Dmitry Yu. Sherbakov

Genotyping of Capreolus pygargus Fossil DNA from Denisova Cave Reveals Phylogenetic Relationships between Ancient and Modern Populations

Background The extant roe deer (Capreolus Gray, 1821) includes two species: the European roe deer (C. capreolus) and the Siberian roe deer (C. pygargus) that are distinguished by morphological and karyotypical differences. The Siberian roe deer occupies a vast area of Asia and is considerably less studied than the European roe deer. Modern systematics of the Siberian roe deer remain controversial with 4 morphological subspecies. Roe deer fossilized bones are quite abundant in Denisova cave (Altai Mountains, South Siberia), where dozens of both extant and extinct mammalian species from modern Holocene to Middle Pleistocene have been retrieved. Methodology/Principal Findings We analyzed a 629 bp fragment of the mitochondrial control region from ancient bones of 10 Holocene and four Pleistocene Siberian roe deer from Denisova cave as well as 37 modern specimen belonging to populations from Altai, Tian Shan (Kyrgyzstan), Yakutia, Novosibirsk region and the Russian Far East. Genealogical reconstructions indicated that most Holocene haplotypes were probably ancestral for modern roe deer populations of Western Siberia and Tian Shan. One of the Pleistocene haplotypes was possibly ancestral for modern Yakutian populations, and two extinct Pleistocene haplotypes were close to modern roe deer from Tian Shan and Yakutia. Most modern geographical populations (except for West Siberian Plains) are heterogeneous and there is some tentative evidence for structure. However, we did not find any distinct phylogenetic signal characterizing particular subspecies in either modern or ancient samples. Conclusion/Significance Analysis of mitochondrial DNA from both ancient and modern samples of Siberian roe deer shed new light on understanding the evolutionary history of roe deer. Our data indicate that during the last 50,000 years multiple replacements of populations of the Siberian roe deer took place in the Altai Mountains correlating with climatic changes. The Siberian roe deer represent a complex and heterogeneous species with high migration rates and without evident subspecies structure. Low genetic diversity of the West Siberian Plain population indicates a recent bottleneck or founder effect.

Palaearctic gastropod gains a foothold in the dominion of endemics: range expansion and morphological change of Lymnaea (Radix) auricularia in Lake Baikal

In and around the endemic-dominated Lake Baikal, palaearctic species are generally restricted to shallow, sheltered bays and in- and out-flowing river floodplains. However, we observed populations of the palaearctic snail Lymnaea (Radix) auricularia on the steep, rocky littoral of Lake Baikal proper. We compared the morphology of 542 shells sampled from this new habitat with potential source populations from conventional habitats. A size-free Discriminant Analysis indicated a strong morphological differentiation of the newly established populations from their likely sources. The new populations had a more compact shell shape with a wide aperture, which may be advantageous in wave-exposed habitats where a firm attachment to the substrate is needed. Shells from the conventional habitats were more elongated, with a narrow aperture, which may be advantageous in habitats that have a dry period where retreating into the mud is required and water loss should be limited. These results may suggest that selection is acting on shell shape in Lake Baikal. The apparent recent arrival of this pandemic gastropod in a habitat previously dominated by endemics constitutes a potential ecological threat and an alert to possible ecological change.

Evolution of mitochondrial genomes in Baikalian amphipods

BackgroundAmphipods (Crustacea) of Lake Baikal are a very numerous and diverse group of invertebrates generally believed to have originated by adaptive radiation. The evolutionary history and phylogenetic relationships in Baikalian amphipods still remain poorly understood. Sequencing of mitochondrial genomes is a relatively feasible way for obtaining a set of gene sequences suitable for robust phylogenetic inferences. The architecture of mitochondrial genomes also may provide additional information on the mechanisms of evolution of amphipods in Lake Baikal.ResultsThree complete and four nearly complete mitochondrial genomes of Baikalian amphipods were obtained by high-throughput sequencing using the Illumina platform. A phylogenetic inference based on the nucleotide sequences of all mitochondrial protein coding genes revealed the Baikalian species to be a monophyletic group relative to the nearest non-Baikalian species with a completely sequenced mitochondrial genome - Gammarus duebeni. The phylogeny of Baikalian amphipods also suggests that the shallow-water species Eulimnogammarus has likely evolved from a deep-water ancestor, however many other species have to be added to the analysis to test this hypothesis.The gene order in all mitochondrial genomes of studied Baikalian amphipods differs from the pancrustacean ground pattern. Mitochondrial genomes of four species possess 23 tRNA genes, and in three genomes the extra tRNA gene copies have likely undergone remolding. Widely varying lengths of putative control regions and other intergenic spacers are typical for the mitochondrial genomes of Baikalian amphipods.ConclusionsThe mitochondrial genomes of Baikalian amphipods display varying organization suggesting an intense rearrangement process during their evolution. Comparison of complete mitochondrial genomes is a potent approach for studying the amphipod evolution in Lake Baikal.

The complete mitochondrial genome of a deep-water Baikalian amphipoda Brachyuropus grewingkii (Dybowsky, 1874)

Abstract In this study, we present a complete mitochondrial genome of a deep-water amphipoda Brachyuropus grewingkii (Dybowsky, 1874) from Lake Baikal. A circular mitochondrial DNA has 17,118 bp in length and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, a putative control region, and five intergenic spacers. An extended control region and altered positions of some tRNA genes distinguish mitochondrial genome of B. grewingkii from the mitochondrial genomes described for other Baikalian amphipoda species.

