Analysis of microsatellite variation in the rainbow trout (Parasalmo (Oncorhynchus) mykiss) from Kamchatka

Genetic variation of Kamchatka rainbow trout Parasalmo (O.) mykiss was examined using 10 microsatellite DNA loci, and phylogeographic comparison with other representatives of the species across the distribution range was performed. It was demonstrated that Kamchatka populations differed from other geographic groups of rainbow trout in a number of microsatellite loci. These populations also displayed distinct clustering and were characterized by lower genetic diversity. Analysis of a set of 26 different microsatellite loci (personal and literature data) demonstrated that most of the populations within the Kamchatka region were separated from one another, characterized by marked geographic differentiation, and affiliation to certain river basins. In Kamchatka rainbow trout, with high degree of probability, three geographic clusters (northwestern, southwestern, and eastern) were identified. In general, analysis of microsatellite DNA supported the data on low genetic diversity of the Kamchatka group Parasalmo (O.) mykiss, based on the variation estimates for a number of genes of nuclear and mitochondrial DNA, and allozyme loci.     

Genetic divergence of mykizha (<Emphasis Type="Italic">Parasalmo</Emphasis> (<Emphasis Type="Italic">Oncorhynchus</Emphasis>) <Emphasis Type="Italic">mykiss</Emphasis>) from Kamchatka inferred from restriction analysis and sequencing of mtDNA cytochrome b gene

The populations of mykizha Parasalmo (O.) mykiss from western and eastern coasts of Kamchatka were studied by restriction analysis of a fragment of fish mitochondrial genome that included the control region and the region of the cytochrome b gene ( cytb). The restriction patterns obtained with five enzymes ( MspI; Tru1I; RsaI; BsuRI; DdeI) were identical in all studied individuals. Sequencing of the cytb gene showed high similarity between all samples (99.6–100%). In general, the geographical group of mykiss from Kamchatka is monophyletic with low genetic divergence at the population level. Shantarian mykiss originates most likely from that native to Kamchatka.Translated from Genetika, Vol. 40, No. 12, 2004, pp. 1695–1701.Original Russian Text Copyright © 2004 by Pavlov, Kolesnikov, Melnikova, Ushakova.     

Allozyme variability and genetic divergence of Pacific trout (species Parasalmo) from western Kamchatka

Genetic variation in several populations of Parasalmo (Onchorhyncus) mykiss from Kamchatka was examined on the basis of data obtained by the author and results from literature. Three (sSOD-1*, LDH-C*, and EST-1*) out of 44 protein-coding loci were highly polymorphic. Low-frequency alternative alleles occurred at sAAT-1,2*, LDH-A2*, EST-5*, IDDH-1,2*, and sMDH-1,2*. The results of the present work and comparison with evidence on North American species indicated that, in the Kamchatka part of the range, P. mykiss is represented by several populations carrying unique alleles and forming a genetically independent group. Gene exchange between North American and Western Kamchatka populations is mainly determined by straying in the feeding stock of the American coastal form entering the Sea of Okhotsk. The genetic divergence and mean heterozygosities in the Kamchatka populations were low (D magnitude of 0.0002-0.0275; HS magnitude of 0.011-0.0371). The difference between the Western Kamchatka populations from the North American coastal form was so small (D magnitude of 0.0109-0.0241) that these forms clustered together. Genetic divergence of the Kamchatka populations and the inland North American P. mykiss is an order of magnitude higher (D magnitude of 0.1973-0.2367).     

Parasites of underyearling kamchatka mykiss Parasalmo mykiss mykiss (Osteichithyes:Salmonidae) in the Utkholok River (North-Western Kamchatka)

Eight species of parasites, Apiosoma piscicolum piscicolum, Apatemon sp., Diplostomum sp., Bunoderidae gen. sp., Crepidostomum metoecus, Hysterothylacium gadi aduncum, Salvelinema salmonicola, and Cucullanus truttae had been found in underyearling Kamchatka mykiss (with fork length 28-41 mm) from the Utkholok River, North-Western Kamchatka. Infestation rate of the fishes with each parasite species was rather low. Presence of C. truttae in underyearling Kamchatka mykiss could not be explained by the conceptual model of its life cycle proposed by Moravec (1979). Spatial and temporal isolation of underyearling Kamchatka mykiss and ammocoetes, as the elements of a local food web, suggest that the lamprey larvae do not participate in the transmission of C. truttae to underyearling Kamchatka mykiss.     

