Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity

Abstract

The processes that shaped modern European mitochondrial DNA (mtDNA) variation remain unclear. The initial peopling by Palaeolithic hunter-gatherers ~42,000 years ago and the immigration of Neolithic farmers into Europe ~8000 years ago appear to have played important roles but do not explain present-day mtDNA diversity. We generated mtDNA profiles of 364 individuals from prehistoric cultures in Central Europe to perform a chronological study, spanning the Early Neolithic to the Early Bronze Age (5500 to 1550 calibrated years before the common era). We used this transect through time to identify four marked shifts in genetic composition during the Neolithic period, revealing a key role for Late Neolithic cultures in shaping modern Central European genetic diversity.

Fig. 1. Location of Mittelelbe-Saale and prehistoric comparative data, as well as PCA and Ward clustering

Map A show the location of study sites in the Mittelelbe-Saale region in Saxony-Anhalt, Germany of the Early Neolithic (LBK=Linear Pottery culture, RSC=Rössen culture, SCG=Schöningen group), Middle Neolithic (BAC=Baalberge culture, SMC=Salzmünde culture, BEC=Bernburg culture), Late Neolithic (CWC=Corded Ware culture, BBC=Bell Beaker culture), and Early Bronze Age (UC=Unetice culture) cultures. Map B display the location of published data from eleven Mesolithic (HGC=hunter-gatherer Central Europe, HGS=hunter-gatherer South Europe, HGE=hunter-gatherer East Europe, PWC=Pitted Ware culture), Neolithic (CAR=(Epi)Cardial, NPO=Neolithic Portugal, NBQ=Neolithic Basque Country & Navarre, FBC=Funnel Beaker culture, TRE=Treilles culture), and Bronze Age (BAS=Bronze Age Siberia, BAK=Bronze Age Kazakhstan (not shown)) populations. Symbols indicate populations from Central Europe (squares and diamonds), southern Scandinavia (circles), the Iberian Peninsula (triangles), and East Europe/Asia (stars). Colour shading of data points denote to hunter-gatherer (grey), Early Neolithic (brown), Middle Neolithic (orange), and Late Neolithic/EBA (yellow) samples (for further information see 13, Figs. S1-S2, and Table S1-S4). The haplogroup frequencies of these populations (Table S9) were used to perform PCA (C) and Ward clustering (D). The first two principal components of the PCA display 32.8 % of the total genetic variation. We superimposed each haplogroup as component loading vectors (grey), proportionally to their contribution. P-values of the clusters are given in percent of reproduced clusters based on 10.000 bootstrap replicates.

Fig. 2. Ward clustering, genetic distances and test of population continuity

Haplogroup frequencies of Central European hunter-gatherers (HGC), the nine Mittelelbe-Saale cultures (see Fig. 1 for abbreviations), and a modern Central European metapopulation (CEM, n=500) (Table S5) were used for hierarchical Ward clustering (A). Cluster significance is given as percent of reproduced clusters on 10,000 bootstrap replicates. We computed genetic distances (F_st) (Table S6) based on HVS-I sequences (np 16059–16400) between all cultures (B) and pools of Early/Middle and Late Neolithic/EBA cultures (C). The shading indicates the degree of genetic distance between the cultures ranging from white (small distances/high similarities) to green (large distance/dissimilarities). Significant differences are indicated by + (after 10,000 permutations and post-hoc Benjamini-Hochberg correction) (Table S6). The upper diagonal (D) summarises the results of the test of population continuity to evaluate possible effects of genetic drift. The p-values (Table S8) describe the probability that changes in haplogroup frequencies between two populations cannot be explained by genetic drift alone (white areas=non significant, green areas=significant (13).

Fig. 3. Development of mtDNA components from the Late Mesolithic to present-day

Population data from Central European hunter-gatherers (HGC), the nine Mittelelbe-Saale cultures (see Fig. 1. for abbreviations), and a modern Central European metapopulation (CEM, n=500) were placed in chronological order (x-axis) and the amount of lineages ascribed to particular time periods were evaluated in each population. The characterising haplogroups of the hunter-gather (U, U4, U5, U8, grey), Early/Middle Neolithic (N1a, T2, K, J, HV, V, W, X, brown), and Late Neolithic/Early Bronze Age (LN/EBA, I, U2, T1, R, yellow) period were summarised into three respective components (y-axis) (Table S5) accordingly to the differentiation in the PCA (Fig. 1C). Haplogroups that could not be ascertained unambiguously to one of the three components were reported as ‘other’ (H, U3, other African and Asian lineages of the CEM) (13). Error bars of component frequencies indicate the 95% confidence interval of 10,000 bootstrap replicates (Table S5). Horizontal shading denotes the population dynamic events (A, B₁, B₂, C and D) inferred from the synthesis of all population genetic analyses (see main text).