We studied the distribution of the mitochondrial DNA haplotypes and microsatellite genotypes at 8 loci in 102 gray 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 more than 13% of the studied wolves had detectable dog ancestry and more than 10% of the dogs had detectable wolf ancestry. About 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 gray 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 gray wolves and 2) since very recent time, when humans started to more tightly control contacts of purebred dogs.

Aim Genome‐wide genetic data can provide key input for both taxonomy and conservation, but its use in this context remains limited. In this study, we performed the first genome‐wide assessment of genetic variation in two populations of the Eurasian lynx, the Balkan population, the most threatened, and the Caucasian population, a possible glacial refugium, with the aim to place them in the context of the species, investigate their demographic history and evaluate their genetic status. Location The Balkans and the Caucasus. Methods We obtained whole genome resequencing data from seven Balkan and 12 Caucasian lynx, and analysed them along with novel and existing data from other populations. Based on a total 105 whole genome and 114 mitogenome sequences, we reconstructed phylogenetic and historical relationships, ancient and recent demography, and patterns of genetic diversity and inbreeding. Results Both the Balkan and the Caucasian lynx appear as distinct mitochondrial lineages that diverged from the rest of the Eurasian lynx lineages ca. 92.6 kya, and from each other ca. 46.4 kya. Autosomal data suggest, however, that the Balkan lynx is closely related with the Carpathian population, and revealing alarmingly low genetic diversity and high inbreeding. In contrast, the Caucasian lynx shows a longer history of relative isolation from the rest of lynx populations and high genetic diversity, consistent with its large long‐term effective population size. Main conclusions The taxonomic status of the Balkan lynx remains unresolved due to the evidence of long‐term isolation in the mitogenome, contrasting with extensive autosomal admixture and intense recent genetic drift in the nuclear genome. Our results alert on genetic risks and call for the consideration of genetic rescue from closely related Carpathian lynxes. In contrast, substantial mitogenomic and autosomal divergence with no signs of genetic drift supports the identification of the Caucasian lynx as a separate subspecies with good genetic health.

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It has recently been suggested that goitered gazelles (Gazella subgutturosa and Gazella marica) have paraphyletic maternal origin, and that the mitochondrial cytochrome b gene fragment can be used for species identification prior to reintroduction of the gazelles. Although there is a large geographic area where the gazelles have intermediate morphology, previous researchers have not inferred any signs of mitochondrial haplotype introgression, and it is thought that the introgression, if it exists, is malebiased. We studied mitochondrial haplotypes of morphologically typical G. subgutturosa from two geographic locations. Goitered gazelles from eastern Turkey, morphologically identical to G. subgutturosa, had haplotypes identical to G. marica. This finding confirms ongoing maternal gene introgression from G. marica to G. subgutturosa. Our suggestion is that there is a natural gene flow between these two nominal species, and morphological characters together with recombinant genetic markers rather than mitochondrial DNA should be used to differentiate among individuals from areas close to the contact zone.

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Grey wolf and golden jackal are both common in Georgia, although they have different habitat preferences. The wolf is more common in mountain areas of the country, and jackals are more common in the lowland part of Georgia, with its milder and warmer climate. In recent decades, the abundance of both species increased. Simultaneously, the jackals are increasingly often sighted at higher elevations than previously recorded, and simultaneously, there are increased sightings of the wolves in lowlands of western Georgia, including the areas close to the Black Sea Coast. The analysis of partial mitochondrial DNA sequences and 20 microsatellite markers suggest substantially higher genetic diversity of wolves than the jackals in Georgia, which could be related to the late expansion of jackals into the Caucasus region (not before the Bronze Age). Clustering using a Bayesian approach based on the microsatellite markers suggests that the vast majority of both jackals and wolves sampled in western Georgia descend from recent migrants from the east of the country. The expansion of the two species may be related to the conservation efforts in the latest decades or/and climate change that explains the appearance of jackals in the mountain regions of Georgia, as well as in northern Europe. Population genetics of wolfs and jackals in Georgia M. Shakarashvili et al.

11Three species of cetaceans, Phocoena phocoena, Delphinus delphis and Tursiops truncatus 12 ponticus are found in the Black Sea. The Black Sea populations of all three species show 13 morpho-ecological peculiarities that leaded to their subspecific status: P. p. relicta (PPR), D. 14 d. ponticus (DDP), and T. t. ponticus (TTP). It is not clear how long-lasting was their 15 isolation from the core conspecific populations that ensured the development of adaptive 16 features of PPR, DDP, and TTP. The analysis of mitochondrial haplotypes of PPR suggests 17 that the split time of the at least maternal lineage of the Black Sea population of harbour 18 porpoise lasted for over 100 ky (i.e. they should survive at least the latest glacial maximum 19within the Black Sea). However, the analysis of multiple microsatellite genotypes leaded 20 some authors to suggest that the isolation is much less long, since middle Holocene. We re-21 analysed published mitochondrial sequences of all three Black Sea cetaceans along with 22 several tens of sequences obtained from the stranded cetaceans. Our analyses suggest that 23 Black Sea populations of all three cetacean species have an important input of populations 24 that survived the last (and maybe earlier) glacial maxima within the Black Sea, most likely in 25 its south-eastern fragment, which did not freeze in winter time even during the glacial peaks. 26This analysis is supported by both molecular clock approach and simple population 27 modelling based on the assumption on the effective population size range. Different from the 28 PPR, whose Black Sea population is currently fully isolated, there is a limited migration 29 between the Black Sea and Atlantic populations of T. truncatus and D. delphis, through the 30 Mediterranean "bridge" population. However, the migration rates are not sufficient to 31 overweight differential selection between the Black Sea and Mediterranean populations, and 32 the local morpho-ecological specifics is successfully maintained. 33 34 35 65 the Atlantic and Black Sea populations of harbour porpoise suggests their separation at least 66 for 175 kyr (Tolley & Rosel, 2006; Viaud-Martínez et al., 2007). However, Fontaine et al. 67 4 (2010, 2012, 2014) disputed this dating, using the Bayesian model of divergence, based on 68 ten microsatellite loci analysis, as an argument. 69 The inference of Fontain et al. (2012; 2014) is however based on an assumption about strong 70 selection underlining the evolution of mitochondrial genome, and the authors acknowledge 71 this complication in the interpretation of the time of divergence between the Black Sea and 72 the Atlantic population of harbor porpoises. Besides, the Model for Interdisciplinary 73 Research on Climate (MIROC) (Braconnot et al., 2007) that was shown to be more realistic 74 than the other palaeoclimatic models (Tarkhnishvili et al., 2012) suggests positive winter 75 temperature at least at the south-eastern Black Sea Coast, which excludes complete freezing 76 of the Black Sea surface and does n...