[Exon and Intron Variability in Salmonidae Growth Hormone Genes].

Gene duplication is one of the main mechanisms of formation of new genetic material in evolution. The occurrence of a gene duplication is believed to relax selection pressure on one of the copies. Consequently, this gene accumulates mutations at a higher rate, and over time it acquires a new function. As a result of several rounds of polyploidization, many genes in salmon are duplicated, including the growth hormone gene. The analysis of nucleotide diversity in the paralogous genes of growth hormone, gh1 and gh2, demonstrated that the level of variability in their introns was higher than in the exons. In addition, the variability of each exon weakly correlated with its length, and seems to be determined by the functional significance of the protein region encoded. The level of variability in the exons of the gh2 gene was higher than that in the gh1 one, which was probably due to the current process of gene subfunctionalization.

[Divergence of paralogous growth-hormone-encoding genes and their promoters in Salmonidae].

In many fish species, including salmonids, the growth-hormone is encoded by two duplicated paralogous genes, gh1 and gh2. Both genes were already in place at the time of divergence of species in this group. A comparison of the entire sequence of these genes of salmonids has shown that their conserved regions are associated with exons, while their most variable regions correspond to introns. Introns C and D include putative regulatory elements (sites Pit-1, CRE, and ERE), that are also conserved. In chars, the degree of polymorphism of gh2 gene is 2-3 times as large as that in gh1 gene. However, a comparison across all Salmonidae species would not extent this observation to other species. In both these chars' genes, the promoters are conserved mainly because they correspond to putative regulatory sequences (TATA box, binding sites for the pituitary transcription factor Pit-1 (F1-F4), CRE, GRE and RAR/RXR elements). The promoter of gh2 gene has a greater degree of polymorphism compared with gh1 gene promoter in all investigated species of salmonids. The observed differences in the rates of accumulation of changes in growth hormone encoding paralogs could be explained by differences in the intensity of selection.

[Fish growth hormone genes: Divergence of coding sequences in salmonid fishes].

Comparison of coding nucleotide sequences of the paralogous GH1 and GH2 genes, as well as of the growth hormone amino acid sequences, in the species of closely related salmonid genera Salvelinus, Oncorhynchus, and Salmo was performed. It was demonstrated that, in different groups of salmonids, the amino acid substitution rates were considerably different. In some cases, an obvious discrepancy between the divergence of growth hormone genes and phylogenetic schemes based on other methods and approaches was revealed. These findings suggest that the reason may be multidirectional selection at duplicated genes at different stages of evolution.

Specific features of root aerenchyma formation in Sium latifolium L. (Apiaceae).

Types of aerenchyma formation in adventive roots of wild plant S. latifolium L. are described for the first time. Specific cell divisions and patterns of cell growth in the inner and outer root cortex at the initial stages of aerenchyma formation are highlighted in detail. Destructive processes in cells occurred under aerenchyma formation are considered in the view of known stages of programmed cell death in plants.

[Fish growth-hormone genes: functionality evidence of paralogous genes in Levanidov's charr].

In the genome of most vertebrates growth-hormone gene is presented in a single copy, while in salmonids after one of the duplication events many genes were multiplied, including growth hormone gene. In salmonids, the growth-hormone gene exists as two independently inherited functional paralogues, gh1 and gh2. In this study, we performed a comparative analysis of gh1 and gh2 growth-hormone genes and their adjacent sequences in Levanidov's charr Salvelinus levanidovi to determine their functionality and define the potential differences. We found that both genes have the same gene structure and are composed of six exons (I-VI) and five introns (A, B, C, D, E). However, the respective gene sequences differ in length. A comparison of exons showed that the size of each exon is identical in both paralogues. The overall length of genes differs due to the varying lengths of introns. Coding sequence of both genes contains an open reading frame for 210 amino acids. We identified regulatory elements in the promoter region of both genes: TATA box, A/T-rich regions that contain binding sites for pituitary-specific transcriptional activator Pit-1, and regions responsible for interaction with other transcriptional activators and initiators, in particular hormone receptors. The obtained data indicate that both genes are functional.

[Analysis of mtDNA and Nuclear Markers Points to Homoploid Hybrid Origin of the New Species of Far Eastern Redfins of the Genus Tribolodon (Pisces, Cyprinidae)].

The nucleotide sequences of two mitochondrial genes (cytochrome c oxidase subunit I, COI, and cytochrome b, cyt b) and four nuclear genes (growth hormone gene GH1, ribosomal protein S7 gene RP1, recombination activating gene RAG1, and rhodopsin gene RH) from the Far Eastern redfins of the genus Tribolodon were examined to clarify the status of the southern form of T. hakonensis. Nucleotide sequence analysis of the mitochondrial genes showed differences of 2.6% between individuals of T. hakonensis inhabiting the north and south of the range. Analysis of the nuclear genes showed that Tribolodon sp. (southern form of T. hakonensis) has a mosaic of nuclear genes received from the Pacific redfin T. brandtii and big-scaled redfin T. hakonensis. It is suggested that the new species could have formed as a result of homoploid hybridization between the true T. hakonensis (by original description) and T. brandtii, which probably made it possible for this species to occupy a new ecological niche.

