qpAdm is a statistical tool that is often used for testing large sets of alternative admixture models for a target population. Despite its popularity, qpAdm remains untested on two-dimensional stepping-stone landscapes and in situations with low pre-study odds (low ratio of true to false models). We tested high-throughput qpAdm protocols with typical properties such as number of source combinations per target, model complexity, model feasibility criteria, etc. Those protocols were applied to admixture-graph-shaped and stepping-stone simulated histories sampled randomly or systematically. We demonstrate that false discovery rates of high-throughput qpAdm protocols exceed 50% for many parameter combinations since: 1) pre-study odds are low and fall rapidly with increasing model complexity; 2) complex migration networks violate the assumptions of the method, hence there is poor correlation between qpAdm p-values and model optimality, contributing to low but non-zero false positive rate and low power; 3) although admixture fraction estimates between 0 and 1 are largely restricted to symmetric configurations of sources around a target, a small fraction of asymmetric highly non-optimal models have estimates in the same interval, contributing to the false positive rate. We also re-interpret large sets of qpAdm models from two studies in terms of source-target distance and symmetry and suggest improvements to qpAdm protocols: 1) temporal stratification of targets and proxy sources in the case of admixture-graph-shaped histories; 2) focused exploration of few models for increasing pre-study odds; 3) dense landscape sampling for increasing power and stringent conditions on estimated admixture fractions for decreasing the false positive rate.

Department of Biological Sciences Middle East Technical University Üniversiteler Mahallesi Dumlupınar Bulvarı No 1 06800 Çankaya Ankara Türkiye

Department of Biology and Ecology Faculty of Science University of Ostrava Chittussiho 1077 10 710 00 Ostrava Czechia

Department of Biology Eberly College of Science Pennsylvania State University 168 Curtin Road University Park PA 16802 USA

Department of Human Evolutionary Biology Harvard University 11 Divinity Avenue Cambridge MA 02138 USA

Institute of Parasitology Biology Centre of the Czech Academy of Sciences Branišovská 1160 31 370 05 České Budějovice Czechia

Leibniz Institute on Aging Fritz Lipmann Institute Beutenbergstraße 11 07745 Jena Germany

Aktualizováno

Genetics. 2025 Apr 02:iyaf047. doi: 10.1093/genetics/iyaf047. PubMed

Zobrazit více v PubMed

Al-Asadi H, Petkova D, Stephens M, Novembre J. 2019. Estimating recent migration and populationsize surfaces. PLoS Genet. 15(1):e1007908. doi: 10.1371/journal.pgen.1007908. PubMed DOI PMC

Alexander DH, Novembre J, Lange K. 2009. Fast model-based estimation of ancestry in unrelated individuals, Genome Res. 19(9):1655–1664. doi: 10.1101/gr.094052.109. PubMed DOI PMC

Allentoft ME, Sikora M, Refoyo-Martínez A, Irving-Pease EK, Fischer A, Barrie W, Ingason A, Stenderup J, Sjögren KG, Pearson A, et al. 2024. Population genomics of post-glacial western Eurasia. Nature. 625(7994):301–311. doi: 10.1038/s41586-023-06865-0. PubMed DOI PMC

Antonio ML, Gao Z, Moots HM, Lucci M, Candilio F, Sawyer S, Oberreiter V, Calderon D, Devitofranceschi K, Aikens RC, et al. 2019. Ancient Rome: A genetic crossroads of Europe and the Mediterranean. Science. 366(6466):708–714. doi: 10.1126/science.aay6826. PubMed DOI PMC

Baumdicker F, Bisschop G, Goldstein D, Gower G, Ragsdale AP, Tsambos G, Zhu S, Eldon B, Ellerman EC, Galloway JG, et al. 2022. Efficient ancestry and mutation simulation with msprime 1.0. Genetics. 220(3):iyab229. doi: 10.1093/genetics/iyab229. PubMed DOI PMC

Baxter K. 2004. Extrinsic factors that effect the preservation of bone. The Nebraska Anthropologist. 19:38–45.