The Spring-Run Ecotype of the Steelhead Trout Parasalmo (Oncorhynchus) mykiss (Walbaum, 1792) (Salmonidae,Salmoniformes) in the Kamchatka Peninsula

Russian Journal of Marine Biology - A seasonal spring-run (vernal) ecotype of the Steelhead Trout Parasalmo (Oncorhynchus) mykiss (Walbaum, 1792) has been found in western Kamchatka for the first...     

Phylogenetic divergence in leatherside chub (Gila copei) inferred from mitochondrial cytochrome b sequences

We examined intra-specific phylogenetic relationships in leatherside chub, Gila copei. The complete mitochondrial (mt) cytochrome b gene (1140 bp) was sequenced for 30 individuals from 10 populations that span the geographical distribution of this species. Traditional phylogenetic analyses revealed two deeply divergent and evolutionarily distinct mtDNA clades that are geographically separated in northern and southern drainage basins. Interpopulation sequence variation between clades ranged from 7.7 to 8.1%. The northern clade was genetically more similar and phylogenetically more closely related to the selected out-group Lepidomeda m. mollispinus than to the southern clade, suggesting that the taxonomy of this species may require revision. Sequence variation among populations within clades ranged from 0 to 0.3% in the north and from 0 to 0.7% in the south. Statistical parsimony was used to construct phylogenetic networks of haplotypes within clades. Nested clade analysis revealed that geographical fragmentation has played an important role in genetic structuring within northern and southern clades.     

Variation of cytochrome b gene in sympatric chars from kronotsky lake (Kamchatka Peninsula)

In previously identified sympatric char forms (species) from Kronotsky Lake (Kamchatka Peninsula) and a number of other chars from the genus Salvelinus, nucleotide sequences of the mtDNA cytochrome b gene were determined and phylogenetic analysis of these chars was performed. The divergence estimate of the cytochrome b gene in the Kronotsky char group (0.48%) coincided with the interpopulation difference estimates in northern Dolly Varden, which indicates a relatively recent divergence of the chars from Kronotsky Lake. Haplotypes of each form of the Kronotsky Lake chars are divided into two groups, which belonged to two different phylogenetic mtDNA lineages of northern Dolly Varden from Chukotka and Kamchatka. The formation of the Kronotsky char forms proved to be unrelated to the observed variability of the mtDNA cytochrome b gene.     

Variation of cytochrome b gene in sympatric chars from Kronotsky Lake (Kamchatka oblast)

In previously identified sympatric char forms (species) from Kronotsky Lake (Kamchatka Peninsula) and a number of other chars from the genus Salvelinus, nucleotide sequences of the mtDNA cytochrome b gene were determined and phylogenetic analysis of these forms was performed. The divergence of the cytochrome b gene in the Kronotsky char group (0.48%) coincided with the interpopulation difference estimates in northern Dolly Varden, which indicates a relatively recent divergence of the chars from Kronotsky Lake. Haplotypes of each form of the Kronotsky Lake chars are divided into two groups, which belonged to two different phylogenetic mtDNA lineages of northern Dolly Varden from Chukotka and Kamchatka. The formation of the Kronotsky char forms proved to be unrelated to the observed variability of the mtDNA cytochrome b gene.     

