Phylogeography of ancient and modern brown bears from eastern Eurasia

The brown bear (Ursus arctos) is an iconic carnivoran species of the Northern Hemisphere. Its population history has been studied extensively using mitochondrial markers, which demonstrated signatures of multiple waves of migration, arguably connected with glaciation periods. Among Eurasian brown bears, Siberian populations remain understudied. We have sequenced complete mitochondrial genomes of four ancient (~4.5-40 kya) bears from South Siberia and 19 modern bears from South Siberia and the Russian Far East. Reconstruction of phylogenetic relationships between haplotypes and evaluation of modern population structure have demonstrated that all the studied samples belong to the most widespread Eurasian clade 3. One of the ancient haplotypes takes a basal position relative to the whole of clade 3; the second is basal to the haplogroup 3a (the most common subclade), and two others belong to clades 3a1 and 3b. Modern Siberian bears retain at least some of this diversity; apart from the most common haplogroup 3a, we demonstrate the presence of clade 3b, which was previously found mainly in mainland Eurasia and Northern Japan. Our findings highlight the importance of South Siberia as a refugium for northern Eurasian brown bears and further corroborate the hypothesis of several waves of migration in the Pleistocene.

Vocal phenotype of male rutting roars and genetic markers delineate East European red deer (Cervus elaphus) from Central and West European populations

This study investigates a population of red deer Cervus elaphus, founded by 10 individuals introduced in the nineteenth century from Germany to the Voronezh region of the European part of Southern Russia and then developed without further introductions. We characterize for the first time the vocal phenotype of the Voronezh red deer male rutting calls in comparison with similar data on the Pannonian (native Central European) and Iberian (native West European) red deer obtained by the authors during preceding studies. In addition, we provide for the first time the genetic data on Pannonian red deer. In Voronezh stags, the number of roars per bout (2.85 ± 1.79) was lower than in Pannonian (3.18 ± 2.17) but higher than in Iberian (2.11 ± 1.71) stags. In Voronezh stags, the duration of main (the longest within bouts) roars was longer (2.46 ± 1.14 s) than in Pannonian (1.13 ± 0.50 s) or Iberian (1.90 ± 0.50 s) stags. The maximum fundamental frequency of main roars was similar between Voronezh (175 ± 60 Hz) and Pannonian (168 ± 61 Hz) but higher in Iberian stags (223 ± 35 Hz). Mitochondrial cytochrome b gene analysis of red deer from the three study populations partially supports the bioacoustical data, of closer similarity between Voronezh and Pannonian populations. In contrast, microsatellite DNA analysis delineates Voronezh red deer from either Pannonian or Iberian red deer. We discuss that population bottlenecking might affect the acoustics of the rutting roars, in addition to genotype.

Genetic Specificity of the Siberian Forest Reindeer (Rangifer tarandus valentinae Flerov, 1932) of the Kuznetsk Alatau

This is the first study to show the genetic identity of the Altai-Sayan population of the forest reindeer of the Kuznetsk Alatau (Rangifer tarandus valentinae). The population is characterized by the existence of unique mitochondrial lines, the absence of signs of introgression of domestic rein deer mtDNA, as well as a low level of genetic diversity. In the sample studied, only two nucleotide substitutions (both of them transitions) were revealed, the nucleotide diversity (0.0015 ± 0.00136) was almost ten times lower than in most populations of wild reindeer in Russia and was comparable only with that of some wild reindeer populations of Norway and Svalbard. The haplotype diversity (h) was also relatively low (0.615 ± 0.102).

Colonizing the High Arctic: Mitochondrial DNA Reveals Common Origin of Eurasian Archipelagic Reindeer (Rangifer tarandus)

In light of current debates on global climate change it has become important to know more on how large, roaming species have responded to environmental change in the past. Using the highly variable mitochondrial control region, we revisit theories of Rangifer colonization and propose that the High Arctic archipelagos of Svalbard, Franz Josef Land, and Novaia Zemlia were colonized by reindeer from the Eurasian mainland after the last glacial maximum. Comparing mtDNA control region sequences from the three Arctic archipelagos showed a strong genetic connection between the populations, supporting a common origin in the past. A genetic connection between the three archipelagos and two Russian mainland populations was also found, suggesting colonization of the Eurasian high Arctic archipelagos from the Eurasian mainland. The age of the Franz Josef Land material (>2000 years before present) implies that Arctic indigenous reindeer colonized the Eurasian Arctic archipelagos through natural dispersal, before humans approached this region.

