Original methods of spectral-statistical approach have been elaborated for recognizing a new type of latent periodicity in DNA, called latent profile periodicity (or latent profility). Search of the latent profility allows revealing different levels of information encoding in the genes, and in local DNA regions included.

Application of multilocus sequence typing for investigation of Legionella pneumophyla strains isolated in Russia allowed us to obtain data for molecular-ecological analysis of the situation. Strains from subterranean waters demonstrated similar allelic profiles in different distant regions of country. The mutation process had similar direction in conditions of cooling towers and water stagnations in autonomous water supply system. Recombinations predominated during clonal complexes forming. On the bases of comparision of allelic profiles with EWGLI data base epidemiological appreciation of investigated strains was given.

On a set of real protein sequences, comparison of several protein phylogeny reconstruction methods has been performed. The programs of PHYLIP package and programs FastME, PhyML and TreeTop have been tested. In contrast to several studies that used simulated sequences, our results demonstrate superiority of distance methods over the maximum likelihood method.

A web-available computer system for analyzing the molecular evolution modes of genes and proteins was developed (SAMEM: http://pixie.bionet.nsc.ru/samem/). SAMEM computations are based on the ratio of radical to conservative amino acid replacements, on the rate of amino acid changes in the course of protein evolution, and on the statistical relations between evolutionary change of all known amino acid properties and user defined phenotypical features of organisms.

During last decade traditional morphological paradigm of evolutionary biology has been challenged. Despite on technological advancements the current evolutionary paradigm still lacking organism shape changing theory. The links between evolution, ontogeny, systematics and phylogentics are prima facie obvious, but similarly greatly underestimated currently, though the field of the "Evo-devo" is continuously growing. As a synthesis (or more exactly, re-synthesis) of still in considerable degree developed independently major biological fields, i.e. ontogeny, evolution and ta­xonomy, new conception of ontogenetic systematics is therefore suggested and illustrated by the examples from the nudibranch molluscs.

14 chloroplast microsatellite markers were used for analysis of diversity and phylogenetic rela­tionships of chloroplast genomes of 71 accessions of six D-genome Aegilops species. The highest intraspecies variation was observed for Ae. tauschii. The highes haplotype diversity among polyploid species was revealed for Ae. ventricosa (DN). All haplotypes of Ae. ventricosa were remarkably dif­fer from haplotypes of Ae. tauschii. All accessions of Ae. cylindrica analyzed had closely related haplotypes similar with haplotypes of Ae. tauschii.

Five RAPD primers out of 20 and 6 SSR primers out of 13 were selected to discriminate 33 accessions of parsley (Petroselinum crispum [Mill] Nym. ex A.W. Hill). In the total, 51 RAPD and 66 ISSR bands were generated with these primers. The UPGMA dendrogram based on the Jaccard's coefficients was constructed. The two clusters of leaf and root plant forms were the most distant at similarity 0,292 from each other. Consequently, root form-specific markers were observed. Not all flat leaf and curly-leaf forms have been clearly separated, but some of curly-leaf accessions formed their own sub-cluster.

Bioinformatics analyses and site-directed mutagenesis enabled us to identify determinants of catalysis by CYP74 family enzymes in I-helix central domain and ERR-triad. Substitutions K302S and T366Y in tomato allene oxide synthase LeAOS3 led to hydroperoxide lyase activity appearance. Mutant forms F284I, F287V, G288I, N285A and N285T of alfalfa hydroperoxide lyase MtHPL, unlike wild-type enzyme produced predominantly 02-aldoacid, synthesized С13- and СИ-frag- ments. The data obtained confirm the evolutionary origin of CYP74 family diversity from a common ancestor with hydroperoxide lyase activity.

The nucleotide sequences of cytochromoxidase COI gene from 76 specimens of blue butter­flies of subgenus Polyommatus (s. str.) were determined. These speciments belong to 36 taxa with species and subspecies status. Phylogenetic reconstruction by neigbour joining method reveals among all the diversity of taxa studied only 12 monophyletic clades corresponding to species-level taxa: P. icarus, P. ciloicus, P. icadius, P. amorata, P. eros, P. forsteri, P. celina, P. venus, P. ariana, P. sto- liczkanus, P. erigone, P. amor.

