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, 10 (5), e1004353
eCollection

Population Genomic Analysis of Ancient and Modern Genomes Yields New Insights Into the Genetic Ancestry of the Tyrolean Iceman and the Genetic Structure of Europe

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Population Genomic Analysis of Ancient and Modern Genomes Yields New Insights Into the Genetic Ancestry of the Tyrolean Iceman and the Genetic Structure of Europe

Martin Sikora et al. PLoS Genet.

Abstract

Genome sequencing of the 5,300-year-old mummy of the Tyrolean Iceman, found in 1991 on a glacier near the border of Italy and Austria, has yielded new insights into his origin and relationship to modern European populations. A key finding of that study was an apparent recent common ancestry with individuals from Sardinia, based largely on the Y chromosome haplogroup and common autosomal SNP variation. Here, we compiled and analyzed genomic datasets from both modern and ancient Europeans, including genome sequence data from over 400 Sardinians and two ancient Thracians from Bulgaria, to investigate this result in greater detail and determine its implications for the genetic structure of Neolithic Europe. Using whole-genome sequencing data, we confirm that the Iceman is, indeed, most closely related to Sardinians. Furthermore, we show that this relationship extends to other individuals from cultural contexts associated with the spread of agriculture during the Neolithic transition, in contrast to individuals from a hunter-gatherer context. We hypothesize that this genetic affinity of ancient samples from different parts of Europe with Sardinians represents a common genetic component that was geographically widespread across Europe during the Neolithic, likely related to migrations and population expansions associated with the spread of agriculture.

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Geographic origin of ancient samples and ADMIXTURE results.
(A) Map of Europe indicating the discovery sites for each of the ancient samples used in this study. (B) Ancestral population clusters inferred using ADMIXTURE on the HGDP dataset, for k = 6 ancestral clusters. The width of the bars of the ancient samples was increased to aid visualization.
Figure 2
Figure 2. Allele sharing and D-tests with whole-genome datasets.
(A) Normalized derived allele sharing rate of the Iceman with Eurasian whole genomes from Complete Genomics. Each circle represents the rate of sharing with a particular genome, grouped by population of origin. Positions on the y-axis have added jitter for ease of visualization. Populations with EUR suffix correspond to the European ancestry tracts of individuals of populations with known European admixture (ASW, MXL). Due to differences in admixture proportions among individuals from those populations, the total number of observations varies between individuals, indicated by the size of the circles. (B) D-test results for the ancient samples compared to populations from the 1000 Genomes project and Sardinia. Each panel shows results for a particular ancient sample, grouped by cultural context. Diamonds indicates the value of the D-statistic for a single D-test involving the ancient sample and a pair of modern populations, shown on the left and right of the panels. Significance at Z = 3 is indicated with filled diamonds, and the line shows the corresponding standard error of the D-statistic. Plot colors indicate different pairs of geographic regions within Europe (blue: Europe S/Europe N; green: Europe S/Europe S).
Figure 3
Figure 3. Results of TreeMix analysis of the Iceman with 1000G/Sardinia.
Shown are maximum-likelihood trees and the matrices of pairwise residuals (inset) for a model allowing (A) m = 0 and (B) m = 3 mixture events. Large positive values in the residual matrix indicate a poor fit for the respective pair of populations. Edges representing mixture events are colored according to weight of the inferred edge.
Figure 4
Figure 4. A simplified model for recent demographic history of Europeans.
The panels indicate a possible demographic scenario consistent with the observed signals. (A) Mesolithic HGs present in mainland Europe prior to the arrival of agriculture. (B) Initial spread of farming from the Middle East beginning from 7,000 YBP into SE Europe. (C) Expansion of farming to N Europe from SE European gene pool and establishment of main S-N gradient of genetic diversity. Wave of migration also reaches Sardinia. (D) Continuous population expansion and admixture with local HGs as well as additional migrations continues to shape genetic diversity in mainland Europe, but Sardinia remains mostly isolated (IBD: isolation by distance).

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