Over the past few years, studies of DNA isolated from human fossils and archaeological remains have generated considerable novel insight into the history of our species. Several landmark papers have described the genomes of ancient humans across West Eurasia, demonstrating the presence of large-scale, dynamic population movements over the last 10,000 years, such that ancestry across present-day populations is likely to be a mixture of several ancient groups [ 1–7 ]. While these efforts are bringing the details of West Eurasian prehistory into increasing focus, studies aimed at understanding the processes behind the generation of the current West Eurasian genetic landscape have been limited by the number of populations sampled or have been either too regional or global in their outlook [ 8–11 ]. Here, using recently described haplotype-based techniques [ 11 ], we present the results of a systematic survey of recent admixture history across Western Eurasia and show that admixture is a universal property across almost all groups. Admixture in all regions except North Western Europe involved the influx of genetic material from outside of West Eurasia, which we date to specific time periods. Within Northern, Western, and Central Europe, admixture tended to occur between local groups during the period 300 to 1200 CE. Comparisons of the genetic profiles of West Eurasians before and after admixture show that population movements within the last 1,500 years are likely to have maintained differentiation among groups. Our analysis provides a timeline of the gene flow events that have generated the contemporary genetic landscape of West Eurasia.
Recent Gene Flow into West Eurasia from Surrounding World Regions In contrast to relatively low levels in Northern Europe, ancestry from East Asia is much more visible in the West Central Asian, Caucasus, and Turkish clusters, where the influence of Mongolia (mon) in particular can be seen through the pink links and bars in Figure 2B and in Figure 4A. In West Central Asia (WA), some Central (cas) and East Asian (eas) ancestry is also present across this region. Within Anatolia (here defined as Armenia and Iran, IA, and Turkey, TK), West Central Asia (WA; including Nogai, Tajik, and Turkmen individuals), and several other groups from the Caucasus (EC and WC), events largely involve Asian sources, with the period after 1000 CE appearing to be important in the generation of the ancestry of this region (Figure 3B). Interestingly, the three events that do involve a Mongolian-like source in Northern Europe, in the Chuvash (CH; chuva16: 829 CE [627–940 CE]), Russians (russi25: 913 CE [754–1007 CE]), and Mordovians (mordo13: 792 CE [564–975 CE]) all date prior to 1000 CE, suggesting an origin from a different historical event to the more eastern groups (Figure 3B). Of the other Asian world regions, we only see direct admixture from North Siberia (nsib) into a Finnish cluster (finni3: 469 CE [213 BCE–1011 CE]; Figure 3B and Table S4) and from India (ind) into a cluster of two Romanians (roman2: 990 CE [741–1245 CE]), putatively of Romany origin. Nevertheless, observable ancestral components from Afghanistan and Pakistan groups (afp and bal) in WA, EC, WC, and IA suggests that ancestry from across Asia is shared with the more easterly West Eurasian groups.
Southern European groups (SEE, SCE, SDN, SWE, and BA) on the other hand derive ancestry from African and Near Eastern World Regions. In particular, ancestry from groups most similar to contemporary populations from in and around the Levant (lev; which we define as the World Region containing individuals from Syria, Palestine, Lebanon, Jordan, Saudi, Yemen, and Egypt) is present across Italy (SCE), Sardinia (SDN), France and Spain (SWE), and Armenia (IA; Figure 2B). Interestingly, North (nafII) and West (waf) African ancestry is also seen entering Southern Europe, suggesting a key role for the Mediterranean in supporting gene flow back into Europe [8, 26, 27]. Dates for the influx of this admixture are broad and generally fall within the first millennium CE (Figure 3B) although are more recent in BA and SWE, including French (frenc24: 728 CE [424–1011 CE]) and Spanish (spani27: 1042 CE [740–1201 CE]; spani9: 668 CE [286–876 CE]) clusters, consistent with migrations associated with the Arabic Conquest of the Iberian peninsula [8, 11, 28] and earlier movements in and around Italy [29].
Movement within Europe during the Medieval Migration Period When we consider the composition of sources from within West Eurasia (minor sources in Figure 2C and major sources in Figure 2D), while the majority of a group’s ancestry tends to come from its own regional area, there is a substantial contribution of both Northern European (light and dark blue) and Armenian groups (light green) to most WA, EC, WC, and TK clusters, as well as some clusters from both SEE and SCE. As previously reported [11], the formation of the Slavic people at around 1000 CE had a significant impact on the populations of Northern and Eastern Europe, a result that is supported by an analysis of identity by descent segments in European populations [10]. Here, despite characterizing populations by genetic similarity rather than geographic labels, we infer the same events involving a “Slavic” source (represented here by a cluster of Lithuanians; lithu11 and colored light blue) across all Balkan groups in the analysis (Greece, Bulgaria, Romania, Croatia, and Hungary) as well as in a large cluster of Germanic origin (germa36) and a composite cluster of eastern European individuals (ukrai48; Figures 4A and 4B ). Dates for these events mostly overlap, although are older in Croatia and Greece, and appear to concentrate at the end of the first millennium CE (Figure 2B), a time known as the European Migration Period, or Völkerwanderung [25]. We additionally infer events during the period 300–1200 CE across Northern and Western Europe involving minor West Eurasian source groups from Europe (Figures 2D, 3B, and 4C). The date and composition of these events suggest a substantial amount of movement during the Völkerwanderung [25], providing persuasive evidence that this period had a visible effect on contemporary populations across Northern, Western, and Central Europe (Figure 4C).
