{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T21:33:43Z","timestamp":1792445623141,"version":"4.5.0"},"reference-count":106,"publisher":"Springer Science and Business Media LLC","issue":"8057","license":[{"start":{"date-parts":[[2024,12,18]],"date-time":"2024-12-18T00:00:00Z","timestamp":1734480000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,12,18]],"date-time":"2024-12-18T00:00:00Z","timestamp":1734480000000},"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":[[2025,4,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Human treponemal infections are caused by a family of closely related\n                    <jats:italic>Treponema pallidum<\/jats:italic>\n                    that give rise to the diseases yaws, bejel, pinta and, most notably, syphilis\n                    <jats:sup>1<\/jats:sup>\n                    . Debates on a common origin for these pathogens and the history of syphilis itself have weighed evidence for the \u2018Columbian hypothesis\u2019\n                    <jats:sup>2<\/jats:sup>\n                    , which argues for an American origin, against that for the \u2018pre-Columbian hypothesis\u2019\n                    <jats:sup>3<\/jats:sup>\n                    , which argues for the presence of the disease in Eurasia in the Medieval period and possibly earlier. Although molecular data has provided a genetic basis for distinction of the typed subspecies\n                    <jats:sup>4<\/jats:sup>\n                    , deep evolution of the complex has remained unresolved owing to limitations in the conclusions that can be drawn from the sparse palaeogenomic data that are currently available. Here we explore this evolutionary history through analyses of five pre- and peri-contact ancient treponemal genomes from the Americas that represent ancient relatives of the\n                    <jats:italic>T. pallidum<\/jats:italic>\n                    subsp.\u00a0\n                    <jats:italic>pallidum<\/jats:italic>\n                    \u00a0(syphilis),\n                    <jats:italic>T. pallidum<\/jats:italic>\n                    subsp.\n                    <jats:italic>pertenue<\/jats:italic>\n                    (yaws) and\n                    <jats:italic>T. pallidum<\/jats:italic>\n                    subsp.\n                    <jats:italic>endemicum<\/jats:italic>\n                    \u00a0(bejel) lineages. Our data indicate unexplored diversity and an emergence of\n                    <jats:italic>T. pallidum<\/jats:italic>\n                    that post-dates human occupation in the Americas. Together, these results support an American origin for all\n                    <jats:italic>T. pallidum<\/jats:italic>\n                    characterized at the genomic level, both modern and ancient.\n                  <\/jats:p>","DOI":"10.1038\/s41586-024-08515-5","type":"journal-article","created":{"date-parts":[[2024,12,18]],"date-time":"2024-12-18T11:02:04Z","timestamp":1734519724000},"page":"186-193","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Ancient genomes reveal a deep history of Treponema pallidum in the Americas"],"prefix":"10.1038","volume":"640","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0518-4518","authenticated-orcid":false,"given":"Rodrigo","family":"Barquera","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7160-6240","authenticated-orcid":false,"given":"T. Lesley","family":"Sitter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9755-6459","authenticated-orcid":false,"given":"Casey L.","family":"Kirkpatrick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8982-2550","authenticated-orcid":false,"given":"Dar\u00edo A.","family":"Ramirez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arthur","family":"Kocher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3615-3936","authenticated-orcid":false,"given":"Maria A.","family":"Spyrou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lourdes R.","family":"Couoh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorge A.","family":"Talavera-Gonz\u00e1lez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mario","family":"Castro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanya","family":"von Hunnius","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5174-1376","authenticated-orcid":false,"given":"Evelyn K.","family":"Guevara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4019-3823","authenticated-orcid":false,"given":"W. Derek","family":"Hamilton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4403-7548","authenticated-orcid":false,"given":"Patrick","family":"Roberts","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erin","family":"Scott","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariana","family":"Fabra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3410-3027","authenticated-orcid":false,"given":"Gabriela