Early farmers from across Europe directly descended from Neolithic Aegeans—Hofmanová et al., 3D figure S4

Three-dimensional PCA of modern reference populations and projected ancient individuals. The Greek and Anatolian samples reported here cluster tightly with other European farmers close to modern-day Sardinians, however, are clearly distinct from previously published Caucasian hunter-gatherers. This excludes the latter as potential ancestral source population for early European farmers and suggests strong genetic structure in hunter-gatherers of southwest Asia. A two-dimensional version including the legend explaining the colour code are part of Figure 2 of the main text

CHROMOPAINTER/fineSTRUCTURE analysis.

<p><b>(A)</b> PCA estimated from the CHROMOPAINTER coancestry matrix of 67 ancient samples ranging from the Paleolithic to the Anglo-Saxon period. The samples belonging to each one of the 19 populations identified with fineSTRUCTURE are connected by a dashed line. Samples are placed geographically in 3 panels (with random jitter for visual purposes): <b>(B)</b> Hunter-gatherers; (<b>C)</b> Neolithic Farmers (including Ötzi) and (<b>D)</b> Copper Age to Anglo-Saxon samples. The Portuguese Bronze Age samples (D, labelled in red) formed a distinct population (<i>Portuguese_BronzeAge</i>), while the Middle and Late Neolithic samples from Portugal clustered with Spanish, Irish and Scandinavian Neolithic farmers, which are termed “<i>Atlantic_Neolithic</i>” (C, in green).</p

Patterns of hunter-gatherer haplotype donation to ancient Eurasians.

<p>This was estimated by subtracting the vector of haplotype donation of Hungarian HG from a vector of hunter-gatherer X, where X = {LaBrana, Bichon, Loschbour}. Legend: E—Early; M—Middle; L—Late; N—Neolithic; PT—Portugal; SP—Spain. Note: HG individuals were removed from the tree.</p

Total variation distance between vectors of median haplotype donation from Bronze Age (purple) and Neolithic (green) samples from different regions in Europe to modern populations.

<p>Circle size varies according to the absolute difference between Neolithic and Bronze Age samples in terms of the number of haplotypes donated to present day populations. Regardless of the geographical locations of the ancient samples, Neolithic samples tend to donate comparatively more haplotypes to Southern populations, while Bronze Age show the opposite pattern, with an excess of haplotype contribution to Northern Europeans. This pattern is present, but distinctly weaker in the Portuguese Neolithic-Bronze Age comparison.</p

ADMIXTURE analysis of 1941 modern and 176 ancient individuals. Selected profiles of 227 ancient samples, alongside individuals from nine present-day Eurasian populations are displayed here for K = 10 ancestral clusters.

<p>Individuals are ordered within a grid, partitioned by approximate time period and geographic region. Where possible, ancient individuals have been grouped under common population labels, based on archaeological context. For populations containing three or less individuals, bar plots have been narrowed, leaving empty space within the grid box. Samples from the current study are highlighted in bold.</p

Extended haplotype homozygosity in regions under selection.

<p>Panels on the left represent the decay of EHH, or the probability of homozygosity at a certain base across 2 randomly chosen chromosomes in a population. Plots on the right represent existing haplotypes in a population, with the lower portion of the graph depicting haplotypes with the derived allele (red) and the upper part showing haplotypes carrying the ancestral allele (blue). Unique haplotypes in a population are not represented. Legend: CEU—Utah Residents (CEPH) with Northern and Western Ancestry; YRI—Yoruba in Ibadan, Nigeria; CHB—Han Chinese in Beijing, China; 1KG: 1000 Genomes Project. * Earliest appearance of the homozygous derived allele in the samples analysed.</p

Summary of the samples sequenced in the present study.

<p>Summary of the samples sequenced in the present study.</p

Average genomic height for each of the Western Eurasian samples in the imputed dataset, plotted against its approximate date, highlighting temporal trends in genetic height.

<p>We excluded from this analysis Russian Bronze and Iron Age individuals containing variable amounts of Siberian admixture, but polygenic scores for all imputed samples can be seen in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006852#pgen.1006852.s007" target="_blank">S7 Text</a>.</p