Phylogenetic history of patrilineages rare in northern and eastern Europe from large-scale re-sequencing of human Y-chromosomes

Abstract

The most frequent Y-chromosomal (chrY) haplogroups in northern and eastern Europe (NEE) are well-known and thoroughly characterised. Yet a considerable number of men in every population carry rare paternal lineages with estimated frequencies around 5%. So far, limited sample-sizes and insufficient resolution of genotyping have obstructed a truly comprehensive look into the variety of rare paternal lineages segregating within populations and potential signals of population history that such lineages might convey. Here we harness the power of massive re-sequencing of human Y chromosomes to identify previously unknown population-specific clusters among rare paternal lineages in NEE. We construct dated phylogenies for haplogroups E2-M215, J2-M172, G-M201 and Q-M242 on the basis of 421 (of them 282 novel) high-coverage chrY sequences collected from large-scale databases focusing on populations of NEE. Within these otherwise rare haplogroups we disclose lineages that began to radiate ~1-3 thousand years ago in Estonia and Sweden and reveal male phylogenetic patterns testifying of comparatively recent local demographic expansions. Conversely, haplogroup Q lineages bear evidence of ancient Siberian influence lingering in the modern paternal gene pool of northern Europe. We assess the possible direction of influx of ancestral carriers for some of these male lineages. In addition, we demonstrate the congruency of paternal haplogroup composition of our dataset with two independent population-based cohorts from Estonia and Sweden.

Fig. 1. Schematic phylogenetic trees of hg E2a and J2b.

The calibrated trees were constructed using BEAST v.1.7.5 software package. Internal nodes, sub-clade names and population names (numbers show the number of samples) are indicated. Internal nodes with posterior probabilities <0.73 are not shown. Samples from Estonia and Sweden are marked in blue and orange, respectively. a A schematic phylogenetic tree of hg E2a is based on 132 high-coverage chrY sequences. Neighbour-clade E2b and its sublineages are marked in grey. Detailed tree can be found in Supplementary Materials (Supplementary Fig. S5). Age estimates can be found in Supplementary Table S8. All the subclade (node) defining mutations and marker names are presented in Supplementary Table S4. b A schematic phylogenetic tree of hg J2b is based on 136 high-coverage chrY sequences. Neighbour-clade J2a and its sublineages are marked in grey. Detailed tree can be found in Supplementary Materials (Supplementary Fig. S6). Age estimates can be found in Supplementary Table S9. All the sub-clade (node) defining mutations and marker names are presented in Supplementary Table S5.

Fig. 2. Detailed phylogenetic tree of hg Q.

A detailed phylogenetic tree of hg Q-M242 is based on 84 high-coverage chrY sequences. Two hg R1a sequences were used for an outgroup. The detailed calibrated tree was constructed using BEAST v.1.7.5 software package. Internal nodes, sub-clade names and population names are indicated. Internal nodes with posterior probabilities <0.73 are not shown. Age estimates can be found in Supplementary Table S10. All the subclade (node) defining mutations and marker names are presented in Supplementary Table S6. Samples from Estonia and Sweden are marked in blue and orange, respectively.

Fig. 3. Phylogeographic spread maps of hgs J2b2-L283 and E2a1-CTS1273 in Europe.

Maps indicate the phylogeographic spread of a J2b2-L283 around 6 kya, 4 kya, 2 kya and in the present, and b E2a1-CTS1273 around 5–6 kya, 4 kya, 2 kya and in the present. Shaded in pink are the 80% HPD areas of the node locations inferred by Bayesian continuous phylogeographic analysis with Beast v1.10.4 software. White circles indicate the median locations of the nodes, while black lines indicate the branches of the maximum clade credibility tree.