Our understanding of population history in deep time has been assisted by fitting admixture graphs (AGs) to data: models that specify the ordering of population splits and mixtures, which along with the amount of genetic drift and the proportions of mixture, is the only information needed to predict the patterns of allele frequency correlation among populations. The space of possible AGs relating populations is vast, and thus most published studies have identified fitting AGs through a manual process driven by prior hypotheses, leaving the majority of alternative models unexplored. Here, we develop a method for systematically searching the space of all AGs that can incorporate non-genetic information in the form of topology constraints. We implement this findGraphs tool within a software package, ADMIXTOOLS 2, which is a reimplementation of the ADMIXTOOLS software with new features and large performance gains. We apply this methodology to identify alternative models to AGs that played key roles in eight publications and find that in nearly all cases many alternative models fit nominally or significantly better than the published one. Our results suggest that strong claims about population history from AGs should only be made when all well-fitting and temporally plausible models share common topological features. Our re-evaluation of published data also provides insight into the population histories of humans, dogs, and horses, identifying features that are stable across the models we explored, as well as scenarios of populations relationships that differ in important ways from models that have been highlighted in the literature.

Broad Institute of Harvard and MIT Cambridge United States

Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czech Republic

Department of Genetics Harvard Medical School Boston United States

Department of Human Evolutionary Biology Harvard University Cambridge United States

Howard Hughes Medical Institute Harvard Medical School Boston United States

Před aktualizací

doi: 10.1101/2022.05.08.491072 PubMed

Zobrazit více v PubMed

Baumdicker F, Bisschop G, Goldstein D, Gower G, Ragsdale AP, Tsambos G, Zhu S, Eldon B, Ellerman EC, Galloway JG, Gladstein AL, Gorjanc G, Guo B, Jeffery B, Kretzschumar WW, Lohse K, Matschiner M, Nelson D, Pope NS, Quinto-Cortés CD, Rodrigues MF, Saunack K, Sellinger T, Thornton K, van Kemenade H, Wohns AW, Wong Y, Gravel S, Kern AD, Koskela J, Ralph PL, Kelleher J. Efficient ancestry and mutation simulation with msprime 1.0. Genetics. 2022;220:iyab229. doi: 10.1093/genetics/iyab229. PubMed DOI PMC

Bellwood P. The checkered prehistory of rice movement southwards as a domesticated cereal—from the yangzi to the equator. Rice. 2011;4:93–103. doi: 10.1007/s12284-011-9068-9. DOI

Bergström A, Frantz L, Schmidt R, Ersmark E, Lebrasseur O, Girdland-Flink L, Lin AT, Storå J, Sjögren KG, Anthony D, Antipina E, Amiri S, Bar-Oz G, Bazaliiskii VI, Bulatović J, Brown D, Carmagnini A, Davy T, Fedorov S, Fiore I, Fulton D, Germonpré M, Haile J, Irving-Pease EK, Jamieson A, Janssens L, Kirillova I, Horwitz LK, Kuzmanovic-Cvetković J, Kuzmin Y, Losey RJ, Dizdar DL, Mashkour M, Novak M, Onar V, Orton D, Pasarić M, Radivojević M, Rajković D, Roberts B, Ryan H, Sablin M, Shidlovskiy F, Stojanović I, Tagliacozzo A, Trantalidou K, Ullén I, Villaluenga A, Wapnish P, Dobney K, Götherström A, Linderholm A, Dalén L, Pinhasi R, Larson G, Skoglund P. Origins and genetic legacy of prehistoric dogs. Science. 2020;370:557–564. doi: 10.1126/science.aba9572. PubMed DOI PMC

Bergström A, Stanton DWG, Taron UH, Frantz L, Sinding M-HS, Ersmark E, Pfrengle S, Cassatt-Johnstone M, Lebrasseur O, Girdland-Flink L, Fernandes DM, Ollivier M, Speidel L, Gopalakrishnan S, Westbury MV, Ramos-Madrigal J, Feuerborn TR, Reiter E, Gretzinger J, Münzel SC, Swali P, Conard NJ, Carøe C, Haile J, Linderholm A, Androsov S, Barnes I, Baumann C, Benecke N, Bocherens H, Brace S, Carden RF, Drucker DG, Fedorov S, Gasparik M, Germonpré M, Grigoriev S, Groves P, Hertwig ST, Ivanova VV, Janssens L, Jennings RP, Kasparov AK, Kirillova IV, Kurmaniyazov I, Kuzmin YV, Kosintsev PA, Lázničková-Galetová M, Leduc C, Nikolskiy P, Nussbaumer M, O’Drisceoil C, Orlando L, Outram A, Pavlova EY, Perri AR, Pilot M, Pitulko VV, Plotnikov VV, Protopopov AV, Rehazek A, Sablin M, Seguin-Orlando A, Storå J, Verjux C, Zaibert VF, Zazula G, Crombé P, Hansen AJ, Willerslev E, Leonard JA, Götherström A, Pinhasi R, Schuenemann VJ, Hofreiter M, Gilbert MTP, Shapiro B, Larson G, Krause J, Dalén L, Skoglund P. Grey wolf genomic history reveals a dual ancestry of dogs. Nature. 2022;607:313–320. doi: 10.1038/s41586-022-04824-9. PubMed DOI PMC

Boos DD. Introduction to the bootstrap world. Statistical Science. 2003;18:168–174. doi: 10.1214/ss/1063994971. DOI

Border R, Johnson EC, Evans LM, Smolen A, Berley N, Sullivan PF, Keller MC. No support for historical candidate gene or candidate gene-by-interaction hypotheses for major depression across multiple large samples. The American Journal of Psychiatry. 2019;176:376–387. doi: 10.1176/appi.ajp.2018.18070881. PubMed DOI PMC

Campbell MC, Tishkoff SA. African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping. Annual Review of Genomics and Human Genetics. 2008;9:403–433. doi: 10.1146/annurev.genom.9.081307.164258. PubMed DOI PMC

Carlhoff S, Duli A, Nägele K, Nur M, Skov L, Sumantri I, Oktaviana AA, Hakim B, Burhan B, Syahdar FA, McGahan DP, Bulbeck D, Perston YL, Newman K, Saiful AM, Ririmasse M, Chia S, Pulubuhu DAT, Jeong C, Peter BM, Prüfer K, Powell A, Krause J, Posth C, Brumm A. Genome of a middle Holocene Hunter-Gatherer from Wallacea. Nature. 2021;596:543–547. doi: 10.1038/s41586-021-03823-6. PubMed DOI PMC