The sequence analysis of b/c intron of nadl mitochondrial gene in 13 Fagopyrum species was carried out and demonstrated ability of this intron to use in phylogenetic studies. The length of the mitochondrial nadl b/c intron varied from 1217 bp in F. tataricum, F. cymosum, F. giganteum to 1239 bp in F. capillatum. Species- and accession- specific SNPs and indels were detected. For obtained molecular phylogeny of Fagopyrum species a good agreement with the recognized taxo- nomic divisions within the genus was observed. NJ and MP trees showed a clear clustering into two major genetic groups: cymosum and urophyllum. The urophyllum group was characterized by the presence of several synapomorphic characters including 11 bp insert flanked by directrepeats.

Systematics of oligochaete worms during all 20th century caused discussions of experts. With development of computing and implementation of molecular methods, there was an opportunity to built phylogenetically justified system. Nevertheless eliminating of some paraphyletic lineages has not caused unanimous approval of the broad audience of biologists (taxonomists, ecologists, etc.). Molecular systematics has helped to clear up position of many disputable species and genera, simultaneously having raised the doubts in classification of high rank taxa seemed to be logical and firm until recently.

Phylogenetic relationships of two Mesozoa group were inferred on the base of analysis of nearly complete combined nucleotide sequences of 18 and 28S rRNA genes. Two Mesozoa groups, Ortonectida and Dicyemida, comprise in phylogenetic trees well statistically supported clade. In phylogenetic trees inferred, Mesozoa put into alliance Spiralia within Lophotrochozoa group exhibiting a tendency to unite with one of Annelida group.

The article concerned to phylogenic relationships among Niviventer species inhabited Indo­china. 15 separated species-level clades were revealed in the genus. The data obtained performed us to argue new conception on intrageneric structure and established new, more complex taxo- nomical structure of the genus. Four to five additional division may well been established in genus along with one (andersoni division) currently accepted: niviventer, fulvescens, brahma, culturatus and may be langbianis. These divisions combine together 13 from 15 currently genetically characterized Niviventer species, the other not least than 2 Sundaic and Malayan species hardly if any can be faultlessly attributed to any of these taxa. Additional investigations based on more complex data have to be performed to make clear their position in the genus.

The geographic variability of Harmonia axyridis was studied by three morphological features. The authors started a study of cytochrome c oxydase subunit I (COI) polymorphism too. The authors' results revealed two geographically separated zones inside Russian part of the spe­cies range. Interpopulational differences detected by complex of polymorphic features are minimal inside both zones. At the same time, the differences between populations of Western and Eastern zones satisfy to subspecies level. A zone of clinal variability of morphological traits is located in Transbaikalia, obviously, it is originated by secondary contact of "Western" and "Eastern" groups of populations separated during last glaciation and then joined again.

Phylogenetic relationships of Baikalian endemic Chironomid Paratanytarsus baicalensis (Tshern.) and other representaives of tribe Tanytarsini have been studied using 117 partial sequences of mito­chondrial gene COI belonging to 33 species of Paratanytarsus и Micropsectra. It was shown that the Baikalian species is closely related to two European species P. austriacus, P. hyperboreus and itself it splits into two genetically distinctive clades.

Two species investigated (Stratiomys singularior and Oxycera pardalina) belong to the family Stratiomyidae. Their larvae inhabit contrasting thermal (semi)aquatic environments. The goal was to compare the hsp70 genes clusters cloned from the genomes of these species. It has been demonst­rated that in S. singularior five hsp70 copies form a highly polymorphic gene cluster which occupies ~ 29 kb. In O. pardalina we have shown the presence of four hsp70 copies and hsp68 gene in the common cluster, and two hsp70 pseudogenes. The distance between tandem orientated O. pardalina hsp70 genes is more than 9 kb. We suggest that conservative hsp70 genes may be used with some limitations to assess time of divergence of distantly related species.

Overview of own and literary molecular phylogenetic studies on intraspecies variability in wi­dely distributed Asian fishes, amphibians, birds and mammals is presented. In many cases the populations from South-Eastern parts of the species ranges demonstrate distinct sets of haplotypes and increased variability. This means such populations might have experienced isolation in refugia, and East Asia might have served as a hotspot in the speciation process for many Asian animals.

A new SCAR- and ISSR-gene marker systems, were created for genetic analysis of populations of kamchatka mykiss Parasalmo (O.) mykiss and other salmonides. Both systems has demonstrated a high level of variability between newborn populations of mykiss, but can used for analysis in other salmonides with complex structure of populations.

BLAST Search of the markers used for Kuril Island Dolly Varden population structure studies revealed homologies of these markers either with structural genes or at least with expressed sequ­ences from dbEST resources of GeneBank. Such nature of markers allows to suppose the adaptive character of their evolution.

