{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T09:12:39Z","timestamp":1790759559419,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.pgen.1010931","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,9,19]],"date-time":"2023-09-19T00:00:00Z","timestamp":1695081600000}}],"reference-count":86,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2023,9,7]],"date-time":"2023-09-07T00:00:00Z","timestamp":1694044800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001823","name":"Czech Ministry of Education, Youth and Sports","doi-asserted-by":"crossref","award":["LL2103"],"award-info":[{"award-number":["LL2103"]}],"id":[{"id":"10.13039\/501100001823","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001824","name":"Czech Science Foundation","doi-asserted-by":"crossref","award":["21-27624S"],"award-info":[{"award-number":["21-27624S"]}],"id":[{"id":"10.13039\/501100001824","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Russian federal budget","award":["075-15-2019-1879"],"award-info":[{"award-number":["075-15-2019-1879"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HG012287"],"award-info":[{"award-number":["HG012287"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000952","name":"Paul G. Allen Family Foundation","doi-asserted-by":"publisher","award":["Allen Discovery Center"],"award-info":[{"award-number":["Allen Discovery Center"]}],"id":[{"id":"10.13039\/100000952","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000925","name":"John Templeton Foundation","doi-asserted-by":"publisher","award":["61220"],"award-info":[{"award-number":["61220"]}],"id":[{"id":"10.13039\/100000925","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Jean-Francois Clin","award":["private gift"],"award-info":[{"award-number":["private gift"]}]},{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001823","name":"Czech Ministry of Education, Youth and Sports","doi-asserted-by":"crossref","award":["e-INFRA CZ LM2018140"],"award-info":[{"award-number":["e-INFRA CZ LM2018140"]}],"id":[{"id":"10.13039\/501100001823","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001823","name":"Czech Ministry of Education, Youth and Sports","doi-asserted-by":"crossref","award":["LM2015070"],"award-info":[{"award-number":["LM2015070"]}],"id":[{"id":"10.13039\/501100001823","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"abstract":"<jats:p>\n                    <jats:italic>f<\/jats:italic>\n                    -statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. Not only are they guaranteed to allow robust tests of the fits of proposed models of population history to data when analyzing full genome sequencing data\u2014that is, all single nucleotide polymorphisms (SNPs) in the individuals being analyzed\u2014but they are also guaranteed to allow robust tests of models for SNPs ascertained as polymorphic in a population that is an outgroup in a phylogenetic sense to all groups being analyzed. True \u201coutgroup ascertainment\u201d is in practice impossible in humans because our species has arisen from a substructured ancestral population that does not descend from a homogeneous ancestral population going back many hundreds of thousands of years into the past. However, initial studies suggested that non-outgroup-ascertainment schemes might produce robust enough results using\n                    <jats:italic>f<\/jats:italic>\n                    -statistics, and that motivated widespread fitting of models to data using non-outgroup-ascertained SNP panels such as the \u201cAffymetrix Human Origins array\u201d which has been genotyped on thousands of modern individuals from hundreds of populations, or the \u201c1240k\u201d in-solution enrichment reagent which has been the source of about 70% of published genome-wide data for ancient humans. In this study, we show that while analyses of population history using such panels work well for studies of relationships among non-African populations and one African outgroup, when co-modeling more than one sub-Saharan African and\/or archaic human groups (Neanderthals and Denisovans), fitting of\n                    <jats:italic>f<\/jats:italic>\n                    -statistics to such SNP sets is expected to frequently lead to false rejection of true demographic histories, and failure to reject incorrect models. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, has limited statistical power and retains important biases. However, by carrying out simulations of diverse demographic histories, we show that bias in inferences based on\n                    <jats:italic>f<\/jats:italic>\n                    -statistics can be minimized by ascertaining on variants common in a union of diverse African groups; such ascertainment retains high statistical power while allowing co-analysis of archaic and modern groups.