Phylogenetic analysis in chicken breeds inferred from complete cytochrome b gene information

Complete cytochrome b (cyt b) gene (1140 bp) nucleotide sequences were used to investigate characteristics of the genetic constitution of Chunky broiler chickens, and these were compared with the Hy-Line and WL-GM (Garber) line of White Leghorn, the GSP line of Fayoumi, the BM-C line of Black Minorca (egg-chickens), and an outgroup of wild-origin Japanese quail. A high genetic difference (five haplotypes) was observed at the cytochrome b region in the Chunky broiler in contrast to the high homologies observed among the other chicken breeds (egg-purpose). Chunky broilers can be distinguished from the other breeds (White Leghorn, Fayoumi, and Black Minorca) at positions 552 and 779. The molecular phylogenetic tree exhibited genetic differences within Chunky broilers, and between Chunky broilers and the other three chicken breeds. As a result, some chicken strains or breeds apparently different from the other egg-chickens may have contributed to the Chunky broiler formation. Artificial selection may be one of the biggest factors causing nucleotide diversity in the chicken breeds.     

Genetic evidence of extensive introgression of short-tailed ground squirrel genes in a hybridization zone of Spermophilus major and S. erythrogenys, inferred from sequencing of the mtDNA cytochrome b gene

We have completely sequenced the mtDNA cytochrome b gene of ground squirrels from the zone of overlapping ranges of Spermophilus major and S. erythrogenys in the Tobol-Ishim interfluve, which is a putative hybridization zone of these species. The results of the sequencing showed extensive introgression of mtDNA genes of the short-tailed ground squirrel S. e. brevicauda, whose haplotype had fully replaced the S. major haplotype. All of the ground squirrels from the Tobol-Ishim interfluve had a variant of the S. e. brevicauda mtDNA haplotype that was specific for this zone. On average, 119 substitutions (10.44%) were found between S. major from Ul'yanovsk oblast and S. e. brevicauda from the northern Kazakhstan, the mean genetic distance (D) between them being 0.115, which conforms to the corresponding parameters for the S. e. brevicauda-S. pygmaeus pair (122 substitutions, D = 0.118). Insignificant differences (seven substitutions, D = 0.043) were found between the S. major and S. pygmaeus haplotypes, which suggest that these species have similar mitochondrial haplotypes. Five to ten nucleotide substitutions (0.44–0.88%) were detected between the animals from the Tobol-Ishim interfluve and S. e. brevicauda. The mtDNA haplotype divergence D within the genus Spermophilus (ten species) for all codon positions ranged from 0.035 to 0.158. Phylogenetic reconstructions (MP, ML, and NJ trees) showed two well-differentiated clusters with high bootstrap support. However, there was different branching topology within the cluster and their species composition varied. The maximum likelihood tree, ML, differentiating the species into two subgenera, Citellus and Colobotis, most reliably reflected taxonomic relationships of the species from the genus Spermophilus, inferred from morphological and genetic biochemical data. The morphologically pure S. major (subgenus Colobotis) animals, used in the analysis, proved to carry the haplotype of another species, S. pygmaeus (subgenus Citellus). This poses a question on the existence of the specific haplotype of S. major, the reason of its replacement by haplotype of other species, and possible consequences of this phenomenon for survival of the species.     

Genetic evidence of extensive introgression of short-tailed ground squirrel genes in a hybridization zone of Spermophilus major and S. erythrogenys, inferred from sequencing of the mtDNA cytochrome b gene