Chen FH, Dong GH, Zhang DJ, Liu XY, Jia X, An CB, Ma MM, Xie YW, Barton L, Ren XY, Zhao ZJ, Wu XH, Jones MK. Agriculture facilitated permanent human occupation of the Tibetan Plateau after 3600 B.P. Science. 2015;347:248–250. doi: 10.1126/science.1259172. PubMed DOI

Collins AL, Kim Y, Sklar P, O’Donovan MC, Sullivan PF, International Schizophrenia Consortium Hypothesis-driven candidate genes for schizophrenia compared to genome-wide association results. Psychological Medicine. 2012;42:607–616. doi: 10.1017/S0033291711001607. PubMed DOI PMC

David Reich Lab Admixtools. ed1d857GitHub. 2023 https://github.com/DReichLab/AdmixTools

Duncan LE, Ostacher M, Ballon J. How genome-wide association studies (GWAS) made traditional candidate gene studies obsolete. Neuropsychopharmacology. 2019;44:1518–1523. doi: 10.1038/s41386-019-0389-5. PubMed DOI PMC

Excoffier L, Dupanloup I, Huerta-Sánchez E, Sousa VC, Foll M. Robust demographic inference from genomic and SNP data. PLOS Genetics. 2013;9:e1003905. doi: 10.1371/journal.pgen.1003905. PubMed DOI PMC

Flegontov P, Altınışık NE, Changmai P, Rohland N, Mallick S, Adamski N, Bolnick DA, Broomandkhoshbacht N, Candilio F, Culleton BJ, Flegontova O, Friesen TM, Jeong C, Harper TK, Keating D, Kennett DJ, Kim AM, Lamnidis TC, Lawson AM, Olalde I, Oppenheimer J, Potter BA, Raff J, Sattler RA, Skoglund P, Stewardson K, Vajda EJ, Vasilyev S, Veselovskaya E, Hayes MG, O’Rourke DH, Krause J, Pinhasi R, Reich D, Schiffels S. Palaeo-eskimo genetic ancestry and the peopling of chukotka and North America. Nature. 2019;570:236–240. doi: 10.1038/s41586-019-1251-y. PubMed DOI PMC

Fu Q, Posth C, Hajdinjak M, Petr M, Mallick S, Fernandes D, Furtwängler A, Haak W, Meyer M, Mittnik A, Nickel B, Peltzer A, Rohland N, Slon V, Talamo S, Lazaridis I, Lipson M, Mathieson I, Schiffels S, Skoglund P, Derevianko AP, Drozdov N, Slavinsky V, Tsybankov A, Cremonesi RG, Mallegni F, Gély B, Vacca E, Morales MRG, Straus LG, Neugebauer-Maresch C, Teschler-Nicola M, Constantin S, Moldovan OT, Benazzi S, Peresani M, Coppola D, Lari M, Ricci S, Ronchitelli A, Valentin F, Thevenet C, Wehrberger K, Grigorescu D, Rougier H, Crevecoeur I, Flas D, Semal P, Mannino MA, Cupillard C, Bocherens H, Conard NJ, Harvati K, Moiseyev V, Drucker DG, Svoboda J, Richards MP, Caramelli D, Pinhasi R, Kelso J, Patterson N, Krause J, Pääbo S, Reich D. The genetic history of ice age Europe. Nature. 2016;534:200–205. doi: 10.1038/nature17993. PubMed DOI PMC

Gray RD, Jordan FM. Language trees support the express-train sequence of austronesian expansion. Nature. 2000;405:1052–1055. doi: 10.1038/35016575. PubMed DOI

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH-Y, Hansen NF, Durand EY, Malaspinas A-S, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. A draft sequence of the Neandertal genome. Science. 2010;328:710–722. doi: 10.1126/science.1188021. PubMed DOI PMC

Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. Bayesian inference of ancient human demography from individual genome sequences. Nature Genetics. 2011;43:1031–1034. doi: 10.1038/ng.937. PubMed DOI PMC

Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLOS Genetics. 2009;5:e1000695. doi: 10.1371/journal.pgen.1000695. PubMed DOI PMC

Haak W, Lazaridis I, Patterson N, Rohland N, Mallick S, Llamas B, Brandt G, Nordenfelt S, Harney E, Stewardson K, Fu Q, Mittnik A, Bánffy E, Economou C, Francken M, Friederich S, Pena RG, Hallgren F, Khartanovich V, Khokhlov A, Kunst M, Kuznetsov P, Meller H, Mochalov O, Moiseyev V, Nicklisch N, Pichler SL, Risch R, Rojo Guerra MA, Roth C, Szécsényi-Nagy A, Wahl J, Meyer M, Krause J, Brown D, Anthony D, Cooper A, Alt KW, Reich D. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature. 2015;522:207–211. doi: 10.1038/nature14317. PubMed DOI PMC

Hajdinjak M, Mafessoni F, Skov L, Vernot B, Hübner A, Fu Q, Essel E, Nagel S, Nickel B, Richter J, Moldovan OT, Constantin S, Endarova E, Zahariev N, Spasov R, Welker F, Smith GM, Sinet-Mathiot V, Paskulin L, Fewlass H, Talamo S, Rezek Z, Sirakova S, Sirakov N, McPherron SP, Tsanova T, Hublin JJ, Peter BM, Meyer M, Skoglund P, Kelso J, Pääbo S. Initial upper Palaeolithic humans in Europe had recent neanderthal ancestry. Nature. 2021;592:253–257. doi: 10.1038/s41586-021-03335-3. PubMed DOI PMC

Hammer MF, Woerner AE, Mendez FL, Watkins JC, Wall JD. Genetic evidence for archaic admixture in Africa. PNAS. 2011;108:15123–15128. doi: 10.1073/pnas.1109300108. PubMed DOI PMC

Harney É, Patterson N, Reich D, Wakeley J. Assessing the performance of qpAdm: a statistical tool for studying population Admixture. Genetics. 2021;217:iyaa045. doi: 10.1093/genetics/iyaa045. PubMed DOI PMC

Hirschhorn JN, Daly MJ. Genome-Wide association studies for common diseases and complex traits. Nature Reviews. Genetics. 2005;6:95–108. doi: 10.1038/nrg1521. PubMed DOI

Hubisz M, Siepel A. Inference of ancestral recombination graphs using argweaver. Methods in Molecular Biology. 2020;2090:231–266. doi: 10.1007/978-1-0716-0199-0_10. PubMed DOI

