Genetic Differentiation of Populations of Three Megalopolises by DNA Markers of the Y-Chromosome in Connection with the Problem of Developing Genetic Databases

The purpose of the study was to consider the distribution of Y-chromosome DNA markers in samples from the populations of the three largest megalopolises (Moscow, Saint Petersburg, and Novosibirsk) in the Russian Federation, in the context of developing genetic databases. The study aimed to compare the frequency profiles of 18 Y-chromosome STRs (Short tandem repeats) and the level of genetic differentiation. Based on FST estimates for the distribution of these 18 Y-chromosome STRs, the senior generations of Moscow and Novosibirsk were found to be similar. Statistically significant differences were detected between the Novosibirsk sample and the samples from Saint-Petersburg and from the young generation of Moscow (FST = 0.0087, p < 0.05 and FST = 0.0084, p < 0.01, respectively). For probability prediction of Y-chromosome haplotypes, analysis of 18 STR-haplotypes using Internet-predictor - Whit Athey’s Haplogroup Predictor was performed. The distribution of Y-chromosome haplogroups in the studied samples from the three megalopolises largely corresponds to the Russian gene pool, with the most frequent haplogroups being R1a, R1b, E1b1b1, N, I1, I2, J1, and J2 — predominantly R1a. This aligns with the predominance of ethnic Russians within the populations of these large urban centers. Significant differences for two samples representing senior generations in two megalopolises were detected by the “Southern origin” haplogroups (G2a, G2c, J1, J2, L, O2, O3, Q, R2, and T): 3.4% in Novosibirsk and 11.2% in Moscow (G = 6.1081, df = 1, p < 0.05). These frequencies are notably higher in the sample from the young generation of Moscow (21%) and in the sample from Saint-Petersburg (16%). The observed distribution of Y-chromosome DNA markers is consistent with the observed migration parameters, reinforcing the conclusion regarding the necessity of developing reference databases of Y-chromosome DNA markers specific to each megalopolis, based on both molecular studies and genetic-demographic questionnaires. These databases must be subject to timely updates to account for the changes in the gene pool, particularly those driven by migration. Such an approach is particularly relevant for monitoring the gene pool dynamics of populations in megalopolises and ensuring the ongoing applicability of genetic databases.