Bergström A, Stanton DWG, Taron UH, Frantz L, Sinding MS, Ersmark E, Pfrengle S, Cassatt-Johnstone M, Lebrasseur O, Girdland-Flink L, et al. 2022. Grey wolf genomic history reveals a dual ancestry of dogs. Nature. 607(7918):313–320. doi: 10.1038/s41586-022-04824-9. PubMed DOI PMC

Brielle ES, Fleisher J, Wynne-Jones S, Sirak K, Broomandkhoshbacht N, Callan K, Curtis E, Iliev L, Lawson AM, Oppenheimer J, et al. 2023. Entwined African and Asian genetic roots of medieval peoples of the Swahili coast. Nature. 615(7954):866–873. doi: 10.1038/s41586-023-05754-w. PubMed DOI PMC

Carlhoff S, Duli A, Nägele K, Nur M, Skov L, Sumantri I, Oktaviana AA, Hakim B, Burhan B, Syahdar FA, et al. 2021. Genome of a middle Holocene hunter-gatherer from Wallacea. Nature. 596(7873):543–547. doi: 10.1038/s41586-021-03823-6. PubMed DOI PMC

Carlhoff S, Kutanan W, Rohrlach AB, Posth C, Stoneking M, Nägele K, Shoocongdej R, Krause J. 2023. Genomic portrait and relatedness patterns of the Iron Age Log Coffin culture in northwestern Thailand. Nat Commun. 14(1):8527. doi: 10.1038/s41467-023-44328-2. PubMed DOI PMC

Cerezo-Román JI, Wessman A, Williams H (eds.). 2017. Cremation and the Archaeology of Death. Oxford: Oxford University Press.

Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. 2015. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 4:7. doi: 10.1186/s13742-015-0047-8. PubMed DOI PMC

Changmai P, Jaisamut K, Kampuansai J, Kutanan W, Altınışık NE, Flegontova O, Inta A, Yüncü E, Boonthai W, Pamjav H, et al. 2022a. Indian genetic heritage in Southeast Asian populations. PLoS Genet. 18(2):e1010036. doi: 10.1371/journal.pgen.1010036. PubMed DOI PMC

Changmai P, Pinhasi R, Pietrusewsky M, Stark MT, Ikehara-Quebral RM, Reich D, Flegontov P. 2022b. Ancient DNA from Protohistoric Period Cambodia indicates that South Asians admixed with local populations as early as 1st-3rd centuries CE. Sci Rep. 12(1):22507. doi: 10.1038/s41598-022-26799-3. PubMed DOI PMC

Duforet-Frebourg N, Slatkin M. 2016. Isolation-by-distance-and-time in a stepping-stone model. Theor Popul Biol. 108:24–35. doi: 10.1016/j.tpb.2015.11.003. PubMed DOI PMC

Durand EY, Patterson N, Reich D, Slatkin M. 2011. Testing for ancient admixture between closely related populations. Mol Biol Evol. 28(8):2239–2252. doi: 10.1093/molbev/msr048. PubMed DOI PMC

Estavoyer M, François O. 2022. Theoretical analysis of principal components in an umbrella model of intraspecific evolution. Theor Popul Biol. 148:11–21. doi: 10.1016/j.tpb.2022.08.002. PubMed DOI

Fernandes DM, Mittnik A, Olalde I, Lazaridis I, Cheronet O, Rohland N, Mallick S, Bernardos R, Broomandkhoshbacht N, Carlsson J, et al. 2020. The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean. Nat Ecol Evol. 4(3):334–345. doi: 10.1038/s41559-020-1102-0. PubMed DOI PMC

Fernandes DM, Sirak KA, Ringbauer H, Sedig J, Rohland N, Cheronet O, Mah M, Mallick S, Olalde I, Culleton BJ, et al. 2021. A genetic history of the pre-contact Caribbean. Nature. 590(7844):103–110. doi: 10.1038/s41586-020-03053-2. PubMed DOI PMC

Flegontov P, Işıldak U, Maier R, Yüncü E, Changmai P, Reich D. 2023. Modeling of African population history using f-statistics is biased when applying all previously proposed SNP ascertainment schemes. PLoS Genet. 19(9):e1010931. doi: 10.1371/journal.pgen.1010931. PubMed DOI PMC

