Evgeniy Simonov

Implications of hybridization, NUMTs, and overlooked diversity for DNA Barcoding of Eurasian ground squirrels.

The utility of DNA Barcoding for species identification and discovery has catalyzed a concerted effort to build the global reference library; however, many animal groups of economical or conservational importance remain poorly represented. This study aims to contribute DNA barcode records for all ground squirrel species (Xerinae, Sciuridae, Rodentia) inhabiting Eurasia and to test efficiency of this approach for species discrimination. Cytochrome c oxidase subunit 1 (COI) gene sequences were obtained for 97 individuals representing 16 ground squirrel species of which 12 were correctly identified. Taxonomic allocation of some specimens within four species was complicated by geographically restricted mtDNA introgression. Exclusion of individuals with introgressed mtDNA allowed reaching a 91.6% identification success rate. Significant COI divergence (3.5–4.4%) was observed within the most widespread ground squirrel species (Spermophilus erythrogenys, S. pygmaeus, S. suslicus, Urocitellus undulatus), suggesting the presence of cryptic species. A single putative NUMT (nuclear mitochondrial pseudogene) sequence was recovered during molecular analysis; mitochondrial COI from this sample was amplified following re-extraction of DNA. Our data show high discrimination ability of 100 bp COI fragments for Eurasian ground squirrels (84.3%) with no incorrect assessments, underscoring the potential utility of the existing reference librariy for the development of diagnostic ‘mini-barcodes’.

DNA extraction protocols may influence biodiversity detected in the intestinal microbiome: a case study from wild Prussian carp, Carassius gibelio.

&NA; In this investigation, we examined the influence of different DNA extraction protocols on results obtained for intestinal microbiota of Prussian carp. We showed that significant differences were observed in numbers of reads, OTUs, Shannon index and taxonomic composition between two different DNA extraction protocols for intestine of Prussian carp (Carassius gibelio), and differences were also evident between microbial communities in the intestinal mucosa and intestinal content. Statistical analyses of 25 published articles also revealed a significant relationship between methods of DNA extraction and bacterial diversity in fish intestine of freshwater species. Microbial diversity, community structure, proportions of read numbers derived from each OTU and the total number of OTUs obtained by different DNA extraction protocols could lead to a bias in results obtained in some cases, and therefore researchers should be conservative in conclusions about community structures.

Alai! Alai! - a new species of the Gloydius halys (Pallas, 1776) complex (Viperidae, Crotalinae), including a brief review of the complex

During a scientific field expedition to the Alai-Pamir range five specimens of the genus Gloydius have been collected in the larger Alai. A morphological and genetical examination of the specimens has shown that they are part of the G. halys complex, but represent a new taxon which is characterized by the following unique character combination: It is a slender and moderately stout small snake, up to 479 mm total length. The head has nine symmetrical plates on the upper head, 7 supralabial and 8-9 infralabial scales. Body scales in 20-22 rows around midbody, 143-156 ventral and 35-45 usually paired subcaudal scales. The cloacal plate not divided. The general coloration consists of various different tones of olive, tan and brown, having a distinct head, but an indistinct body pattern with, excluding the tail, 26-29 transverse crossbands, which are not extending to the sides of the body. The haplotype network shows the new species within the G. halys complex and close related to both, G. h. halys and G. h. caraganus. So far the new described species is only known from the Alai range. However, various Gloydius specimens are found in Kyrgyzstan and because of the complicated taxonomy those specimens have to re-identified to clarify their status and the status of the new species.

Two complete mitochondrial genomes of extinct form of the Sevan trout Salmo ischchan danilewskii

Abstract The mitochondrial genomes from two individuals of the extinct subspecies of the Sevan trout Salmo ischchan danilewskii are published in this paper. The mitochondrial DNA (mtDNA) is 16,665 base pairs (bp) in length and contained 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. The overall base composition of the genome in descending order was 27.9% of A, 29.4% of C, 16.7% of G, and 26.0% of T without a significant AT bias of 53.9%.

Sequencing of two mitochondrial genomes of endangered form of the Sevan trout Salmo ischchan aestivalis

Abstract The two complete mitochondrial genomes of endangered form of the Sevan trout Salmo ischchan aestivalis are published in this paper. The mitochondrial DNA (mtDNA) is 16,677 base pairs (bp) in length and contained 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. The overall base composition of the genome in descending order was 29.4% – C, 27.9% – A, 26.0% – T, 16.7% – G, without a significant AT bias of 53.9%.

