Objective: To elucidate the genetic relationships between Estonian, Latvian and Lithuanian men by studying Y-chromosomal variation in these people. Methods: The allelic status of five deep-rooted marker loci (YAP, Tat, M9, 92R7 and SRY-1532) was determined for 346 Baltic males. On the basis of single nucleotide polymorphism (SNP) haplotypes, Y chromosomes were divided into six haplogroups, and the Baltic haplogroup distribution compared with that in 7 European reference populations. Haplogroup frequencies, diversities and genetic distances (FST values) were calculated. The relationships between populations were further illustrated using Mantel test, neighbor-joining tree and principal-component map. Results: We found the Indo-European-speaking Latvians and Lithuanians to be genetically very similar to the Finno-Ugric-speaking Estonians. When compared to the reference populations, Baltic males were most closely related to the Finno-Ugric-speaking Mari, followed by their Finnish and Slavonic neighbors. Conclusions: The genetic similarity existing between Estonian, Latvian and Lithuanian men suggests that they originate from the same male founder population. Since the Baltic Y-chromosomal haplogroup distribution more closely resembles that of Finno-Ugric than Indo-European-speaking populations, we propose a hypothesis that Baltic males share a common Finno-Ugric ancestry.

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