Ancient Admixture in Human History

Abstract

Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples that provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present-day Basques and Sardinians and the other related to present-day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean "Iceman."A DMIXTURE between populations is a fundamental process that shapes genetic variation and disease risk. For example, African Americans and Latinos derive their genomes from mixtures of individuals who trace their ancestry to divergent populations. Study of the ancestral origin of the admixed individuals provides an opportunity to infer the history of the ancestral groups, some of whom may no longer be extant. The two main classes of methods in this field are local ancestry-based methods and global ancestry-based methods. Local ancestry-based methods such as LAMP (Sankararaman et al. 2008), HAPMIX (Price et al. 2009), and PCADMIX (Brisbin 2010) deconvolve ancestry at each locus in the genome and provide individual-level information about ancestry. While these methods provide valuable insights into the recent history of populations, they have reduced power to detect older events. The most commonly used methods for studying global ancestry are principal component analysis (PCA) (Patterson et al. 2006) and model-based clustering methods such as STRUCTURE (Pritchard et al. 2000) and ADMIXTURE (Alexander et al. 2009). While these are powerful tools for detecting population substructure, they do not provide any formal tests for admixture (the patterns in data detected using these methods can be generated by multiple population histories). For instance, Novembre et al. (2008) showed that isolation-by-distance can generate PCA gradients that are similar to those that arise from long-distance historical migrations, making PCA results difficult to interpret from a historical perspective. STRUCTURE/ADMIXTURE results are also difficult to interpret historically, because these methods work either without explicitly fitting a historical model or by fitting a model that assumes that all the populations have radiated from a single ancestral group, which is unr...

The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists

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“…The genetic data from the Birka warrior was merged with three different population reference data‐sets consisting of genotype SNP data from: the Human Origins dataset (Patterson et al, 2012; Lazaridis et al, 2014), the Swedish reference (Salmela et al, 2011), and the Population Reference Sample–POPRES (Nelson et al, 2008) merged with 60 Yoruban individuals from the pilot phase of the 1000 Genomes Project (The 1000 Genome Project Consortium, 2010). The analyses were restricted to nucleotide positions with minimum mapping and base quality of 30.…”

“…The analyses were performed with pseudo‐haploid genomes and excluding of transition sites. To obtain information on genetic affinities between the Birka individual and the modern populations, we performed f3 ‐outgroup statistics using qp3Pop v. 204 (Patterson et al, 2012) and D statistics which were calculated using qpDstat of ADMIXTOOLS (Durand, Patterson, Reich, & Slatkin, 2011; Patterson et al, 2012). The results are summarized in Figure 4 and Supporting Information Figure S4.2a‐b, S4.3, S4.4, Table S4.4, and Supplementary Excel Table.…”

“…Maps visualizing the results of f 3 ‐statistic in which the individual from grave Bj 581 was compared to (a) Human Origins population reference panel (Lazaridis et al, 2014; Patterson et al, 2012) and (b) Population Reference Sample (POPRES) (Nelson et al, 2008). (c) The Birka warrior plotted against PC1 values for 21 Swedish subpopulations representing all counties and the total of 1525 individuals (Salmela et al, 2011).…”

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“…Reich, a population geneticist at Harvard Medical School in Boston, Massachusetts, and his team were reconstructing the history of Europe using genomes from modern people, when they found a connection between northern Europeans and Native Americans. They proposed that a now-extinct population in northern Eurasia had interbred with both the ancestors of Europeans and a Siberian group that later migrated to the Americas 6 . Reich calls such groups ghost populations, because they are identified by the echoes that they leave in genomes -not by bones or ancient DNA.…”