Complete mitochondrial genomes of Gritzenko's charr Salvelinus gritzenkoi and Miyabe charr Salvelinus malma miyabei and their interpretation regarding intraspecific taxonomy.

BACKGROUND: Salvelinus is one the most species-rich genera of salmonids (Salmoniformes: Salmonidae), and mitogenomic sequence data have served as a rich source of information for resolving fish phylogenies and identifying new charr species. However, current reference databases contain limited mitochondrial genome information on narrow-ranged, endemic charrs with disputable origin and systematic status. More comprehensive mitochondrial genome-based phylogenetics will help enhance understanding of the relationship and delineate charr species. METHODS AND RESULTS: In the present study, the complete mitochondrial genomes of three taxa (S. gritzenkoi, S malma miyabei, and S. curilus) were sequenced (PCR and Sanger dideoxy sequencing) and compared with those of other charr species whose mitochondrial genomes are already reported. Results indicate that the mitochondrial genomes of the three taxa were similar in length (16,652 bp and 16,653 bp for S. curilus and S. malma miyabei, to 16,658 bp for S. gritzenkoi). Analyses of nucleotide composition showed that the newly sequenced five mitochondrial genomes skewed strongly towards high AT (54.4%) content, which is typical of Salvelinus. No large deletions and insertions were found in the mitochondrial genomes, including samples from isolated populations. Heteroplasmy associated with single-nucleotide substitution in the ND1 gene was found in one case (S. gritzenkoi). In maximum likelihood and Bayesian inference trees, S. gritzenkoi and S malma miyabei were clustered with S. curilus with strong branch support. Our results provide the basis for a possible reclassification of S. gritzenkoi to S. curilus. CONCLUSION: The results of this study may be useful for future genetic studies on charrs of the genus Salvelinus toward the in-depth phylogenetic study and proper assessment of the conservation status of the disputed taxa.

Complete mitochondrial genomes of endemic charr of the genus Salvelinus from Lake Nachikinskoe (Kamchatka, Russia).

The complete mitochondrial genomes were sequenced from three individuals of the endemic charr Salvelinus sp. 4 [ from Lake Nachikinskoe (Kamchatka, Russia). The complete mitochondrial genomes were 16,654 bp in size; the genome organization and GC content (45.6%) was consistent with charr mitochondrial genomes published previously. The low level of sequence divergence detected between the Salvelinus sp. 4 and the GenBank Salvelinus taranetzi genomes indicated recent divergence and their origin from a common ancestor. Our results could play an essential role in resolving the conflict over current taxonomic status of endemic charr in genus Salvelinus.

Complete mitochondrial genomes of the charr Salvelinus alpinus erythrinus (Salmoniformes: Salmonidae) from Arctic Canada.

The complete mitochondrial genomes were sequenced in two individuals of charr Salvelinus alpinus erythrinus from Arctic Canada. The genome sequences were 16,652 bp in length; the genome organization and GC content (45.6%) are consistent with those of charr mitochondrial genomes published previously. The difference between the two genomes studied is low, 0.02%. Our results indicate the phylogenetic closeness of S. alpinus erythrinus and Salvelinus sp. 4 from Lake Nachikinskoe, Kamchatka and their origin from a common ancestor.

Complete mitochondrial genome and phylogenetic position of the Levanidov's charr Salvelinus levanidovi Chereshnev, Skopetz et Gudkov, 1989 (Salmoniformes, Salmonidae).

The complete mitochondrial genome was sequenced in Levanidov's charr Salvelinus levanidovi. The genome sequences are 16,624 bp, and the gene arrangement, composition, and size are similar to the charr genomes. The level of divergence between S. levanidovi and charr belonging to the genus Salvelinus was in the range from 4.80% to 3.65%. Molecular phylogeny provides new evidence that S. levanidovi is closely related to the common ancestor of the genus Salvelinus. The present study confirms that S. fontinalis, S. levanidovi, S. leucomaensis, and S. namaycus form a basal group of taxa, each of them belongs to an independent evolutionary line.

Complete mitochondrial genomes of the Arctic charr Salvelinus alpinus alpinus Linnaeus (Salmoniformes: Salmonidae).

The complete mitochondrial genomes were sequenced in three individuals of Arctic charr Salvelinus alpinus alpinus. The genome sequences were 16,655 and 16,657 bp in length, and the gene arrangement, composition, and size are very similar to the charr genomes published previously. The difference between the three genomes studied is low, 0.09%. The level of sequence divergence between S. alpinus alpinus and S. alpinus oquassa inferred from the complete mitochondrial genomes is relatively low (0.36%), indicating recent divergence of the taxa and/or potential historical hybridization between different lineages upon secondary contact.

First report of three complete mitochondrial genomes of the long-finned charr Salvethymus svetovidovi Chereshnev et Skopetz, 1990 (Salmoniformes: Salmonidae) with phylogenetic consideration.

The complete mitochondrial genome was sequenced in three individuals of long-finned charr Salvethymus svetovidovi from Lake El'gygytgyn (Chukotka Peninsula, Russia). The genome sequences are 16,655 bp in size and the gene arrangement, composition, and size are similar to the charr genomes published previously. The difference between the three genomes studied is low, 0.07%. Our results support the phylogenetic closeness of Sl. svetovidovi with representatives of the genus Salvelinus and their origin from a common ancestor. A placement of Sl. svetovidovi in the phylogenetic tree is strictly defined and this taxon should be included in the genus Salvelinus.

Complete mitochondrial genome and phylogenetic position of the Taranetz charr Salvelinus taranetzi Kaganovsky, 1955 (Salmoniformes: Salmonidae).

The complete mitochondrial genome was sequenced in two individuals of Taranetz charr Salvelinus taranetzi. The genome sequences are 16,654  bp in size, and the gene arrangement, composition, and size are very similar to the charr genomes published previously. The difference between the two genomes studied is low, 0.05%. The present study confirms the independent taxonomic status of S. taranetzi within the genus Salvelinus. The level of sequence divergence between S. taranetzi and Salvelinus alpinus inferred from the complete mitochondrial genomes is relatively low (1.1%), indicating recent divergence of the species.

First report of the mitochondrial DNA sequences of Chukchi Charr (Salvelinus andriashevi, Salmonidae).

Three mitochondrial DNA regions were sequenced in two individuals of the Chukchi charr Salvelinus andriashevi from Lake Istihed (Chukotka): the entire gene sequences of cytochrome b and cytochrome c oxidase-1, and control region. The low level of sequence divergence detected between the sequences suggests that S. andriashevi is probably an isolated population of the Taranetz charr S. taranetzi. The genealogy of mtDNA haplotypes confirms the phylogenetic closeness of S. andriashevi, S. taranetzi, Salvelinus sp. 4 (Lake Nachikinskoe), S. krogiusae (Lake Dal'nee), S. boganidae and S. elgyticus (Lake Elgygytgyn), and S. a. erythrinus (NWT).

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.