Frichot E, Schoville S, Bouchard G, François O. 2012. Correcting principal component maps for effects of spatial autocorrelation in population genetic data. Front Genet. 3:254. doi: 10.3389/fgene.2012.00254. PubMed DOI PMC

Gill H, Lee J, Jeong C. 2024. Reconstructing the genetic relationship between ancient and present-day Siberian populations. Genome Biol Evol. 16(4):evae063. doi: 10.1093/gbe/evae063. PubMed DOI PMC

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, et al. 2010. A draft sequence of the Neandertal genome. Science. 328(5979):710–722. doi: 10.1126/science.1188021. PubMed DOI PMC

Gnecchi-Ruscone GA, Szécsényi-Nagy A, Koncz I, Csiky G, Rácz Z, Rohrlach AB, Brandt G, Rohland N, Csáky V, Cheronet O, et al. 2022. Ancient genomes reveal origin and rapid trans-Eurasian migration of 7th century Avar elites. Cell. 185(8):1402–1413.e21. doi: 10.1016/j.cell.2022.03.007. PubMed DOI PMC

Grundler MC, Terhorst J, Bradburd GS. 2024. A geographic history of human genetic ancestry. doi: 10.1101/2024.03.27.586858. [accessed 2025 Jan 22]. https://www.biorxiv.org/content/10.1101/2024.03.27.586858v2. PubMed DOI

Haak W, Lazaridis I, Patterson N, Rohland N, Mallick S, Llamas B, Brandt G, Nordenfelt S, Harney E, Stewardson K, et al. 2015. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature. 522(7555):207–211. doi: 10.1038/nature14317. PubMed DOI PMC

Harney É, May H, Shalem D, Rohland N, Mallick S, Lazaridis I, Sarig R, Stewardson K, Nordenfelt S, Patterson N, et al. 2018. Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation. Nat Commun. 9(1):3336. doi: 10.1038/s41467-018-05649-9. PubMed DOI PMC

Harney É, Nayak A, Patterson N, Joglekar P, Mushrif-Tripathy V, Mallick S, Rohland N, Sedig J, Adamski N, Bernardos R, et al. 2019. Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India. Nat Commun. 10(1):3670. doi: 10.1038/s41467-019-11357-9. PubMed DOI PMC

Harney É, Patterson N, Reich D, Wakeley J. 2021. Assessing the performance of qpAdm: a statistical tool for studying population admixture. Genetics. 217(4):iyaa045. doi: 10.1093/GENETICS/IYAA045. PubMed DOI PMC

Ioannidis JP. 2005. Why most published research findings are false. PLoS Med. 2(8):e124. doi: 10.1371/journal.pmed.0020124. PubMed DOI PMC

Kerdoncuff E, Skov L, Patterson N, Zhao W, Lueng YY, Schellenberg GD, Smith JA, Dey S, Ganna A, Dey AB, et al. 2024. 50,000 years of evolutionary history of India: Insights from ~2,700 whole genome sequences. doi: 10.1101/2024.02.15.580575. [accessed 2025 Jan 22]. https://www.biorxiv.org/content/10.1101/2024.02.15.580575v2. DOI

Lawson DJ, van Dorp L, Falush D. 2018. A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots. Nat Commun. 9(1):3258. doi: 10.1038/s41467-018-05257-7. PubMed DOI PMC

Lazaridis I, Nadel D, Rollefson G, Merrett DC, Rohland N, Mallick S, Fernandes D, Novak M, Gamarra B, Sirak K, et al. 2016. Genomic insights into the origin of farming in the ancient Near East. Nature. 536(7617):419–424. doi: 10.1038/nature19310. PubMed DOI PMC

Lazaridis I, Mittnik A, Patterson N, Mallick S, Rohland N, Pfrengle S, Furtwängler A, Peltzer A, Posth C, Vasilakis A, et al. 2017. Genetic origins of the Minoans and Mycenaeans. Nature. 548(7666):214–218. doi: 10.1038/nature23310. PubMed DOI PMC