[Comparative analysis of mitochondrial DNA variation in four species of far eastern redfins of the genus Tribolodon (Pisces, Cyprinidae)].

MtDNA variations were examined in four endemic species of the Far Eastern redfins of the genus Tribolodon across considerable parts of their ranges. No close correlation was revealed between the lifespan of the species and the level of mtDNA variations. An association was revealed between the degree of manifestation of the genetic structure population and the degree ofamphidromy in the species. The presence of differing mtDNA phylogroups in three out of four species indicates that the history of these species included long period of independent intraspecific divergent evolution. This period occurred at approximately the same historical time and was probably caused by the same factors. The period appeared to be not long enough and ended with the association of genetically independent units into single species.

[Ultrastructure and metabolic activity of pea mitochondria under clinorotation].

Experimental data on the mitochondrial ultrastructure and tissue respiration in root apex as well as metabolic activity of the organelles isolated from pea seedling roots after 5-day of clinorotation are presented. It was shown that mitochondrial condensation in the distal elongation zone correlated with an increased rate of oxygen uptake on 7%. We also observed increase in rate of malate oxidation and respiratory control ratio increased simultaneously with a decreased in efficiency of oxidative phosphorylation. Such character of mitochondrial rearrangements in simulated microgravity is assumed to be a consequence of adaptation to these conditions.

[Phylogenetic relationships of silver crucian carp in Carassius auratus complex based on mtDNA analysis].

The phylogenetic relationships of Carassius genus subspecies were investigated based on the data of the variability of nucleotide sequences of the mtDNA cytochrome b (cyt b) and control region (CR). Dendrograms constructed based on the BA, ML, NJ, and MP methods revealed five clusters of the congruent topologies that substantially corresponded to geographical localities and taxonomic conception of the C. auratus complex. An analysis of two mtDNA fragment topologies demonstrated that the island forms of Japanese crucian carps C. cuvieri and C. auratus langsdorfii diverged later compared to the divergence of continental C. auratus forms (4.0-4.5 mln years ago, by molecular calibration). Among the continental silver crucian carps, C. a. gibelio forms two clusters corresponding to two phylogroups with a mean uncorrected genetic distance p = 0.044. The genealogical combination of haplotypes with the first C. a. gibelio phylogroup was observed in C. auratus clade. According to the data of mtDNA analysis, these subspecies represent sister lineages with a level of intergroup divergence of p = 0.022-0.036. No genetic differences were observed between diploid (except for the two C. a. gibelio phylogroups) and polyploid C a. auratus, as well as monophyly in polyploid forms. New approaches based on a comparative study of the nuclear markers might help to unravel the origin of gynogenetic forms and phylogenetic relationships within the C. auratus complex.

[Phylogenetic relationships of silver crucian carp Carassius auratus gibelio, C. auratus cuvieri, crucian carp C. carassius, and common carp Cyprinus carpio as inferred from mitochondrial DNA variation].

PCR-RFLP analysis of the ND3/ND4L/ND4 and 12S/16S rRNA regions and nucleotide sequence variation of the cytochrome b gene were used to study the mtDNA divergence in species of the family Cyprinidae, to examine the phylogenetic relationships of the species, and to identify their taxonomic status. The results indicated that an ancestral form diverged into silver crucian carp and crucian carp after its separation from the common carp lineage. The divergence of continental Carassius auratus gibelio and Japanese C. auratus cuvieri occurred more recently. Two well distinguishable mtDNA phylogroups, suggesting divergent evolution, were observed in continental C. auratus gibelio populations. The divergence was possibly related to the formation of two silver crucian carp groups with different types of reproduction, triploid gynogenetic and diploid gonochoric. At the same time, the results supported the high probability of current genetic exchange between the forms. In view of these findings and high morphological similarity of the two forms, they were not considered to be separate species.

[Phylogeographic analysis reveals two periods of divergence in large-scaled redfin Tribolodon hakonensis (Pisces, Cyprinidae)].

Analysis of mtDNA variation in one of the amphidromic Far Eastern redfins, Tribolodon hakonensis, revealed the presence of three considerably genetically different mtDNA phylogroups in the individuals from the Russian part of the range. These data suggest the presence of the two periods of divergent evolution in the history of the species examined. Comparison of the haplotype distributions from different phylogroups over the species range revealed geographic localization of only one phylogroup in the population samples from southern continental coastal regions of the Sea of Japan. At the same time, two other phylogroups were found in almost equal ratios in northern continental samples and near the Sakhalin Island. These results suggest that the first stage of the divergent evolution, which occured between Pliocene and Pleistocene, resulted in the formation of genetically isolated form (probably, a species) in the region of the Sea of Japan. The second, later period of divergence, probably associated with the separation of the Sea of Okhotsk from the Pacific Ocean then ended with the integration of earlier genetically separated forms into one species with the common gene pool.