The Effect of Recent Admixture on Genomic Variation in West Eurasia All peripheral populations analyzed have experienced recent admixture from World Regions (Figure 4A), and we also inferred recent mixing between many of the groups within West Eurasia (Figure 4C). We performed a variety of analyses using total variation distance (TVD) to understand and quantify the effect of these events on genetic variation (Figure 4 and Supplemental Information). Using the output of GLOBETROTTER, we considered “pre-admixture” variation in two ways: by using the inferred major source copying vectors directly and by removing the minor admixing source from the original cluster copying vector. Likewise, “post-admixture” variation can be inferred either by combining the inferred major and minor admixture sources in the appropriate admixture proportions or by using the cluster copying vectors directly. While the two sets of pre- and post-admixture copying vectors should be similar, in practice, they are unlikely to be identical, both because the admixture inference is unlikely to be perfect and because GLOBETROTTER is unable to fully account for genetic drift that may have occurred after admixture [11]. Comparisons of TVD between pairs of copying vectors inferred in these two ways show that when we re-generate a cluster from the admixture inference (Figure S4J), we systematically underestimate variation compared to the variation we observe when we use the contemporary clusters. In fact, for a given group, the differences between the two pre-admixture copying vectors and the two post-admixture copying vectors are highly correlated (Figure S4K), suggesting that the variation is mainly down to differences between the (observed) cluster copying vectors and GLOBETROTTER’s inferred sources of admixture. If this error is in part due to drift, then this suggests that drift after admixture may have acted to increase genetic differentiation.
When we compare the relative differences between pre- and post-admixture groups, we observe no appreciable difference between them, suggesting that admixture has not had a significant impact on genetic variation in West Eurasia (Figure 4G). Median TVD does, however, marginally decrease in the pre-admixture variation estimates (Figure 4G), which appears to be driven by differences between western (top left quadrant of Figures 4E and 4F) and eastern (lower right quadrant) West Eurasian groups. When we plot all admixture sources on a PCA based on contemporary individuals (Figure 4D), they tend to occur closer to the center of the plot, resembling the West Eurasian population structure inferred in a recent study of Bronze Age individuals [6]. Additional recent research using ancient DNA from multiple populations and time points in West Eurasia has demonstrated that there has been large-scale genetic turnover in Europe over the last 5,000 years [4, 5, 6, 30]. Our analysis supports this work by providing evidence that recent population movements have acted on top of this Bronze Age structure but also highlights a potential role for admixture and/or genetic drift in contributing to the genetic variation present in West Eurasia today.
Our results show that it is possible to draw complex inferences about recent human evolutionary past through the genomes of people alive today that are complementary to those made from ancient DNA. We caution that we are unlikely to have included individuals from all potential genetic donor groups to the current West Eurasian gene pool, and therefore, the gene flow events that we present should be viewed in the context of the dataset that we have used. Future work providing a better understanding of the phenotypic effects of World Region ancestry on contemporary populations as well as placing this work within the context of ancient DNA samples will further aid our understanding of Eurasian prehistory and disease. Nonetheless, the current analysis demonstrates that admixture has left a record in the genomes of all contemporary West Eurasians.
(A) For each geographic sampling location, we estimated the proportion of ancestry coming from outside of West Eurasia by averaging GLOBETROTTER’s admixture inference across individuals from a sampling location. The sampling locations of each point are shown in Figure S4A; Caucasus populations are spread out to aid visibility. Points are stacked vertically in cases where multiple ancestries are present in a population.
(B) Copying vectors of 82 West Eurasian fineSTRUCTURE clusters projected onto PCA based on the copying vectors of 1,000 West Eurasian individuals (faded colors; symbols and colors are as in Figure 1B); lines link World Region admixture sources to the clusters in which admixture from them is inferred.
(C) Gene flow within West Eurasia is shown by lines linking the best-matching donor group to the sources of admixture with recipient clusters (arrowhead). Line colors represent the regional identity of the donor group, and line thickness represents the proportion of DNA coming from the donor group. Ranges of the dates (point estimates) for events involving sources most similar to selected donor groups are shown.
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