A. G. Oleinik

Phylogeography of the Salmonid Fish, Dolly Varden Salvelinus malma: Multiple Glacial Refugia in the North Pacific Rim

The geographic distribution pattern of mitochondrial DNA (control region) sequence polymorphisms from 73 populations of a salmonid fish, Dolly Varden Salvelinus malma, over most of its range in the North Pacific rim, was examined to assess how its spatial population genetic structure has been molded. The observed 68 haplotypes were grouped into three main lineages, which correspond to western, central, and eastern regions in the North Pacific. The two outlier-haplotype groups gave close agreement with DNA types from two congeneric species, white-spotted charr S. leucomaenis and Arctic charr S. alpinus, respectively. These results suggest that the present-day genetic structure of S. malma reflects historical patterns of isolation and re-colonization, and also historical hybridization with co-distributed species. We also placed the haplotypes of S. malma within our study areas into a pre-existing evolutionary relationship of S. alpinus and S. malma throughout the Northern Hemisphere. Phylogenetic analysis revealed that the Western Lineage S. malma was basal to all other lineages of S. malma and S. alpinus. Our data serve as a biogeographic hypothesis for salmonid fishes that the Sea of Japan and/or Sea of Okhotsk regions represents a place of origin for S. malma and S. alpinus groups currently distributed in circumpolar regions.

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.

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 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.

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 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.

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.

Phylogenetic relationships of Sakhalin taimen Parahucho perryi inferred from PCR-RFLP analysis of mitochondrial DNA

RFLP analysis of three amplified mtDNA fragments (Cytb/D-loop, ND1/ND2, and ND3/ND4L/ND4) was performed in the following taxa: Parahucho perryi, Hucho taimen, Brachymystax lenok, B. tumensis, Salmo salar, Salvelinus leucomaenis, and S. levanidovi. For mtDNA of P. perryi, a substantial decrease in the haplotype and nucleotide diversity was observed as a result of random genetic drift, caused by a reduction in the effective population size. Nucleotide divergence estimates between the mtDNA haplotypes were determined. Sakhalin taimen P. perryi was found to be approximately equally diverged from S. salar and from the charrs of the genus Salvelinus, by 11.0 and 10.0%, respectively. The divergence between P. perryi and H. taimen constituted 14.6%, between P. perryi and lenoks of the genus Brachymystax, 14.2%, and between H. taimen and Brachymystax, 7.7%. The analysis of possible phylogenetic relationships of the mtDNA from P. perryi among the group of taxa examined confirmed validity of the genus Parahucho. Phylogenetic reconstructions performed showed that robustness of the trees constructed for the complex of phylogenetically informative characters over three mtDNA fragments was considerably higher than that of the trees constructed for individual genes.