Lazaridis I, Alpaslan-Roodenberg S, Acar A, Açıkkol A, Agelarakis A, Aghikyan L, Akyüz U, Andreeva D, Andrijašević G, Antonović D, et al. 2022. The genetic history of the Southern Arc: A bridge between West Asia and Europe. Science. 377(6609):eabm4247. doi: 10.1126/science.abm4247. PubMed DOI PMC

Lee J, Miller BK, Bayarsaikhan J, Johannesson E, Ventresca Miller A, Warinner C, Jeong C. 2023. Genetic population structure of the Xiongnu Empire at imperial and local scales. Sci Adv. 9(15):eadf3904. doi: 10.1126/sciadv.adf3904. PubMed DOI PMC

Librado P, Khan N, Fages A, Kusliy MA, Suchan T, Tonasso-Calvière L, Schiavinato S, Alioglu D, Fromentier A, Perdereau A, et al. 2021. The origins and spread of domestic horses from the Western Eurasian steppes. Nature. 598(7882):634–640. doi: 10.1038/s41586-021-04018-9. PubMed DOI PMC

Librado P, Tressières G, Chauvey L, Fages A, Khan N, Schiavinato S, Calvière-Tonasso L, Kusliy MA, Gaunitz C, Liu X, et al. 2024. Widespread horse-based mobility arose around 2200 BCE in Eurasia. Nature. 631(8022):819–825. doi: 10.1038/s41586-024-07597-5. PubMed DOI PMC

Lindig WH. 1964. Tree burial among the Seri Indians. Ethnology. 3(3):284–286. doi: 10.2307/3772884. DOI

Lipson M. 2020. Applying f4-statistics and admixture graphs: Theory and examples. Mol Ecol Resour. 20(6):1658–1667. doi: 10.1111/1755-0998.13230. PubMed DOI PMC

Maier R, Flegontov P, Flegontova O, Işıldak U, Changmai P, Reich D. 2023. On the limits of fitting complex models of population history to f-statistics. eLife. 12:e85492. doi: 10.7554/eLife.85492. PubMed DOI PMC

Marcus JH, Posth C, Ringbauer H, Lai L, Skeates R, Sidore C, Beckett J, Furtwängler A, Olivieri A, Chiang CWK, et al. 2020. Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia. Nat Commun. 11(1):939. doi: 10.1038/s41467-020-14523-6. PubMed DOI PMC

Maróti Z, Neparáczki E, Schütz O, Maár K, Varga GIB, Kovács B, Kalmár T, Nyerki E, Nagy I, Latinovics D, et al. 2022. The genetic origin of Huns, Avars, and conquering Hungarians. Curr Biol. 32(13):2858–2870.e7. doi: 10.1016/j.cub.2022.04.093. PubMed DOI

Martin SH, Davey JW, Jiggins CD. 2015. Evaluating the use of ABBA-BABA statistics to locate introgressed loci. Mol Biol Evol. 32(1):244–257. doi: 10.1093/molbev/msu269. PubMed DOI PMC

Mathieson I, Lazaridis I, Rohland N, Mallick S, Patterson N, Roodenberg SA, Harney E, Stewardson K, Fernandes D, Novak M, et al. 2015. Genome-wide patterns of selection in 230 ancient Eurasians. Nature. 528(7583):499–503. doi: 10.1038/nature16152. PubMed DOI PMC

Mathieson I, Alpaslan-Roodenberg S, Posth C, Szécsényi-Nagy A, Rohland N, Mallick S, Olalde I, Broomandkhoshbacht N, Candilio F, Cheronet O, et al. 2018. The genomic history of southeastern Europe. Nature. 555(7695):197–203. doi: 10.1038/nature25778. PubMed DOI PMC

McRae BH. 2006. Isolation-by-resistance. Evolution. 60(8):1551–1561. doi: 10.1554/05-321.1. PubMed DOI

McVean G. 2009. A genealogical interpretation of principal components analysis. PLoS Genet. 5(10):e1000686. doi: 10.1371/journal.pgen.1000686. PubMed DOI PMC

