Molecular phylogeny of one extinct and two critically endangered Central Asian sturgeon species (genus Pseudoscaphirhynchus) based on their mitochondrial genomes

The enigmatic and poorly studied sturgeon genus Pseudoscaphirhynchus (Scaphirhynchinae: Acipenseridae) comprises three species: the Amu Darya shovelnose sturgeon (Pseudoscaphirhynchus kaufmanni (Bogdanow)), dwarf Amu Darya shovelnose sturgeon P. hermanni (Kessler), and Syr Darya shovelnose sturgeon (P. fedtschenkoi (Bogdanow). Two species – P. hermanni and P. kaufmanni – are critically endangered due to the Aral Sea area ecological disaster, caused by massive water use for irrigation to support cotton agriculture, subsequent pesticide pollution and habitat degradation. For another species – P. fedtschenkoi – no sightings have been reported since 1960-s and it is believed to be extinct, both in nature and in captivity. In this study, complete mitochondrial (mt) genomes of these three species of Pseudoscaphirhynchus were characterized using Illumina and Sanger sequencing platforms. Phylogenetic analyses showed the significant divergence between Amu Darya and Syr Darya freshwater sturgeons and supported the monophyletic origin of the Pseudoscaphirhynchus species. We confirmed that two sympatric Amu Darya species P. kaufmanni and P. hermanni form a single genetic cluster, which may require further morphological and genetic study to assess possible hybridization, intraspecific variation and taxonomic status and to develop conservation measures to protect these unique fishes.publishedVersio

Phylogeny, phylogeography and hybridization of Caucasian barbels of the genus Barbus (Actinopterygii, Cyprinidae)

Phylogenetic relationships and phylogeography of six species of Caucasian barbels, the genus Barbus s. str., were studied based on extended geographic coverage and using mtDNA and nDNA markers. Based on 27 species studied, matrilineal phylogeny of the genus Barbus is composed of two clades ¿ (a) West European clade, (b) Central and East European clade. The latter comprises two subclades: (b1) Balkanian subclade, and (b2) Ponto-Caspian one that includes 11 lineages mainly from Black and Caspian Sea drainages. Caucasian barbels are not monophyletic and subdivided for two groups. The Black Sea group encompasses species from tributaries of Black Sea including re-erected B. rionicus and excluding B. kubanicus. The Caspian group includes B. ciscaucasicus, B. cyri (with B. goktschaicus that might be synonymized with B. cyri), B. lacerta from the Tigris-Euphrates basin and B. kubanicus from the Kuban basin. Genetic structure of Black Sea barbels was influenced by glaciation-deglaciation periods accompanying by freshwater phases, periods of migration and colonization of Black Sea tributaries. Intra- and intergeneric hybridization among Caucasian barbines was revealed. In the present study, we report about finding of B. tauricus in the Kuban basin, where only B. kubanicus was thought to inhabit. Hybrids between these species were detected based on both mtDNA and nDNA markers. Remarkably, Kuban population of B. tauricus is distant to closely located conspecific populations and we consider it as relic. We highlight revealing the intergeneric hybridization between evolutionary tetraploid (2n=100) B. goktschaicus and evolutionary hexaploid (2n=150) Capoeta sevangi in Lake Sevan.The study was supported by Russian Science Foundation (grant no. 15-14-10020); final stage of the study was supported by Russian Foundation for Basic Research (grants nos. 18-54-05003 and 19-04-00719)

Complete mitochondrial genomes of representatives of two endemic sculpin families (Perciformes: Cottoidei) from Baikal – the world’s largest and deepest lake

In this study, five new mitogenomes from four endemic Lake Baikal sculpins were determined: Cottocomephorus grewingkii (Dybowski, 1874) (GB#MW732165), Cottocomephorus inermis (Yakovlev, 1890) (GB#MW732163), and Paracottus knerii (Dybowski, 1874) (GB#MW732164) (Family Cottocomephoridae – Bighead sculpins), and from two specimens of Procottus major Taliev, 1949 (GB##MW732166, MW732167) from Family Abyssocottidae (Deep-water sculpins). Together with recently published mitogenomes of Baikal Oilfishes (Sandel et al. ), the first mitogenome-based phylogenetic tree for all three endemic Baikal sculpin families is presented. Complete mitogenome phylogeny supports the monophyletic origin of the lake Baikal sculpins species flock, but does not support the monophyly of the family Cottocomephoridae (Bighead sculpins)

