\/eager. PeerJ 9, e10947 (2021).","journal-title":"PeerJ"},{"key":"7546_CR84","doi-asserted-by":"crossref","DOI":"10.1186\/s13104-016-1900-2","volume":"9","author":"M Schubert","year":"2016","unstructured":"Schubert, M., Lindgreen, S. & Orlando, L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res. Notes 9, 88 (2016).","journal-title":"BMC Res. Notes"},{"key":"7546_CR85","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","volume":"34","author":"S Chen","year":"2018","unstructured":"Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884\u2013i890 (2018).","journal-title":"Bioinformatics"},{"key":"7546_CR86","doi-asserted-by":"crossref","DOI":"10.1038\/s41597-021-00816-y","volume":"8","author":"JA Fellows Yates","year":"2021","unstructured":"Fellows Yates, J. A. et al. Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Scientific Data 8, 31 (2021).","journal-title":"Scientific Data"},{"key":"7546_CR87","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","volume":"43","author":"MA DePristo","year":"2011","unstructured":"DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491\u2013498 (2011).","journal-title":"Nat. Genet."},{"key":"7546_CR88","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/nature13591","volume":"514","author":"KI Bos","year":"2014","unstructured":"Bos, K. I. et al. Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature 514, 494\u2013497 (2014).","journal-title":"Nature"},{"key":"7546_CR89","doi-asserted-by":"crossref","first-page":"e2116722119","DOI":"10.1073\/pnas.2116722119","volume":"119","author":"AA Valtue\u00f1a","year":"2022","unstructured":"Valtue\u00f1a, A. A. et al. Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague. Proc. Natl Acad. Sci. USA 119, e2116722119 (2022).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7546_CR90","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841\u2013842 (2010).","journal-title":"Bioinformatics"},{"key":"7546_CR91","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1038\/nature01097","volume":"419","author":"MJ Gardner","year":"2002","unstructured":"Gardner, M. J. et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419, 498\u2013511 (2002).","journal-title":"Nature"},{"key":"7546_CR92","doi-asserted-by":"crossref","first-page":"58","DOI":"10.12688\/wellcomeopenres.15194.1","volume":"4","author":"U B\u00f6hme","year":"2019","unstructured":"B\u00f6hme, U., Otto, T. D., Sanders, M., Newbold, C. I. & Berriman, M. Progression of the canonical reference malaria parasite genome from 2002\u20132019 [version 2; peer review: 3 approved]. Wellcome Open Res 4, 58 (2019).","journal-title":"Wellcome Open Res"},{"key":"7546_CR93","doi-asserted-by":"crossref","first-page":"4","DOI":"10.12688\/wellcomeopenres.9876.1","volume":"1","author":"S Auburn","year":"2016","unstructured":"Auburn, S. et al. A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes [version 1; peer review: 2 approved]. Wellcome Open Res 1, 4 (2016).","journal-title":"Wellcome Open Res"},{"key":"7546_CR94","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1101\/gr.176552.114","volume":"25","author":"G Jun","year":"2015","unstructured":"Jun, G., Wing, M. K., Abecasis, G. R. & Kang, H. M. An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data. Genome Res. 25, 918\u2013925 (2015).","journal-title":"Genome Res."},{"key":"7546_CR95","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1038\/ng1847","volume":"38","author":"AL Price","year":"2006","unstructured":"Price, A. L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904\u2013909 (2006).","journal-title":"Nat. Genet."},{"key":"7546_CR96","doi-asserted-by":"crossref","first-page":"2074","DOI":"10.1371\/journal.pgen.0020190","volume":"2","author":"N Patterson","year":"2006","unstructured":"Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, 2074\u20132093 (2006).","journal-title":"PLoS Genet."},{"key":"7546_CR97","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.094052.109","volume":"19","author":"DH Alexander","year":"2009","unstructured":"Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655\u20131664 (2009).","journal-title":"Genome Res."},{"key":"7546_CR98","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","volume":"81","author":"S Purcell","year":"2007","unstructured":"Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559\u2013575 (2007).","journal-title":"Am. J. Hum. Genet."},{"key":"7546_CR99","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1534\/genetics.112.145037","volume":"192","author":"N Patterson","year":"2012","unstructured":"Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065\u20131093 (2012).","journal-title":"Genetics"},{"key":"7546_CR100","doi-asserted-by":"crossref","first-page":"2685","DOI":"10.1093\/bioinformatics\/bts507","volume":"28","author":"S Kumar","year":"2012","unstructured":"Kumar, S., Stecher, G., Peterson, D. & Tamura, K. MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis. Bioinformatics 28, 2685\u20132686 (2012).","journal-title":"Bioinformatics"},{"key":"7546_CR101","doi-asserted-by":"crossref","first-page":"W293","DOI":"10.1093\/nar\/gkab301","volume":"49","author":"I Letunic","year":"2021","unstructured":"Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293\u2013W296 (2021).","journal-title":"Nucleic Acids Res."}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07546-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07546-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07546-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,3]],"date-time":"2024-07-03T15:15:17Z","timestamp":1720019717000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07546-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6,12]]},"references-count":101,"journal-issue":{"issue":"8019","published-print":{"date-parts":[[2024,7,4]]}},"alternative-id":["7546"],"URL":"https:\/\/doi.org\/10.1038\/s41586-024-07546-2","relation":{},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,6,12]]},"assertion":[{"value":"10 September 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 May 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 June 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}