New data on birds and mammals population of the Sette-Daban Mountain Ridge

Original materials on the fauna of the northern macroslope of the Sette-Daban Mountain Ridge are presented. Birds and mammals population in different habitats in the basin of the Allakh-Yun River are characterized.     

Genome‐wide SNP analysis unveils genetic structure and phylogeographic history of snow sheep (Ovis nivicola) populations inhabiting the Verkhoyansk Mountains and Momsky Ridge (northeastern Siberia)

Insights into the genetic characteristics of a species provide important information for wildlife conservation programs. Here, we used the OvineSNP50 BeadChip developed for domestic sheep to examine population structure and evaluate genetic diversity of snow sheep (Ovis nivicola) inhabiting Verkhoyansk Range and Momsky Ridge. A total of 1,121 polymorphic SNPs were used to test 80 specimens representing five populations, including four populations of the Verkhoyansk Mountain chain: Kharaulakh Ridge–Tiksi Bay (TIK, n = 22), Orulgan Ridge (ORU, n = 22), the central part of Verkhoyansk Range (VER, n = 15), Suntar‐Khayata Ridge (SKH, n = 13), and Momsky Ridge (MOM, n = 8). We showed that the studied populations were genetically structured according to a geographic pattern. Pairwise F_ST values ranged from 0.044 to 0.205. Admixture analysis identified K = 2 as the most likely number of ancestral populations. A Neighbor‐Net tree showed that TIK was an isolated group related to the main network through ORU. TreeMix analysis revealed that TIK and MOM originated from two different ancestral populations and detected gene flow from MOM to ORU. This was supported by the f3 statistic, which showed that ORU is an admixed population with TIK and MOM/SKH heritage. Genetic diversity in the studied groups was increasing southward. Minimum values of observed (Ho) and expected (He) heterozygosity and allelic richness (Ar) were observed in the most northern population—TIK, and maximum values were observed in the most southern population—SKH. Thus, our results revealed clear genetic structure in the studied populations of snow sheep and showed that TIK has a different origin from MOM, SKH, and VER even though they are conventionally considered a single subspecies known as Yakut snow sheep (Ovis nivicola lydekkeri). Most likely, TIK was an isolated group during the Late Pleistocene glaciations of Verkhoyansk Range.     

Genetic characteristics of Kodar snow sheep using SNP markers

For the first time nuclear DNA polymorphisms were studied in Kodar snow sheep (Ovis nivicola kodarensis, KOD). KOD is a representative of a small isolated population of Asian snow sheep (Ovis nivicola Eschscholtz, 1829) inhabiting the Kodar Ridge (Irkutsk oblast, Transbaikal krai). We compared KOD with the geographically closest Yakut subspecies (Ovis nivicola lydekkeri). Genome-wide study of single-nucleotide polymorphisms (SNPs) was performed using the Illumina OvineSNP50 BeadChip (Illumina, United States). The final set of markers for analysis included 1030 SNPs. We found that Kodar snow sheep had almost 10 times lower level of genetic diversity evaluated by multilocus heterozygosity—MLH (0.027 for KOD vs 0.215–0.270 for individuals of Yakut subspecies) and standardized MLH—stMLH (0.116 against 0.910–1.147). The results of multidimensional scaling (MDS), Nei distances calculations (D_N) and STRUCTURE analysis showed a clear genetic differentiation of Kodar snow sheep from Yakut subspecies. Our data is the first step to understanding the demographic history of the original Kodar population of snow sheep.     

Genomic patterns in the widespread Eurasian lynx shaped by Late Quaternary climatic fluctuations and anthropogenic impacts

Disentangling the contribution of long‐term evolutionary processes and recent anthropogenic impacts to current genetic patterns of wildlife species is key to assessing genetic risks and designing conservation strategies. Here, we used 80 whole nuclear genomes and 96 mitogenomes from populations of the Eurasian lynx covering a range of conservation statuses, climatic zones and subspecies across Eurasia to infer the demographic history, reconstruct genetic patterns, and discuss the influence of long‐term isolation and/or more recent human‐driven changes. Our results show that Eurasian lynx populations shared a common history until 100,000 years ago, when Asian and European populations started to diverge and both entered a period of continuous and widespread decline, with western populations, except Kirov, maintaining lower effective sizes than eastern populations. Population declines and increased isolation in more recent times probably drove the genetic differentiation between geographically and ecologically close westernmost European populations. By contrast, and despite the wide range of habitats covered, populations are quite homogeneous genetically across the Asian range, showing a pattern of isolation by distance and providing little genetic support for the several proposed subspecies. Mitogenomic and nuclear divergences and population declines starting during the Late Pleistocene can be mostly attributed to climatic fluctuations and early human influence, but the widespread and sustained decline since the Holocene is more probably the consequence of anthropogenic impacts which intensified in recent centuries, especially in western Europe. Genetic erosion in isolated European populations and lack of evidence for long‐term isolation argue for the restoration of lost population connectivity.     

