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

Phenotypic divergence, convergence and evolution of Caucasian rock lizards (Darevskia)

Phenotypic evolution can cause either divergent or convergent phenotypic patterns. Even adaptation to the same environment may result in divergence of some elements of phenotype, whereas for other morphological traits it could cause phenotypic convergence. We hypothesize that at least some phenotypic characters diverge monotonically, hence they evolve irreversibly even in very closely related species, and this happens in spite of multiple convergent adaptive patterns. We studied the evolution of phenotype in 13 closely related Caucasian rock lizards (Darevskia), whose phylogenetic relationships are well known. We used head shape and the outlines of three important scales, using geometric morphometrics. We studied the association of the overall head shape, individual principal components of head shape and scale outlines with four predictors: phylogeny, habitat, sex and size. The overall head shape was not correlated with any of these predictors, whereas some principal components were correlated with habitat or phylogeny. Habitat type explained the highest fraction of variation in head shape and anal scale area. The relatedness inferred from the components of phenotype not correlated with habitat was congruent with the phylogenetic tree inferred from molecular data. Although adaptation to local environments may obscure the phylogenetic signal present in phenotype, there are components of phenotype whose evolution is irreversible

Use of three-dimensional geometric morphometrics for the identification of closely related species of Caucasian rock lizards (Lacertidae: Darevskia)

Geometric morphometrics is a better tool to evaluate the variation of shape than ‘traditional’ morphometrics. In reptiles, it outperforms morphometrics based on linear measurements and scalation. In an earlier study, two-dimensional outline-based geometric morphometrics in six species of rock lizards (Darevskia) showed that their shapes reflected the species divergence pattern. This allowed us to separate species from different clades, but we could not distinguish closely related species within a clade. We hypothesized that three-dimensional (3D) head shape data would be sufficiently discriminative to identify closely related species. To test this hypothesis, we compared head shapes of three closely related species of the ‘rudis’ clade, Darevskia portschinskii, Darevskia valentini and Darevskia rudis, with the last species treated as two distinct groups (D. r. obscura vs. D. r. rudis), using 3D landmark data. The 3D analysis isolated the species of the ‘rudis’ clade from each other and even separated individuals from populations that showed a genetic introgression pattern. The analysis showed that D. r. obscura is morphologically as distinct from D. r. rudis as from the other nominal species. For this reason, we suggest elevating the status of D. r. obscura to species level, i.e. Darevskia obscura Lantz & Cyrén, 1936

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

Data from: Gene flow between wolf and shepherd dog populations in Georgia (Caucasus)

We studied the distribution of the mitochondrial DNA haplotypes and microsatellite genotypes at eight loci in 102 grey wolves, 57 livestock guarding dogs, and 9 mongrel dogs from Georgia (Caucasus). Most of the studied dogs had mitochondrial haplotypes clustered with presumably East Asian dog lineages, and most of the studied wolves had the haplotypes clustered with European wolves, but 20% of wolves and 37% of dogs shared the same mitochondrial haplotypes. Bayesian inference with STRUCTURE software suggested that over 13% of the studied wolves had detectable dog ancestry and over 10% of the dogs had detectable wolf ancestry. 2-3% of the sampled wolves and dogs were identified, with a high probability, as first generation hybrids. These results were supported by the relatedness analysis which showed that 10% of wolves and 20% of dogs had closest relatives from an opposite group. The results of the study suggest that wolf-dog hybridization is a common event in the areas where large livestock guarding dogs are held in a traditional way, and that gene flow between dogs and grey wolves was an important force influencing gene pool of dogs for millennia since early domestication events. This process may have been terminated (1) in areas outside the natural range of grey wolves and (2) since very recent time, when humans started to more tightly control contacts of purebred dogs

on Pre-Pleistocene Refugia and Differentiation between Populations of the Caucasian Salamander (Mertensiella caucasica)

A350-bp fragment of the mitochondrial cytochrome-b gene was sequenced in the Caucasian salamander, Mertensiella caucasica, representing 10 populations from across its range along the Black Sea coast. Five haplotypes were discovered among 65 fragments analyzed, differing at 2–50 positions. The highest differentiation between haplotypes was observed in animals from the eastern part of the species ’ range (Borjomi) compared to those from the remainder of the species’ range. Randomly amplified nuclear DNA revealed a pattern of spatial genetic variation similar to that of the mitochondrial genome. M. caucasica, as currently known, represents two evolutionary lineages that evolved independently, perhaps since the lower Pliocene. These lineages represent taxa, possibly to be described as species, distributed in the Borjomi area in central Georgia and in southwestern Georgia and northeastern Turkey. The multivariate analysis of morphological data did not reveal significant differences between the taxa. However, substantial morphological differentiation was observed within both lineages, showing parallel patterns in body proportions and coloration patterns. This variation is possibly associated with extant ecological conditions. Salamanders with reduced pigmentation from southwestern Georgia were not genetically distinguishable from neighbor-ing populations. � 2000 Academic Pres