Hubisz MJ, Williams AL, Siepel A. Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLOS Genetics. 2020;16:e1008895. doi: 10.1371/journal.pgen.1008895. PubMed DOI PMC

Ioannidis JPA. Why most published research findings are false. PLOS Medicine. 2005;2:e124. doi: 10.1371/journal.pmed.0020124. PubMed DOI PMC

Jeong C, Balanovsky O, Lukianova E, Kahbatkyzy N, Flegontov P, Zaporozhchenko V, Immel A, Wang CC, Ixan O, Khussainova E, Bekmanov B, Zaibert V, Lavryashina M, Pocheshkhova E, Yusupov Y, Agdzhoyan A, Koshel S, Bukin A, Nymadawa P, Turdikulova S, Dalimova D, Churnosov M, Skhalyakho R, Daragan D, Bogunov Y, Bogunova A, Shtrunov A, Dubova N, Zhabagin M, Yepiskoposyan L, Churakov V, Pislegin N, Damba L, Saroyants L, Dibirova K, Atramentova L, Utevska O, Idrisov E, Kamenshchikova E, Evseeva I, Metspalu M, Outram AK, Robbeets M, Djansugurova L, Balanovska E, Schiffels S, Haak W, Reich D, Krause J. The genetic history of admixture across inner Eurasia. Nature Ecology & Evolution. 2019;3:966–976. doi: 10.1038/s41559-019-0878-2. PubMed DOI PMC

Kamm J, Terhorst J, Durbin R, Song YS. Efficiently inferring the demographic history of many populations with allele count data. Journal of the American Statistical Association. 2020;115:1472–1487. doi: 10.1080/01621459.2019.1635482. PubMed DOI PMC

Ko AM-S, Chen C-Y, Fu Q, Delfin F, Li M, Chiu H-L, Stoneking M, Ko Y-C. Early Austronesians: into and out of Taiwan. American Journal of Human Genetics. 2014;94:426–436. doi: 10.1016/j.ajhg.2014.02.003. PubMed DOI PMC

Kutanan W, Liu D, Kampuansai J, Srikummool M, Srithawong S, Shoocongdej R, Sangkhano S, Ruangchai S, Pittayaporn P, Arias L, Stoneking M. Reconstructing the human genetic history of mainland Southeast Asia: insights from genome-wide data from Thailand and laos. Molecular Biology and Evolution. 2021;38:3459–3477. doi: 10.1093/molbev/msab124. PubMed DOI PMC

Lachance J, Vernot B, Elbers CC, Ferwerda B, Froment A, Bodo JM, Lema G, Fu W, Nyambo TB, Rebbeck TR, Zhang K, Akey JM, Tishkoff SA. Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers. Cell. 2012;150:457–469. doi: 10.1016/j.cell.2012.07.009. PubMed DOI PMC

Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M, Berger B, Economou C, Bollongino R, Fu Q, Bos KI, Nordenfelt S, Li H, de Filippo C, Prüfer K, Sawyer S, Posth C, Haak W, Hallgren F, Fornander E, Rohland N, Delsate D, Francken M, Guinet JM, Wahl J, Ayodo G, Babiker HA, Bailliet G, Balanovska E, Balanovsky O, Barrantes R, Bedoya G, Ben-Ami H, Bene J, Berrada F, Bravi CM, Brisighelli F, Busby GBJ, Cali F, Churnosov M, Cole DEC, Corach D, Damba L, van Driem G, Dryomov S, Dugoujon JM, Fedorova SA, Gallego Romero I, Gubina M, Hammer M, Henn BM, Hervig T, Hodoglugil U, Jha AR, Karachanak-Yankova S, Khusainova R, Khusnutdinova E, Kittles R, Kivisild T, Klitz W, Kučinskas V, Kushniarevich A, Laredj L, Litvinov S, Loukidis T, Mahley RW, Melegh B, Metspalu E, Molina J, Mountain J, Näkkäläjärvi K, Nesheva D, Nyambo T, Osipova L, Parik J, Platonov F, Posukh O, Romano V, Rothhammer F, Rudan I, Ruizbakiev R, Sahakyan H, Sajantila A, Salas A, Starikovskaya EB, Tarekegn A, Toncheva D, Turdikulova S, Uktveryte I, Utevska O, Vasquez R, Villena M, Voevoda M, Winkler CA, Yepiskoposyan L, Zalloua P, Zemunik T, Cooper A, Capelli C, Thomas MG, Ruiz-Linares A, Tishkoff SA, Singh L, Thangaraj K, Villems R, Comas D, Sukernik R, Metspalu M, Meyer M, Eichler EE, Burger J, Slatkin M, Pääbo S, Kelso J, Reich D, Krause J. Ancient human Genomes suggest three ancestral populations for present-day Europeans. Nature. 2014;513:409–413. doi: 10.1038/nature13673. PubMed DOI PMC

Lazaridis I, Nadel D, Rollefson G, Merrett DC, Rohland N, Mallick S, Fernandes D, Novak M, Gamarra B, Sirak K, Connell S, Stewardson K, Harney E, Fu Q, Gonzalez-Fortes G, Jones ER, Roodenberg SA, Lengyel G, Bocquentin F, Gasparian B, Monge JM, Gregg M, Eshed V, Mizrahi AS, Meiklejohn C, Gerritsen F, Bejenaru L, Blüher M, Campbell A, Cavalleri G, Comas D, Froguel P, Gilbert E, Kerr SM, Kovacs P, Krause J, McGettigan D, Merrigan M, Merriwether DA, O’Reilly S, Richards MB, Semino O, Shamoon-Pour M, Stefanescu G, Stumvoll M, Tönjes A, Torroni A, Wilson JF, Yengo L, Hovhannisyan NA, Patterson N, Pinhasi R, Reich D. Genomic insights into the origin of farming in the ancient near East. Nature. 2016;536:419–424. doi: 10.1038/nature19310. PubMed DOI PMC

Leppälä K, Nielsen SV, Mailund T. Admixturegraph: an R package for admixture graph manipulation and fitting. Bioinformatics. 2017;33:1738–1740. doi: 10.1093/bioinformatics/btx048. PubMed DOI PMC

