The Divergence of the Dolly Varden Char Salvelinus malma in the Asian Northern Pacific Populations Inferred from the PCR–RFLP Analysis of Mitochondrial DNA

Genetic differentiation of the Dolly Varden char Salvelinus malmaWalbaum was studied in five populations from the western part of the Northern Pacific. Using restriction analysis (RFLP), we examined polymorphism of three mitochondrial DNA (mtDNA) fragments amplified in polymerase chain reaction (PCR). MtDNA haplotypes were shown to fall into two phylogenetic groups, which probably reflect the existence of two previously described subspecies of Asian Dolly Varden,S. malma malma and S. malma krascheninnikovi. The divergence of mtDNA nucleotide sequences in the Dolly Varden subspecies (about 4%) corresponds to the differences between the valid char species from the genus Salvelinus.     

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.     

Microsatellite genetic variation of Asian populations of Dolly Varden char

Genetic variation at eight microsatellite loci was examined in 21 populations of Dolly Varden charrs, Salvelinus malma, representing five geographical regions (Kamchatka Peninsula, Sea of Okhotsk coast, Sea of Japan coast, Sakhalin Island, and Kuril islands). Hierarchical analysis of molecular variance showed that 11% (58% in terms of R-statistics) of the variation was distributed among of northern subspecies of Dolly Varden, Salvelinus malma malma and southern Asian Dolly Varden, S. m. krascheninnikovi while similar values were attributed to the among-regional level within northern Dolly Varden 9% (7%) and southern Asian Dolly Varden 11% (14%). Permutation-based tests indicated a mutational component to genetic differentiation based on allelic size variance and suggested that divergence of the two subspecies had occurred at least 3,000 generations ago. On large spatial scales (within the Asian range of the species), populations clustered according to their geographical location. On smaller scales (within regions and subregions) correlation between genetic and geographic distances was not significant. Northern Dolly Varden has higher allelic diversity and more private alleles than southern subspecies, this probably indicating differences in demographic history.     

Allozyme Diversity and Genetic Divergence of the Dolly Varden Salvelinus malma Walbaum from the Kuril Islands

Genetic variation was studied in the southern subspecies of the Asian Dolly Varden Salvelinus malma krascheninnikovi from the Kuril Islands. Thirty-six genetic loci controlling 19 enzyme systems were analyzed in 13 Dolly Varden populations from the Shumshu, Paramushir, Onekotan, Rasshua, Simushir, Urup, Iturup, and Kunashir islands. In the studied populations, the proportion of polymorphic loci was 35 to 85% and the mean heterozygosity was 0.104 to 0.173; populations from the Kunashir Island were characterized by maximum heterozygosity. In the island populations examined, significant interpopulation heterogeneity of allele frequencies was found for all studied population pairs. For the all island populations, the interpopulation diversity (G _ST = 0.188) was comparable to this parameter for the populations from the Kunashir Island only (G _ST = 0.170). Genetic distances between populations did not correlate with the corresponding geographical distances, which indicates the lack of a pronounced gene exchange between the island populations. Cluster analysis and multidimensional scaling based on genetic distances did not reveal clear groups among the studied populations but indicated greater similarity within the Iturup–Simushir–Urup–Paramushir group and a greater genetic divergence of the Kunashir, Onekotan, Rasshua, and especially Shumshu populations. In the Shumshu population, allele frequencies indicate the admixture of genes of the northern Dolly Varden. The observed pattern of genetic differentiation was probably caused largely by genetic drift under the conditions of a limited gene flow because of homing (which is typical of the Dolly Varden) and the presence of isolated nonanadromous populations. The population–genetic analysis of the Dolly Varden from the Kuril Islands does not give grounds to distinguish any other isolated char species in this region than S. malma, which is represented by the southern form S. m. krascheninnikovi with an admixture of the northern form S. m. malma in the Shumshu Island.     