Moreno-Mayar JV, Vinner L, de Barros Damgaard P, de la Fuente C, Chan J, Spence JP, Allentoft ME, Vimala T, Racimo F, Pinotti T, et al. 2018. Early human dispersals within the Americas. Science. 362(6419):eaav2621. doi: 10.1126/science.aav2621. PubMed DOI

Nakatsuka N, Holguin B, Sedig J, Langenwalter PE 2nd, Carpenter J, Culleton BJ, García-Moreno C, Harper TK, Martin D, Martínez-Ramírez J, et al. 2023. Genetic continuity and change among the Indigenous peoples of California. Nature. 624(7990):122–129. doi: 10.1038/s41586-023-06771-5. PubMed DOI PMC

Narasimhan VM, Patterson N, Moorjani P, Rohland N, Bernardos R, Mallick S, Lazaridis I, Nakatsuka N, Olalde I, Lipson M, et al. 2019. The formation of human populations in South and Central Asia. Science. 365(6457):eaat7487. doi: 10.1126/science.aat7487. PubMed DOI PMC

Nelson D, Kelleher J, Ragsdale AP, Moreau C, McVean G, Gravel S. 2020. Accounting for long-range correlations in genome-wide simulations of large cohorts. PLoS Genet. 16(5):e1008619. doi: 10.1371/journal.pgen.1008619. PubMed DOI PMC

Ning C, Li T, Wang K, Zhang F, Li T, Wu X, Gao S, Zhang Q, Zhang H, Hudson MJ, et al. 2020a. Ancient genomes from northern China suggest links between subsistence changes and human migration. Nat Commun. 11(1):2700. doi: 10.1038/s41467-020-16557-2. PubMed DOI PMC

Ning C, Fernandes D, Changmai P, Flegontova O, Yüncü E, Maier R, Altınışık NE, Kassian AS, Krause J., Lalueza-Fox C, et al. 2020b. The genomic formation of First American ancestors in East and Northeast Asia. doi: 10.1101/2020.10.12.336628. [accessed 2025 Jan 22]. https://www.biorxiv.org/content/10.1101/2020.10.12.336628v1. DOI

Novembre J, Stephens M. 2008. Interpreting principal component analyses of spatial population genetic variation. Nat Genet. 40(5):646–649. doi: 10.1038/ng.139. PubMed DOI PMC

Olalde I, Mallick S, Patterson N, Rohland N, Villalba-Mouco V, Silva M, Dulias K, Edwards CJ, Gandini F, Pala M, et al. 2019. The genomic history of the Iberian Peninsula over the past 8000 years. Science. 363(6432):1230–1234. doi: 10.1126/science.aav4040. PubMed DOI PMC

Oliveira S, Nägele K, Carlhoff S, Pugach I, Koesbardiati T, Hübner A, Meyer M, Oktaviana AA, Takenaka M, Katagiri C, et al. 2022. Ancient genomes from the last three millennia support multiple human dispersals into Wallacea. Nat Ecol Evol. 6(7):1024–1034. doi: 10.1038/s41559-022-01775-2. PubMed DOI PMC

Papac L, Ernée M, Dobeš M, Langová M, Rohrlach AB, Aron F, Neumann GU, Spyrou MA, Rohland N, Velemínský P, et al. 2021. Dynamic changes in genomic and social structures in third millennium BCE central Europe. Sci Adv. 7(35):eabi6941. doi: 10.1126/sciadv.abi6941. PubMed DOI PMC

Patterson N, Price AL, Reich D. 2006. Population structure and eigenanalysis. PLoS Genet. 2(12):e190. doi: 10.1371/journal.pgen.0020190. PubMed DOI PMC

Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D. 2012. Ancient admixture in human history. Genetics. 192(3):1065–1093. doi: 10.1534/genetics.112.145037. PubMed DOI PMC

Patterson N, Isakov M, Booth T, Büster L, Fischer CE, Olalde I, Ringbauer H, Akbari A, Cheronet O, Bleasdale M, et al. 2022. Large-scale migration into Britain during the Middle to Late Bronze Age. Nature. 601(7894):588–594. doi: 10.1038/s41586-021-04287-4. PubMed DOI PMC

Pavlinskaya LR (ed.). 2009. Sibirskij sbornik-1: Pogrebalnyj obryad narodov Sibiri i sopredelnych territorij (book 2). St. Petersburg: Museum of Antrhopology and Ethnography of the Russian Academy of Sciences.