Librado P, Khan N, Fages A, Kusliy MA, Suchan T, Tonasso-Calvière L, Schiavinato S, Alioglu D, Fromentier A, Perdereau A, Aury J-M, Gaunitz C, Chauvey L, Seguin-Orlando A, Der Sarkissian C, Southon J, Shapiro B, Tishkin AA, Kovalev AA, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Seregély T, Klassen L, Iversen R, Bignon-Lau O, Bodu P, Olive M, Castel J-C, Boudadi-Maligne M, Alvarez N, Germonpré M, Moskal-Del Hoyo M, Wilczyński J, Pospuła S, Lasota-Kuś A, Tunia K, Nowak M, Rannamäe E, Saarma U, Boeskorov G, Lōugas L, Kyselý R, Peške L, Bălășescu A, Dumitrașcu V, Dobrescu R, Gerber D, Kiss V, Szécsényi-Nagy A, Mende BG, Gallina Z, Somogyi K, Kulcsár G, Gál E, Bendrey R, Allentoft ME, Sirbu G, Dergachev V, Shephard H, Tomadini N, Grouard S, Kasparov A, Basilyan AE, Anisimov MA, Nikolskiy PA, Pavlova EY, Pitulko V, Brem G, Wallner B, Schwall C, Keller M, Kitagawa K, Bessudnov AN, Bessudnov A, Taylor W, Magail J, Gantulga J-O, Bayarsaikhan J, Erdenebaatar D, Tabaldiev K, Mijiddorj E, Boldgiv B, Tsagaan T, Pruvost M, Olsen S, Makarewicz CA, Valenzuela Lamas S, Albizuri Canadell S, Nieto Espinet A, Iborra MP, Lira Garrido J, Rodríguez González E, Celestino S, Olària C, Arsuaga JL, Kotova N, Pryor A, Crabtree P, Zhumatayev R, Toleubaev A, Morgunova NL, Kuznetsova T, Lordkipanize D, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Clavel B, Lepetz S, Davoudi H, Mashkour M, Berezina NY, Stockhammer PW, Krause J, Haak W, Morales-Muñiz A, Benecke N, Hofreiter M, Ludwig A, Graphodatsky AS, Peters J, Kiryushin KY, Iderkhangai T-O, Bokovenko NA, Vasiliev SK, Seregin NN, Chugunov KV, Plasteeva NA, Baryshnikov GF, Petrova E, Sablin M, Ananyevskaya E, Logvin A, Shevnina I, Logvin V, Kalieva S, Loman V, Kukushkin I, Merz I, Merz V, Sakenov S, Varfolomeyev V, Usmanova E, Zaibert V, Arbuckle B, Belinskiy AB, Kalmykov A, Reinhold S, Hansen S, Yudin AI, Vybornov AA, Epimakhov A, Berezina NS, Roslyakova N, Kosintsev PA, Kuznetsov PF, Anthony D, Kroonen GJ, Kristiansen K, Wincker P, Outram A, Orlando L. The origins and spread of domestic horses from the Western Eurasian steppes. Nature. 2021;598:634–640. doi: 10.1038/s41586-021-04018-9. PubMed DOI PMC

Lipson M, Loh PR, Levin A, Reich D, Patterson N, Berger B. Efficient moment-based inference of admixture parameters and sources of gene flow. Molecular Biology and Evolution. 2013;30:1788–1802. doi: 10.1093/molbev/mst099. PubMed DOI PMC

Lipson M, Szécsényi-Nagy A, Mallick S, Pósa A, Stégmár B, Keerl V, Rohland N, Stewardson K, Ferry M, Michel M, Oppenheimer J, Broomandkhoshbacht N, Harney E, Nordenfelt S, Llamas B, Gusztáv Mende B, Köhler K, Oross K, Bondár M, Marton T, Osztás A, Jakucs J, Paluch T, Horváth F, Csengeri P, Koós J, Sebők K, Anders A, Raczky P, Regenye J, Barna JP, Fábián S, Serlegi G, Toldi Z, Gyöngyvér Nagy E, Dani J, Molnár E, Pálfi G, Márk L, Melegh B, Bánfai Z, Domboróczki L, Fernández-Eraso J, Antonio Mujika-Alustiza J, Alonso Fernández C, Jiménez Echevarría J, Bollongino R, Orschiedt J, Schierhold K, Meller H, Cooper A, Burger J, Bánffy E, Alt KW, Lalueza-Fox C, Haak W, Reich D. Parallel palaeogenomic transects reveal complex genetic history of early European farmers. Nature. 2017;551:368–372. doi: 10.1038/nature24476. PubMed DOI PMC

Lipson M. Applying f4-statistics and admixture graphs: theory and examples. Molecular Ecology Resources. 2020a;20:1658–1667. doi: 10.1111/1755-0998.13230. PubMed DOI

Lipson M, Ribot I, Mallick S, Rohland N, Olalde I, Adamski N, Broomandkhoshbacht N, Lawson AM, López S, Oppenheimer J, Stewardson K, Asombang RN, Bocherens H, Bradman N, Culleton BJ, Cornelissen E, Crevecoeur I, de Maret P, Fomine FLM, Lavachery P, Mindzie CM, Orban R, Sawchuk E, Semal P, Thomas MG, Van Neer W, Veeramah KR, Kennett DJ, Patterson N, Hellenthal G, Lalueza-Fox C, MacEachern S, Prendergast ME, Reich D. Ancient West African foragers in the context of African population history. Nature. 2020b;577:665–670. doi: 10.1038/s41586-020-1929-1. PubMed DOI PMC

Lipson M, Sawchuk EA, Thompson JC, Oppenheimer J, Tryon CA, Ranhorn KL, de Luna KM, Sirak KA, Olalde I, Ambrose SH, Arthur JW, Arthur KJW, Ayodo G, Bertacchi A, Cerezo-Román JI, Culleton BJ, Curtis MC, Davis J, Gidna AO, Hanson A, Kaliba P, Katongo M, Kwekason A, Laird MF, Lewis J, Mabulla AZP, Mapemba F, Morris A, Mudenda G, Mwafulirwa R, Mwangomba D, Ndiema E, Ogola C, Schilt F, Willoughby PR, Wright DK, Zipkin A, Pinhasi R, Kennett DJ, Manthi FK, Rohland N, Patterson N, Reich D, Prendergast ME. Ancient DNA and deep population structure in sub-Saharan African foragers. Nature. 2022;603:290–296. doi: 10.1038/s41586-022-04430-9. PubMed DOI PMC