V.","family":"Da Pe\u00f1a","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5569-2281","authenticated-orcid":false,"given":"Aryel","family":"Pacheco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M\u00f3nica","family":"Rodriguez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eugenio","family":"Aspillaga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthi","family":"Tiliakou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth A.","family":"Nelson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen L.","family":"Giffin","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\/0000-0002-4204-5018","authenticated-orcid":false,"given":"Adam B.","family":"Rohrlach","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mar\u00eda","family":"de los \u00c1ngeles Garc\u00eda Mart\u00ednez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabiola A.","family":"Ballesteros Sol\u00eds","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":"Shelley R.","family":"Saunders","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9153-0626","authenticated-orcid":false,"given":"Rodrigo","family":"Nores","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"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2937-3006","authenticated-orcid":false,"given":"Kirsten I.","family":"Bos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,12,18]]},"reference":[{"key":"8515_CR1","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1128\/CMR.00070-13","volume":"27","author":"L Giacani","year":"2014","unstructured":"Giacani, L. & Lukehart, S. A. The endemic treponematoses. Clin. Microbio. Rev. 27, 89 (2014).","journal-title":"Clin. Microbio. Rev."},{"key":"8515_CR2","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1525\/aa.1969.71.2.02a00020","volume":"71","author":"AW Crosby Jr","year":"1969","unstructured":"Crosby, A. W. Jr. The early history of syphilis: a reappraisal. Am. Anthropol. 71, 218\u2013227 (1969).","journal-title":"Am. Anthropol."},{"key":"8515_CR3","first-page":"7","volume":"29","author":"CJ Hackett","year":"1963","unstructured":"Hackett, C. J. On the origin of the human treponematoses (pinta, yaws, endemic syphilis, and venereal syphilis). Bull. World Health Organ. 29, 7\u201341 (1963).","journal-title":"Bull. World Health Organ."},{"key":"8515_CR4","doi-asserted-by":"publisher","first-page":"e3261","DOI":"10.1371\/journal.pntd.0003261","volume":"8","author":"B \u0160taudov\u00e1","year":"2014","unstructured":"\u0160taudov\u00e1, B. et al. Whole genome sequence of the Treponema pallidum subsp. endemicum strain Bosnia A: the genome is related to yaws treponemes but contains few loci similar to syphilis treponemes. PLOS Negl. Trop. Dis. 8, e3261 (2014).","journal-title":"PLOS Negl. Trop. Dis."},{"key":"8515_CR5","unstructured":"Qu\u00e9tel, C. History of Syphilis (Johns Hopkins Univ. Press, 1990)."},{"key":"8515_CR6","doi-asserted-by":"publisher","first-page":"1549","DOI":"10.1038\/s41564-021-01000-z","volume":"6","author":"MA Beale","year":"2021","unstructured":"Beale, M. A. et al. Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis. Nat. Microbiol. 6, 1549\u20131560 (2021).","journal-title":"Nat. Microbiol."},{"key":"8515_CR7","doi-asserted-by":"publisher","first-page":"e0011602","DOI":"10.1371\/journal.pntd.0011602","volume":"17","author":"K Jane\u010dkoc\u00e1","year":"2023","unstructured":"Jane\u010dkoc\u00e1, K. et al. The genomes of the yaws bacterium, Treponema pallidum subsp. pertenue, of nonhuman primate and human origin are not genomically distinct. PLOS Negl. Trop. Dis. 17, e0011602 (2023).","journal-title":"PLOS Negl. Trop. Dis."},{"key":"8515_CR8","doi-asserted-by":"publisher","first-page":"3219","DOI":"10.1128\/IAI.68.6.3219-3225.2000","volume":"68","author":"K Wicher","year":"2000","unstructured":"Wicher, K., Wicher, V., Abbruscatom, F. & Baugh, R. E. Treponema pallidum subspecies pertenue displays pathogenic properties different from those of T. pallidum subsp. pallidum. Infect. Immun. 68, 3219\u20133225 (2000).","journal-title":"Infect. Immun."},{"key":"8515_CR9","doi-asserted-by":"publisher","first-page":"e0006447","DOI":"10.1371\/journal.pntd.0006447","volume":"12","author":"VJ Schuenemann","year":"2018","unstructured":"Schuenemann, V. J. et al. Historic Treponema pallidum genomes from colonial Mexico retrieved from archaeological remains. PLOS Negl. Trop. Dis. 12, e0006447 (2018).","journal-title":"PLOS Negl. Trop. Dis."