Single nucleotide polymorphisms in chum salmon (Oncorhynchus keta) mitochondrial DNA derived from restriction site haplotype information.

Single nucleotide polymorphisms (SNPs) are useful genetic markers for the management and conservation of commercially important species such as salmon. Informative markers can be derived from data obtained for other purposes. We used restriction endonuclease data from earlier work to identify potentially useful restriction sites in chum salmon (Oncorhynchus keta). With the aid of a newly generated complete mitochondrial DNA sequence (accession number AP010773), we identified the SNP responsible for each restriction site variant, designed rapid genotyping assays, and surveyed the SNPs in more than 400 individuals. The restriction site analysis and the SNP genotyping assays were almost perfectly concordant. Some reasons for the non-concordance were identified and discussed.

[Incomplete congruence between morphobiological characters and sex-specific molecular markers in Pacific salmons: II. Population and temporal variability of the phenomenon].

The congruence between secondary sexual characters and molecular markers, linked to the Y chromosome was examined in Asian populations of five Pacific salmon species of the genus Oncorhynchus. Our results support the existence of discrepancy between secondary sexual characters and sex-linked molecular markers in all species examined, which suggests the existence of similar or identical mechanism responsible for this phenomenon in Pacific salmons. Clinal latitudinal directional variation of the character confirmed the possibility that this phenomenon could be adaptively important, including its importance for regulation of the population number. In addition to natural factors affecting the degree of discrepancy between morphobiological characters and molecular markers in the Pacific salmon populations, anthropogenic factors, in particular intense fishery of certain population or population group, is also important.

[Sex ratio control in pink salmon (Oncorhynchus gorbuscha) and chum salmon (O. keta) populations: the possible causes and mechanisms of changes in the sex ratio].

Long-term changes in the sex ratio have been studied in pink salmon (Oncorhynchus gorbuscha) and chum salmon (O. keta) populations of Kamchatka and Sakhalin. It has been demonstrated that these changes are an adaptation to population dynamics: an increase in the population size is accompanied by a shift towards a higher proportion of males; a decrease in population size, by a shift towards a higher proportion of females. The correspondence between morphological and molecular characters in populations of the two species has been analyzed in order to determine the mechanism of sex ratio control. In some pink salmon and chum salmon populations, there is a discrepancy between sex identifications based on morphological characters and molecular markers. This discrepancy is assumed to be accounted for by sex inversion mechanisms, which may be population- or region-specific. In two cases, it has been found that the sex ratio discrepancy in populations is related to the numbers of fish in subsequent generations. These findings suggest that sex inversion may be related to population size control.

[Variation of mitochondrial DNA in Chinook salmon Oncorhynchus tschawytscha Walbaum populations from Kamchatka].

The variation in mitochondrial DNA (mtDNA) structure among Chinook Salmon Oncorhynchus tschawytscha Walbaum populations from Kamchatka was inferred from restriction length polymorphism analysis using eight restriction endonucleases. The nucleotide sequence variation in three amplified mtDNA regions was examined at seven polymorphic restriction sites in 579 fish from 13 localities. Based on the frequencies of 11 combined haplotypes and the number of nucleotide substitutions, the among- and within-population variation was estimated. The heterogeneity test showed highly significant differences among all the populations. The estimated maximum time of independent divergence of the Asian Chinook salmon populations, whose differences was about 0.02% nucleotide substitutions, did not exceed 10000-20000 years. Apparently, the retreat of the late Pleistocene glacier triggered spreading, recolonization, and formation of the present-day pattern of the species subdivision into structural components.

[Collation of data on the ploidy levels and mitochondrial DNA phylogenetic lineages in the silver crucian carp Carassius auratus gibelio from Far Eastern and Central Asian populations].