Lu D, Lou H, Yuan K, Wang X, Wang Y, Zhang C, Lu Y, Yang X, Deng L, Zhou Y, Feng Q, Hu Y, Ding Q, Yang Y, Li S, Jin L, Guan Y, Su B, Kang L, Xu S. Ancestral origins and genetic history of Tibetan highlanders. American Journal of Human Genetics. 2016;99:580–594. doi: 10.1016/j.ajhg.2016.07.002. PubMed DOI PMC

Maier R, Isildak U, rmmaier Admixtools. swh:1:rev:45fcc41768d88559863d6dfae9ccaceaf247f81eSoftware Heritage. 2022 https://archive.softwareheritage.org/swh:1:dir:38fceb428451354c86a1c41fa7291ea117a15d2b;origin=https://github.com/uqrmaie1/admixtools;visit=swh:1:snp:ec5ab16d631d19a1943b1f874db5a4df0cee6ced;anchor=swh:1:rev:45fcc41768d88559863d6dfae9ccaceaf247f81e

Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A, Skoglund P, Lazaridis I, Sankararaman S, Fu Q, Rohland N, Renaud G, Erlich Y, Willems T, Gallo C, Spence JP, Song YS, Poletti G, Balloux F, van Driem G, de Knijff P, Romero IG, Jha AR, Behar DM, Bravi CM, Capelli C, Hervig T, Moreno-Estrada A, Posukh OL, Balanovska E, Balanovsky O, Karachanak-Yankova S, Sahakyan H, Toncheva D, Yepiskoposyan L, Tyler-Smith C, Xue Y, Abdullah MS, Ruiz-Linares A, Beall CM, Di Rienzo A, Jeong C, Starikovskaya EB, Metspalu E, Parik J, Villems R, Henn BM, Hodoglugil U, Mahley R, Sajantila A, Stamatoyannopoulos G, Wee JTS, Khusainova R, Khusnutdinova E, Litvinov S, Ayodo G, Comas D, Hammer MF, Kivisild T, Klitz W, Winkler CA, Labuda D, Bamshad M, Jorde LB, Tishkoff SA, Watkins WS, Metspalu M, Dryomov S, Sukernik R, Singh L, Thangaraj K, Pääbo S, Kelso J, Patterson N, Reich D. The simons genome diversity project: 300 genomes from 142 diverse populations. Nature. 2016;538:201–206. doi: 10.1038/nature18964. 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, Fernandes D, Ferry M, Gamarra B, Fortes GG, Haak W, Harney E, Jones E, Keating D, Krause-Kyora B, Kucukkalipci I, Michel M, Mittnik A, Nägele K, Novak M, Oppenheimer J, Patterson N, Pfrengle S, Sirak K, Stewardson K, Vai S, Alexandrov S, Alt KW, Andreescu R, Antonović D, Ash A, Atanassova N, Bacvarov K, Gusztáv MB, Bocherens H, Bolus M, Boroneanţ A, Boyadzhiev Y, Budnik A, Burmaz J, Chohadzhiev S, Conard NJ, Cottiaux R, Čuka M, Cupillard C, Drucker DG, Elenski N, Francken M, Galabova B, Ganetsovski G, Gély B, Hajdu T, Handzhyiska V, Harvati K, Higham T, Iliev S, Janković I, Karavanić I, Kennett DJ, Komšo D, Kozak A, Labuda D, Lari M, Lazar C, Leppek M, Leshtakov K, Vetro DL, Los D, Lozanov I, Malina M, Martini F, McSweeney K, Meller H, Menđušić M, Mirea P, Moiseyev V, Petrova V, Price TD, Simalcsik A, Sineo L, Šlaus M, Slavchev V, Stanev P, Starović A, Szeniczey T, Talamo S, Teschler-Nicola M, Thevenet C, Valchev I, Valentin F, Vasilyev S, Veljanovska F, Venelinova S, Veselovskaya E, Viola B, Virag C, Zaninović J, Zäuner S, Stockhammer PW, Catalano G, Krauß R, Caramelli D, Zariņa G, Gaydarska B, Lillie M, Nikitin AG, Potekhina I, Papathanasiou A, Borić D, Bonsall C, Krause J, Pinhasi R, Reich D. The genomic history of southeastern Europe. Nature. 2018;555:197–203. doi: 10.1038/nature25778. PubMed DOI PMC

McColl H, Racimo F, Vinner L, Demeter F, Gakuhari T, Moreno-Mayar JV, van Driem G, Gram Wilken U, Seguin-Orlando A, de la Fuente Castro C, Wasef S, Shoocongdej R, Souksavatdy V, Sayavongkhamdy T, Saidin MM, Allentoft ME, Sato T, Malaspinas A-S, Aghakhanian FA, Korneliussen T, Prohaska A, Margaryan A, de Barros Damgaard P, Kaewsutthi S, Lertrit P, Nguyen TMH, Hung H-C, Minh Tran T, Nghia Truong H, Nguyen GH, Shahidan S, Wiradnyana K, Matsumae H, Shigehara N, Yoneda M, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Hanihara T, Nakagome S, Deviese T, Bacon A-M, Duringer P, Ponche J-L, Shackelford L, Patole-Edoumba E, Nguyen AT, Bellina-Pryce B, Galipaud J-C, Kinaston R, Buckley H, Pottier C, Rasmussen S, Higham T, Foley RA, Lahr MM, Orlando L, Sikora M, Phipps ME, Oota H, Higham C, Lambert DM, Willerslev E. The prehistoric peopling of Southeast Asia. Science. 2018;361:88–92. doi: 10.1126/science.aat3628. PubMed DOI

Molloy EK, Durvasula A, Sankararaman S. Advancing admixture graph estimation via maximum likelihood network orientation. Bioinformatics. 2021;37:i142–i150. doi: 10.1093/bioinformatics/btab267. 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, Rasmussen S, Margaryan A, Iraeta Orbegozo M, Mylopotamitaki D, Wooller M, Bataille C, Becerra-Valdivia L, Chivall D, Comeskey D, Devièse T, Grayson DK, George L, Harry H, Alexandersen V, Primeau C, Erlandson J, Rodrigues-Carvalho C, Reis S, Bastos MQR, Cybulski J, Vullo C, Morello F, Vilar M, Wells S, Gregersen K, Hansen KL, Lynnerup N, Mirazón Lahr M, Kjær K, Strauss A, Alfonso-Durruty M, Salas A, Schroeder H, Higham T, Malhi RS, Rasic JT, Souza L, Santos FR, Malaspinas AS, Sikora M, Nielsen R, Song YS, Meltzer DJ, Willerslev E. Early human dispersals within the Americas. Science. 2018;362:2621. doi: 10.1126/science.aav2621. PubMed DOI