Differences Between two Subspecies of Dolly Varden, Salvelinus malma, Revealed by RFLP—PCR Analysis of Mitochondrial DNA

Genetic differences between two subspecies of Dolly Varden, northern Salvelinus malma malma and southern Salvelinus malma krascheninnikovi, from rivers of eastern Russia were studied. Mitochondrial DNA was analyzed by restriction fragment length polymorphisms (RFLP) performed on products amplified with polymerase chain reaction. Three adjacent segments (approximately 7670 bp), comprising 47% of the mitochondrial genome were used: two encoding the five complete NADH dehydrogenase subunits and the other the cytochrome b gene and the control region (D-loop). Total composite haplotypes 46 were found among 136 fishes using RFLP analysis with 14 restriction enzymes. The amount of nucleotide divergence between haplotypes of two subspecies of Dolly Varden was estimated to be approximately 4%. The differences in the level of nucleotide diversity, mismatch distribution between haplotypes, and population-genetic structure of two subspecies of Dolly Varden suggest that these two forms have existed separately for a long time.     

Phylogeography of southern Asian Dolly Varden char <Emphasis Type="Italic">Salvelinus malma krascheninnikovi</Emphasis>: Genealogical analysis of mitochondrial DNA

Phylogeography of southern Asian Dolly Varden char was studied using the data on mtDNA variation (regions ND1/ND2, ND5/ND6, and Cytb/D loop) obtained using PCR-RFLP analysis. Analysis of contemporary population genetic structure showed that Salvelinus malma krascheninnikovi throughout the whole species range was characterized by high population differentiation in combination with rather small differences between the populations from remote regions. The genealogy of mtDNA haplotypes was reconstructed and nested clade analysis of geographical distances was performed. Geographical distribution of mtDNA haplotypes of S. m. krascheninnikovi was explained by population genetic processes (restricted gene flow), as well as by historical demographic events (range expansion and fragmentation). It was demonstrated that the main demographic events were associated with cyclic processes of the geological formation of the Sea of Japan and adjacent territories. Furthermore, genealogical tree of S. m. krascheninnikovi contained the traces of secondary contact between isolated phylogeographical lineages.     

Population genetic structure of northern Dolly Varden char <Emphasis Type="Italic">Salvelinus malma malma</Emphasis> in Asia and North America

The level of genetic differentiation of northern Dolly Varden char Salvelinus malma malma from Asia and North America was evaluated using the data on mtDNA variation (regions ND1/ND2, ND5/ND6, and Cytb/D-loop) obtained by means of PCR-RFLP analysis. For S. m. malma, the mean values of haplo-type and nucleotide diversity were 0.5261 ± 0.00388 and 0.001558, respectively. The mean estimate of the population nucleotide divergence constituted 0.055%. It was demonstrated that S. m. malma on the most part of the species range examined (drainages of the Beaufort Sea, Chukotka Sea, Bering Sea, and the Sea of Okhotsk) was characterized by the population genetic structure with the low level of genetic differentiation and divergence. At the same time, populations from the Pacific Ocean Gulf of Alaska demonstrated marked genetic differentiation, supported by the high pairwise G4ST values (from 0.4198 to 0.5211) and nucleotide divergence estimates (mean divergence, 0.129%), from Asian and North American populations. Analysis of molecular variance (AMOVA) showed that most of the mtDNA variation in S. m. malma fell in the intrapopulation component (72.5%). At the same time, the differences between the populations (21.1%) and between the regions (6.4%) made lower contribution to the total variation.     

Genetic divergence of mitochondrial DNA in white char <Emphasis Type="Italic">Salvelinus albus</Emphasis> and northern Dolly Varden char <Emphasis Type="Italic">Salvelinus malma malma</Emphasis>

Comparative analysis of mitochondrial DNA variation was performed in white char Salvelinus albus Glubokovsky and in its putative ancestor species, northern Dolly Varden char Salvelinus malma malma Walbaum. Highly statistically significant differentiation of S. albus and S. m. malma in the areas of sympatric (Kamchatka River basin) and allopatric (Kronotskoe Lake and Kronotskaya River) residence was demonstrated. The mtDNA divergence between S. albus and S. m. malma did not exceed the range of intraspecific variation in the populations of northern Dolly Varden char. At the same time, clusterization pattern of the Salvelinus chars provides hypothesis on the common origin of two allopatric populations of white char. Genealogical analysis of haplotypes indicates that S. albus and S. m. malma currently demonstrate incomplete divergence of mitochondrial lineages. The low nucleotide divergence estimates between S. albus and S. m. malma reflect the short time period since the beginning of the divergence of ancestral lineages. These estimates are determined by ancestral polymorphism and haplotype exchange between the diverged phylogenetic groups as a result of introgressive hybridization.     