},{"key":"8515_CR10","doi-asserted-by":"publisher","first-page":"e148","DOI":"10.1371\/journal.pntd.0000148","volume":"2","author":"KN Harper","year":"2008","unstructured":"Harper, K. N. et al. On the origin of the treponematoses: a phylogenetic approach. PLOS Negl. Trop. Dis. 2, e148 (2008).","journal-title":"PLOS Negl. Trop. Dis."},{"key":"8515_CR11","unstructured":"Hudson, E. H. Treponematosis (Oxford Univ. Press, 1946)."},{"key":"8515_CR12","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1002\/ajpa.21613","volume":"146","author":"KN Harper","year":"2011","unstructured":"Harper, K. N., Zuckerman, M. K., Harper, M. L., Kingston, J. D. & Armelagos, G. J. The origin and antiquity of syphilis revisited: an appraisal of Old World pre-Columbian evidence for treponemal infection. Am. J. Phys. Anthropol. 146, 99\u2013133 (2011).","journal-title":"Am. J. Phys. Anthropol."},{"key":"8515_CR13","unstructured":"Holcomb, R. C. Who Gave the World Syphilis? The Haitian Myth (Froben Press, 1930)."},{"key":"8515_CR14","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1099\/00207713-31-1-82","volume":"31","author":"DR Brothwell","year":"1981","unstructured":"Brothwell, D. R. Microevolutionary change in the human pathogenic treponemes: an alternative hypothesis. Int. J. Syst. Bacteriol. 31, 82\u201387 (1981).","journal-title":"Int. J. Syst. Bacteriol."},{"key":"8515_CR15","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1086\/204004","volume":"32","author":"FB Livingstone","year":"1991","unstructured":"Livingstone, F. B. On the origin of syphilis: an alternative hypothesis. Curr. Anthropol. 32, 587\u2013590 (1991).","journal-title":"Curr. Anthropol."},{"key":"8515_CR16","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1002\/oa.1390010106","volume":"1","author":"A Striland","year":"1991","unstructured":"Striland, A. Pre-Columbian treponematosis in medieval Britain. Int. J. of Osteoarchaeol. 1, 39\u201347 (1991).","journal-title":"Int. J. of Osteoarchaeol."},{"key":"8515_CR17","unstructured":"Dutour, O. et al. L\u2019origine de la Syphilis en Europe Avant our Apr\u00e8s 1493? (Editions Errance, 1994)."},{"key":"8515_CR18","unstructured":"Powell, M. L. & Cook, D. C. The Myth of Syphilis: the Natural History of Treponematosis in North America (Univ. Florida Press, 2005)."},{"key":"8515_CR19","doi-asserted-by":"crossref","unstructured":"Hackett C. J. Diagnostic Criteria of Syphilis, Yaws, and Treponarid (Treponematoses) and Some Other Diseases in Dry Bone (for Use in Osteo-archaeology) (Springer, 1976).","DOI":"10.1007\/978-3-662-06583-9"},{"key":"8515_CR20","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1002\/(SICI)1096-8644(199809)107:1<25::AID-AJPA3>3.0.CO;2-C","volume":"107","author":"SC Hillson","year":"1998","unstructured":"Hillson, S. C. et al. Dental defects of congenital syphilis. Am. J. Phys. Anthropol. 107, 25\u201340 (1998).","journal-title":"Am. J. Phys. Anthropol."},{"key":"8515_CR21","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1002\/ajpa.23988","volume":"171","author":"B Baker","year":"2020","unstructured":"Baker, B. et al. Advancing the understanding of treponemal disease in the past and present. Am. J. Phys. Anthropol. 171, 5\u201341 (2020).","journal-title":"Am. J. Phys. Anthropol."},{"key":"8515_CR22","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1016\/j.jas.2004.11.014","volume":"32","author":"AS Bouwman","year":"2005","unstructured":"Bouwman, A. S. & Brown, T. A. The limits of biomolecular palaeopathology: ancient DNA cannot be used to study venereal syphilis. J. Archaeol. Sci. 32, 703\u2013713 (2005).","journal-title":"J. Archaeol. Sci."},{"key":"8515_CR23","doi-asserted-by":"publisher","first-page":"2060","DOI":"10.1086\/315151","volume":"180","author":"CJ Kolman","year":"1999","unstructured":"Kolman, C. J., Centurion-Lara, A., Lukehart, S. A., Owsley, D. W. & Tuross, N. Identification of Treponema pallidum subspecies pallidum in a 200-year-old skeletal specimen. J. Infect. Dis. 180, 2060\u20132063 (1999).","journal-title":"J. Infect. Dis."},{"key":"8515_CR24","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1016\/j.cub.2020.04.002","volume":"30","author":"R Barquera","year":"2020","unstructured":"Barquera, R. et al. Origin and health status of first-generation Africans from early colonial Mexico. Curr. Biol. 30, 2078\u20132091.e11 (2020).","journal-title":"Curr. Biol."},{"key":"8515_CR25","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-66012-x","volume":"10","author":"KL Giffin","year":"2020","unstructured":"Giffin, K. L. et al. A treponemal genome from an historic plague victim supports a recent emergence of yaws and its presence in 15th century Europe. Sci Rep. 10, 9499 (2020).","journal-title":"Sci Rep."