Narasimhan VM, Patterson N, Moorjani P, Rohland N, Bernardos R, Mallick S, Lazaridis I, Nakatsuka N, Olalde I, Lipson M, Kim AM, Olivieri LM, Coppa A, Vidale M, Mallory J, Moiseyev V, Kitov E, Monge J, Adamski N, Alex N, Broomandkhoshbacht N, Candilio F, Callan K, Cheronet O, Culleton BJ, Ferry M, Fernandes D, Freilich S, Gamarra B, Gaudio D, Hajdinjak M, Harney É, Harper TK, Keating D, Lawson AM, Mah M, Mandl K, Michel M, Novak M, Oppenheimer J, Rai N, Sirak K, Slon V, Stewardson K, Zalzala F, Zhang Z, Akhatov G, Bagashev AN, Bagnera A, Baitanayev B, Bendezu-Sarmiento J, Bissembaev AA, Bonora GL, Chargynov TT, Chikisheva T, Dashkovskiy PK, Derevianko A, Dobeš M, Douka K, Dubova N, Duisengali MN, Enshin D, Epimakhov A, Fribus AV, Fuller D, Goryachev A, Gromov A, Grushin SP, Hanks B, Judd M, Kazizov E, Khokhlov A, Krygin AP, Kupriyanova E, Kuznetsov P, Luiselli D, Maksudov F, Mamedov AM, Mamirov TB, Meiklejohn C, Merrett DC, Micheli R, Mochalov O, Mustafokulov S, Nayak A, Pettener D, Potts R, Razhev D, Rykun M, Sarno S, Savenkova TM, Sikhymbaeva K, Slepchenko SM, Soltobaev OA, Stepanova N, Svyatko S, Tabaldiev K, Teschler-Nicola M, Tishkin AA, Tkachev VV, Vasilyev S, Velemínský P, Voyakin D, Yermolayeva A, Zahir M, Zubkov VS, Zubova A, Shinde VS, Lalueza-Fox C, Meyer M, Anthony D, Boivin N, Thangaraj K, Kennett DJ, Frachetti M, Pinhasi R, Reich D. The formation of human populations in South and central Asia. Science. 2019;365:7487. doi: 10.1126/science.aat7487. PubMed DOI PMC

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

Nielsen SV, Vaughn AH, Leppälä K, Landis MJ, Mailund T, Nielsen R. Bayesian inference of Admixture graphs on native American and Arctic populations. PLOS Genetics. 2023;1:1010410. doi: 10.1371/journal.pgen.1010410. PubMed DOI PMC

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

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

Pickrell JK, Pritchard JK. Inference of population splits and mixtures from genome-wide allele frequency data. PLOS Genetics. 2012;8:e1002967. doi: 10.1371/journal.pgen.1002967. PubMed DOI PMC

Posth C, Nakatsuka N, Lazaridis I, Skoglund P, Mallick S, Lamnidis TC, Rohland N, Nägele K, Adamski N, Bertolini E, Broomandkhoshbacht N, Cooper A, Culleton BJ, Ferraz T, Ferry M, Furtwängler A, Haak W, Harkins K, Harper TK, Hünemeier T, Lawson AM, Llamas B, Michel M, Nelson E, Oppenheimer J, Patterson N, Schiffels S, Sedig J, Stewardson K, Talamo S, Wang CC, Hublin JJ, Hubbe M, Harvati K, Nuevo Delaunay A, Beier J, Francken M, Kaulicke P, Reyes-Centeno H, Rademaker K, Trask WR, Robinson M, Gutierrez SM, Prufer KM, Salazar-García DC, Chim EN, Müller Plumm Gomes L, Alves ML, Liryo A, Inglez M, Oliveira RE, Bernardo DV, Barioni A, Wesolowski V, Scheifler NA, Rivera MA, Plens CR, Messineo PG, Figuti L, Corach D, Scabuzzo C, Eggers S, DeBlasis P, Reindel M, Méndez C, Politis G, Tomasto-Cagigao E, Kennett DJ, Strauss A, Fehren-Schmitz L, Krause J, Reich D. Reconstructing the deep population history of central and South America. Cell. 2018;175:1185–1197. doi: 10.1016/j.cell.2018.10.027. PubMed DOI PMC

Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PLF, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S. The complete genome sequence of a Neanderthal from the altai mountains. Nature. 2014;505:43–49. doi: 10.1038/nature12886. PubMed DOI PMC

Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A, Moltke I, Rasmussen S, Stafford TW, Orlando L, Metspalu E, Karmin M, Tambets K, Rootsi S, Mägi R, Campos PF, Balanovska E, Balanovsky O, Khusnutdinova E, Litvinov S, Osipova LP, Fedorova SA, Voevoda MI, DeGiorgio M, Sicheritz-Ponten T, Brunak S, Demeshchenko S, Kivisild T, Villems R, Nielsen R, Jakobsson M, Willerslev E. Upper Palaeolithic Siberian genome reveals dual ancestry of native Americans. Nature. 2014;505:87–91. doi: 10.1038/nature12736. PubMed DOI PMC

Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas A-S, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, Cornejo OE, Moreno-Mayar JV, Korneliussen TS, Pierre T, Rasmussen M, Campos PF, de Barros Damgaard P, Allentoft ME, Lindo J, Metspalu E, Rodríguez-Varela R, Mansilla J, Henrickson C, Seguin-Orlando A, Malmström H, Stafford T, Shringarpure SS, Moreno-Estrada A, Karmin M, Tambets K, Bergström A, Xue Y, Warmuth V, Friend AD, Singarayer J, Valdes P, Balloux F, Leboreiro I, Vera JL, Rangel-Villalobos H, Pettener D, Luiselli D, Davis LG, Heyer E, Zollikofer CPE, Ponce de León MS, Smith CI, Grimes V, Pike K-A, Deal M, Fuller BT, Arriaza B, Standen V, Luz MF, Ricaut F, Guidon N, Osipova L, Voevoda MI, Posukh OL, Balanovsky O, Lavryashina M, Bogunov Y, Khusnutdinova E, Gubina M, Balanovska E, Fedorova S, Litvinov S, Malyarchuk B, Derenko M, Mosher MJ, Archer D, Cybulski J, Petzelt B, Mitchell J, Worl R, Norman PJ, Parham P, Kemp BM, Kivisild T, Tyler-Smith C, Sandhu MS, Crawford M, Villems R, Smith DG, Waters MR, Goebel T, Johnson JR, Malhi RS, Jakobsson M, Meltzer DJ, Manica A, Durbin R, Bustamante CD, Song YS, Nielsen R, Willerslev E. Population genetics: genomic evidence for the Pleistocene and recent population history of native Americans. Science. 2015;349:aab3884. doi: 10.1126/science.aab3884. PubMed DOI PMC