Peter BM. 2016. Admixture, population structure, and F-statistics. Genetics. 202(4):1485–1501. doi: 10.1534/genetics.115.183913. PubMed DOI PMC

Peter BM. 2022. A geometric relationship of F2, F3 and F4-statistics with principal component analysis. Philos Trans R Soc Lond B Biol Sci. 377(1852):20200413. doi: 10.1098/rstb.2020.0413. PubMed DOI PMC

Petkova D, Novembre J, Stephens M. 2016. Visualizing spatial population structure with estimated effective migration surfaces. Nat Genet. 48(1):94–100. doi: 10.1038/ng.3464. PubMed DOI PMC

Posth C, Yu H, Ghalichi A, Rougier H, Crevecoeur I, Huang Y, Ringbauer H, Rohrlach AB, Nägele K, Villalba-Mouco V, et al. 2023. Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers. Nature. 615(7950):117–126. doi: 10.1038/s41586-023-05726-0. PubMed DOI PMC

Prendergast ME, Lipson M, Sawchuk EA, Olalde I, Ogola CA, Rohland N, Sirak KA, Adamski N, Bernardos R, Broomandkhoshbacht N, et al. 2019. Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa. Science. 365(6448):eaaw6275. doi: 10.1126/science.aaw6275. PubMed DOI PMC

Privé F, Luu K, Blum MGB, McGrath JJ, Vilhjálmsson BJ. 2020. Efficient toolkit implementing best practices for principal component analysis of population genetic data. Bioinformatics. 36(16):4449–4457. doi: 10.1093/bioinformatics/btaa520. PubMed DOI PMC

Reich D, Thangaraj K, Patterson N, Price AL, Singh L. 2009. Reconstructing Indian population history. Nature. 461(7263):489–494. doi: 10.1038/nature08365. PubMed DOI PMC

Reich D, Patterson N, Campbell D, Tandon A, Mazieres S, Ray N, Parra MV, Rojas W, Duque C, Mesa N, et al. 2012. Reconstructing Native American population history. Nature. 488(7411):370–374. doi: 10.1038/nature11258. PubMed DOI PMC

Scally A, Durbin R. 2012. Revising the human mutation rate: implications for understanding human evolution. Nat Rev Genet. 13(10):745–753. doi: 10.1038/nrg3295. PubMed DOI

Sikora M, Pitulko VV, Sousa VC, Allentoft ME, Vinner L, Rasmussen S, Margaryan A, de Barros Damgaard P, de la Fuente C, Renaud G, et al. 2019. The population history of northeastern Siberia since the Pleistocene. Nature. 570(7760):182–188. doi: 10.1038/s41586-019-1279-z. PubMed DOI PMC

Sirak KA, Fernandes DM, Lipson M, Mallick S, Mah M, Olalde I, Ringbauer H, Rohland N, Hadden CS, Harney É, et al. 2021. Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia. Nat Commun. 12(1):7283. doi: 10.1038/s41467-021-27356-8. PubMed DOI PMC

Skoglund P, Thompson JC, Prendergast ME, Mittnik A, Sirak K, Hajdinjak M, Salie T, Rohland N, Mallick S, Peltzer A, et al. 2017. Reconstructing prehistoric African population structure. Cell. 171(1):59–71.e21. doi: 10.1016/j.cell.2017.08.049. PubMed DOI PMC

Soraggi S, Wiuf C. 2019. General theory for stochastic admixture graphs and F-statistics. Theor Popul Biol. 125:56–66. doi: 10.1016/j.tpb.2018.12.002. PubMed DOI

Speidel L, Silva M, Booth T, Raffield B, Anastasiadou K, Barrington C, Götherström A, Heather P, Skoglund P. 2024. High-resolution genomic ancestry reveals mobility in early medieval Europe. doi: 10.1101/2024.03.15.585102. [accessed 2025 Jan 22]. https://www.biorxiv.org/content/10.1101/2024.03.15.585102v1. PubMed DOI PMC

