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.     

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.     

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.     

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.     

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.     

The divergence of the dolly varden char Salvelinus malma in Asian Northern Pacific populations inferred from the PCR-RFLP analysis of the mitochondrial DNA

Genetic differentiation of the dolly varden char Salvelinus malma Walbaum 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.     

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 inter-population heterogeneity of allele frequencies was found for all studied population pairs. For the total population of all islands, the inter-population diversity (GST = 0.188) was comparable to this parameter for the total population from the Kunashir Island (GST = 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 Dolly Varden 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.     

Genetic differentiation of three sympatric charr species from genus Salvelinus inferred from PCR-RFLP analysis of mitochondrial DNA

We examined differentiation of three sympatric charr species Dolly Varden charr Salvelinus malma Walbaum, white-spotted charr S. leucomaenis Pallas, and Levanidov charr S. 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 between S. levanidovi and S. leucomaenis was about 9.7%, between S. levanidovi and S. malma, 8.7%, and between S. malma and S. 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 sympatric charrs of the genus Salvelinus 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 Cytb/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.     

Mitochondrial DNA variation in Pacific capelin (<Emphasis Type="Italic">Mallotus villosus catervarius</Emphasis>) from the Sea of Okhotsk,inferred from PCR-RFLP analysis

Four population samples of Pacific capelin Mallotus villosus catervarius (Pennat, 1784) from geographically distant localities in the Sea of Okhotsk, Tauy Bay and the eastern coast of the Sakhalin Island, were examined using PCR-RFLP analysis of three mitochondrial DNA regions (A8/A6/COIII/ND3, ND3/ND4L/ND4, and ND5/ND6). The nucleotide divergence of mtDNA sequences among the samples, as well as the analysis of geographic heterogeneity of the haplotype frequencies and quantitative estimation of genetic differentiation performed by means of AMOVA, showed that the samples examined belonged to one panmictic population. Genealogic analysis of the mtDNA variation structure was carried out. It was demonstrated that the high level of haplotype diversity (0.9639 ± 0.00015) along with the low level of nucleotide diversity (0.003818 ± 0.0000003) pointed to the exponential rate of population growth of the capelin from the Sea of Okhotsk, which rather recently in its evolutionary history faced the bottleneck effect.     

Mitochondrial DNA variation in Pacific capelin (Mallotus villosus catervarius) from the Sea of Okhotsk, inferred from PCR-RFLP analysis

Four population samples of Pacific capelin Mallotus villosus catervarius (Pennant, 1784) from geographically distant localities in the Sea of Okhotsk, Tauy Bay and the eastern coast of the Sakhalin Island, were examined using PCR-RFLP analysis of three mitochondrial DNA regions (A8/A6/COIII/ND3, ND3/ND4L/ND4, and ND5/ND6). The nucleotide divergence of mtDNA sequences among the samples, as well as the analysis of geographic heterogeneity of the haplotype frequencies and quantitative estimation of genetic differentiation performed by means of AMOVA, showed that the samples examined belonged to one panmictic population. Genealogic analysis of the mtDNA variation structure was carried out. It was demonstrated that the high level of haplotype diversity (0.9639 +/- 0.00015) along with the low level of nucleotide diversity (0.003818 +/- 0.0000003) pointed to the exponential rate of population growth of the capelin from the Sea of Okhotsk, which rather recently in its evolutionary history faced the bottleneck effect.     

Spatial and temporal variation in invertebrate consumer diets in forested and herbaceous wetlands

Lake Kronotskoye (the Kronotsky Biosphere State Reserve, south-eastern Kamchatka Peninsula) contains three closely related resident morphotypes charrs, which are considered to be either independent species (white charr Salvelinus albus, longhead charr Salvelinus kronocius, Schmidt’s charr Salvelinus schmidti) or a united lacustrine-riverine charrs, represented by several phenotypes. Salvelinus malma malma is isolated from the lake charr populations by an upstream migration barrier in the Kronotskaya River, which flows out of the lake. We examined the level of genetic variability and divergence of mtDNA both between charrs from Kronotsky Lake and between resident lacustrine charrs and the hypothetical ancestor species S. m. malma. The RFLP-PCR analysis was used to examine six regions (ND1/ND2, ND3/ND4L/ND4, ND5/ND6, COI/COII/A8, A8/A6/COIII/ND3, and Cytb/D-loop), comprising ~80% of the mtDNA. Significantly different levels of diversity were found among the populations of lacustrine charrs. S. albus and S. schmidti had the highest indices of mtDNA diversity among the investigated populations from the different habitats. Heterogeneity tests revealed highly significant differentiation among lake populations and among riverine (Kronotskaya River) and lake (Lake Kronotskoye) populations of charrs, indicating their reproductive isolation. Hierarchical analysis of molecular variance revealed the following regularities of diversity distribution: the high proportion of interpopulation variation (93.25%) and low but statistically significant subdivision between charr populations (6.75%, P < 0.001). Results of the present study suggest that the populations of S. albus, S. kronocius, S. schmidti belong to the S. m. malma phylogenetic group. The divergence value of mtDNA of resident charrs (0.0357–0.0010%) does not exceed the intraspecific variability of S. m. malma. The analysis of the mtDNA haplotypes genealogy of charrs showed that the low values of nucleotide divergence reflect a short period from the beginning of divergence from the ancestral lineages and are due to ancestral polymorphism, as well as to haplotype exchange between the diverged phylogenetic groups as a result of introgressive hybridization.     

