Yu. S. Bukin

Genetic differentiation of the endemic Baikalian mollusk Baicalia carinata (Mollusca: Caenogastropoda)

In gastropod mollusk Baicalia carinata Dybowski, 1875, sampled in different sites of the Lake Baikal, comparison of 81 sequences of internal transcribed spacer 1 (ITS1) located between the genes for 18S rRNA and 5.8S rRNA, and of 100 sequences of the fragment of mitochondrial DNA cytochrome-c-oxidase subunit 1 gene (CO1) was performed. Molecular phylogenetic analysis showed that the endemic mollusk species studied formed at least two distinct populations, Southwestern and Eastern. Statistical significance of the species subdivision into two populations was evaluated using the Mann-Whitney rank test.

Genetic differentiation of populations of Baikal endemic Sergentia baicalensis Tshern. (Diptera, Chironomidae)

The population structure of endemic species Sergentia baicalensis Tshern. (Diptera, Chironomidae) from Lake Baikal was studied using the first subunit of the cytochrome c oxidase mitochondrial gene (CO1). Two populations inhabiting different basins of this lake, the southern-central and northern, were detected. It was confirmed that the divergence time of this species was dated to Late Miocene (9.53 ± 3.9 Mya), during the period when geographically separated basins existed in the Baikal rift zone.

Substrate Specificity of Methanogenic Communities from Lake Baikal Bottom Sediments Associated with Hydrocarbon Gas Discharge

Methane production by microbial communities from Lake Baikal bottom sediments with different chemical composition of pore water was studied. Methane production was more active in the media supplemented with H2: CO2 and H2 + CH3COONa, rather than on media with acetate as the sole source of carbon and energy. Addition of methanol stimulated methane production only in the case of microbial communities from upper silts. Ability of the communities to produce methane correlated reliably with the concentrations of the NO3–, SO42−, Cl–, and CH3COO– ions in the pore water of the relevant sediments. Cultivation of communities from the mud volcano sediments resulted in development of methanogenic archaea of the family Methanocellaсеае in the media supplemented with H2: CO2 and H2 + CH3COONa, while methanogenic archaea in the communities cultivated without additional substrates belonged to the genera Methanoregula, Methanobacterium, and Methanosaeta.

A comparative analysis on the physicochemical properties of tick-borne encephalitis virus envelope protein residues that affect its antigenic properties

This work is dedicated to the study of the variability of the main antigenic envelope protein E among different strains of tick-borne encephalitis virus at the level of physical and chemical properties of the amino acid residues. E protein variants were extracted from then NCBI database. Four amino acid residues properties in the polypeptide sequences were investigated: the average volume of the amino acid residue in the protein tertiary structure, the number of amino acid residue hydrogen bond donors, the charge of amino acid residue lateral radical and the dipole moment of the amino acid residue. These physico-chemical properties are involved in antigen-antibody interactions. As a result, 103 different variants of the antigenic determinants of the tick-borne encephalitis virus E protein were found, significantly different by physical and chemical properties of the amino acid residues in their structure. This means that some strains among the natural variants of tick-borne encephalitis virus can potentially escape the immune response induced by the standard vaccine.

Formation of Pectobacterium carotovorum biofilms depending of the carbon source

Microbial biofilms are a basic form of existence of bacteria in the environment, as well as in the animal and plant organisms. The patterns of biofilm formation depending on cultivation conditions is presently insufficiently studied. This paper presents experimental results on the effect of carbon sources on biofilm formation and movement on the swarming type in a phytopathogenic bacterium Pectobacterium carotovorum. A polyol inositol was shown to cause a significant activation of these processes.

Molecular phylogenetic analysis of the ant genus Formica L. (Hymenoptera: Formicidae) from Palearctic region

Sixty-five sequences of the mitochondrial DNA cytochrome b gene fragment (759 bp) and 23 sequences of the NADH dehydrogenase subunit 6 gene fragment (224 bp) were compared in ants of the genus Formica L. from different regions of the Palearctic and in Polyergus rufescens Latr. as outgroup. In total, 28 species of the genus Formica were examined. As a result, dated trees with a molecular clock were constructed showing the phylogenetic relationships of Formica ants. The topology of the obtained tree based on the Cyt-b sequences was found to be not consistent with the generally accepted opinion on the Formica rufa and F. rufibarbis groups. New data on the formation history of the present-day fauna of Formica ants of the Palearctic were obtained. It was demonstrated that a considerable fraction of the examined species (about a third) were formed in the Quaternary Period.