Speidel L, Silva M, Booth T, Raffield B, Anastasiadou K, Barrington C, Götherström A, Heather P, Skoglund P. 2025. High-resolution genomic history of early medieval Europe. Nature. 637(8044):118–126. doi: 10.1038/s41586-024-08275-2. PubMed DOI PMC

Taylor WTT, Librado P, American Horse CJ, Shield Chief Gover C, Arterberry J, Afraid of Bear-Cook AL, Left Heron H, Yellow Hair RM, Gonzalez M, Means B, et al. 2023. Early dispersal of domestic horses into the Great Plains and northern Rockies. Science. 379(6639):1316–1323. doi: 10.1126/science.adc9691. PubMed DOI

Tricou T, Tannier E, de Vienne DM. 2022. Ghost lineages highly influence the interpretation of introgression tests. Syst Biol. 71(5):1147–1158. doi: 10.1093/sysbio/syac011. PubMed DOI PMC

van de Loosdrecht M, Bouzouggar A, Humphrey L, Posth C, Barton N, Aximu-Petri A, Nickel B, Nagel S, Talbi EH, El Hajraoui MA, et al. 2018. Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations. Science. 360(6388):548–552. doi: 10.1126/science.aar8380. PubMed DOI

Villalba-Mouco V, van de Loosdrecht MS, Rohrlach AB, Fewlass H, Talamo S, Yu H, Aron F, Lalueza-Fox C, Cabello L, Cantalejo Duarte P, et al. 2023. A 23,000-year-old southern Iberian individual links human groups that lived in Western Europe before and after the Last Glacial Maximum. Nat Ecol Evol. 7(4):597–609. doi: 10.1038/s41559-023-01987-0. PubMed DOI PMC

Wang K, Goldstein S, Bleasdale M, Clist B, Bostoen K, Bakwa-Lufu P, Buck LT, Crowther A, Dème A, McIntosh RJ, et al. 2020. Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa. Sci. Adv. 6(24):eaaz0183. doi: 10.1126/sciadv.aaz0183. PubMed DOI PMC

Wang CC, Yeh HY, Popov AN, Zhang HQ, Matsumura H, Sirak K, Cheronet O, Kovalev A, Rohland N, Kim AM, et al. 2021. Genomic insights into the formation of human populations in East Asia. Nature. 591(7850):413–419. doi: 10.1038/s41586-021-03336-2. PubMed DOI PMC

Williams MP, Flegontov P, Maier R, Huber CD. 2024. Testing times: Disentangling admixture histories in recent and complex demographies using ancient DNA. Genetics. 228(1):iyae110. doi: 10.1093/genetics/iyae110. PubMed DOI PMC

Yaka R, Mapelli I, Kaptan D, Doğu A, Chyleński M, Erdal ÖD, Koptekin D, Vural KB, Bayliss A, Mazzucato C, et al. 2021. Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes. Curr Biol. 31(11):2455–2468.e18. doi: 10.1016/j.cub.2021.03.050. PubMed DOI PMC

Yang MA, Fan X, Sun B, Chen C, Lang J, Ko YC, Tsang CH, Chiu H, Wang T, Bao Q, et al. 2020. Ancient DNA indicates human population shifts and admixture in northern and southern China. Science. 369(6501):282–288. doi: 10.1126/science.aba0909. PubMed DOI

Zeng TC, Vyazov LA, Kim A, Flegontov P, Sirak K, Maier R, Lazaridis I, Akbari A, Frachetti M, Tishkin AA, et al. 2023. Postglacial genomes from foragers across Northern Eurasia reveal prehistoric mobility associated with the spread of the Uralic and Yeniseian languages. doi: 10.1101/2023.10.01.560332. [accessed 2025 Jan 22]. https://www.biorxiv.org/content/10.1101/2023.10.01.560332v2. DOI

Zhang F, Ning C, Scott A, Fu Q, Bjørn R, Li W, Wei D, Wang W, Fan L, Abuduresule I, et al. 2021. The genomic origins of the Bronze Age Tarim Basin mummies. Nature. 599(7884):256–261. doi: 10.1038/s41586-021-04052-7. PubMed DOI PMC