},{"key":"8515_CR26","doi-asserted-by":"publisher","first-page":"3788","DOI":"10.1016\/j.cub.2020.07.058","volume":"30","author":"K Majander","year":"2020","unstructured":"Majander, K. et al. Ancient bacterial genomes reveal a high diversity of Treponema pallidum strains in Early Modern Europe. Curr. Biol. 30, 3788\u20133803.e10 (2020).","journal-title":"Curr. Biol."},{"key":"8515_CR27","doi-asserted-by":"publisher","first-page":"16245","DOI":"10.1038\/nmicrobiol.2016.245","volume":"2","author":"N Arora","year":"2016","unstructured":"Arora, N. et al. Origin of modern syphilis and emergence of a pandemic Treponema pallidum cluster. Nat. Microbiol. 2, 16245 (2016).","journal-title":"Nat. Microbiol."},{"key":"8515_CR28","doi-asserted-by":"publisher","first-page":"pdb.prot5448","DOI":"10.1101\/pdb.prot5448","volume":"6","author":"M Meyer","year":"2010","unstructured":"Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 6, pdb.prot5448 (2010).","journal-title":"Cold Spring Harb. Protoc."},{"key":"8515_CR29","doi-asserted-by":"publisher","first-page":"2279","DOI":"10.1038\/s41596-020-0338-0","volume":"15","author":"M-T Gansauge","year":"2020","unstructured":"Gansauge, M.-T. et al. 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":"8515_CR30","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1903-0","volume":"20","author":"R Huebler","year":"2019","unstructured":"Huebler, R. et al. HOPS: automated detection and authentication of pathogen DNA in archaeological remains. Genome Biol. 20, 280 (2019).","journal-title":"Genome Biol."},{"key":"8515_CR31","doi-asserted-by":"publisher","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":"8515_CR32","doi-asserted-by":"publisher","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":"8515_CR33","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1038\/s41586-023-06965-x","volume":"627","author":"K Majander","year":"2024","unstructured":"Majander, K. et al. Redefining the treponemal history through pre-Columbian genomes from Brazil. Nature 627, 184\u2013188 (2024).","journal-title":"Nature"},{"key":"8515_CR34","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/gku1196","volume":"43","author":"NJ Croucher","year":"2015","unstructured":"Croucher, N. J. et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 43, e15 (2015).","journal-title":"Nucleic Acids Res."},{"key":"8515_CR35","doi-asserted-by":"publisher","first-page":"e1004041","DOI":"10.1371\/journal.pcbi.1004041","volume":"11","author":"X Didelot","year":"2015","unstructured":"Didelot, X. & Wilson, D. J. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput. Biol. 11, e1004041 (2015).","journal-title":"PLoS Comput. Biol."},{"key":"8515_CR36","doi-asserted-by":"publisher","first-page":"4453","DOI":"10.1093\/bioinformatics\/btz305","volume":"35","author":"AM Kozlov","year":"2019","unstructured":"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\u20134455 (2019).","journal-title":"Bioinformatics"},{"key":"8515_CR37","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1016\/j.gde.2016.08.004","volume":"41","author":"M Slatkin","year":"2016","unstructured":"Slatkin, M. Statistical methods for analyzing ancient DNA from hominins. Curr. Opin. Genet. Dev. 41, 72\u201376 (2016).","journal-title":"Curr. Opin. Genet. Dev."},{"key":"8515_CR38","doi-asserted-by":"publisher","first-page":"e1003537","DOI":"10.1371\/journal.pcbi.1003537","volume":"10","author":"R Bouckaert","year":"2014","unstructured":"Bouckaert, R. et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 10, e1003537 (2014).","journal-title":"PLoS Comput. Biol."},{"key":"8515_CR39","doi-asserted-by":"crossref","unstructured":"Featherstone, L. A., Rambaut, A., Duchene, S. & Wirth, W. Clockor2: inferring global and local strict molecular clocks using root-to-tip regression. Syst. Biol. 73, 623\u2013628 (2024).","DOI":"10.1093\/sysbio\/syae003"},{"key":"8515_CR40","doi-asserted-by":"publisher","first-page":"3363","DOI":"10.1093\/molbev\/msaa163","volume":"37","author":"S Duchene","year":"2020","unstructured":"Duchene, S. et al. Bayesian evaluation of temporal signal in measurably evolving populations. Mol. Biol. Evol. 37, 3363\u20133379 (2020).","journal-title":"Mol. Biol. Evol."},{"key":"8515_CR41","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1080\/10635150500433722","volume":"55","author":"N Lartillot","year":"2006","unstructured":"Lartillot, N. & Philippe, H. Computing Bayes factors using thermodynamic integration. Syst. Biol. 55, 195\u2013207 (2006).","journal-title":"Syst. Biol."