L. A. Skurikhina

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.

Genetic divergence and relationships among smelts of the genus Osmerus from the Russian waters

Smelts of the genus Osmerus, O. eperlanus and O. mordax dentes, inhabiting the basins of the Atlantic, Arctic, and Pacific oceans were investigated using RFLP analysis of the mitochondrial DNA segments A8/A6/COIII/ND3 and ND3/ND4, and sequencing of the cytb and COI genes (mtDNA), and intron 1 of the rpS7 gene (nDNA). A total of 14 samples from the populations from most part of the Russian range were examined. The mean values of haplotype and nucleotide diversity constituted 0.5997 ± 0.11264 and 0.003201 for O. m. dentex, and 0.3086 ± 0.09892 and 0.000431 for O. eperlanus, respectively. The high level of interspecific diversity (12.94%) along with the low level of intraspercific diversity (0.049% for O. m. dentex, and 0.001% for O. eperlanus was observed. The dendrograms (UPGMA, NJ, MP, and BA) constructed using the data of RFLP analysis of mtDNA, along with the sequencing data of mitochondrial and nuclear genes were congruent. The representatives of O. eperlanus and O. m. dentex formed steady clusters in accordance with their species affiliation, albeit without subdivision into local populations depending on their geographic locality.

Phylogeny of charrs of the genus Salvelinus based on mitochondrial DNA data

Charrs of the genus Salvelinus (including Salvethymus) represent a monophyletic group of salmonid fishes that diverged from the common ancestor without subdivision into subgenera. The phylogenesis of the genus is characterized by four cycles of mitochondrial genome divergence. The first one, belonging to the Late Miocene—the border between Miocene and Pliocene (6 to 4 million years ago)—was associated with the consecutive divergence of the S. fontinalis, S. namaycush, S. levanidovi, and S. leucomaenis basal branches. Two divergence events, including separation of the ancestral lineage of Western Pacific group of S. m. krascheninnikovi and the following segregation of the common ancestor into two mitochondrial phyla, happened within the period of 3 to 2 million years ago. The next cycle is attributed to the time interval of about 1 million years ago and includes the divergence of both phyla. In one phylum, a relatively quick isolation of Arctic and Eastern Pacific phylogroups, along with the divergence of the latter phylogroup into S. confluentus and S. m. lordi lineages, took place. At the same time, the second phylum diverged into the S. m. malma and S. alpinus phylogenetic groups. At the final stage (Middle to Late Pleistocene), differentiation of the taxa within the phylogenetic groups took place.

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.

Phylogenetic analysis of smelts (Osmeridae) based on the variation of cytochrome b gene

Putative phylogenetic relationships between all smelt species inhabiting Russian waters were studied using RFLP and the data on divergence between nucleotide sequences of the mitochondrial gene encoding cytochrome b. All types of phylogenetic trees (NJ, MP, and Bayesian) displayed stable clustering into isolated groups corresponding to the division of the subfamily Osmerinae into three genera, Mallotus, Osmerus, and Hypomesus. It was demonstrated that the Mallotus phylum was the first to diverge from a hypothetical common ancestor of the smelts. Later, it divided into two clusters corresponding to the modern subspecies Mallotus villosus villosus and M. v. catervarius. The phylum of the genus Osmerus diverged later than the genus Mallotus and also divided into two clusters, one including O. mordax of the Pacific (Sea of Japan) and Arctic (Kara and Barents Seas) basins and the other, anadromous and resident ecotypes of the O. eperlanus from the Baltic Sea basin. The smelts of the genus Hypomesus is the youngest phylogenetic group among the taxa studied; it forms three individual clusters matching the species H. olidus, H. nipponensis, and H. japonicus. The proposed phylogenetic hypothesis is discussed from the standpoint of its compliance with the phylogenetic constructions based on the external morphological and osteological traits.

Punctuate divergent evolution in fish from the Northern Pacific

The mtDNA divergence was examined in some families of anadromous and semi-anadromous fish. Heterogeneous distribution of the divergence values along the scale was demonstrated. Statistically significantly higher number of the species pairs were characterized by divergence values ranging from 2 to 4% and 5 to 12% of nucleotide substitutions. These results suggest that in different monophyletic groups occupying common historical ranges, divergence-associated speciation often happened within similar time intervals. Comparison of the species divergence time calculated using the molecular clock pointed to the coincidence of the radiation periods in the taxa with paleogeological and paleoclimatic global changes in the history of Northern Pacific.

[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 (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.

Genetic divergence of mitochondrial DNA in white char Salvelinus albus and northern Dolly Varden char Salvelinus malma malma

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.

Intraspecific polymorphism of mtDNA in Sakhalin taimen Parahucho perryi

The intraspecific polymorphism of Sakhalin taimen Parahucho perryi (Brevoort, 1856), Salmonidae, was assessed via the RFLP analysis of mitochondrial DNA fragments that contain Cytb, the control region (D loop), and the genes for the NADH dehydrogenase subunits 1–4, as well as the sequencing of the mitochondrial DNA COI gene. The statistically significant differentiation of the populations from the mainland coast of the Sea of Japan and the eastern and western coasts of Sakhalin Island was demonstrated. The higher level of haplotype diversity in Sakhalin populations compared to Primorye populations and the structure of haplotype genealogies suggested that all populations of Parahucho perryi originated from a common ancestor, which probably lived on the western coast of the Sakhalin Island.

Analysis of the mitochondrial DNA variation in pond smelt Hypomesus olidus (Osmeridae)

Pond smelt Hypomesus olidus (Pallas, 1814), one of the five species of the genus Hypomesus, family Osmeridae, was examined for intraspecific variation of the mitochondrial DNA cytb (1062 bp) and COI (567 bp) genes. Among the ten single substitutions discovered, only one, leading to the substitution of isoleucine by valine, was nonsynonymous, while the remaining substitutions were synonymous. The degree of genetic divergence among pooled nucleotide sequences in H. olidus populations examined constituted 0.4% on average, ranging from 0.2 to 0.6%. These values were not higher than the levels of divergence between the individuals within the populations. Phylogenetic analysis of the populations examined did not reveal their subdivision depending of their geographic location, and pointed to the absence of intraspecific differentiation of the species.