Landscape Complexity in the Caucasus impedes Genetic Assimilation of Human Populations More Effectively than Language or Ethnicity

The analyses of 15 autosomal and 23 Y-chromosome DNA STR loci in five rural populations from the Caucasus, namely four ethnically Georgian and one ethnically Armenian populations, indicated that two populations of Georgians - one from the west and the other one from the east of the Greater Caucasus Mountains - were both patrilineally and autosomally most differentiated from each other, and the other populations of Georgians and Armenians held an intermediate position between those two. This pattern may be due to human dispersal from two distinct glacial refugia in the last glacial period and the early Holocene, followed by less gene flow among the populations from the Greater Caucasus than those from the rest of the Caucasus, where the populations have undergone substantial admixture in historical time. This hypothesis is supported by a strong correlation between genetic differentiation among the populations and landscape permeability to human migrations. The latter is determined by terrain ruggedness, forest cover, and snow cover. Although geographic patterns of autosomal and Y-chromosome DNA are not fully concordant, both are influenced by landscape permeability, and show a similar east-west gradient. Our results suggest that this permeability was a stronger factor limiting gene flow among human populations in the Caucasus than ethnic or linguistic boundaries

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2

Landscape Complexity in the Caucasus impedes Genetic Assimilation of Human Populations More Effectively than Language or Ethnicity

The analyses of 15 autosomal and 23 Y-chromosome DNA single-tandem-repeat loci in five rural populations from the Caucasus (four ethnically Georgian and one ethnically Armenian) indicated that two Georgian populations, one from the west and the other from the east of the Greater Caucasus Mountains, were both patrilineally and autosomally most differentiated from each other, and the other populations of Georgians and Armenians held an intermediate position between those two. This pattern may be due to human dispersal from two distinct glacial refugia in the last glacial period and the early Holocene, followed by less gene flow among the populations from the Greater Caucasus than among those from the rest of the Caucasus, where the populations have undergone substantial admixture in historical time. This hypothesis is supported by a strong correlation between genetic differentiation among the populations and landscape permeability to human migrations as determined by terrain ruggedness, forest cover, and snow cover. Although geographic patterns of autosomal and Y-chromosome DNA are not fully concordant, both are influenced by landscape permeability and show a similar east-west gradient. Our results suggest that this permeability was a stronger factor limiting gene flow among human populations in the Caucasus than were ethnic or linguistic boundaries

Phylogeny of caucasian rock lizards (Darevskia) and other true lizards based on mitogenome analysis: Optimisation of the algorithms and gene selection.

We generated a phylogeny for Caucasian rock lizards (Darevskia), and included six other families of true lizards (Lacertini), based on complete mitochondrial genome analysis. Next-generation sequencing (NGS) of genomic DNA was used to obtain 16 new mitogenomes of Darevskia. These, along with 35 sequences downloaded from GenBank: genera Darevskia, Zootoca, Podarcis, Phoenicolacerta, Takydromus, Lacerta, and Eremias-were used in the analysis. All four analytical methods (Bayesian Inference, BI; Maximum Likelihood, ML; Maximum Parsimony, MP; and Neighbor-Joining, NJ) showed almost congruent intra-generic topologies for Darevskia and other lizard genera. However, ML and NJ methods on one side, and BI and MP methods on the other harvested conflicting phylogenies. The ML/NJ topology supports earlier published separation of Darevskia into three mitochondrial clades (Murphy, Fu, Macculloch, Darevsky, and Kupinova, 2000), but BI and MP topologies support that the basal branching occurred between D. parvula from the western Lesser Caucasus and the rest of Darevskia. All topologies altered the phylogenetic position of some individual species, including D. daghestanica, D. derjugini, and D. chlorogaster. Reanalysis after excluding four saturated genes from the data set, and excluding genus Eremias gives fully convergent topologies. The most basal branching for true lizards was between Far Eastern Takydromus and the Western Eurasian genera (BI). Comparing phylogenetic performance of individual genes relative to whole mitogenome data, concatenated 16S RNA (the least saturated gene in our analyses) and Cytochrome b genes generate a robust phylogeny that is fully congruent with that based on the complete mitogenome

Human Paternal Lineages, Languages, and Environment in the Caucasus

Publications that describe the composition of the human Y-DNA haplogroup in different ethnic or linguistic groups and geographic regions provide no explicit explanation of the distribution of human paternal lineages in relation to specific ecological conditions. Our research attempts to address this topic for the Caucasus, a geographic region that encompasses a relatively small area but harbors high linguistic, ethnic, and Y-DNA haplogroup diversity. We genotyped 224 men that identified themselves as ethnic Georgian for 23 Y-chromosome short tandem-repeat markers and assigned them to their geographic places of origin. The genotyped data were supplemented with the published data on haplogroup composition and location of the other ethnic groups of the Caucasus. We used multivariate statistical methods to see if linguistics, climate, and landscape accounted for geographical differences in frequencies of the Y-DNA haplogroups G2, J2, R1b, J1, and R1a. The analysis showed significant associations of (1) haplogroup G2 with well-forested mountains, (2) haplogroup J2 with warm areas or poorly forested mountains, and (3) haplogroup J1 with poorly forested mountains. R1b showed no association with environment. Haplogroups J1 and R1a significantly associated with Daghestanian and Kypchak speakers, respectively, but the other haplogroups showed no such simple associations with languages. Climate and landscape in the context of competition over productive areas among different paternal lineages, arriving in the Caucasus in different times, have played an important role in shaping the present-day spatial distribution of patrilineages in the Caucasus. This spatial pattern had formed before linguistic subdivisions were finally shaped, probably in Neolithic to Bronze Age. Later historical turmoil had little influence on the patrilineage composition and spatial distribution. Based on our results, the plausible scenario of postglacial expansions of humans and their languages to the Caucasus from the Middle East, western Eurasia, and the East European Plain is discussed