},{"key":"8515_CR42","doi-asserted-by":"publisher","first-page":"17931803","DOI":"10.1093\/molbev\/msz094","volume":"36","author":"JV Membrebe","year":"2019","unstructured":"Membrebe, J. V., Suchard, M. A., Rambaut, A., Baele, G. & Lemey, P. Bayesian inference of evolutionary histories under time-dependent substitution rates. Mol. Biol. Evol. 36, 17931803 (2019).","journal-title":"Mol. Biol. Evol."},{"key":"8515_CR43","doi-asserted-by":"publisher","first-page":"6250","DOI":"10.1126\/science.aab3884","volume":"349","author":"M Raghavan","year":"2015","unstructured":"Raghavan, M. et al. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 349, 6250 (2015).","journal-title":"Science"},{"key":"8515_CR44","doi-asserted-by":"publisher","first-page":"891","DOI":"10.1126\/science.aax9830","volume":"365","author":"LG Davis","year":"2019","unstructured":"Davis, L. G. et al. Late upper paleolithic occupation at Cooper\u2019s Ferry, Idaho, USA, similar to 16,000 years ago. Science 365, 891\u2013897 (2019).","journal-title":"Science"},{"key":"8515_CR45","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/j.gde.2016.06.016","volume":"41","author":"P Skoglund","year":"2016","unstructured":"Skoglund, P. & Reich, D. A genomic view of the peopling of the Americas. Curr. Opin. Genet. Dev. 41, 27\u201335 (2016).","journal-title":"Curr. Opin. Genet. Dev."},{"key":"8515_CR46","unstructured":"Buret, F. Syphilis Today and Among the Ancient (F. A. Davis, 1891)."},{"key":"8515_CR47","doi-asserted-by":"publisher","first-page":"S174","DOI":"10.1098\/rsbl.2003.0131","volume":"271","author":"RJ Knell","year":"2004","unstructured":"Knell, R. J. Syphilis in renaissance Europe: rapid evolution of an introduced sexually transmitted disease? Proc. Biol. Sci. 271, S174\u2013S176 (2004).","journal-title":"Proc. Biol. Sci."},{"key":"8515_CR48","unstructured":"Weaver, D. S. et al. in The Myth of Syphilis (eds Powell M. L. & Cook D. C.) 77\u201391 (Univ. Florida Press, 2005)."},{"key":"8515_CR49","doi-asserted-by":"publisher","first-page":"e3016","DOI":"10.1371\/journal.pntd.0003016","volume":"8","author":"K Asiedu","year":"2014","unstructured":"Asiedu, K. et al. Eradication of yaws: historical efforts and achieving WHO\u2019s 2020 target. PLOS Negl. Trop. Dis. 8, e3016 (2014).","journal-title":"PLOS Negl. Trop. Dis."},{"key":"8515_CR50","unstructured":"Cook, D. C. & Powell M. L. in The Myth of Syphilis (eds Powell, M. L. & Cook, D. C.) 443\u2013479 (Univ. Florida Press, 2005)."},{"key":"8515_CR51","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1017\/S0033822200033865","volume":"51","author":"C Bronk Ramsey","year":"2009","unstructured":"Bronk Ramsey, C. Bayesian analysis of radiocarbon dates. Radiocarbon 51, 337\u2013360 (2009).","journal-title":"Radiocarbon"},{"key":"8515_CR52","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1017\/RDC.2020.59","volume":"62","author":"AG Hogg","year":"2020","unstructured":"Hogg, A. G. et al. SHCal20 Southern Hemisphere calibration, 0\u201355,000 years cal bp. Radiocarbon 62, 759\u2013778 (2020).","journal-title":"Radiocarbon"},{"key":"8515_CR53","doi-asserted-by":"publisher","first-page":"725","DOI":"10.1017\/RDC.2020.41","volume":"62","author":"PJ Reimer","year":"2020","unstructured":"Reimer, P. J. et al. The IntCal20 Northern Hemisphere radiocarbon age calibration curve (0\u201355 cal kbp). Radiocarbon 62, 725\u2013757 (2020).","journal-title":"Radiocarbon"},{"key":"8515_CR54","doi-asserted-by":"crossref","unstructured":"Heaton, T. J. et al. Marine20\u2014The marine radiocarbon age calibration curve (0\u201355,000 cal bp). Radiocarbon 62, 779\u2013820 (2020).","DOI":"10.1017\/RDC.2020.68"},{"key":"8515_CR55","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1038\/230241a0","volume":"230","author":"R Longin","year":"1971","unstructured":"Longin, R. New method of collagen extraction for radiocarbon dating. Nature 230, 241\u2013242 (1971).","journal-title":"Nature"},{"key":"8515_CR56","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1017\/S0033822200045069","volume":"52","author":"F Brock","year":"2010","unstructured":"Brock, F., Higham, T., Ditchfield, P. & Bronk Ramsey, C. Current pretreatment methods for AMS radiocarbon dating at the Oxford Radiocarbon Accelerator Unit (ORAU). Radiocarbon 52, 103\u2013112 (2010).","journal-title":"Radiocarbon"},{"key":"8515_CR57","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1016\/0305-4403(90)90007-R","volume":"17","author":"SH Ambrose","year":"1990","unstructured":"Ambrose, S. H. Preparation and characterization of bone and tooth collagen for isotopic analysis. J. Archaeol. Sci. 17, 431\u2013451 (1990).","journal-title":"J. Archaeol. Sci."