Complete mitochondrial genomes and phylogenetic analysis of four Baikal endemic Batrachocottus species (Scorpaeniformes: Cottoidei).

Baikal sculpins are the most species-rich and ecologically diverse group of fishes in the Lake. We analyzed complete mitochondrial genomes from four species of the endemic Baikal genus Batrachocottus (B. baicalensis, B. multiradiatus, B. talievi, and B. nikolski). Mitogenome sequences are 16,523-16,535 bp in length with a mitogenomic organization and gene arrangement identical to that of typical teleosts. Phylogenetic analysis using the Bayesian method positioned B. baicalensis outside the monophyletic clades of the genus Batrachocottus. Batrachocottus multiradiatus and B. talievi are sister species.

Diversification along a benthic to pelagic gradient contributes to fish diversity in the world's largest lake (Lake Baikal, Russia).

Insights into the generation of diversity in both plants and animals have relied heavily on studying speciation in adaptive radiations. Russia's Lake Baikal has facilitated a putative adaptive radiation of cottid fishes (sculpins), some of which are highly specialized to inhabit novel niches created by the lake's unique geology and ecology. Here, we test evolutionary relationships and novel morphological adaptation in a piece of this radiation: the Baikal cottid genus, Cottocomephorus, a morphologically derived benthopelagic genus of three described species. We used a combination of mitochondrial DNA and restriction site associated DNA sequencing from all Cottocomephorus species. Analysis of mitochondrial cytochrome b haplotypes was only able to two resolve two lineages: C. grewingkii and C. comephoroides/inermis. Phylogenetic inference, principal component analysis, and faststructure of genome-wide SNPs uncovered three lineages within Cottocomephorus: C. comephoroides, C. inermis and C. grewingkii. We found recent divergence and admixture between C. comephoroides and C. inermis and deep divergence between these two species and C. grewingkii. Contrasting other fish radiations, we found no evidence of ancient hybridization among Cottocomephorus species. Digital morphology revealed highly derived pelagic phenotypes that reflect divergence by specialization to the benthopelagic niche in Cottocomephorus. Among Cottocomephorus species, we found evidence of ongoing adaptation to the pelagic zone. This pattern highlights the importance of speciation along a benthic-pelagic gradient seen in Cottocomephorus and across other adaptive fish radiations.

Amazing Discoveries of Benthic Fauna from the Abyssal Zone of Lake Baikal.

Lake Baikal is a natural laboratory for the study of species diversity and evolution, as a unique freshwater ecosystem meeting the all of the main criteria of the World Heritage Convention. However, despite many years of research, the true biodiversity of the lake is clearly insufficiently studied, especially that of deep-water benthic sessile organisms. For the first time, plastic waste was raised from depths of 110 to 190 m of Lake Baikal. The aim of this study was to examine the biological community inhabiting the plastic substrate using morphological and molecular genetic analysis. Fragments of plastic packaging materials were densely populated: bryozoans, leeches and their cocoons, capsules of gastropod eggs, and turbellaria cocoons were found. All the data obtained as a result of an analysis of the nucleotide sequences of the standard bar-coding fragment of the mitochondrial genome turned out to be unique. Our results demonstrate the prospects for conducting comprehensive studies of artificial substrates to determine the true biodiversity of benthos in the abyssal zone of Lake Baikal.

Complete mitochondrial genomes of Baikal endemic coregonids: omul and lacustrine whitefish (Salmonidae: Coregonus sp.).

Coregonid fishes are among the most successful groups in the subarctic, boreal, and subalpine fresh waters of the northern hemisphere. Limnetic-benthic sympatric species-pairs from two different evolutionary lineages, the North American lake whitefish (Coregonus clupeaformis species complex), and the European whitefish (Coregonus lavaretus species complex), are becoming the subject of close attention to explore the role of natural selection during the ecological speciation. Baikal endemic coregonids, limnetic omul (Coregonus migratorius), and benthic lacustrine whitefish (Coregonus baicalensis) are the only representatives of another unique lineage that has not left the lake since the divergence from the two above. Due to Pleistocene oscillations sympatric limnetic-benthic divergence has been replicated here many times within the same water body over a long geological period in contrast to both Europe and America where sympatric species-pairs are the results of post-glacial secondary-contacts between glacial isolates during the Late Pleistocene on the territory of each continent. Mitochondrial genomes encode genes that are essential for respiration and metabolism. Data on complete mitogenomes of Baikal endemic coregonids provided here will complement ongoing investigations on energy metabolism as the main biological function involved in the divergence between limnetic and benthic whitefish.