Phylogeography of northern Dolly Varden Salvelinus malma malma based on analysis of mitochondrial DNA

The northern Dolly Varden, Salvelinus malma malma, is a typical representative of arctic fauna distributed in northeastern Asia and northwestern North America. Because its spawning habitats were affected by Pleistocene glacial advances over most of its natural range, S. m. malma is among the most interesting objects of phylogeographic and microevolutionary studies. We reconstructed the genealogy of mtDNA haplotypes from 27 Alaskan and Asian populations to study the influence of glacial and geological vicariance events on the contemporary population genetic structure, phylogeographic subdivision and distribution of the northern Dolly Varden. Analysis of restriction site states in three PCR‐amplified mtDNA regions (ND1/ND2, ND5/ND6, Cytb/D‐loop; 47% of the mitochondrial genome) resolved 75 haplotypes in 436 fish. Similar patterns of subspecific variation apparent from hierarchical diversity and nested clade analyses of mtDNA haplotypes identify weak spatial differentiation and low levels of divergence. Our results suggest that (1) demographic history has been influenced by historical range expansions and recent isolation by distance, (2) present populations from Asia and North America were colonized from one main Beringian Refugium, and (3) that this taxon's ancestral population probably experienced a bottleneck in the Beringian Refugium during the late Pleistocene (Wisconsin) glacial period.     

Introgressive hybridization of chars of the genus <Emphasis Type="Italic">Salvelinus</Emphasis> as inferred from mitochondrial DNA variation

Nucleotide sequence analysis of the mitochondrial cytochrome b gene in the genus Salvelinus revealed hybrids with S. leucomaenis in S. malma malma populations of the Northern Okhotsk Sea basin. Hybrids of S. m. malma and S. m. krascheninnikovi were found in S. m. malma populations from the Northern Okhotsk Sea basin and Kamchatka. The findings testify to a secondary contact and mtDNA transfer between these species and forms. It was assumed that introgressive hybridization took place both long ago and relatively recently and occurred in one direction: from S. leucomaenis or S. m. krascheninnikovi to S. m. malma.Translated from Genetika, Vol. 40, No. 12, 2004, pp. 1678–1685.Original Russian Text Copyright © 2004 by Radchenko.     

On morphological diversity of southern Dolly Varden trout Salvelinus malma krascheninnikovi from water bodies of Sakhalin

Morphological and some biological specific features of nine samples of the southern form of Dolly Varden trout Salvelinus malma krascheninnikovi from water bodies of Sakhalin were studied. Comparative analysis was performed of our own estimates and estimates made by other authors of meristic characters of Sakhalin populations of Dolly Varden trout, as well as of samples from water bodies of the Kuril Islands and Western Kamchatka. Sakhalin populations of S. malma krascheninnikovi are characterized by a low level of morphological differentiation and the absence of geographic structure. No clinal latitudinal variation in sample averages was revealed in either of the nine studied meristic characters, including the number of vertebrae for populations of S. malma krascheninnikovi in the range from Bol’shoi Shantar Island to the south of Sakhalin. The cline in vertebral number from Kamchatka, along the Kuril Islands to Hokkaido, is most likely explained by specific features of distribution and introgressive hybridization at the secondary contact of populations of the northern and southern forms of Dolly Varden trout that originated from different glacial refugia and had a different vertebral number rather than by the temperature gradient.     

Differentiation of the Dolly Varden Char (Salvelinus malma) and the Taranetz Char (Salvelinus taranetzi) Inferred from the PCR–RFLP Analysis of Mitochondrial DNA

Genetic differentiation of two sympatric char species, the Dolly Varden char (Salvelinus malma Walbaum) and the Taranetz char (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 char and the Taranetz char are genetically isolated and confirm that S. taranetzimay be regarded as a separate species.     