},{"key":"8515_CR58","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1006\/jasc.1998.0385","volume":"26","author":"GJ van Klinken","year":"1999","unstructured":"van Klinken, G. J. Bone collagen quality indicators for palaeodietary and radiocarbon measurements. J. Archaeol. Sci. 26, 687\u2013695 (1999).","journal-title":"J. Archaeol. Sci."},{"key":"8515_CR59","unstructured":"Powell, R. L. & Still, C. J. Biogeography of C3 and C4 vegetation in South America. In Proc. XIV Simp\u00f3sio Brasileiro de Sensoriamento Remoto 2935\u20132942 (INPE, 2009)."},{"key":"8515_CR60","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1016\/S0278-4165(03)00040-0","volume":"22","author":"DR Yesner","year":"2003","unstructured":"Yesner, D. R., Figuerero Torres, M. J., Guichon, R. A. & Borrero, L. A. Stable isotope analysis of human bone and ethnohistoric subsistence patterns in Tierra del Fuego. J. Anthropol. Archaeol. 22, 279\u2013291 (2003).","journal-title":"J. Anthropol. Archaeol."},{"key":"8515_CR61","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1016\/j.quascirev.2017.06.035","volume":"170","author":"E Gonz\u00e1lez-Guarda","year":"2017","unstructured":"Gonz\u00e1lez-Guarda, E. et al. Late Pleistocene ecological, environmental and climatic reconstruction based on megafauna stable isotopes from northwestern Chilean Patagonia. Quat. Sci. Rev. 170, 188\u2013202 (2017).","journal-title":"Quat. Sci. Rev."},{"key":"8515_CR62","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1017\/S0033822200019512","volume":"41","author":"J Arneborg","year":"1999","unstructured":"Arneborg, J. et al. Change of diet of the Greenland Vikings determined from stable carbon isotope analysis and 14C dating of their bones. Radiocarbon 41, 157\u2013168 (1999).","journal-title":"Radiocarbon"},{"key":"8515_CR63","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1016\/j.quageo.2015.02.024","volume":"27","author":"GT Cook","year":"2015","unstructured":"Cook, G. T. et al. Best practice methodology for 14C calibration of marine and mixed terrestrial\/marine samples. Quat. Geochronol. 27, 164\u2013171 (2015).","journal-title":"Quat. Geochronol."},{"key":"8515_CR64","doi-asserted-by":"publisher","first-page":"925","DOI":"10.1017\/RDC.2018.16","volume":"60","author":"EJ Marsh","year":"2018","unstructured":"Marsh, E. J. et al. IntCal, SHCal, or a mixed curve? Choosing a 14C calibration curve for archaeological and palaeoenvironmental records from tropical South America. Radiocarbon 60, 925\u2013940 (2018).","journal-title":"Radiocarbon"},{"key":"8515_CR65","doi-asserted-by":"publisher","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":"8515_CR66","doi-asserted-by":"publisher","first-page":"2447","DOI":"10.1038\/s41596-018-0050-5","volume":"13","author":"N Rohland","year":"2018","unstructured":"Rohland, N. et al. 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":"8515_CR67","doi-asserted-by":"publisher","first-page":"20130624","DOI":"10.1098\/rstb.2013.0624","volume":"370","author":"N Rohland","year":"2015","unstructured":"Rohland, N. et al. Partial uracil-DNA-glycosylase treatment for screening of ancient DNA. Philos. Trans. R. Soc. B 370, 20130624 (2015).","journal-title":"Philos. Trans. R. Soc. B"},{"key":"8515_CR68","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":"8515_CR69","doi-asserted-by":"publisher","unstructured":"Herbig, A. et al. MALT: fast alignment and analysis of metagenomic DNA sequence data applied to the Tyrolean Iceman. Preprint at BioRxiv https:\/\/doi.org\/10.1101\/050559 (2016).","DOI":"10.1101\/050559"},{"key":"8515_CR70","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1038\/nbt.3820","volume":"35","author":"P di Tommaso","year":"2017","unstructured":"di Tommaso, P. et al. Nextflow enables reproducible computational workflows. Nat. Biotechnol. 35, 316\u2013319 (2017).","journal-title":"Nat. Biotechnol."},{"key":"8515_CR71","doi-asserted-by":"publisher","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":"8515_CR72","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754\u20131760 (2009).","journal-title":"Bioinformatics"},{"key":"8515_CR73","doi-asserted-by":"publisher","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":"8515_CR74","doi-asserted-by":"publisher","first-page":"3652","DOI":"10.1093\/bioinformatics\/btab190","volume":"37","author":"J Neukamm","year":"2021","unstructured":"Neukamm, J., Peltzer, A. & Nieselt, K. DamageProfiler: fast damage pattern calculation for ancient DNA. Bioinformatics 37, 3652\u20133653 (2021).","journal-title":"Bioinformatics"},{"key":"8515_CR75","doi-asserted-by":"publisher","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. 