The distribution of the diploid and triploid forms and the correspondence between ploidy and mitochondrial DNA (mtDNA) phylogenetic lineages of the silver crucian carp have been studied in Far Eastern water bodies and the Syr Darya River. Both diploid and triploid forms have been found in large river systems (the Amur, Suifun, Tumangan, and Syr Darya river basins). Only the diploid form has been detected in lakes of Bol'shoi Pelis Island (Peter the Great Bay of the Sea of Japan), Sakhalin Island, and the Kamchatka River basin (the Kamchatka Peninsula). It has been confirmed that there are two mtDNA phylogroups in the silver crucian carp in the area studied. Both mtDNA phylogenetic lineages are present in the Suifun and Tumangan river basins. Only one mtDNA phylogroup (characteristic of the gynogenetic form) has been detected in two samples from the Amur River and in the Syr Darya population. The other mtDNA phylogroup is predominant in insular populations and in Kamchatka. The gynogenetic form carries only mtDNA phylogroup I, whereas both phylogroups have been found in diploid bisexual fish. The existence of only two mtDNA phylogroups substantially differing from each other indicates that the gynogenetic form has emerged from the diploid form only once and evolved independently for a long time after that. The absence of haplotypes transitional between the two mtDNA phylogroups suggests that the secondary contact between the gynogenetic and bisexual forms in continental populations occurred within recent historical time. The obtained data confirm that genetic (though asymmetric) exchange between the two forms is possible, which explains the high morphological and, probably, genetic similarity between them.

[The variation in chum salmon Oncorhynchus keta (Walbaum) mitochondrial DNA and its connection with the paleogeographic events in the Northwest Pacific].

The results of examining mtDNA variation in populations of chum salmon Oncorhynchus keta from the rivers of the basins of the seas of Japan and Okhotsk and in the chum salmon seasonal races of the Amur River are presented. A significant level of polymorphism between the majority of the populations studied was detected. The groups of chum salmon from the Japan and Okhotsk Seas displayed the most pronounced differences. Analysis of genetic variation demonstrated that periodic paleontologic and climatic changes in the past of this region were the most probable factor that caused the divergence of these populations. The advances and retreats of glaciers and the accompanying regressions and transgressions of the ocean level caused isolation of chum salmon in the refugia belonging hypothetically to the paleo-Suifun and paleo-Amur regions. These population groups diverged presumably 350-450 thousand years ago. Differences between the seasonal races of the Amur chum salmon are insignificant, and their emergence dates back to the period of the last Wisconsin glaciation. Probably, the main isolation factor now is the genetically determined time of spawning.

[The effect of reproduction biotopes on the genetic differentiation of populations of sockeye salmon Oncorhynchus nerka].

Variation of mitochondrial DNA (mtDNA) was examined in nine populations from three lake-river systems of Chukotka and Kamchatka. Significant differences were found between most of the sockeye salmon samples studied. The genetic differences among populations were not high and often did not correlate with the geographical distances between them. The low population divergence is explained by a short time of existence of most of them, having been formed after the recession of the upper Pleistocene glacier. When the populations were grouped according to their spawning biotopes (river or lake), they in general appeared more genetically similar than upon their grouping by geographical location (the lake-river systems). The differences between the river and lake populations in the lake--river systems increased from north to south.

[Differentiation of Dolly Varden char Salvelinus malma from Asia and North America inferred from PCR-RFLP analysis of mitochondrial DNA].

Genetic differentiation of Dolly Varden char Salvelinus malma Walbaum from the Asian and North American Pacific coasts was studied. We examined restriction fragment length polymorphism of three mitochondrial DNA (mtDNA) fragments amplified in polymerase chain reaction, which encoded four NADH dehydrogenase subunits, the cytochrome b gene, and a D-loop segment. The mtDNA haplotypes were shown to form three phylogenetic groups, whose geographic distribution corresponded to three Dolly Varden subspecies: S. malma malma, S. malma krascheninnikovi, and S. malma lordi. The nucleotide sequence divergence between S. malma malma and S. malma krascheninnikovi was 3.8%; between S. malma malma and S. malma lordi, 3.1%; and between S. malma krascheninnikovi and S. malma lordi, 2.5%. The northern Dolly Varden S. malma malma from Asia was shown to be genetically identical to that from North America.

[Differentiation of Salvelinus malma charr and Taranetz Charr Salvelinus taranetzi from PCR-RFLP analysis of mitochondrial DNA]. / Differentsiatsiia mal'my Salvelinus malma i gol'tsa tarantsa Salvelinus taranetzi po dannym PCR-RFLP-analiza mitokhondrial'noi DNK.

Genetic differentiation of two sympatric charr species, the Dolly Varden charr (Salvelinus malma Walbaum) and the Taranetz charr (S. taranetzi Kaganovski), has been studied. Restriction fragment length polymorphism (RFLP) analysis has been used to compare three mitochondrial DNA (mtDNA) fragments (ND1/ND2, ND5/ND6, and Cytb/D-loop) amplified via polymerase chain reaction (PCR). The divergence between S. malma and S. taranetzi inferred from mtDNA nucleotide sequences is 2.8%; between S. leucomaenis and S. taranetzi, 7.1%; and between S. malma and S. leucomaenis, 7.5%. The absence of common haplotypes and the degree of divergence indicate that the Dolly Varden charr and the Taranetz charr are genetically isolated and confirm that S. taranetzi may be regarded as a separate species.