Change in nucleotide sequence of mitochondrial DNA from cytochrome b gene in chars of Salvelinus genus

Nucleotide sequences of two (405- and 1050-bp) regions of mitochondrial DNA (mtDNA) cytochrome c gene were established in chars of the genus Salvelinus from Russian Far East and Siberia. Based on the divergence and phylogenetic analysis of nucleotide sequences of the mtDNA cytochrome c gene, S. laecomaenis was shown to carry the most ancient mitochondrial lineage, which is close to the ancestral one. The archaic mtDNA of S. levanidovi occupied an isolated position on the phylogenetic trees. The mtDNA lineage of the southern S. malma was close to the S. alpinus-S. malma complex group. Within the S. alpinus-S. malma complex, three groups of mtDNA types having particular geographic distributions were distinguished. The Kolyma-Chukotka group includes lake S. taranetzi, S. boganidae and S. elgyticus from Chukotka, lake chars from Kolyma. The Okhotsk group is represented by northern S. malma, lake chars from northern Sea of Okhotsk, and anadromous S. taranetzi. The Siberian group is close to the Okhotsk one and consists of Taimyr and Baikal region chars as well as Arctic char from Finland. The divergence of char mitochondrial lineages was dated to the Pliocene-Pleistocene.     

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.     

Differentiation of Dolly Varden Char <Emphasis Type="Italic">Salvelinus malma</Emphasis> 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.__________Translated from Genetika, Vol. 41, No. 5, 2005, pp. 626–634.Original Russian Text Copyright © 2005 by Oleinik, Skurikhina, Brykov, Crane, Wenburg.     

Mitochondrial DNA phylogeography in northern grasshopper mice (Onychomys leucogaster) — the influence of Quaternary climatic oscillations on population dispersion and divergence

The details of mitochondrial DNA (mtDNA) phylogenetic structure of the northern grasshopper mouse Onychomys leucogaster were examined using populations from a postulated area of endemism that includes three arid regions (Colorado Plateaus, Interior Plains, and Wyoming Basins) in western North America. Fifteen tetra- and heptanucleotide restriction enzymes were used to assay restriction-site variation in a 2150-bp PCR-amplified fragment of mtDNA representing the ND2 and part of the COI gene regions. A total of 18 mtDNA haplotypes were detected. Although overall genetic divergence among these haplotypes was low (average = 1.1%), phylogeographic structuring was apparent. Notably, a clear phylogenetic split separated one group of haplotypes restricted to the Wyoming Basins from all others. This phylogenetic split was further corroborated by examination of nucleotide sequence variation from a 270-bp stretch of the mtDNA cytochrome b gene. Overall geographic and phylogenetic patterns suggest a complex history of geographic structuring and subsequent mixing of populations of grasshopper mice throughout the late Pleistocene. These patterns of variation are evaluated relative to alternative hypotheses about biotic responses to Quaternary climatic oscillations in western North American arid 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 RT-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 modem structure of the isolated populations is discussed in terms of phylogeography.     

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.     

Genetic differentiation of Mediterranean horse mackerel (Trachurus mediterraneus) populations as revealed by mtDNA PCR-RFLP analysis

The genetic population structure of Mediterranean horse mackerel, Trachurus mediterraneus , from seven locations throughout the Black, Marmara, Aegean and eastern Mediterranean seas was investigated using restriction fragment length polymorphism (RFLP) analysis of the mtDNA 16S rDNA region. An approximately 2000-bp segment was screened in 280 individuals using six restriction enzymes, resulting in 10 composite haplotypes. The most common haplotype was present in 56.42% individuals; the next most frequent haplotype was present in 22.85% individuals. Average haplotype diversity within samples was moderate (0.38), and nucleotide diversity was low (0.00435). Mean nucleotide divergence for the seven sampling sites was 0.0028. Nucleotide divergence among samples was moderate, with the highest value detected between the Aegean Sea (Izmir) and the eastern Black Sea (Trabzon) populations (0.007055), and the lowest (−0.000043) between the Marmara Sea (Adalar) and the western Black Sea (Sile) populations. In Monte Carlo pairwise comparisons of haplotype frequencies, the Sinop from the middle Black Sea, Trabzon from the eastern Black Sea, and Iskenderun Bay from the north-eastern Mediterranean Sea exhibited highly significant (P   <   0.001) geographical differentiation from each other and from all other populations. Mantel's test indicated that the nucleotide divergence among populations of T. mediterraneus was not significantly associated with their geographical isolation ( r  = −0.2963; P   >   0.05). Consequently, the mtDNA 16S rDNA region provided evidence for the existence of three distinct T. mediterraneus populations (Sinop, Trabzon and Iskenderun Bay) in the Black and north-eastern Mediterranean seas.