Whole genome SNP scanning of snow sheep (<Emphasis Type="Italic">Ovis nivicola</Emphasis>)

This is the first report performing the whole genome SNP scanning of snow sheep (Ovis nivicola). Samples of snow sheep (n = 18) collected in six different regions of the Republic of Sakha (Yakutia) from 64° to 71° N. For SNP genotyping, we applied Ovine 50K SNP BeadChip (Illumina, United States), designed for domestic sheep. The total number of genotyped SNPs (call rate 90%) was 47796 (88.1% of total SNPs), wherein 1006 SNPs were polymorphic (2.1%). Principal component analysis (PCA) showed the clear differentiation within the species O. nivicola: studied individuals were distributed among five distinct arrays corresponding to the geographical locations of sampling points. Our results demonstrate that the DNA chip designed for domestic sheep can be successfully used to study the allele pool and the genetic structure of snow sheep populations.     

On the origin of mongrels: evolutionary history of free-breeding dogs in Eurasia

Although a large part of the global domestic dog population is free-ranging and free-breeding, knowledge of genetic diversity in these free-breeding dogs (FBDs) and their ancestry relations to pure-breed dogs is limited, and the indigenous status of FBDs in Asia is still uncertain. We analyse genome-wide SNP variability of FBDs across Eurasia, and show that they display weak genetic structure and are genetically distinct from pure-breed dogs rather than constituting an admixture of breeds. Our results suggest that modern European breeds originated locally from European FBDs. East Asian and Arctic breeds show closest affinity to East Asian FBDs, and they both represent the earliest branching lineages in the phylogeny of extant Eurasian dogs. Our biogeographic reconstruction of ancestral distributions indicates a gradual westward expansion of East Asian indigenous dogs to the Middle East and Europe through Central and West Asia, providing evidence for a major expansion that shaped the patterns of genetic differentiation in modern dogs. This expansion was probably secondary and could have led to the replacement of earlier resident populations in Western Eurasia. This could explain why earlier studies based on modern DNA suggest East Asia as the region of dog origin, while ancient DNA and archaeological data point to Western Eurasia.     

Comparative analysis of the effectiveness of STR and SNP markers for intraspecific and interspecific differentiation of the genus <Emphasis Type="Italic">Ovis</Emphasis>

A comparative study of the informativeness of SNP and STR markers for interspecific and intraspecific differentiation of the two species of the genus Ovis, snow sheep (O. nivicola) and domestic sheep (O. aries), was conducted. Eleven STR loci combined into two multiplex panels were examined. SNP analysis was performed with the DNA microarray OvineSNP50K BeadChip featuring 54241 SNPs. The possibility of clear differentiation of the studied Ovis species with both types of genetic markers was demonstrated. The advantages of SNP markers for intraspecific differentiation of the O. aries breeds and O. nivicola geographical groups were revealed. The areas of application of the studied types of DNA markers are discussed.     

Characteristics of the Genetic Structure of Snow Sheep (<Emphasis Type="Italic">Ovis nivicola lydekkeri</Emphasis>) of the Verkhoyansk Mountain Chain

Genetic characteristics of the allele pool of four groups of the Yakut snow sheep subspecies (Ovis nivicola lydekkeri) inhabiting various parts of the Verkhoyansk Mountain Range such as Kharaulakh Ridge, Orulgan Ridge, ridges of the Central Verkhoyansk, and Suntar-Khayata Ridge is presented. Fragment analysis using 17 microsatellite loci was carried out using the ABI 3131xl genetic analyzer. Significant heterozygote deficiency was detected in all investigated snow sheep populations. Differentiation of the studied groups in accordance to their geographical origin was revealed.     

Coat Polymorphism in Eurasian Lynx: Adaptation to Environment or Phylogeographic Legacy?

Journal of Mammalian Evolution - We studied the relationship between the variability and contemporary distribution of pelage phenotypes in one of most widely distributed felid species and an array...