Mitotypical Peculiarities of the Population of Moose Alces alces of Southeastern West Siberia

Based on the structure of the D-loop control region of mitochondrial DNA, the genetic diversity of moose of West Siberia was evaluated and their placement within the structure of current species population was determined. It was noted that the values of genetic diversity exceed the values of analogous indices obtained for western groups of the species. Three haplogroups were identified in the population structure: European- Ural, West Siberian, and American.

[A Detection of Allelic Variants at Microsatellite Markers by Using Capillary and Traditional Electrophoresis]

Microsatellite alleles are detected by PCR (polymerase chain reaction) that provides a manifold increase in the number of copies (amplification) of a given DNA fragment. The fragment visualization can be reached by two different methods. These are fragment analysis by capillary electrophoresis in denaturing gel and frag- ment separation in non-denaturing gel with subsequent gel staining. The first method is more accurate and automated, but expensive. The second method is much cheaper but less convenient. It requires manual pro- cessing and is presumably less accurate. In this study, we present the results of comparison of the allele typing at nine microsatellite loci using these two methods for one of the species of Pacific salmon, sockeye salmon Oncorhynchus nerka Walbaum. In most cases, both methods give identical fragment sizes or a constant differ- ence if the alleles are relatively small (not larger than 200-220 bp).

Superb winter fur insulation in the small Siberian musk deer (Moschus moschiferus)

We compared the morphology and thermal characteristics of winter pelage from two Siberian musk deer Moschus moschiferus (aged 5 and 41 mo.; 5.7 and 9.5 kg) and two Eurasian reindeer Rangifer tarandus tarandus (aged >48 mo.; 73 and 79 kg).  The depth of the fur over the back of musk deer was less (approximately 30 mm) than in reindeer (approximately 40 mm).  Guard hairs of musk deer were longer (mean = 50.0 mm) and had greater diameter at half-length (mean = 314.4 μm) than those of reindeer (mean = 38.6mm and = 243.9 μm, respectively).  The thermal characteristics (thermal conductivity and resistance) of the winter pelage of the two species were nevertheless similar (0.057 W·m-1·K-1 and 0.79 K·m2·W-1; and 0.037 W·m-1 ·K-1 and 1.00 K·m2·W-1, respectively) despite a tenfold difference in their body mass.

[The role of the Urals in the genetic diversity of the European moose subspecies (Alces alces alces)]

The genetic diversity of the Uralian moose population and the role of the Ural region in the phylogeographic structure of the European moose were evaluated based on sequence polymorphisms of the mtDNA control region. The nucleotide diversity of the Ural moose was low, whereas haplotype diversity was rather high. It was found that the haplotype pool of the Ural moose reflects both the unique features of their mitochondrial lineages and their connection with Alces alces alces populations of Europe and West Siberia. The structure of median networks and the territorial haplotype distribution support the hypothesis that the mitochondrial lineages typical for this part of the European moose area originate from a late Pleistocene refugium that was located in the Urals.

[Identification of European (Capreolus capreolus L.) and Siberian (C. pygargus Pall.) roe deer hybrids by microsatellite marker analysis]

An analysis of 130 tissue specimens of the European (Capreolus capreolus) and the Siberian (C. pygargus) roe deer from nine regions of Russia and Ukraine using microsatellite loci analysis was conducted, aimed at the identification of hybrid animals. An optimized complex of 21 microsatellite loci was selected for the determination of species specificity and the search for interspecies hybrids. Hybrid animals were revealed in the Moscow and Volgograd regions. Their ratio in the total sample obtained in the European part of Russia was 11.9%.

[Major histocompatibility complex (MHC) in mammals' and its importance for studies of rare species (with Felidae family as an example)]

Major histocompatibility complex (MHC) appears to be a suitable tool for solving various tasks of popu- lationgenetics. Information on genetic basis of immunity facilitates understanding of evolutionary his- tory and assessment of current state and prospects of studied population/species survival. On the one hand, MHC variability is maintained through pathogen dependent mechanisms, i.e., directional selection of individuals resistant to diseases, that are present in the environment and balancing selection which gives advantage to those individuals carrying unusual or rare alleles of MHC genes. On the other hand, MHC genes have an influence on reproduction efficiency of individuals. Because of MHC polygeny, its studying requires an application of methods that introduce additional stages between amplification of a certain gene segment and its sequencing. In the article, different tech- niques of allele separation are considered, as well as a simplified version of MHC variability analysis based on the examination of microsatellite loci. Despite the high information value of MHC, it is still not used in zoological studies as often as it deserves. Using as an example predatory mammals of Felidae family which contains quite a few threatened species, we show that a majority of studies on MHC in wild cats is descriptive ones and only few of them deal with genes comparative analysis. The rise of interest to the studies of major histocompatibility complex in non-model species may help not only in solving the fundamental problems of evolution and phylogenetic structure of the family but also in planning the measures for conservation of rare and endangered species exposed to various anthropogenic stresses.

