Patterns of genetic structure and adaptive positive selection in the Lithuanian population from high-density SNP data

Abstract

The analysis of geographically specific regions and the characterization of fine-scale patterns of genetic diversity may facilitate a much better understanding of the microevolutionary processes affecting local human populations. Here we generated genome-wide high-density SNP genotype data in 425 individuals from six geographical regions in Lithuania and combined our dataset with available ancient and modern data to explore genetic population structure, ancestry components and signatures of natural positive selection in the Lithuanian population. Our results show that Lithuanians are a homogenous population, genetically differentiated from neighbouring populations but within the general expected European context. Moreover, we not only confirm that Lithuanians preserve one of the highest proportions of western, Scandinavian and eastern hunter-gather ancestry components found in European populations but also that of an steppe Early to Middle Bronze Age pastoralists, which together configure the genetic distinctiveness of the Lithuanian population. Finally, among the top signatures of positive selection detected in Lithuanians, we identified several candidate genes related with diet ( PNLIP , PPARD ), pigmentation ( SLC 2 4A5 , TYRP1 and PPARD ) and the immune response ( BRD2 , HLA-DOA , IL26 and IL22 ).

Inferring Effective Population Size and Divergence Time in the Lithuanian Population According to High-Density Genotyping Data

“…The recent Ne was estimated for 50 generations (g), or 1250 years from the present (Table S5). Considering the Lithuanian population, we observed that ancestors of the contemporary Lithuanians first split from Africans in 52,886 YBP, CI (43,394-62,378), and only much later from East Asians-in 27,353 YBP, CI (11,909). The split from Central South and Middle Eastern Asians happened around the same time-in 8278 CI (7354-9201) and in 8895 YBP, CI (6290-11,501), respectively.…”

“…People in the different regions of Lithuania seemed to have lived in a relative isolation for a long time because of an inaccessible nature of the terrain. On the landward side, their territory was bounded by the vast forests and swamps, which could have resulted in partial genetic isolation of the Lithuanians, as explained by Urnikyte et al (2019) [11,22,23]. Interestingly, the phylogenetic tree ( Figure 5), which represents the divergence between the ethnolinguistic regions of Lithuania, contradicts the division of the Lithuanian population into two main monophyletic groups (three groups of Žemaitija and three groups of Aukštaitija) on the basis of linguistic differentiation.…”

“…The Lithuanian population is rather homogeneous with a subtle population structure. It is partially isolated by genetic distinctiveness of preserved ancient genetic composition within the European context [11]. Analysis of such geographically specific regions as is Lithuania may facilitate a much deeper understanding of the micro-evolutionary processes affecting local human populations.…”

The evolution of skin pigmentation associated variation in West Eurasia

“…4C). The TYRP1 locus has been previously identified as a target of selection in Europeans (5,8,9,71,72) although some studies (73,74) have questioned this finding. Our analysis supports the hypothesis of selection at this locus, with a window centered around rs1325132 in the top 0.77% of genome-wide PBS windows on the hunter-gatherer lineage.…”

Ethnicity-dependent allele frequencies are correlated with COVID-19 case fatality rate

“…We propose that the structural deviation causes TMPRSS2 to be less stable, resulting in a reduced overall infection rate that led to reduced CFR in East Asians. We collected and analyzed 221,498 genomes from public databases [19][20][21] and 2,262 whole genomes from the Korean Genome Project 22 . We also traced TMPRSS2 AF distribution in ancient populations by region and time period.…”