The computer approach is developed to reveal the significant oligonucleotide motives in regulatory regions of eukaryotic genes. The regulatory signals, specific for promoter regions of miRNA genes, which are expressed in different tissues of mammalians, are obtained and classified.

Molecular and morphometric data were used to study relationships among tall and dwarf forms of apple-trees growing in the territory of Buryatia. Phylogenetic analysis based on six polymorphic loci has shown that dwarf apple-trees are descended from tall forms of Malus baccata. Statistical approach based on morphological data has suggested that two forms of the studied apple-trees belong to the same species of Siberian apple. Taking into account obtained results a dwarf form of apple-trees is considered as the ecological form of M. baccata and it is probably initial stage of the parapatric speciation.

The spatial genetic structure of the metapopulation of Melittis sarmatica Klok. on the territory of Volkovysk Elevation (Grodno region of Belarus) was investigated. The RAPD method used for genetic analysis of similarity of populations within the metapopulation revealed exchange of genetic information between matapopulation components. The most stable links, main and problem elements in its structure and some genetically separate groups were revealed. There was a negative linear dependence of the degree of genetic similarity of populations from the distance between them.

To estimate the haplotype diversity of red deer (Cervus elaphus L.) from Balkan Peninsula, а fragment of cytochrome b (427 bp) was analyzed. In the investigated red deer from Bulgaria (16 individuals) 6 haplotypes were revealed. In the comparative analyses were included 32 sequences (15 from GenBank and 17 our samples from different locations of Cervus elaphus area). As outgroup we used a sequence C. e. xanthopygus. Four Bulgarian red deer haplotypes were closely related to other European haplotypes, when two other haplotypes formed a separate branch, encompassing also two samples from Sardinia and Tunisia. Thereby, our results indicated an existence in Bulgaria at least two different genetic lines of red deer.

Comparative sequence analysis of the ITS1-2 region of the rDNA of D. antarctica indicate that genetically distinct plants of the species migrated to Antarctica during the post-glacial period. Application of RAPD-markers revealed the difference in the levels of polymorphism between populations of D. antarctica from different latitudes as well as the limited gene flow between them.

We report a conserved motif upstream genes proA and proB widely represented among y-pro- teobacteria, particularly in the genera Pseudomonas, Marinobacter and Shewanella. The conserved protein-DNA binding sites are 8 bp-long. Some genes have a duplet of sites for cooperative factor binding. The phylogenetic profiles of binding sites and all protein factors were compared. We iden­tify a tetR family protein, an ortholog of the NP_249058 protein from P. aeruginosa PAO1, as a transcription factor. Our algorithm was applied to construct the tree of species with predicted regulation of the pro genes. The phylogeny of pro genes, transcription factors phylogeny and their binding sites phylogeny were mapped onto the tree of species with our algorithm. The obtained scenario displays important HGT and the related events.

191 plant homologues of human protein kinases phosphorylating microtubular proteins and regulating cell cycle have been identified. Similarity of plant protein kinases was analysed by neighbor joining clustering.

Phylogeny of the DroSophila viriliS species group is studied on the base of five nuclear and mi- tochondrial genes: Adh, NonA, Fu, RaSl и 16S-12S rRNA. Mathematical simulation to estimate uneven accumulation of replacements in lineages of closely related species using arbitrary number of sequences was suggested. It accounts for multiple, parallel and reverse mutations. Periods of evolution with irregular rates in the viriliS species group were reconstructed. Phylogeny tree for the group given on the base of neutral variability was constructed.

Influenza virus is one of human pathogens, responsible for several pandemics with high death rate. For statistical analysis of coding regions of genes from extensive sample of Influenza A viruses two programs were written. While inner viral proteins appeared to be evolutionary stable, surface antigens and non structural protein NS1 are highly variable. Using written programs to predict evolutionary variable regions inside M1 protein sequence it was shown that N-domain is the most conservative one while M- and C-domains are more variable. In addition, C-domain was shown to be the most unfolded one according to DISOPRED algorithm prediction and, thus, possesses the most structural plasticity.

An analysis of the complete sequence of D. littoralis mitochondrial genome (mt-genome) is presented. The basic characters of the mt-genome, such as size, nucleotide composition, genes order, as well as a degree of purifying selection pressure on different parts of the mt-genome are reported. The features of protein-coding genes and tRNA genes are discussed. The structure of mtDNA control region and intergenic spacers in the virilis group are presented. The fragments of mitochondrial genes atp6 and cox3 were found in the nuclear genome of D. virilis. The evolution history of mitochondrial and nuclear genes data indicates that mitochondrial gene transfer to the nucleus is a recent event and connected to the activity of retrotransposons.