[New data on the phylogeography and genetic diversity of the brown bear Ursus arctos Linnaeus, 1758 of northeastern Eurasia (mtDNA control region polymorphism analysis)]

An analysis of polymorphism of the fragment of the control region of mitochondrial DNA of 53 tissue samples of the brown bear Ursus arctos from several regions of the eastern part of Russia was carried out. It was found that most of the described haplotypes belong to cluster 3a, the most common in Eurasia, and do not form regionally specific haplogroups. However, among the bears from Western and Eastern Siberia, as well as the island of Kunashir, three haplotypes were identified, which are close to the haplogroup typical of Eastern Hokkaido bears. The assumption was made of the existence in Siberia and the Far East of one or more Pleistocene refugia.

[Polymorphism of the mtDNA control region in wild reindeer Rangifer tarandus (Mammalia: Artiodactyla) from the European part of Russia]

Genetic diversity ofwild reindeer (Rangifer tarandus) inhabiting the European part of Russia, including Komi Republic, Arkhangelsk oblast, Murmansk oblast, and the Republic of Karelia was characterized using sequence polymorphism of the mtDNA control region. Despite of currently low population number of wild reindeer, they were characterized by a high level of genetic diversity (pi = 0.018; H= 0.872 to 0.914). Phylogenetic analysis showed close relationships between European reindeer and wild reindeer of Siberia. In reindeer from Murmansk oblast a haplotype in common with the wild reindeer form Southwestern Norway was described. The reindeer sample examined contained no haplotypes earlier described for the reindeer of Central Norway. It is suggested that in recent past wild reindeer from the European north of Russia formed one population with the reindeer from the north of the Asian part of Eurasia.

[Phylogeography of red deer (Cervus elaphus): data of analysis of polymorphism of the mitochondrial gene for cytochrome b]

Analysis of polymorphism of the gene for cytochrome b (1140 bp) of 106 samples of red deer (Cervus elaphus) of Eurasia is carried out, and the phylogenetic relationships of groups throughout the entire geographic range, including North America, are reconstructed. In total, the paper describes 75 haplotypes, 33 of them for the European and 42 for the Asian part of the geographic range. Common haplotypes for these two parts of the range were not found. The genetic kinship of Asian Siberian stags and North American wapiti is confirmed. Red deer living in Yakutia are close to the Siberian stags of Altai and Tuva, whereas red deer that live in Krasnoyarsk krai and Irkutsk oblast form a separate group. Overall, the reconstructed phylogeographic structure of the species is significantly different from the accepted subspecies differentiation based on morphological characters.

[Genetic diversity and relatives of the goitered gazelle (Gazella subgutturosa) groups from Uzbekistan, Turkmenistan, and Azerbaijan: analysis of the D-loop of mitochondrial DNA]

Polymorphism of the nucleotide sequence of a hypervariable fragment of the D-loop (985 bp) of mtDNA in 76 Goitered gazelles of subspecies Gazella subgutturosa subgutturosa from Uzbekistan, Turkmenistan, and Azerbaijan was studied. The genetic similarity of gazelles from Turkmenistan and Uzbekistan has been identified. The population of gazelles from Shirvanskaya steppe reserve (Azerbaijan) is unique and strictly isolated from other groups studied. A high haplotypic (H = 0.9649 +/- 0.0091) and relatively low nucleotide diversity (pi = 0.0212 +/- 0.0105) were noted for all investigated groups of gazelle based on this mtDNA fragment, which is probably related to ecological peculiarities of the species and the history of formation of regional populations.

[Analysis of the variability of the control region and cytochrome b gene of mtDNA of Capreolus pygargus Pall]

Analysis the of cytochrome b gene (1140 b.p.) polymorphism and polymorphism of 79 specimens of the control region (934 b.p.) of mtDNA of the Siberian roe deer Capreolus pygargus from 23 regions of Russia and Kazakhstan has been carried out. The combined alignment of two fragments ofmitochondrial DNA revealed 36 haplotypes, which are distributed in three haplogroups. The net distance was 0.8, 1.3, and 1.3%. The specific pattern of haplogroups was described for roe deer of each region (Ural, trans-Ural, Eastern Siberia, Far East, Northeastern China). Unrelated haplogroups were found in populations of the Urals and Siberia. The variation pattern and spatial distribution of mitochondrial lines allowed us to suggest that a haplogroup that initially belongs to C. p. tianschanicus occurs secondarily in C. p. pygargus.