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

Reich D, Patterson N, Kircher M, Delfin F, Nandineni MR, Pugach I, Ko AM-S, Ko Y-C, Jinam TA, Phipps ME, Saitou N, Wollstein A, Kayser M, Pääbo S, Stoneking M. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. The American Journal of Human Genetics. 2011;89:516–528. doi: 10.1016/j.ajhg.2011.09.005. PubMed DOI PMC

Reich D, Patterson N, Campbell D, Tandon A, Mazieres S, Ray N, Parra MV, Rojas W, Duque C, Mesa N, García LF, Triana O, Blair S, Maestre A, Dib JC, Bravi CM, Bailliet G, Corach D, Hünemeier T, Bortolini MC, Salzano FM, Petzl-Erler ML, Acuña-Alonzo V, Aguilar-Salinas C, Canizales-Quinteros S, Tusié-Luna T, Riba L, Rodríguez-Cruz M, Lopez-Alarcón M, Coral-Vazquez R, Canto-Cetina T, Silva-Zolezzi I, Fernandez-Lopez JC, Contreras AV, Jimenez-Sanchez G, Gómez-Vázquez MJ, Molina J, Carracedo A, Salas A, Gallo C, Poletti G, Witonsky DB, Alkorta-Aranburu G, Sukernik RI, Osipova L, Fedorova SA, Vasquez R, Villena M, Moreau C, Barrantes R, Pauls D, Excoffier L, Bedoya G, Rothhammer F, Dugoujon JM, Larrouy G, Klitz W, Labuda D, Kidd J, Kidd K, Di Rienzo A, Freimer NB, Price AL. Ruiz-linares a. Reconstructing Native American Population History. Nature. 2012;488:370–374. doi: 10.1038/nature11258. PubMed DOI PMC

Rogers AR. Legofit: estimating population history from genetic data. BMC Bioinformatics. 2019;20:526. doi: 10.1186/s12859-019-3154-1. PubMed DOI PMC

Scally A, Durbin R. Revising the human mutation rate: implications for understanding human evolution. Nature Reviews. Genetics. 2012;13:745–753. doi: 10.1038/nrg3295. PubMed DOI

Schiffels S, Durbin R. Inferring human population size and separation history from multiple genome sequences. Nature Genetics. 2014;46:919–925. doi: 10.1038/ng.3015. PubMed DOI PMC

Schiffels S, Haak W, Paajanen P, Llamas B, Popescu E, Loe L, Clarke R, Lyons A, Mortimer R, Sayer D, Tyler-Smith C, Cooper A, Durbin R. Iron age and anglo-saxon genomes from East England reveal British migration history. Nature Communications. 2016;7:10408. doi: 10.1038/ncomms10408. PubMed DOI PMC

Seguin-Orlando A, Korneliussen TS, Sikora M, Malaspinas A-S, Manica A, Moltke I, Albrechtsen A, Ko A, Margaryan A, Moiseyev V, Goebel T, Westaway M, Lambert D, Khartanovich V, Wall JD, Nigst PR, Foley RA, Lahr MM, Nielsen R, Orlando L, Willerslev E. Paleogenomics: genomic structure in Europeans dating back at least 36,200 years. Science. 2014;346:1113–1118. doi: 10.1126/science.aaa0114. PubMed DOI

Shinde V, Narasimhan VM, Rohland N, Mallick S, Mah M, Lipson M, Nakatsuka N, Adamski N, Broomandkhoshbacht N, Ferry M, Lawson AM, Michel M, Oppenheimer J, Stewardson K, Jadhav N, Kim YJ, Chatterjee M, Munshi A, Panyam A, Waghmare P, Yadav Y, Patel H, Kaushik A, Thangaraj K, Meyer M, Patterson N, Rai N, Reich D. An ancient harappan genome lacks ancestry from steppe pastoralists or Iranian farmers. Cell. 2019;179:729–735. doi: 10.1016/j.cell.2019.08.048. PubMed DOI PMC

Sikora M, Pitulko VV, Sousa VC, Allentoft ME, Vinner L, Rasmussen S, Margaryan A, de Barros Damgaard P, de la Fuente C, Renaud G, Yang MA, Fu Q, Dupanloup I, Giampoudakis K, Nogués-Bravo D, Rahbek C, Kroonen G, Peyrot M, McColl H, Vasilyev SV, Veselovskaya E, Gerasimova M, Pavlova EY, Chasnyk VG, Nikolskiy PA, Gromov AV, Khartanovich VI, Moiseyev V, Grebenyuk PS, Fedorchenko AYu, Lebedintsev AI, Slobodin SB, Malyarchuk BA, Martiniano R, Meldgaard M, Arppe L, Palo JU, Sundell T, Mannermaa K, Putkonen M, Alexandersen V, Primeau C, Baimukhanov N, Malhi RS, Sjögren K-G, Kristiansen K, Wessman A, Sajantila A, Lahr MM, Durbin R, Nielsen R, Meltzer DJ, Excoffier L, Willerslev E. The population history of northeastern Siberia since the Pleistocene. Nature. 2019;570:182–188. doi: 10.1038/s41586-019-1279-z. PubMed DOI

Skoglund P, Posth C, Sirak K, Spriggs M, Valentin F, Bedford S, Clark GR, Reepmeyer C, Petchey F, Fernandes D, Fu Q, Harney E, Lipson M, Mallick S, Novak M, Rohland N, Stewardson K, Abdullah S, Cox MP, Friedlaender FR, Friedlaender JS, Kivisild T, Koki G, Kusuma P, Merriwether DA, Ricaut F-X, Wee JTS, Patterson N, Krause J, Pinhasi R, Reich D. Genomic insights into the peopling of the southwest Pacific. Nature. 2016;538:510–513. doi: 10.1038/nature19844. PubMed DOI PMC

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

Speidel L, Forest M, Shi S, Myers SR. A method for genome-wide genealogy estimation for thousands of samples. Nature Genetics. 2019;51:1321–1329. doi: 10.1038/s41588-019-0484-x. PubMed DOI PMC