Data from: Species and hybrid identification of sturgeon caviar: a new molecular approach to detect illegal trade

Overexploitation of wild populations due to the high economic value of caviar has driven sturgeons to near extinction. The high prices commanded by caviar on world markets have made it a magnet for illegal and fraudulent caviar trade, often involving low-value farmed caviar being sold as top-quality caviar. We present a new molecular approach for the identification of pure sturgeon species and hybrids that are among the most commercialized species in Europe and North America. Our test is based on the discovery of species-specific single nucleotide polymorphisms (SNPs) in the ribosomal protein S7, supplemented with the Vimentin gene and the mitochondrial D-loop. Test validations performed in 702 specimens of target and nontarget sturgeon species demonstrated a 100% identification success for Acipenser naccarii, A. fulvescens, A. stellatus, A. sinensis and A. transmontanus. In addition to species identification, our approach allows the identification of Bester and AL hybrids, two of the most economically important hybrids in the world, with 80% and 100% success, respectively. Moreover, the approach has the potential to identify many other existing sturgeon hybrids. The development of a standardized sturgeon identification tool will directly benefit trade law enforcement, providing the tools to monitor and regulate the legal trade of caviar and protect sturgeon stocks from illicit producers and traders, hence contributing to safeguarding this group of heavily threatened species

Complete mitochondrial genomes of the critically endangered Ship sturgeon <i>Acipenser nudiventris</i> from two seas

<p>Two complete mitochondrial genome sequences of ship sturgeon <i>Acipenser nudiventris</i> from the Caspian Sea and from Balkhash Lake (introduced from the Aral Sea during the last century) were determined by PCR-based sequencing method. The whole mitogenome sequences have been deposited in GenBank under accession numbers KU321568 and KU321569.</p

Alignment Figure S3

Alignment of the first intron (locus A) of the gene RPS7 gene obtained from different species. The alignment was used to identify diagnostic polymorphisms which are highlighted in the published version (figure S3 of the supplementaty material)

Alignment figure S2

The alignment of sequences obtained by PCR amplification of putative RPS7 gene with universal primers was used to built the tree reported in Figure S2 of supplementary material

Molecular phylogeny of one extinct and two critically endangered Central Asian sturgeon species (genus Pseudoscaphirhynchus) based on their mitochondrial genomes

The enigmatic and poorly studied sturgeon genus Pseudoscaphirhynchus (Scaphirhynchinae: Acipenseridae) comprises three species: the Amu Darya shovelnose sturgeon (Pseudoscaphirhynchus kaufmanni (Bogdanow)), dwarf Amu Darya shovelnose sturgeon P. hermanni (Kessler), and Syr Darya shovelnose sturgeon (P. fedtschenkoi (Bogdanow). Two species – P. hermanni and P. kaufmanni – are critically endangered due to the Aral Sea area ecological disaster, caused by massive water use for irrigation to support cotton agriculture, subsequent pesticide pollution and habitat degradation. For another species – P. fedtschenkoi – no sightings have been reported since 1960-s and it is believed to be extinct, both in nature and in captivity. In this study, complete mitochondrial (mt) genomes of these three species of Pseudoscaphirhynchus were characterized using Illumina and Sanger sequencing platforms. Phylogenetic analyses showed the significant divergence between Amu Darya and Syr Darya freshwater sturgeons and supported the monophyletic origin of the Pseudoscaphirhynchus species. We confirmed that two sympatric Amu Darya species P. kaufmanni and P. hermanni form a single genetic cluster, which may require further morphological and genetic study to assess possible hybridization, intraspecific variation and taxonomic status and to develop conservation measures to protect these unique fishes