Genetic divergence of sympatric charrs of the genus <Emphasis Type="Italic">Salvelinus</Emphasis> from Nachikinskoe Lake (Kamchatka)

We studied genetic differentiation of two charr species, Dolly Varden Salvelinus malma malma Walbaum and resident lacustrine charr Salvelinus sp., which sympatrically inhabit Nachikinskoe Lake (the Bol’shaya River basin) in southwestern Kamchatka Peninsula. Using restriction analysis (RFLP), three mitochondrial DNA fragments (ND1/ND2, ND5/ND6, and Cyt b/D-loop) amplified in polymerase chain reaction (PCR) were compared. The divergence of the mtDNA sequences between Salvelinus sp. and S. malma malma was 2.8%; Salvelinus sp. and S. taranetzi, 0.36%; Salvelinus sp. and S. krogiusae, 0.21%; Salvelinus sp. and S. alpinus, 3.0%. These results point to reproductive isolation of charrs in Nachikinskoe Lake and support the earlier suggestion on a close relationship between Salvelinus sp., S. taranetzi, and S. krogiusae.     

Phylogeography of northern Dolly Varden Salvelinus malma (Salmoniformes: Salmonidae) from Asia and North America: An analysis based on the mitochondrial DNA genealogy

Spawning in habitats affected by Pleistocene glacial advances over most of its natural range, northern Dolly Varden Salvelinus malma malma typifies Arctic fauna distributed in northeastern Asia and northwestern North America. We reconstructed a genealogy of mtDNA haplotypes from 27 Alaskan and Asian populations to study the influence of historical events on the phylogeography and contemporary population genetic structure. Analysis of molecular variance partitioned most of the mtDNA variability to the intrapopulation component (72.5%) with much reduced differences between populations (21.1%) and regions (6.4%). Similar patterns of variation apparent from hierarchical diversity and nested clade phylogeographical analysis (NCPA) of mtDNA haplotypes identify weak spatial differentiation and low levels of divergence. These findings suggest (1) that demographic history has been influenced by historical range expansions and recent isolation by distance, (2) that present populations from Asia and North America were colonized from one main Beringian Refugium, and (3) that this taxon’s ancestral population probably experienced a bottleneck in the Beringian Refugium during the late Pleistocene (Wisconsin) glacial period. The genealogical and NCPA analyses, and mismatch distribution of S. m. malma mtDNA haplotypes do not confirm the assumptions about presence of the two refugia on the territories of the Beringian Land, in which allopatric S. m. malma ancestral populations evolved, and independent origin of the Sea of Okhotsk populations.     

Differentiation of Salvelinus malma charr and Taranetz Charr Salvelinus taranetzi from PCR-RFLP analysis of mitochondrial DNA

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.     

Karyological Differentiation of Northern Dolly Varden and Sympatric Chars of the Genus <Emphasis Type="Italic">Salvelinus</Emphasis> in Northeastern Russia

In many cases the taxonomic status of sympatric chars (with exception of white-spotted char Salvelinus leucomaenis) is not clear and is actively debated. We karyotyped three pairs of sympatric chars inhabiting the Russian Far East-northern Dolly Varden, S. malma malma, and Lavanidov's char, S. levanidovi, from the Yama River (northern coast of the Sea of Okhotsk, Magadan Region), northern Dolly Varden and Taranetz's char, S. taranetzi, from Lake Achchen (east Chukotka), and northern Dolly Varden and white char, S. albus, from the Kamchatka River (Kamchatka Peninsula). Three of them had similar chromosome numbers. But all chars studied had an individual and discrete set of karyotypic characters, which enabled reliable identification each of them by chromosome number, chromosome arm number, and number and location of active nuclear organizer regions.     

Effect of isolation on the genetic characteristics of populations in charrs of the genus Salvelinus

To study the effect of isolation on the genetic variation of mDNA, Salvelinus malma krascheninnikovi and S. malma malma nonanadromous populations from different model ecosystems were examined by RFLI-PCR. The haplotype and nucleotide diversities of mtDNA were significantly decreased in three isolated populations as a result of random gene drift. The genealogy of mtDNA haplotypes was reconstructed. The formation of the modern structure of the isolated populations is discussed in terms of phylogeography.     