Tambets K, Yunusbayev B, Hudjashov G, Ilumäe AM, Rootsi S, Honkola T, Vesakoski O, Atkinson Q, Skoglund P, Kushniarevich A, Litvinov S, Reidla M, Metspalu E, Saag L, Rantanen T, Karmin M, Parik J, Zhadanov SI, Gubina M, Damba LD, Bermisheva M, Reisberg T, Dibirova K, Evseeva I, Nelis M, Klovins J, Metspalu A, Esko T, Balanovsky O, Balanovska E, Khusnutdinova EK, Osipova LP, Voevoda M, Villems R, Kivisild T, Metspalu M. Genes reveal traces of common recent demographic history for most of the uralic-speaking populations. Genome Biology. 2018;19:139. doi: 10.1186/s13059-018-1522-1. PubMed DOI PMC

Terhorst J, Kamm JA, Song YS. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nature Genetics. 2017;49:303–309. doi: 10.1038/ng.3748. PubMed DOI PMC

Vallini L, Marciani G, Aneli S, Bortolini E, Benazzi S, Pievani T, Pagani L. Genetics and material culture support repeated expansions into paleolithic Eurasia from a population hub out of Africa. Genome Biology and Evolution. 2022;14:evac045. doi: 10.1093/gbe/evac045. 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, Amzazi S, Hublin J-J, Pääbo S, Schiffels S, Meyer M, Haak W, Jeong C, Krause J. Pleistocene North African genomes link near eastern and sub-Saharan African human populations. Science. 2018;360:548–552. doi: 10.1126/science.aar8380. PubMed DOI

Wang CC, Reinhold S, Kalmykov A, Wissgott A, Brandt G, Jeong C, Cheronet O, Ferry M, Harney E, Keating D, Mallick S, Rohland N, Stewardson K, Kantorovich AR, Maslov VE, Petrenko VG, Erlikh VR, Atabiev BC, Magomedov RG, Kohl PL, Alt KW, Pichler SL, Gerling C, Meller H, Vardanyan B, Yeganyan L, Rezepkin AD, Mariaschk D, Berezina N, Gresky J, Fuchs K, Knipper C, Schiffels S, Balanovska E, Balanovsky O, Mathieson I, Higham T, Berezin YB, Buzhilova A, Trifonov V, Pinhasi R, Belinskij AB, Reich D, Hansen S, Krause J, Haak W. Ancient human genome-wide data from a 3000-year interval in the Caucasus corresponds with eco-geographic regions. Nature Communications. 2019;10:590. doi: 10.1038/s41467-018-08220-8. PubMed DOI PMC

Wang C-C, Yeh H-Y, Popov AN, Zhang H-Q, Matsumura H, Sirak K, Cheronet O, Kovalev A, Rohland N, Kim AM, Mallick S, Bernardos R, Tumen D, Zhao J, Liu Y-C, Liu J-Y, Mah M, Wang K, Zhang Z, Adamski N, Broomandkhoshbacht N, Callan K, Candilio F, Carlson KSD, Culleton BJ, Eccles L, Freilich S, Keating D, Lawson AM, Mandl K, Michel M, Oppenheimer J, Özdoğan KT, Stewardson K, Wen S, Yan S, Zalzala F, Chuang R, Huang C-J, Looh H, Shiung C-C, Nikitin YG, Tabarev AV, Tishkin AA, Lin S, Sun Z-Y, Wu X-M, Yang T-L, Hu X, Chen L, Du H, Bayarsaikhan J, Mijiddorj E, Erdenebaatar D, Iderkhangai T-O, Myagmar E, Kanzawa-Kiriyama H, Nishino M, Shinoda K, Shubina OA, Guo J, Cai W, Deng Q, Kang L, Li D, Li D, Lin R, Shrestha R, Wang L-X, Wei L, Xie G, Yao H, Zhang M, He G, Yang X, Hu R, Robbeets M, Schiffels S, Kennett DJ, Jin L, Li H, Krause J, Pinhasi R, Reich D. Genomic insights into the formation of human populations in East Asia. Nature. 2021;591:413–419. doi: 10.1038/s41586-021-03336-2. PubMed DOI PMC

Yan J, Patterson N, Narasimhan VM. MiqoGraph: fitting admixture graphs using mixed-integer quadratic optimization. Bioinformatics. 2021;37:2488–2490. doi: 10.1093/bioinformatics/btaa988. PubMed DOI

Yang M.A, Gao X, Theunert C, Tong H, Aximu-Petri A, Nickel B, Slatkin M, Meyer M, Pääbo S, Kelso J, Fu Q. 40,000-year-old individual from Asia provides insight into early population structure in Eurasia. Current Biology. 2017;27:3202–3208. doi: 10.1016/j.cub.2017.09.030. PubMed DOI PMC

Yang MA, Fan X, Sun B, Chen C, Lang J, Ko Y-C, Tsang C, Chiu H, Wang T, Bao Q, Wu X, Hajdinjak M, Ko AM-S, Ding M, Cao P, Yang R, Liu F, Nickel B, Dai Q, Feng X, Zhang L, Sun C, Ning C, Zeng W, Zhao Y, Zhang M, Gao X, Cui Y, Reich D, Stoneking M, Fu Q. Ancient DNA indicates human population shifts and admixture in northern and southern China. Science. 2020;369:282–288. doi: 10.1126/science.aba0909. PubMed DOI

Zhang M, Yan S, Pan W, Jin L. Phylogenetic evidence for sino-tibetan origin in northern China in the late neolithic. Nature. 2019;569:112–115. doi: 10.1038/s41586-019-1153-z. PubMed DOI

Testing times: disentangling admixture histories in recent and complex demographies using ancient DNA

Long shared haplotypes identify the Southern Urals as a primary source for the 10th century Hungarians

Widespread horse-based mobility arose around 2200 BCE in Eurasia

Population genomics of post-glacial western Eurasia

Testing Times: Challenges in Disentangling Admixture Histories in Recent and Complex Demographies

Modeling of African population history using f-statistics is biased when applying all previously proposed SNP ascertainment schemes

Reanalyzing the genetic history of Kra-Dai speakers from Thailand and new insights into their genetic interactions beyond Mainland Southeast Asia

Modeling of African population history using f -statistics can be highly biased and is not addressed by previously suggested SNP ascertainment schemes

Ancient DNA from Protohistoric Period Cambodia indicates that South Asians admixed with local populations as early as 1st-3rd centuries CE