Assessment of genetic variation and evolutionary history of Caucasian Grouse (Lyrurus mlokosiewiczi)

Caucasian Grouse (Lyrurus mlokosiewiczi) is an endemic species found in the Caucasus whose population is declining. Initial assessment of genetic variation and phylogenetic status of the species confirmed the monophyly of L. mlokosiewiczias and indicated a sister relationship between L. mlokosiewiczi and L. tetrix (Black grouse). Further the Caucasian grouse from Georgia, Caucasus and Iran created three genetic groups with no shared haplotype. This separation could be the result of different evolutionary events or geographic distances between them. Four different haplotypes were identified in north-western Iran, distributed inside and outside Arasbaran protected area (APA), suggesting the expansion of APA to include Caucasian grouse habitats in the Kalibar Mountains (western APA) and enhance the protection of the species in the region

Precise paternal ancestry of hybrid unisexual ZW lizards (genus Darevskia: Lacertidae: Squamata) revealed by Z-linked genomic markers

WOS:000786040100001We genotyped multiple populations of all seven parthenogenetic species of rock lizards, genus Darevskia, as well as their putative sexual parental populations, using double digest RAD-sequencing genomic markers. Taking advantage of the conserved homology of the ZW/ZZ sex chromosomes among lacertid lizards, we aligned our short sequence reads to a reference Z chromosome assembly of the common wall lizard Podarcis muralis. This provided unique insight into the origin of all-female hybrid populations, which inherited their single Z chromosome exclusively from a paternal ancestor. The mapped Z-linked loci were used to construct a robust time-calibrated phylogeny. In each parent-offspring species pair, the geographically nearest population of the paternal species was identified as the most likely ancestor of the respective parthenogen, mirroring the trend observed previously on the maternal side in mitochondrial DNA. The estimated splits between the sampled paternal sexual ancestors and their daughter species occurred much earlier than suggested previously and during two narrow time periods: (1) the parthenogenetic Darevskia armeniaca, D. dahli, D. uzzelli and D. rostombekowi dated back to similar to 0.5 or similar to 0.9 Mya, depending on the calibration point used, while (2) D. bendimahiensis, D. sapphirina and D. unisexualis appear to have diverged similar to 1 or similar to 2 Mya

Precise paternal ancestry of hybrid unisexual ZW lizards (genus Darevskia: Lacertidae: Squamata) revealed by Z-linked genomic markers

We genotyped multiple populations of all seven parthenogenetic species of rock lizards, genus Darevskia, as well as their putative sexual parental populations, using double digest RAD-sequencing genomic markers. Taking advantage of the conserved homology of the ZW/ZZ sex chromosomes among lacertid lizards, we aligned our short sequence reads to a reference Z chromosome assembly of the common wall lizard Podarcis muralis. This provided unique insight into the origin of all-female hybrid populations, which inherited their single Z chromosome exclusively from a paternal ancestor. The mapped Z-linked loci were used to construct a robust time-calibrated phylogeny. In each parent-offspring species pair, the geographically nearest population of the paternal species was identified as the most likely ancestor of the respective parthenogen, mirroring the trend observed previously on the maternal side in mitochondrial DNA. The estimated splits between the sampled paternal sexual ancestors and their daughter species occurred much earlier than suggested previously and during two narrow time periods: (1) the parthenogenetic Darevskia armeniaca, D. dahli, D. uzzelli and D. rostombekowi dated back to similar to 0.5 or similar to 0.9 Mya, depending on the calibration point used, while (2) D. bendimahiensis, D. sapphirina and D. unisexualis appear to have diverged similar to 1 or similar to 2 Mya

Genotypic similarities among the parthenogenetic Darevskia rock lizards with different hybrid origins

Abstract Background The majority of parthenogenetic vertebrates derive from hybridization between sexually reproducing species, but the exact number of hybridization events ancestral to currently extant clonal lineages is difficult to determine. Usually, we do not know whether the parental species are able to contribute their genes to the parthenogenetic vertebrate lineages after the initial hybridization. In this paper, we address the hypothesis, whether some genotypes of seven phenotypically distinct parthenogenetic rock lizards (genus Darevskia) could have resulted from back-crosses of parthenogens with their presumed parental species. We also tried to identify, as precise as possible, the ancestral populations of all seven parthenogens. Results We analysed partial mtDNA sequences and microsatellite genotypes of all seven parthenogens and their presumed ansectral species, sampled across the entire geographic range of parthenogenesis in this group. Our results confirm the previous designation of the parental species, but further specify the maternal populations that are likely ancestral to different parthenogenetic lineages. Contrary to the expectation of independent hybrid origins of the unisexual taxa, we found that genotypes at multiple loci were shared frequently between different parthenogenetic species. The highest proportions of shared genotypes were detected between (i) D. sapphirina and D. bendimahiensis and (ii) D. dahli and D. armeniaca, and less often between other parthenogens. In case (ii), genotypes at the remaining loci were notably distinct. Conclusions We suggest that both observations (i-ii) can be explained by two parthenogenetic forms tracing their origin to a single initial hybridization event. In case (ii), however, occasional gene exchange between the unisexual and the parental bisexual species could have taken place after the onset of parthenogenetic reproduction. Indeed, backcrossed polyploid hybrids are relatively frequent in Darevskia, although no direct evidence of recent gene flow has been previously documented. Our results further suggest that parthenogens are losing heterozygosity as a result of allelic conversion, hence their fitness is expected to decline over time as genetic diversity declines. Backcrosses with the parental species could be a rescue mechanism which might prevent this decline, and therefore increase the persistance of unisexual forms