110, 2223\u20132227 (2013).","journal-title":"Proc Natl Acad. Sci."},{"key":"8515_CR76","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1038\/35057062","volume":"409","author":"ES Lander","year":"2001","unstructured":"Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860\u2013921 (2001).","journal-title":"Nature"},{"key":"8515_CR77","doi-asserted-by":"publisher","first-page":"1682","DOI":"10.1093\/bioinformatics\/btt193","volume":"29","author":"H J\u00f3nsson","year":"2013","unstructured":"J\u00f3nsson, 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\u20131684 (2013).","journal-title":"Bioinformatics"},{"key":"8515_CR78","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07483-5","volume":"9","author":"TC Lamnidis","year":"2018","unstructured":"Lamnidis, T. C. et al. Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe. Nat. Commun. 9, 5018 (2018).","journal-title":"Nat. Commun."},{"key":"8515_CR79","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1186\/s12859-014-0356-4","volume":"15","author":"TS Korneliussen","year":"2014","unstructured":"Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinform.\u00a015, 356 (2014).","journal-title":"BMC Bioinform."},{"key":"8515_CR80","unstructured":"Schiffels, S. sequenceTools. GitHub https:\/\/github.com\/stschiff\/sequenceTools.git (2018)."},{"key":"8515_CR81","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1038\/13779","volume":"23","author":"RM Andrews","year":"1999","unstructured":"Andrews, R. M. et al. Reanalysis and revision of the cambridge reference sequence for human mitochondrial DNA. Nat. Genet. 23, 147 (1999).","journal-title":"Nat. Genet."},{"key":"8515_CR82","doi-asserted-by":"publisher","first-page":"W58","DOI":"10.1093\/nar\/gkw233","volume":"44","author":"H Weissensteiner","year":"2016","unstructured":"Weissensteiner, H. et al. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 44, W58\u2013W63 (2016).","journal-title":"Nucleic Acids Res."},{"key":"8515_CR83","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.1002\/humu.22356","volume":"34","author":"D Vianello","year":"2013","unstructured":"Vianello, D. et al. HAPLOFIND: a new method for high-throughput mtDNA haplogroup assignment. Hum. Mutat. 34, 1189\u20131194 (2013).","journal-title":"Hum. Mutat."},{"key":"8515_CR84","doi-asserted-by":"crossref","unstructured":"Weissensteiner, H. et al. Contamination detection in sequencing studies using the mitochondrial phylogeny. Genome Res. 31, 309\u2013316 (2021).","DOI":"10.1101\/gr.256545.119"},{"key":"8515_CR85","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-94491-z","volume":"11","author":"AB Rohrlach","year":"2021","unstructured":"Rohrlach, A. B. et al. Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-Path Neolithic expansion to Western Europe. Sci. Rep. 11, 15005 (2021).","journal-title":"Sci. Rep."},{"key":"8515_CR86","doi-asserted-by":"publisher","first-page":"eaay5012","DOI":"10.1126\/science.aay5012","volume":"367","author":"A Bergstr\u00f6m","year":"2020","unstructured":"Bergstr\u00f6m, A. et al. Insights into human genetic variation and population history from 929 diverse genomes. Science 367, eaay5012 (2020).","journal-title":"Science"},{"key":"8515_CR87","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1038\/nature13673","volume":"513","author":"I Lazaridis","year":"2014","unstructured":"Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409\u2013413 (2014).","journal-title":"Nature"},{"key":"8515_CR88","doi-asserted-by":"publisher","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":"8515_CR89","doi-asserted-by":"publisher","first-page":"941","DOI":"10.1038\/s41431-019-0361-1","volume":"27","author":"SA Biagini","year":"2019","unstructured":"Biagini, S. A. et al. People from Ibiza: an unexpected isolate in the Western Mediterranean. Eur. J. Hum. Genet. 27, 941\u2013951 (2019).","journal-title":"Eur. J. Hum. Genet."},{"key":"8515_CR90","doi-asserted-by":"publisher","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":"8515_CR91","unstructured":"Lamnidis, T. C. AdmixturePlotter. GitHub https:\/\/github.com\/TCLamnidis\/AdmixturePlotter (2019)."},{"key":"8515_CR92","unstructured":"Schiffels, S. Xerxes CLI software. GitHub https:\/\/github.com\/poseidon-framework\/poseidon-framework.github.io\/blob\/master\/xerxes.md (2022)."},{"key":"8515_CR93","doi-asserted-by":"publisher","first-page":"744","DOI":"10.1038\/nrmicro.2016.141","volume":"14","author":"J Radolf","year":"2016","unstructured":"Radolf, J. et al. Treponema pallidum, the syphilis spirochete: making a living as a stealth pathogen. Nat. Rev. Microbiol. 