The Mechanisms for Genetic Diversity of Baikal Endemic Amphipod Gmelinoides fasciatus: Relationships between the Population Processes and Paleoclimatic History of the Lake

Amphipods of the species Gmelinoides fasciatus are one of the dominant species in the littoral zone community of Lake Baikal. Earlier, on the basis of the analysis of the mitochondrial COX1 gene, four isolated populations within the species range were identified, between which there were no distinct geographical barriers. In the present study, a phylogenetic reconstruction of the evolutionary history of G. fasciatus with the molecular clock hypothesis is carried out. The population divergence time is dated back to the onset of global climate changes on the Pleistocene–Pliocene boundary at 1.8–2.3 Ma. As a result, the estimated substitution rate in the COX1 gene for G. fasciatus was 1.2–2.4% of substitutions per Myr, which corresponded to the values determined for other groups of invertebrates. It was demonstrated that geographical barriers that formed the populations of G. fasciatus periodically appeared and disappeared in the past, resulting from climate changes associated with the periods of global cooling and warming.

Molecular evolution of the Lake Baikal endemic caddisflies (Trichoptera)

Phylogenetic relationships of the nine Lake Baikal endemic caddisfly species with the representatives of the genus Apatania (Apataniidae) were reconstructed on the basis on nucleotide sequences of the mitochondrial COI gene. The results of Bayesian analysis pointed to the relationships of the endemics with the North American Apatania incerta (Banks, 1897) and A. sorex (Ross, 1941). The divergence of the genetic lineages of the Baikalian and Nearctic apataniids occurred in the Late Oligocene–Early Miocene. On the dendrogram, endemic species formed two monophyletic clades corresponding to the tribes Thamastini and Baicalinini. It was also found that the genus Protobaicalina was polyphyletic, while the genus Baicalina was a species flock. Our analysis showed that the nearest common ancestor of the studied Baikal caddisfly species existed about 21 Mya, while the modern species composition of endemic fauna dates back to Pliocene–Pleistocene age (2.5–0.7 million years).

Ecological and faunistic characteristics of the leech fauna in the Bukhtarma Reservoir, Eastern Kazakhstan

The taxonomic diversity of the Hirudinea fauna and its dependence on the ecological conditions in the Bukhtarma Reservoir (Eastern Kazakhstan) have been studied. The morphological analysis has shown that these leeches belong to two orders and three families: Rhynchobdellida (families Glossiphoniidae and Piscicolidae) and Arhynchobdellida (family Erpobdellidae). On the whole, eight leech species from five genera (Alboglossiphonia, Helobdella, Theromyzon, Piscicola, and Erpobdella) have been identified. Among them, there are three glossiphoniid species (A. heteroclite, H. stagnalis, and T. tessulatum), two species of piscicolids (Piscicola geometra and Piscicola sp.), and three species of predatory leeches (E. octoculata, E. vilnensis, and Erpobdella sp.). Possible effects of hydrochemical parameters of the aquatic environment on the species diversity have been analyzed. Correlation has been revealed between the abundance of species and the physical and chemical characteristics of the environment.

Coevolution in a predator-prey system: An ecogenetic model

In most natural populations, intraspecies competition for natural resources is supplemented by a predator impact. The mode and intensity of the interaction between a prey and its predator may affect the course of competitive or sympatric speciation among the prey and processes of coevolution or cospeciation. Mathematical methods allow the development of models precisely describing all sides of intra- and interspecies interactions. In this paper, we use mathematical modeling to investigate the effect of the intensity of interspecies interactions on competitive or sympatric speciation inside a prey population. The intensity of the interaction is the average number of prey which predators eat pera unit of time: the higher the average number of prey eaten by predators, the greater the intensity of the interaction. In mathematical models, the intensity of such interaction is determined by many parameters. Changes in these parameters will affect the intensity of the interaction. It was found that a sufficiently high intensity of interaction slows competitive speciation among the prey. By altering their adaptive traits, the preys in this case seek to avoid the impact of predators. Another important result was that speciation of predators follows prey speciation when the probability of mutational changes in the adaptive traits of predators exceeds that in the prey.