We have completely sequenced the mtDNA cytochrome b gene of ground squirrels from the zone of overlapping ranges of Spermophilus major and S. erythrogenys in the Tobol-Ishim interfluve, which is a putative hybridization zone of these species. The results of the sequencing showed extensive introgression of mtDNA genes of the short-tailed ground squirrel S. e. brevicauda, whose haplotype had fully replaced the S. major haplotype. All of the ground squirrels from the Tobol-Ishim interfluve had a variant of the S. e. brevicauda mtDNA haplotype that was specific for this zone. On average, 119 substitutions (10.44%) were found between S. major from Ul'yanovsk oblast and S. e. brevicauda from the northern Kazakhstan, the mean genetic distance (D) between them being 0.115, which conforms to the corresponding parameters for the S. e. brevicauda-S. pygmaeus pair (122 substitutions, D = 118). Insignificant differences (seven substitutions, D = 0.043) were found between the S. major and S. pygmaeus haplotypes, which suggest that these species have similar mitochondrial haplotypes. Five to ten nucleotide substitutions (0.44--0.88%) were detected between the animals from the Tobol--Ishim interfluve and S. e. brevicauda. The mtDNA haplotype divergence D within the genus Spermophilus (ten species) for all codon positions ranged from 0.035 to 0.158. Phylogenetic reconstructions (MP, ML, and NJ trees) showed two well-differentiated clusters with high bootstrap support. However, there was different branching topology within the cluster and their species composition varied. The maximum likelihood tree, ML, differentiating the species into two subgenera, Citellus and Colobotis, most reliably reflected taxonomic relationships of the species from the genus Spermophilus, inferred from morphological and genetic biochemical data. The morphologically pure S. major (subgenus Colobotis) animals, used in the analysis, proved to carry the haplotype of another species, S. pygmaeus (subgenus Citellus). This poses a question on the existence of the specific haplotype of S. major, the reason of its replacement by haplotype of other species, and possible consequences of this phenomenon for survival of the species.     

Intraspecific genetic differentiation of the Siberian Rubythroat (Luscinia calliope): Data of sequencing the mtDNA cytochrome b gene

For the first time, genetic diversity and intraspecific structure of Luscinia calliope was studied according to the data of the mtDNA cytochrome b gene sequencing. The strong differentiation of haplotypes of the Siberian Rubythroat into western and eastern groups, which include subspecies according to their geographical attachment, was revealed. A high-haplotypic (Hd = 0.986) and nucleotide (π= 0.00875) variety was shown for the species as a whole. We revealed considerable genetic distances (D = 0.016) between the western and eastern haplotypes that were four times higher than the intraspecific distances in terms of cytochrome b for passerines (D = 0.004). For three birds from Transbaikal, significant genetic divergence was detected, which could indirectly indicate the existence of the hybrid zone of several subspecies in this part of the area.     

The genetic structure of chum salmon (Oncorhynchus keta Walbaum) populations inferred from the nucleotide variation of the mitochondrial DNA cytochrome b gene

The nucleotide sequences of a fragment of the mitochondrial DNA cytochrome b gene were determined in 12 chum salmon populations from the Russian Far East. The level of genetic diversity in the chum salmon populations from the Iturup Island, northern coast of the Sea of Okhotsk, and Anadyr' River was found to be higher than in the populations from Kamchatka and Sakhalin, which may be related to the history of their origin and dispersal. The proportions of intrapopulation genetic variability (F(ct)) and interpopulation genetic variability within the groups (F(sc)) account for 90.87 and 0.9%, respectively, and the intergroup component (F(st)) comprises 8.23%. The predominance of one haplotype, B1, which is common for all populations studied, and a low share of intergroup variability suggest the beginning of colonization by the species of the given region from a common source (group of founders) and a relatively recent time of divergence of the chum salmon populations from the region examined.     

Genetic population structure of Hemigrammocypris rasborella (Cyprinidae) inferred from mtDNA sequences

The genetic population structure of the small cyprinid Hemigrammocypris rasborella, distributed widely in lowlands of western Japan, was examined using partial sequence data of mitochondrial DNA (mtDNA). Molecular phylogenetic analysis revealed that the populations of the western Kyushu region were markedly differentiated from all eastern populations, such that the groups would be comparable to different species; their divergence was inferred to have occurred in the Late Miocene–Pliocene. Also, a largely divergent mtDNA group (with divergence in the early Pleistocene) was found in the Sanyo and northeastern Shikoku regions, forming a secondary contact zone in the western Kinki with the eastern mtDNA group. To date, these aspects of the population structure of H. rasborella appear to be unique among lowland fishes in western Japan. Deeper understanding of the formation processes of freshwater faunas in western Japan will require further comparisons of the phylogeographic patterns and ecological traits of constituent species.     