Genetic Differentiation of Three Sympatric Charr Species from the Genus SalvelinusInferred from PCR–RFLP Analysis of Mitochondrial DNA

We examined differentiation of three sympatric charr species Dolly Varden charr Salvelinus malmaWalbaum, white-spotted charrS.leucomaenisPallas, and Levanidov charrS. levanidovi Chereshnev, Scopetz, Gudkov. Using restriction fragment length polymorphism analysis (RFLP), three mitochondrial DNA fragments (ND1/ND2, ND5/ND6, and Cytb/D-loop) amplified in PCR were compared. The divergence of mtDNA nucleotide sequences betweenS. levanidovi and S. leucomaenis was about 9.7%, between S. levanidovi and S. malma, 8.7%, and between S. malma andS. laecomaenis, 7.5%. These results indicate genetic isolation of the species examined and support the earlier suggestion on closeness of Levanidov charr to the common ancestor of the genus Salvelinus.     

Genetic Divergence of Chars of the Genus <Emphasis Type="Italic">Salvelinus</Emphasis> from Kronotsky Lake (Kamchatka Peninsula)

Chars of the genus Salvelinus, inhabiting lakes and lake-river systems, comprise morphological and ecological 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 longhead) and riverine Dolly Varden 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 heterozygosity 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 separate forms, and in the total sample of all chars from Kronotsky Lake. For allozyme and microsatellite loci, 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 were found. The genetic differentiation among different forms of lacustrine chars, which corresponds to the interpopulation rather than interspecific level, is thought to be explained by their comparatively recent divergence.__________Translated from Genetika, Vol. 41, No. 8, 2005, pp. 1096–1107.Original Russian Text Copyright © 2005 by Salmenkova, Omel’chenko, Radchenko, Gordeeva, Rubtsova, Romanov.     

Evidence for historical introgression along a contact zone between two species of char (Pisces: Salmonidae) in northwestern North America

Phylogeographic analyses can yield valuable insights into the geographic and historical contexts of contact and hybridization between taxa. Two species of char (Salmonidae), Dolly Varden (Salvelinus malma) and bull trout (S. confluentus) have largely parapatric distributions in watersheds of northwestern North America. They are, however, sympatric in several localities and hybridization and some introgression occurs across a broad area of contact. We conducted a comparative phylogenetic analysis of Dolly Varden and bull trout to gain a historical perspective of hybridization between these species and to test for footprints of historical introgression. We resolved two major Dolly Varden mitochondrial DNA (mtDNA) clades (with 1.4-2.2% sequence divergence between haplotypes) that had different geographical distributions. Clade N is distributed across most of the range of Dolly Varden, from southern British Columbia through to the Kuril Islands in Asia. Clade S had a much more limited distribution, from Washington state, at the southern limit of the Dolly Varden range, to the middle of Vancouver Island. The distribution and inferred ages of the mtDNA clades suggested that Dolly Varden survived the Wisconsinan glaciation in a previously unsuspected refuge south of the ice sheet, and that Dolly Varden and bull trout were probably in continuous contact over most of the last 100,000 years. When bull trout were included in the phylogenetic analysis, however, the mtDNA of neither species was monophyletic: Clade S Dolly Varden clustered within the bull trout mtDNA clade. This pattern was discordant with two nuclear phylogenies produced (growth hormone 2 and rRNA internal transcribed sequence 1), in which Dolly Varden and bull trout were reciprocally monophyletic. This discordance between mtDNA- and nDNA-based phylogenies indicates that historical introgression of bull trout mtDNA into Dolly Varden occurred. Percent sequence divergence within these introgressed Dolly Varden (clade S) was 0.2-0.6%, implying that the introgression occurred prior to the most recent glaciation. Our analysis and other evidence of contact between divergent lineages in northwestern North America strongly suggests that the area may be the site of previously unsuspected suture zones of aquatic biotas.