Complete Mitochondrial Genomes of Baikal Oilfishes (Perciformes: Cottoidei), Earth's Deepest-Swimming Freshwater Fishes.

Sculpins are predominantly benthic sit-and-wait predators that inhabit marine and freshwaters of the Northern Hemisphere. In striking contrast to riverine relatives, sculpins endemic to Lake Baikal have diversified in both form and function, with multiple taxa having adaptations for pelagic and bathyal niches within the world's deepest lake. Baikal Oilfishes (Comephorus spp.) represent a highly apomorphic taxon with unique skeletal morphology, soft anatomy, and reproductive ecology. Selection for novel behavior and life history may be evident in genes responsible for organismal energy balance, including those encoding subunits of the electron transport chain. Complete mitochondrial genomes were sequenced for the Big Baikal Oilfish (Comephorus baicalensis) and Little Baikal Oilfish (Comephorus dybowskii). Mitochondrial genomes encode genes essential for electron transport, and data provided here will complement ongoing investigations of genome-to-phenome maps for teleost respiration and metabolism. Phylogenetic analyses including oilfish mitogenomes and all publicly available cottoid representative sequences are largely concordant with previous studies.

Signs of Selection in Synonymous Sites of the Mitochondrial Cytochrome b Gene of Baikal Oilfish (Comephoridae) by mRNA Secondary Structure Alterations.

Studies over the past decade have shown a significant role of synonymous mutations in posttranscriptional regulation of gene expression, which is particularly associated with messenger RNA (mRNA) secondary structure alterations. Most studies focused on prokaryote genomes and the nuclear genomes of eukaryotes while little is known about the regulation of mitochondrial DNA (mtDNA) gene expression. This paper reveals signs of selection in synonymous sites of the mitochondrial cytochrome b gene (Cytb) of Baikal oilfish or golomyankas (Comephoridae) directed towards altering the secondary structure of the mRNA and probably altering the character of mtDNA gene expression. Our findings are based on comparisons of intraspecific genetic variation patterns of small golomyanka (Comephorus dybowski) and two genetic groups of big golomyanka (Comephorus dybowskii). Two approaches were used: (i) analysis of the distribution of synonymous mutations between weak-AT (W) and strong-GC (S) nucleotides within species and groups in accordance with mutation directions from central to peripheral haplotypes and (ii) approaches based on the predicted mRNA secondary structure.

Endemic diversification of the monophyletic cottoid fish species flock in Lake Baikal explored with mtDNA sequencing.

In the ancient Lake Baikal in East Siberia, cottoid fishes have diversified into an endemic flock of 33 species. From an ancestral shallow-water, benthic life-style, Baikalian cottoids have shifted to deep-water life in environments even below 1500 m, and also colonized the pelagic habitat. We examined phylogenetic relationships among 22 Baikalian and 10 extra-Baikalian cottoid taxa using a total of 2822 bp of mitochondrial DNA sequence, from complete sequences of ATPase 8 and 6 and cytochrome b genes and the control region. Unlike in earlier studies, we found strong support for a monophyly of the whole endemic Baikalian cottoid diversity. The Baikalian clade, currently assigned to three families and 12 genera, appears to be nested within the Holarctic freshwater genus Cottus. In the molecular phylogeny, all but one of the current Baikalian genera formed well-supported monophyletic groups. However, the topology was inconsistent with the present morphology-based familial subdivision; particularly in positioning the genus Batrachocottus of Cottidae within Abyssocottidae. The branching order of the Baikalian genera could not be resolved completely, however; short basal branches indicate rapid diversification early in the history of the species flock. Using synonymous divergence rates from other fish species for calibration, the diversification of the Baikalian cottoids seems to have started in the Pliocene or early Pleistocene.