[Genetic diversity of wild reindeer (Rangifer tarandus) of Taimyr: analysis of polymorphism of the control region of mitochondrial DNA]

Based on an analysis of the polymorphism of nucleotide sequences (n = 111) of the control region (left domain) of mtDNA, the genetic diversity of the largest population of wild reindeer Rangifer tarandus in Eurasia, which inhabits Taimyr peninsula, was studied. High levels of gaplotypic (H) and nucleotide (pi) diversity (0.987 and 0.018, respectively) were revealed, which indicate the long existence of this population and the sufficiently stable growth of the population. The absence of long periods of abrupt decrease in the number of the Taimyr population of wild reindeer and/or facts of formation of its genetic diversity as a result of mixing of genetically distant conspecific populations is supported by the data on the distribution pattern of frequencies of pair differences between nucleotide sequences and the topology of the phylogenetic tree. The low level of genetic differences between reindeer from the western, central, and eastern groups reflects their common origin and close kinship.

[Genetic diversity of Swan goose (Anser cygnoides l.) in Russia: analysis of the mitochondrial DNA control region polymorphism]

Using to analysis of hypervariable fragment polymorphism in the control region of mitochondrial DNA (268 bp), the genetic variability of Swan goose Anser cygnoides L., included in the first category of endangered species in the Russian Red Book, has been investigated. Samples from the two main groups nesting in Russia-the Far Eastern group (Khabarovsk krai, n = 38) and the Dauric group (Chita region, n = 10) were examined. Eleven haplotypes were described. The genetic diversity of Swan geese was low comparable with that observed in some other globally endangered Eurasian goose species. Nucleotide and haplotype diversity of goose from Khabarovsk krai was 0.0031 and 0.65, respectively; in those from Chita region, 0.0041 and 0.80; and for in total group, 0.0074 and 0.77, respectively. No identical haplotypes in Swan goose from Far Eastern and Daurical groups have been demonstrated. However, the small sample size does not allow us to make final conclusions on the degree of genetic differentiation between these groups.

[Comparative phylogeography: molecular methods, ecological interpretation]

This brief review of phylogeohraphy - the new field of study concerned with the principles and processing governing the geographic distribution of genealogical lineages (mainly within and among closely related species), is focused on the importance of the ecological approach in understanding of the molecular-genetic data. The comparative phylogeohraphy as one of the most promising lines of investigation in this respect is considered. Comparisons of the phylogeohraphical patterns and ecological traits of representatives of separate ecosystems, regional faunas, systematically close species, "host-parasite" complexes etc. give an opportunity to touch the ground of the microevolutionary processes.

[Molecular genetic study of the beluga (Delphinapterus leucas: Cetacea, Monodontidae) summering in the southern Sea of Okhotsk as compared to North American populations]

The structure of the left part of the mtDNA control region has been studied in Delphinapterus leucas captured in summer in the southern Sea of Okhotsk. The data have been compared with published results of similar studies on D. leucas at different sites along the American coast. A high specificity of maternal lineages of D. leucas from the southern Sea of Ok.

[Molecular genetic diversity of musk deer Moschus moschiferus L., 1758 (Ruminantia, Artiodactyla) from the northern subspecies group]

Genetic diversity within the northern subspecies group of musk deer Moschus moschiferus L, 1758 was examined based on the mtDNA control region hypervariable fragment (300-bp) sequence polymorphism. Nucleotide diversity, constituting 2.6% for the whole sample (n = 34), varied in the range from 0.6 to 1.9% for individual subspecies. Maximum values of this index were observed for Siberian subspecies (M. m. moschiferus), which had the widest range. Genetic similarity between the haplotypes of the musk deer from the Far East (Russia) and Sakhalin Island, which grouped in one cluster in a phylogenetic tree, was demonstrated. The data obtained indicate that the distribution of musk deer along the territory of Russia occurred from Eastern Siberia to the Far East, and from there to the Sakhalin Island. A currently observed decrease of the musk deer population number along with the increased habitat fragmentation can result in a decrease of the total genetic diversity and in inbreeding depression in the local isolated groups.

