Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

Abstract

European populations display low genetic diversity as the result of long term blending of the small number of ancient founding ancestries. However it is still unclear how the combination of ancient ancestries related to early European foragers, Neolithic farmers and Bronze Age nomadic pastoralists can fully explain genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the overall continental diversity, but to date have been systematically understudied. Here we characterised the ancestry profiles of modern-day Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe and the rest of the world. Italian genomes captured several ancient signatures, including a non-steppe related substantial ancestry contribution ultimately from the Caucasus. Differences in ancestry composition as the result of migration and admixture generated in Italy the largest degree of population structure detected so far in the continent and shaped the amount of Neanderthal DNA present in modern-day populations.

The genomic impact of European colonization of the Americas

“…To minimize the impact of within-source ("donors") genetic heterogeneity in the ancestry characterization process, we grouped the assembled 6,115 individuals ( Supplementary Figure 1, Supplementary Table 1A- Our fineSTRUCTURE results ( Supplementary Figure 2, Supplementary Table 2) confirm the worldwide genetic variation pattern already observed by previous studies at the continental scale [19][20][21][22][23] .…”

“…We assembled 11,15,16,20,21,23,25,32, We used KING to remove one random individual from pairs with kinship parameter higher than 0.0884 71 . The final dataset was therefore composed of 17,722 individuals from 261 populations 11,15,16,20,21,23,25,32, (Supplementary Table 1A-B, Supplementary Figure 1). Of these, 11,607 individuals belonging to 22 admixed American populations were treated as 'recipients', while the remaining 6,115 samples from 239 source populations were considered 'donors'.…”

Genome-wide analysis of Corsican population reveals a close affinity with Northern and Central Italy

“…We focused on Western Eurasian clusters composed by more than five individuals. As geographically close populations tend to share recent ancestry and distant genetic contacts may be masked, we performed two different GLOBETROTTER analyses, "full" and "non-local", as previously reported 37,38 (Fig. 4, Supplementary Fig.…”

“…Lastly, we have evaluated the genetic relationship of Corsica and other Mediterranean populations with ancient Eurasian individuals through PCA and qpAdm ( Fig. 5 38,42 . In fact, we have found a similar proportion of Steppe Bronze Age (~19%) and Iranian Neolithic (~14%) in Corsicans.…”

“…In addition, Corsica harboured a relatively high proportion related to Iranian Neolithic (22%), while the contribution of Western and Eastern Hunter Gatherer (WHG, EHG) was smaller, about 11%. According to previous researches, a substantial proportion of the EHG and Iranian Neolithic (related to Caucasus Hunter Gatherer, CHG) trace back to Bronze Age movements from the Steppe, however, Iranian Neolithic could have arrived to Western Mediterranean with different migration[38][39][40] . This seems to be supported also for Corsica when qpAdm analysis including Steppe_EMBA (Early Middle Bronze Age) and Iranian Neolithic (Iran_N) were considered in the same analysis evaluating the proportions (Anatolia Neolithic: 33%, Steppe_EMBA: 19%, Iran Neolithic: 14%, Europe Middle Neolithic/Chalcolithic: 34%).…”