Acclimatization of salmon Oncorhynchus gorbuscha (Walbaum) in the European north: data from restriction analysis of mtDNA

Pink salmon spawners introduced into the White Sea basin (the Umba River) were compared to the spawners from the basin of the Sea of Okhotsk (the Ola River) using restriction analysis of two fragments of mitochondrial DNA (mtDNA). One of the fragments included genes ND5/ND6, the other, the cytochrome b gene and the control region. It was found that mtDNA variation and diversity at the earlier examined nuclear allozyme genes significantly decreased in the odd broodline of pink salmon 8 years after the introduction. The haplotype diversity in the even broodline was considerably lower than in the odd broodline exhibiting virtually no change two generations after the introduction. Based on the results obtained, a possible role of these changes in adaptation of White Sea pink salmon from the odd broodline to the new environment is discussed.     

从细胞色素b基因全序列探讨大额牛的分子系统发生

大额牛是一种半野生半家养的珍稀牛种, 有关其起源和系统地位一直存在争议。通过PCR扩增、测序等步骤共获得了11头大额牛细胞色素b(Cyt b)基因全序列(1 140 bp)。应用分析软件, 对大额牛11条Cyt b序列进行了分析, 并结合GenBank中牛属动物6个近缘种的同源序列, 以亚洲水牛(Bubalus bubalis)为外群, 分别采用邻接法(NJ)和最大简约法(MP)构建了牛属动物分子系统发育树。序列分析结果表明, 11条大额牛Cyt b序列1 140位点中, 共发现95个变异位点(占分析位点总数的8.33 %), 定义了6种单倍型, 表明大额牛群体的Cyt b基因遗传多态性比较丰富。构建的NJ和MP分子系统树均显示, 大额牛研究群体明显分为3支, 第1支与普通牛(Bos taurus)相聚, 第2支与瘤牛(Bos indicus)相聚, 第3支与印度野牛(Bos gaurus)相聚。系统发育分析表明, 大额牛很可能是印度野牛的家养型或驯化种, 我国大额牛群体可能曾受到其他牛种血缘的入侵。     

Genetic divergence of chars of the genus Salvelinus from Kronotsky Lake (Kamchatka Peninsula)

Chars from the genus Salvelinus, inhabiting lakes and lake-river systems, belong to morphologically and ecologically different forms whose taxonomic status is under dispute. In the present work, we have examined genetic variation and divergence in various chars from the Kronotsky lake basin: the lacustrine chars (white, nose, and long-head) and Dolly Varden char Salvelinus malma. The study was conducted using analysis of allozyme and microsatellite loci, myogens, RAPD, and restriction analysis of two mtDNA segments. The estimates of heterozygoisty at allozyme and microsatellite loci were similar to the corresponding parameters in populations of northern Dolly Varden and Arctic char. Heterozygote deficit was recorded in both samples of individual forms, and in the combined sample of all chars from Kronotsky Lake. For both markers, appreciable genetic differentiation among the samples of different char forms was found, which was comparable to that among the spatially isolated populations of northern Dolly Varden. This result indicates reproductive isolation among the char forms examined. However, this isolation is not complete, because no fixed differences between the forms by any of the genetic systems analyzed was found. The genetic differentiation among different forms of lacustrine chars, which corresponds to the interpopulation rather than interspecies level, is thought to be explained by their comparatively recent divergence.     

Phylogenetic relationships of Caucasian shrew Sorex satunini Ogn. (mammalia) in the superspecies Sorex araneus inferred from the data of karyological analysis and the mtDNA cyt b gene sequencing

Using the data of karyological analysis, the phylogenetic relationships of Caucasian shrew Sorex satunini and the cryptic species of superspecies Sorer araneus were examined. In the population of Sorex satunini from the plain of North Ciscaucasia two deeply radiated cytochrome b genes (A and B) were identified. Genetic distance between haplotype A and B groups constituted 0.0675 +/- 0.008, which is higher than any distance in superspecies S. araneus. Possible introgression of type B haplotypes from the populations of the evolutionary lineage S. subaraneus--S. araneus in Pleistocene and the time of the appearance of the chromosomal polymorphism of S. araneus is discussed. Our results show that the use of only one mitochondrial marker can lead to false conclusions on taxonomic diversity