The complete mitochondrial genome of Baikalian amphipoda Eulimnogammarus vittatus Dybowsky, 1874

Abstract A complete mitochondrial genome sequence of amphipoda Eulimnogammarus vittatus Dybowsky, 1874 from Lake Baikal was obtained using next-generation sequencing approach. Mitochondrial DNA with the length of 15,534 bp contains 13 protein-coding genes, 2 ribosomal RNA, 23 transfer RNA and non-coding sequences: a putative control region and 7 intergenic spacers. A brief comparative analysis of mitochondrial genomes of E. vittatus and its sister species Eulimnogammarus verrucosus was performed.

The evolutionary history of two species of Orthocladiinae (Diptera: Chironomidae) from Lake Baikal (Eastern Siberia)

The evolutionary history of two species belonging to the genus Orthocladius van der Wulp, 1874 (Diptera: Chironomidae) from Lake Baikal was investigated using the mitochondrial gene coding the first subunit of the cytochrome c oxidase (CO1 mtDNA). The phylogenetic analysis indicated that the Baikal Orthocladius species were divided into two well-defined clades where O. (Orthocladius) gregarius Linevitsh, 1970 was a sister species to Palaearctic O. (Orthocladius) nitidoscutellatus Lundstrom, 1915 and the O. (Eudactylocladius) sp. was a sister species to Nearctic O. (Eudactylocladius) subletteorum Cranston, 1998. Divergence time estimates indicated that these species had been evolving independently for about 18 Ma (Neogene, Early Miocene), while emergence of the most recent common ancestors of the modern O. (Orthocladius) gregarius and O. (Eudactylocladius) sp. was dated to about 3.5 Ma (Neogene, Pliocene). The evolution of Baikal orthoclads occurred from the rheophilic fauna under conditions of global climate change during the geological history of the Baikal Depression in the Tertiary Period.

Water motion as a transformation mechanism of algal communities structure in Lake Baikal

The diversity of algal communities of phytoplankton and meio-and macrophytes was investigated in Lake Baikal. Fragments of Spirogyra thallomes were recorded in the phytoplankton community of Southern Baikal, which had never been recorded before in its composition. It was also established that the structure of benthic algal communities changed in comparison with that in 2000 due to intense development of filamentous algae, particularly Spirogyra. Its lowest biomass was recorded in the surf zone and wave breaking, whereas the highest biomass was registered in the area of weakened effect of waves on the bottom. The cover percent of the bottom with filamentous algae in different areas of the coastal zone varied from 0 to 100%. Hydraulic characteristics of Spirogyra were the same as those of planktonic diatoms. The circulation currents and wave effect on the bottom favoured transfer and distribution of Spirogyra from the location of its intense development into the coastal area of Lake Baikal.

Population genetic structure and phylogeography of sterlet (Acipenser ruthenus, Acipenseridae) in the Ob and Yenisei river basins

Abstract The sterlet (Acipenser ruthenus Linnaeus, 1758) is a relatively small sturgeon widely distributed in Eurasian rivers from the Danube to the Yenisei. During the twentieth century, all wild sterlet populations have declined due to anthropogenic factors including: overfishing, poaching, construction of dams, and pollution. Despite the necessity of characterization both wild and captive stocks, few studies of population genetics have been performed thus far. Here we studied the genetic diversity and geographic structure of sterlet populations across the eastern range – Ob-Irtysh and Yenisei basins – by sequencing a 628-bp fragment of mitochondrial DNA control region. We identified 98 new haplotypes, delineated 12 haplogroups and estimated the time of basal haplogroup divergence within the species as over 8 million years ago. Our data suggest that Ob-Irtysh and Yenisei populations are isolated from each other and much lower genetic diversity is present in the Yenisei population than in the Ob-Irtysh population. Our data imply that sterlet populations in Siberian rivers underwent bottleneck or fragmentation, followed by subsequent population expansion. The data obtained here are important for sterlet population monitoring and restocking management.

A new, genetically divergent species of Pseudobaikalia Lindholm, 1909 (Caenogastropoda, Baicaliidae).

Abstract A new gastropod species, Pseudobaikalia michelae Sitnikoiva & Kovalenkova, sp. n., (family Baicaliidae) is described from Lake Baikal. This is the first new species from the Baicaliidae for forty years. The new species is distinguished from its sister taxa by means of comparative morphology as well as analyses of DNA sequences (mtDNA and an intron of alpha-subunit gene of ATP-synthase). It was found in the southern and central-eastern parts of the lake where it occurs sympatrically with three other baicaliid species. Characters of the female reproductive system (i.e., a long oviduct loop with 2–3 narrow tube-like evaginations) and the aperture (i.e., oval shape with a simple outer lip) place these snails in the genus Pseudobaikalia Lindholm, 1909. The new species is most similar in its shell morphology to the northern Baikal species Pseudobaikalia jentteriana (smooth elongated shape) but differs by a more oval aperture that is slightly angled to the columella. Combined mitochondrial and nuclear sequences in a Bayesian analysis showed that all specimens of Pseudobaikalia michelae sp. n. form a well-supported clade.

The complete mitochondrial genome of Baikalospongia intermedia (Lubomirskiidae): description and phylogenetic analysis

Abstract The complete mitochondrial genome of the Lake Baikal sponge Baikalospongia intermedia was sequenced. The circular mitochondrial genome is 28,327 bp in length and includes 14 protein-coding genes, 2 ribosomal RNA genes and 25 transfer RNA genes. Bayesian comparative analysis of molecular evolution rates was found no acceleration of the mtDNA evolution of B. intermedia. This species clustered with other species of the genus Baikalospongia on the Bayesian tree.