\n                  <\/jats:p>","DOI":"10.1371\/journal.pgen.1010931","type":"journal-article","created":{"date-parts":[[2023,9,7]],"date-time":"2023-09-07T13:31:23Z","timestamp":1694093483000},"page":"e1010931","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":17,"title":["Modeling of African population history using f-statistics is biased when applying all previously proposed SNP ascertainment schemes"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9759-4981","authenticated-orcid":true,"given":"Pavel","family":"Flegontov","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6497-6254","authenticated-orcid":true,"given":"Ula\u015f","family":"I\u015f\u0131ldak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Maier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eren","family":"Y\u00fcnc\u00fc","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Piya","family":"Changmai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7037-5292","authenticated-orcid":true,"given":"David","family":"Reich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,9,7]]},"reference":[{"key":"pgen.1010931.ref001","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1146\/annurev-genom-083117-021749","article-title":"Ancient genomics of modern humans: The first decade","volume":"19","author":"P Skoglund","year":"2018","journal-title":"Annu Rev Genomics Hum Genet"},{"key":"pgen.1010931.ref002","doi-asserted-by":"crossref","first-page":"e2209475119","DOI":"10.1073\/pnas.2209475119","article-title":"Genomic perspectives on human dispersals during the Holocene","volume":"120","author":"M Stoneking","year":"2023","journal-title":"Proc Natl Acad Sci USA"},{"key":"pgen.1010931.ref003","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1126\/science.aat3188","article-title":"Ancient genomes document multiple waves of migration in Southeast Asian prehistory","volume":"361","author":"M Lipson","year":"2018","journal-title":"Science"},{"key":"pgen.1010931.ref004","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1038\/s41586-021-03335-3","article-title":"Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry","volume":"592","author":"M Hajdinjak","year":"2021","journal-title":"Nature"},{"key":"pgen.1010931.ref005","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1038\/s41559-021-01443-x","article-title":"A genome sequence from a modern human skull over 45,000 years old from Zlat\u00fd k\u016f\u0148 in Czechia.","volume":"5","author":"K Pr\u00fcfer","year":"2021","journal-title":"Nat Ecol Evol."},{"key":"pgen.1010931.ref006","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.cell.2017.08.049","article-title":"Reconstructing prehistoric African population structure","volume":"171","author":"P Skoglund","year":"2017","journal-title":"Cell"},{"key":"pgen.1010931.ref007","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1126\/science.aar8380","article-title":"Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations","volume":"360","author":"M van de Loosdrecht","year":"2018","journal-title":"Science"},{"key":"pgen.1010931.ref008","doi-asserted-by":"crossref","first-page":"eaaw6275","DOI":"10.1126\/science.aaw6275","article-title":"Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa","volume":"365","author":"ME Prendergast","year":"2019","journal-title":"Science"},{"key":"pgen.1010931.ref009","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1038\/s41586-020-1929-1","article-title":"Ancient West African foragers in the context of African population history","volume":"577","author":"M Lipson","year":"2020","journal-title":"Nature"},{"key":"pgen.1010931.ref010","doi-asserted-by":"crossref","first-page":"eaaz0183","DOI":"10.1126\/sciadv.aaz0183","article-title":"Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa.","volume":"6","author":"K Wang","year":"2020","journal-title":"Sci Adv."},{"key":"pgen.1010931.ref011","doi-asserted-by":"crossref","first-page":"7283","DOI":"10.1038\/s41467-021-27356-8","article-title":"Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia.","volume":"12","author":"KA Sirak","year":"2021","journal-title":"Nat Commun"},{"key":"pgen.1010931.ref012","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/s41586-022-04430-9","article-title":"Ancient DNA and deep population structure in sub-Saharan African foragers","volume":"603","author":"M Lipson","year":"2022","journal-title":"Nature"},{"key":"pgen.1010931.ref013","doi-asserted-by":"crossref","first-page":"866","DOI":"10.1038\/s41586-023-05754-w","article-title":"Entwined African and Asian genetic roots of medieval peoples of the Swahili coast","volume":"615","author":"ES Brielle","year":"2023","journal-title":"Nature"},{"key":"pgen.1010931.ref014","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1038\/nature14558","article-title":"An early modern human from Romania with a recent Neanderthal ancestor","volume":"524","author":"Q Fu","year":"2015","journal-title":"Nature"},{"key":"pgen.1010931.ref015","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/nature16152","article-title":"Genome-wide patterns of selection in 230 ancient Eurasians","volume":"528","author":"I