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


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.

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Fig. 1: Schematic phylogenetic trees of hg E2a and J2b.
Fig. 2: Detailed phylogenetic tree of hg Q.
Fig. 3: Phylogeographic spread maps of hgs J2b2-L283 and E2a1-CTS1273 in Europe.

Data availability

The Estonian WGS data are available on demand through the Estonian Biobank: In accordance to the consent form signed by the customers of Gene by Gene commercial genetic testing company, the sequencing data included in this study is used for the sole purpose of scientific inquiry and is reported here on an aggregate level in the form of phylogenetic trees. For both the Estonian Biobank and the Gene by Gene samples, summary-level data including variable positions and their frequency in the cohort population have been deposited to dbSNP with links to BioProject accession number PRJNA718714 in the NCBI BioProject database ( The Swedish data from the SweGen Project is available upon request from the original authors of the project [23].


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This work was supported by institutional research funding IUT24-1 of the Estonian Ministry of Education and Research, Estonian Research Council grants PRG243, PRG1071 and project No. 2014-2020.4.01.16-0024 (MOBTT53) granted by the European Regional Development Fund, European Union Horizon 2020 research and innovation programme (grant No. 810645), European Regional Development Fund project no. MOBEC008. A-MI is supported by Finnish Academy (DIGIHUM project URKO, decision number 329257). High-coverage genome data for five 1000 Genomes samples were generated at the New York Genome Center with funds provided by NHGRI Grant 3UM1HG008901-03S1.

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Correspondence to Anne-Mai Ilumäe.

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Conflict of interest

DMB and CB declare stock ownership at Gene by Gene, Ltd. LFS in an employee of Gene by Gene.

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All donors have provided informed consent and all experiments were performed in accordance with the relevant guidelines and regulations of collaborating institutions. Access to genetic data in Estonian Biobank was approved by the Research Ethics Committee of the University of Tartu (permission number 1.1.-12/659 granted by the Research Ethics Committee of the University of Tartu, Estonia). The chrY sequences included from customers of the commercial personal genetic testing service were only from individuals who had provided informed consent for the use of their data in scientific research and for publication in aggregated form. The list of IDs along with additional sample information is presented in Supplementary Table S1.

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Ilumäe, AM., Post, H., Flores, R. et al. Phylogenetic history of patrilineages rare in northern and eastern Europe from large-scale re-sequencing of human Y-chromosomes. Eur J Hum Genet (2021).

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