[Genetic diversity of Mongolian gazelle Procapra guttorosa Pallas, 1777]

The mitochondrial DNA D-loop hypervariable fragment sequence polymorphism was examined in 27 Mongolian gazelles from Mongolia, Russia, and China. Intraspecific polymorphism of the D-loop fragment examined was demonstrated. All haplotypes described were unique. The average nucleotide diversity (pi) for the mtDNA fragment investigated constituted 5.85 +/- 2.92%. A relatively high number of insertions and deletions was observed. In particular, a haplotype with the 77-bp insertion was described. The data obtained point to high genetic diversity of Mongolian populations. There was no correlation between the distribution of haplotypes examined and geographical location of the animal tissue sampling sites.

[Molecular phylogeny of deer (Cervidae: Artiodactyla)]

Sequences of mitochondrial genes 12S and 16S rRNA (2 445 bp) and the region of the nuclear beta-spectrin gene (828 bp) were analyzed in members of the family Cervidae and in other artiodactyls. Several molecular synapomorphies characteristic both of Cervidae and musk deer have been found. According to our data, Cervidae is a sister clade to Bovidae, which are very close to Moschidae. The family Giraffidae is exterior to this common clade, while Antilocapridae occupies a more basal position. The family Cervidae proper splits into three clades including the genera Cervus and Muntiacus (1), Capreolus, Hydropotes, Alces (2), and Rangifer, Odocoileus, and the remaining genera (3). In general, our phylogenetic reconstructions conform to the results of earlier molecular genetic studies, but substantially differ from the traditional taxonomy of Ruminantia.

[Phylogenetic analysis of sequences of the 12S and 16S rRNA mitochondrial genes in the family Bovidae: new evidence]

The phylogeny of the family Bovidae has been inferred from our data on the 12S and 16S rRNA gene sequences and from the results of other authors. A considerable (2,460 bp) length of the analyzed fragments of these conserved genes and the use of different methods of cladogram construction allowed us to verify the systematic position of the genera Saiga, Pantholops, Procarpa, and Oreamnos. Saigas were shown to be phylogenetically far closer to gazelles than black-tailed gazelles and pygmy antelopes. In general, the genetic analysis data are in agreement with the results of morphological studies.

Mitochondrial 12S rDNA sequence relationships suggest that the enigmatic bovid "Linh Duong" Pseudonovibos spiralis is closely related to buffalo

The phylogenetic position and taxonomic status of the recently described Southeast Asian endemic bovid Pseudonovibos spiralis were deduced from nearly complete 12S mitochondrial rDNA sequences of this species and Bubalus bubalis alongside 26 sequences of Bovidae from GenBank using Cervus elaphus (Cervidae) as outgroup. Maximum-likelihood analyses performed by PUZZLE and fastDNAml nested P. spiralis at the base of the subtribe buffalo Bovini, suggesting the close relationship of this enigmatic species with buffalo and enabling its distinction into the separate

The "Linh Duong" Pseudonovibos spiralis (Mammalia, Artiodactyla) is a new buffalo

The controversial phylogenetic position of the recently described South-East Asian endemic bovid, Pseudonovibos spiralis, was evaluated on the basis of phylogenetic analyses of originally obtained nearly complete 12S mitochondrial rDNA sequences for this species and Bubalus bubalis and 26 sequences of Bovidae from the Genbank using Cervus elaphus (Cervidae) as outgroup. In most of the phylogenetic analyses performed using PAUP 4.0 (maximum parsimony, maximum likelihood and neighbour-joining), Bovidae consisted of two major clades: Bovinae including the tribes Bovini, Tragelaphini and Boselaphini, and Antilopinae + Caprinae, incorporating all other bovids. In most trees P. spiralis fell within the buffalos (subtribe Bovina) between Bubalus and Syncerus. Therefore, our phylogenetic analyses of bovid mitochondrial 12S rRNA gene sequences suggest the close relationship of this enigmatic species with the buffalos and its placement within the subtribe Bovina.

[The use of fur collected in the field for studying the genetic diversity of wild ungulates]

The methods of studying the genetic diversity of wild animals using tissue samples collected without harming the studied populations are discussed for the red deer (Cervus elaphus) fur samples. The methods are proposed for collection and storage of fur samples in field conditions. The optimal methods of DNA isolation from the fur and other tissues (dry, alcohol-fixed, and frozen skin and muscle) of the red deer and other ungulates were selected, and the conditions of PCR for amplification of the mitochondrial DNA fragments were determined. The comparison between the pure-blood red deers from Central England and the Voronezh State Reserve (Russia) was performed using a cytochrome b fragment of the mitochondrial DNA.