Mathieson","year":"2015","journal-title":"Nature"},{"key":"pgen.1010931.ref016","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1534\/genetics.112.145037","article-title":"Ancient admixture in human history","volume":"192","author":"N Patterson","year":"2012","journal-title":"Genetics"},{"key":"pgen.1010931.ref017","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.gde.2020.05.021","article-title":"Latest trends in archaeogenetic research of west Eurasians","volume":"62","author":"I Olalde","year":"2020","journal-title":"Curr Opin Genet Dev"},{"key":"pgen.1010931.ref018","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1101\/gr.276728.122","article-title":"Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs","volume":"32","author":"N Rohland","year":"2022","journal-title":"Genome Res"},{"key":"pgen.1010931.ref019","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1038\/nature08365","article-title":"Reconstructing Indian population history","volume":"461","author":"D Reich","year":"2009","journal-title":"Nature"},{"key":"pgen.1010931.ref020","doi-asserted-by":"crossref","first-page":"1485","DOI":"10.1534\/genetics.115.183913","article-title":"Admixture, population structure, and F-statistics.","volume":"202","author":"BM Peter","year":"2016","journal-title":"Genetics"},{"key":"pgen.1010931.ref021","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/j.tpb.2018.12.002","article-title":"General theory for stochastic admixture graphs and F-statistics","volume":"125","author":"S Soraggi","year":"2019","journal-title":"Theor Popul Biol"},{"key":"pgen.1010931.ref022","doi-asserted-by":"crossref","first-page":"20200413","DOI":"10.1098\/rstb.2020.0413","article-title":"A geometric relationship of F2, F3 and F4-statistics with principal component analysis.","volume":"377","author":"BM Peter","year":"2022","journal-title":"Philos Trans R Soc B Biol Sci."},{"key":"pgen.1010931.ref023","doi-asserted-by":"crossref","first-page":"e85492","DOI":"10.7554\/eLife.85492","article-title":"On the limits of fitting complex models of population history to f-statistics.","volume":"12","author":"R Maier","year":"2023","journal-title":"eLife"},{"key":"pgen.1010931.ref024","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1126\/science.1188021","article-title":"A draft sequence of the Neandertal genome","volume":"328","author":"RE Green","year":"2010","journal-title":"Science"},{"key":"pgen.1010931.ref025","doi-asserted-by":"crossref","first-page":"2239","DOI":"10.1093\/molbev\/msr048","article-title":"Testing for ancient admixture between closely related populations","volume":"28","author":"EY Durand","year":"2011","journal-title":"Mol Biol Evol"},{"key":"pgen.1010931.ref026","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1111\/1755-0998.13230","article-title":"Applying f4-statistics and admixture graphs: Theory and examples","volume":"20","author":"M. Lipson","year":"2020","journal-title":"Mol Ecol Resour"},{"key":"pgen.1010931.ref027","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature14317","article-title":"Massive migration from the steppe was a source for Indo-European languages in Europe","volume":"522","author":"W Haak","year":"2015","journal-title":"Nature"},{"key":"pgen.1010931.ref028","doi-asserted-by":"crossref","first-page":"iyaa045","DOI":"10.1093\/genetics\/iyaa045","article-title":"Assessing the performance of qpAdm: a statistical tool for studying population admixture","volume":"217","author":"\u00c9 Harney","year":"2021","journal-title":"Genetics"},{"key":"pgen.1010931.ref029","article-title":"Falsemixture","author":"E Y\u00fcnc\u00fc","year":"2023","journal-title":"discovery rates of qpAdm-based screens for genetic adbioRxiv."},{"key":"pgen.1010931.ref030","doi-asserted-by":"crossref","first-page":"eaay5012","DOI":"10.1126\/science.aay5012","article-title":"Insights into human genetic variation and population history from 929 diverse genomes","volume":"367","author":"A Bergstr\u00f6m","year":"2020","journal-title":"Science"},{"key":"pgen.1010931.ref031","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1126\/science.1153717","article-title":"Worldwide human relationships inferred from genome-wide patterns of variation","volume":"319","author":"JZ Li","year":"2008","journal-title":"Science"},{"key":"pgen.1010931.ref032","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/nature12886","article-title":"The complete genome sequence of a Neanderthal from the Altai Mountains","volume":"505","author":"K Pr\u00fcfer","year":"2014","journal-title":"Nature"},{"key":"pgen.1010931.ref033","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1126\/science.aao1887","article-title":"A high-coverage Neandertal genome from Vindija Cave in Croatia","volume":"358","author":"K Pr\u00fcfer","year":"2017","journal-title":"Science"},{"key":"pgen.1010931.ref034","doi-asserted-by":"crossref","first-page":"15132","DOI":"10.1073\/pnas.2004944117","article-title":"A high-coverage Neandertal genome