Comparative morphological and genetic analysis of populations and species of the genus Daphnia O.F. Müller, 1785 (Crustacea; Daphniidae) from Lake Glubokoe and Lake Chany

The results of analysis of the variability of body shape of different Daphnia galeata morphs from geographically distinct populations—Lake Glubokoe (Moscow oblast) and Lake Chany (Novosibirsk oblast) are given. The morphological analysis was combined with the analysis of the variability of fragments of the 16S and 12S genes of the mitochondrial DNA (mtDNA) and the internal transcribed spacer 2 (ITS2) of the nuclear DNA. A reconstruction of the phylogenetic relationships between species of the genus Daphnia has been performed using a combined fragment of the 16S and 12S genes of the mtDNA. An inconsistency in the distribution of the 12S- and ITS2-haplotypes for the species D. galeata has been revealed, which indicates the introgression of mtDNA in the Lake Chany population.

Population genetics of the Halys pit viper (Gloydius halys) at the northern distribution limit in Siberia

We studied the genetic structure and diversity of a vulnerable population of the Halys pit viper (Gloydius halys) living at the northern distribution limit of the species (Novosibirsk Region, West Siberia, Russia) and fairly isolated from the nearest known locations (180-200 km). 157 snakes from three locations (separated by 5-11 km) were genotyped using 8 microsatellite loci. In addition, nucleotide sequences of a mitochondrial marker gene (ND4) were obtained from 30 individuals. Two mitochondrial haplotypes differing by one synonymous substitution could be detected. Haplotype H1 had a prevalence of 96.7%. High levels of genetic diversity (mean H O = 0 . 76 ) were detected and no evidence of a recent bottleneck in any sampling site could be discovered. We found that G. halys exhibits a low, although significant, level of genetic differentiation on a fine geographic scale (overall FST = 0.013). The degree of differentiation is comparably low with regard to values reported for other vipers and more similar to those in Colubridae. In addition, using local based FST estimates, we detected a significant difference in the extent of genetic drift between the centrally located and marginal local populations as predicted by the stepping-stone model of migration. Thus, from a short-term perspective, primary attention should be given to the peripheral local populations, due to limited immigration and stronger influence of genetic drift. Since all habitat patches are situated along the river and have a linear order it is important to preserve each habitat site to maintain gene flow across the metapopulation.

DNA barcoding of the fishes of the genus Alburnoides (Actinopterygii, Cyprinidae) from Caucasus

Abstract Spirlins of the genus Alburnoides are widespread fishes, which taxonomy has been rapidly developing in recent years. Mitochondrial cytochrome c oxidase subunit I (COI) was used as DNA barcode marker to create a reference dataset of Caucasian Alburnoides and to test its barcoding efficiency. All four previously known Caucasian species of Alburnoides were confirmed as valid species with high genetic distances to sister species as well confirmed as Caucasian endemics. Alburnoides samiii, previously known from Sefidroud basin (Iran), was discovered in Transcaucasia. The accuracy of species identification of Ponto-Caspian Alburnoides by DNA barcodes was 100%. In addition, one potentially new species within A. gmelini was revealed. Despite the limited ability of COI to infer phylogenetic relationships, study provided evidence that Ponto-Caspian lineage of Alburnoides includes significantly larger number of species from Caspian Sea basin and inland basins of Central Asia.

Diet and other environmental factors shape the bacterial communities of fish gut in an eutrophic lake

The aim of this work was to study the gut microbial diversity from eight species of wild fish with different feeding habits, digestive physiology (gastric vs agastric) and provide comparative structural analysis of the microbial communities within their environment (food items, water, sediments and macrophytes).

A century in synonymy: molecular and morphological evidence for the revalidation of Glyptosternon osсhanini (Herzenstein, 1889) (Actinopterygii: Sisoridae)

Exostoma oschanini, presently treated as a junior synonym of Glyptosternon reticulatum, is revalidated within Glyptosternon based on a phylogenetic analysis of the CO1 gene and morphological characters. Glyptosternon oschanini is known to occur in tributaries of the Syr Darya River in Uzbekistan and Kyrgyzstan and may also occur in the Amu Darya River drainage. A morphological diagnosis and description are provided for G. oschanini. Exostoma gracile is a junior synonym of G. oschanini rather than of G. reticulatum.