14, 744\u2013759 (2016).","journal-title":"Nat. Rev. Microbiol."},{"key":"8515_CR94","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1111\/j.1574-6976.1998.tb00373.x","volume":"22","author":"GM Weinstock","year":"1998","unstructured":"Weinstock, G. M. et al. The genome of Treponema pallidum: new light on the agent of syphilis. FEMS Microbiol. Rev. 22, 323\u2013332 (1998).","journal-title":"FEMS Microbiol. Rev."},{"key":"8515_CR95","doi-asserted-by":"publisher","first-page":"e15713","DOI":"10.1371\/journal.pone.0015713","volume":"5","author":"L Mikalov\u00e1","year":"2010","unstructured":"Mikalov\u00e1, L. et al. Genome analysis of Treponema pallidum subsp. pallidum and subsp. pertenue strains: most of the genetic differences are localized in six regions. PLoS ONE 5, e15713 (2010).","journal-title":"PLoS ONE"},{"key":"8515_CR96","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-016-3217-x","volume":"17","author":"ES Wright","year":"2016","unstructured":"Wright, E. S. & Vetsigian, K. H. Quality filtering of Illumina index reads mitigates sample cross-talk. BMC Genom.\u00a017, 876 (2016).","journal-title":"BMC Genom."},{"key":"8515_CR97","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinland","year":"2010","unstructured":"Quinland, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841\u2013842 (2010).","journal-title":"Bioinformatics"},{"key":"8515_CR98","doi-asserted-by":"publisher","first-page":"80","DOI":"10.4161\/fly.19695","volume":"6","author":"P Cingolani","year":"2012","unstructured":"Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6, 80\u201392 (2012).","journal-title":"Fly"},{"key":"8515_CR99","doi-asserted-by":"publisher","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":"8515_CR100","unstructured":"Baele, G. & Lemey, P. in Bayesian Phylogenetics, Methods, Algorithms, and Applications (eds Chen, M. H. et al.) 59\u201394 (Chapman and Hall\/CRC press, 2014)."},{"key":"8515_CR101","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1007\/BF00160154","volume":"39","author":"Z Yang","year":"1994","unstructured":"Yang, Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39, 306\u2013314 (1994).","journal-title":"J. Mol. Evol."},{"key":"8515_CR102","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1093\/molbev\/msi103","volume":"22","author":"AJ Drummond","year":"2005","unstructured":"Drummond, A. J., Rambaut, A., Shapiro, B. & Pybus, O. G. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 22, 1185\u20131192 (2005).","journal-title":"Mol. Biol. Evol."},{"key":"8515_CR103","doi-asserted-by":"publisher","first-page":"e88","DOI":"10.1371\/journal.pbio.0040088","volume":"4","author":"AJ Drummond","year":"2006","unstructured":"Drummond, A. J., Ho, S. Y. W., Phillips, M. J. & Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88 (2006).","journal-title":"PLoS Biol."},{"key":"8515_CR104","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1093\/sysbio\/syy032","volume":"67","author":"A Rambaut","year":"2018","unstructured":"Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67, 901\u2013904 (2018).","journal-title":"Syst. Biol."},{"key":"8515_CR105","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1186\/1471-2148-13-221","volume":"13","author":"J Heled","year":"2013","unstructured":"Heled, J. & Bouckaert, R. R. Looking for trees in the forest: summary tree from posterior samples. BMC Evol. Biol. 13, 221 (2013).","journal-title":"BMC Evol. Biol."},{"key":"8515_CR106","doi-asserted-by":"publisher","first-page":"vey016","DOI":"10.1093\/ve\/vey016","volume":"4","author":"A Suchard","year":"2018","unstructured":"Suchard, A. et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 4, vey016 (2018).","journal-title":"Virus Evol."}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-08515-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-08515-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-08515-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,4]],"date-time":"2025-04-04T20:00:22Z","timestamp":1743796822000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-08515-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12,18]]},"references-count":106,"journal-issue":{"issue":"8057","published-print":{"date-parts":[[2025,4,3]]}},"alternative-id":["8515"],"URL":"https:\/\/doi.org\/10.1038\/s41586-024-08515-5","relation":{},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,12,18]]},"assertion":[{"value":"23 June 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 December 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 December 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"}}]}}