from Chagyrskaya Cave","volume":"117","author":"F Mafessoni","year":"2020","journal-title":"Proc Natl Acad Sci USA"},{"key":"pgen.1010931.ref035","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1126\/science.1224344","article-title":"A high-coverage genome sequence from an archaic Denisovan individual","volume":"338","author":"M Meyer","year":"2012","journal-title":"Science"},{"key":"pgen.1010931.ref036","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1038\/nature18964","article-title":"The Simons Genome Diversity Project: 300 genomes from 142 diverse populations","volume":"538","author":"S Mallick","year":"2016","journal-title":"Nature"},{"key":"pgen.1010931.ref037","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1111\/j.1365-294X.2011.05413.x","article-title":"Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias","volume":"21","author":"Y Wang","year":"2012","journal-title":"Mol Ecol"},{"key":"pgen.1010931.ref038","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/S0040-5809(03)00005-4","article-title":"Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium","volume":"63","author":"R Nielsen","year":"2003","journal-title":"Theor Popul Biol"},{"key":"pgen.1010931.ref039","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1186\/1479-7364-1-3-218","article-title":"Population genetic analysis of ascertained SNP data","volume":"1","author":"R. Nielsen","year":"2004","journal-title":"Hum Genomics"},{"key":"pgen.1010931.ref040","doi-asserted-by":"crossref","first-page":"2373","DOI":"10.1534\/genetics.104.031039","article-title":"Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data","volume":"168","author":"R Nielsen","year":"2004","journal-title":"Genetics"},{"key":"pgen.1010931.ref041","doi-asserted-by":"crossref","first-page":"1496","DOI":"10.1101\/gr.4107905","article-title":"Ascertainment bias in studies of human genome-wide polymorphism","volume":"15","author":"AG Clark","year":"2005","journal-title":"Genome Res"},{"key":"pgen.1010931.ref042","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1093\/bioinformatics\/btn665","article-title":"Correcting for ascertainment bias in the inference of population structure","volume":"25","author":"G Guillot","year":"2009","journal-title":"Bioinformatics"},{"key":"pgen.1010931.ref043","doi-asserted-by":"crossref","first-page":"2534","DOI":"10.1093\/molbev\/msq148","article-title":"Ascertainment biases in SNP chips affect measures of population divergence","volume":"27","author":"A Albrechtsen","year":"2010","journal-title":"Mol Biol Evol"},{"key":"pgen.1010931.ref044","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1002\/bies.201300014","article-title":"SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it","volume":"35","author":"J Lachance","year":"2013","journal-title":"BioEssays"},{"key":"pgen.1010931.ref045","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1186\/s12864-015-1469-5","article-title":"How do SNP ascertainment schemes and population demographics affect inferences about population history?","volume":"16","author":"EJ McTavish","year":"2015","journal-title":"BMC Genomics"},{"key":"pgen.1010931.ref046","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/s12864-017-4416-9","article-title":"Efficiency of different strategies to mitigate ascertainment bias when using SNP panels in diversity studies","volume":"19","author":"DK Malomane","year":"2018","journal-title":"BMC Genomics"},{"key":"pgen.1010931.ref047","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0245178","article-title":"How array design creates SNP ascertainment bias","volume":"16","author":"J Geibel","year":"2021","journal-title":"PLOS ONE"},{"key":"pgen.1010931.ref048","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1038\/nature09710","article-title":"Genetic history of an archaic hominin group from Denisova Cave in Siberia","volume":"468","author":"D Reich","year":"2010","journal-title":"Nature"},{"key":"pgen.1010931.ref049","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1016\/j.cell.2020.01.012","article-title":"Identifying and interpreting apparent Neanderthal ancestry in African individuals","volume":"180","author":"L Chen","year":"2020","journal-title":"Cell"},{"key":"pgen.1010931.ref050","doi-asserted-by":"crossref","first-page":"15123","DOI":"10.1073\/pnas.1109300108","article-title":"Genetic evidence for archaic admixture in Africa","volume":"108","author":"MF Hammer","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"key":"pgen.1010931.ref051","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pgen.1008204","article-title":"Models of archaic admixture and recent history from two-locus statistics","volume":"15","author":"AP Ragsdale","year":"2019","journal-title":"PLOS Genet"},{"key":"pgen.1010931.ref052","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1038\/s41588-019-0484-x","article-title":"A method for genome-wide genealogy estimation for thousands of samples","volume":"51","author":"L Speidel","year":"2019","journal-title":"Nat Genet"},{"key":"pgen.1010931.ref053","doi-asserted-by":"crossref","first-page":"eaax5097","DOI":"10.1126\/sciadv.aax5097","article-title":"Recovering signals of ghost archaic introgression in African populations","volume":"6","author":"A Durvasula","year":"2020","journal-title":"Sci Adv"},{"key":"pgen.1010931.ref054","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pgen.1008895","article-title":"Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph","volume":"16","author":"MJ Hubisz","year":"2020","journal-title":"PLOS Genet"},{"key":"pgen.1010931.ref055","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1038\/s41586-023-06055-y","article-title":"A weakly structured stem for human origins in Africa","volume":"617","author":"AP Ragsdale","year":"2023","journal-title":"Nature"},{"key":"pgen.1010931.ref056","doi-asserted-by":"crossref","first-page":"eabc4587","DOI":"10.1126\/sciadv.abc4587","article-title":"Human population dynamics and Yersinia pestis in ancient northeast Asia","volume":"7","author":"GM K\u0131l\u0131n\u00e7","year":"2021","journal-title":"Sci Adv"},{"key":"pgen.1010931.ref057","doi-asserted-by":"crossref","first-page":"2455","DOI":"10.1016\/j.cub.2021.03.050","article-title":"Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes","volume":"31","author":"R Yaka","year":"2021","journal-title":"Curr Biol"},{"key":"pgen.1010931.ref058","doi-asserted-by":"crossref","first-page":"1024","DOI":"10.1038\/s41559-022-01775-2","article-title":"Ancient genomes from the last three millennia support multiple human dispersals into Wallacea","volume":"6","author":"S Oliveira","year":"2022","journal-title":"Nat Ecol Evol"},{"key":"pgen.1010931.ref059","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pgen.1002967","article-title":"Inference of population splits and mixtures from genome-wide allele frequency data","volume":"8","author":"JK Pickrell","year":"2012","journal-title":"PLOS Genet"},{"key":"pgen.1010931.ref060","doi-asserted-by":"crossref","first-page":"i142","DOI":"10.1093\/bioinformatics\/btab267","article-title":"Advancing admixture graph estimation via maximum likelihood network orientation","volume":"37","author":"EK Molloy","year":"2021","journal-title":"Bioinformatics"},{"key":"pgen.1010931.ref061","doi-asserted-by":"crossref","first-page":"1788","DOI":"10.1093\/molbev\/mst099","article-title":"Efficient moment-based inference of admixture parameters and sources of gene flow","volume":"30","author":"M Lipson","year":"2013","journal-title":"Mol Biol Evol"},{"key":"pgen.1010931.ref062","doi-asserted-by":"crossref","first-page":"2488","DOI":"10.1093\/bioinformatics\/btaa988","article-title":"miqoGraph: fitting admixture graphs using mixed-integer quadratic optimization","volume":"37","author":"J Yan","year":"2020","journal-title":"Bioinformatics"},{"key":"pgen.1010931.ref063","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pgen.1010410","article-title":"Bayesian inference of admixture graphs on Native American and Arctic populations","volume":"19","author":"SV Nielsen","year":"2023","journal-title":"PLOS Genet"},{"key":"pgen.1010931.ref064","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1126\/science.aaa0114","article-title":"Genomic structure in Europeans dating back at least 36,200 years","volume":"346","author":"A Seguin-Orlando","year":"2014","journal-title":"Science"},{"key":"pgen.1010931.ref065","first-page":"365","article-title":"The formation of human populations in South and Central Asia","author":"VM Narasimhan","year":"2019","journal-title":"Science"},{"key":"pgen.1010931.ref066","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1038\/s41467-018-08220-8","article-title":"Ancient human genome-wide data from a 3000-year interval in the Caucasus corresponds with eco-geographic regions","volume":"10","author":"C-C Wang","year":"2019","journal-title":"Nat Commun"},{"key":"pgen.1010931.ref067","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1186\/s13059-019-1679-2","article-title":"African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations","volume":"20","author":"S Fan","year":"2019","journal-title":"Genome Biol"},{"key":"pgen.1010931.ref068","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/nature13673","article-title":"Ancient human genomes suggest three ancestral populations for present-day Europeans","volume":"513","author":"I Lazaridis","year":"2014","journal-title":"Nature"},{"key":"pgen.1010931.ref069","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1038\/nature13810","article-title":"Genome sequence of a 45,000-year-old modern human from western Siberia","volume":"514","author":"Q Fu","year":"2014","journal-title":"Nature"},{"key":"pgen.1010931.ref070","doi-asserted-by":"crossref","first-page":"e36317","DOI":"10.7554\/eLife.36317","article-title":"Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences","volume":"7","author":"F Pouyet","year":"2018","journal-title":"eLife"},{"key":"pgen.1010931.ref071","first-page":"889","article-title":"A working model of the deep relationships of diverse modern human genetic lineages outside of Africa","volume":"34","author":"M Lipson","year":"2017","journal-title":"Mol Biol Evol"},{"key":"pgen.1010931.ref072","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1038\/s41586-019-1251-y","article-title":"Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America","volume":"570","author":"P Flegontov","year":"2019","journal-title":"Nature"},{"key":"pgen.1010931.ref073","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1038\/s41586-021-03336-2","article-title":"Genomic insights into the formation of human populations in East Asia","volume":"591","author":"C-C Wang","year":"2021","journal-title":"Nature"},{"key":"pgen.1010931.ref074","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pgen.1010036","article-title":"Indian genetic heritage in Southeast Asian populations","volume":"18","author":"P Changmai","year":"2022","journal-title":"PLOS Genet"},{"key":"pgen.1010931.ref075","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1126\/science.aba9572","article-title":"Origins and genetic legacy of prehistoric dogs","volume":"370","author":"A Bergstr\u00f6m","year":"2020","journal-title":"Science"},{"key":"pgen.1010931.ref076","doi-asserted-by":"crossref","first-page":"iyab229","DOI":"10.1093\/genetics\/iyab229","article-title":"Efficient ancestry and mutation simulation with msprime 1.0","volume":"220","author":"F Baumdicker","year":"2021","journal-title":"Genetics"},{"key":"pgen.1010931.ref077","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1016\/j.cub.2006.04.033","article-title":"Demographic history and genetic differentiation in apes","volume":"16","author":"A Fischer","year":"2006","journal-title":"Curr Biol"},{"key":"pgen.1010931.ref078","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/s41586-023-05726-0","article-title":"Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers","volume":"615","author":"C Posth","year":"2023","journal-title":"Nature"},{"key":"pgen.1010931.ref079","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1093\/molbev\/msaa239","article-title":"Signatures of introgression across the allele frequency spectrum","volume":"38","author":"SH Martin","year":"2020","journal-title":"Mol Biol Evol"},{"key":"pgen.1010931.ref080","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/s41586-022-04824-9","article-title":"Grey wolf genomic history reveals a dual ancestry of dogs","volume":"607","author":"A Bergstr\u00f6m","year":"2022","journal-title":"Nature"},{"key":"pgen.1010931.ref081","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1038\/s41586-021-04018-9","article-title":"The origins and spread of domestic horses from the Western Eurasian steppes","volume":"598","author":"P Librado","year":"2021","journal-title":"Nature"},{"key":"pgen.1010931.ref082","doi-asserted-by":"crossref","first-page":"msad082","DOI":"10.1093\/molbev\/msad082","article-title":"Population genomic evidence of adaptive response during the invasion history of Plasmodium falciparum in the Americas","volume":"40","author":"MJM Lefebvre","year":"2023","journal-title":"Mol Biol Evol"},{"key":"pgen.1010931.ref083","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1038\/nrg3295","article-title":"Revising the human mutation rate: implications for understanding human evolution","volume":"13","author":"A Scally","year":"2012","journal-title":"Nat Rev Genet"},{"key":"pgen.1010931.ref084","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pcbi.1004842","article-title":"Efficient coalescent simulation and genealogical analysis for large sample sizes","volume":"12","author":"J Kelleher","year":"2016","journal-title":"PLOS Comput Biol"},{"key":"pgen.1010931.ref085","first-page":"1","article-title":"Accounting for long-range correlations in genome-wide simulations of large cohorts","volume":"16","author":"D Nelson","year":"2020"},{"key":"pgen.1010931.ref086","doi-asserted-by":"crossref","first-page":"s13742-015","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: rising to the challenge of larger and richer datasets.","volume":"4","author":"CC Chang","year":"2015","journal-title":"GigaScience."}],"updated-by":[{"DOI":"10.1371\/journal.pgen.1010931","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,9,19]],"date-time":"2023-09-19T00:00:00Z","timestamp":1695081600000}}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1010931","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,19]],"date-time":"2023-09-19T13:32:27Z","timestamp":1695130347000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1010931"}},"subtitle":[],"editor":[{"given":"Charleston Wen-Kai","family":"Chiang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,9,7]]},"references-count":86,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2023,9,7]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1010931","relation":{},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,9,7]]}}}