Search

Heteromorphic W and Y sex chromosomes often experience gene loss and heterochromatinization, which is frequently viewed as their “degeneration”. However, the evolutionary trajectories of the heterochromosomes are in fact more complex since they may not only lose but also acquire new sequences. Previously, we found that the heterochromatic W chromosome of a lizard Eremias velox (Lacertidae) is decondensed and thus transcriptionally active during the lampbrush stage. To determine possible sources of this transcription, we sequenced DNA from a microdissected W chromosome sample and a total female DNA sample and analyzed the results of reference-based and de novo assembly. We found a new repetitive sequence, consisting of fragments of an autosomal protein-coding gene ATF7IP2, several SINE elements, and sequences of unknown origin. This repetitive element is distributed across the whole length of the W chromosome, except the centromeric region. Since it retained only 3 out of 10 original ATF7IP2 exons, it remains unclear whether it is able to produce a protein product. Subsequent studies are required to test the presence of this element in other species of Lacertidae and possible functionality. Our results provide further evidence for the view of W and Y chromosomes as not just “degraded” copies of Z and X chromosomes but independent genomic segments in which novel genetic elements may arise.

Multiple repeated patterns of adaptive radiation were revealed in cyprinid fish inhabiting the compact geographic region of the Ethiopian Highlands. We found four independently evolved radiations in the evolutionary hexaploid (2n = 150) Labeobarbus lineage based on matrilineal relationships of >800 individuals. Each radiation displayed similar patterns of mouth phenotype diversification, and included ecomorphs/species of the generalized, lipped, scraping (one or two), and large-mouthed (one to three) types. All radiations were detected in geographically isolated rivers, and originated from different ancestral populations. This is the first documented case in which numerous parallel radiations of fishes occurred–via different ways–in a riverine environment. Some radiations are very recent and monophyletic, while others are older and include ecomorphs that originated in separate mini flocks and later combined into one. The diversification bursts among Ethiopian Labeobarbus were detected in the mid-upper reaches of rivers (1050-1550 m above sea level), which likely offer ecological opportunities that include diverse habitats yet poor fauna (i.e. lower competition and relaxed selection). This promising example of parallel evolution of adaptive radiation warrants further investigation.

Little ground squirrel (Spermophilus pygmaeus) is a polytypic species with a wide geographic range, divided by a number of large rivers (Don, Volga, and Ural rivers). Preliminary analysis of the mtDNA control region revealed substantial genetic differentiation (7%) between populations of little ground squirrel inhabiting the right and left banks of the Volga River, suggesting that large rivers act as geographic barriers for this species. Here, we present the results of the genetic diversity analysis of little ground squirrel (52 individuals from 35 localities) across the species range. The Don and Ural rivers, unlike the Volga River, had no considerable effect on the phylogeographic structure of little ground squirrel. Geographic subdivision found in ground squirrels living to the east of the Volga River could be explained by the influence of a large paleo-river flowing along the Turgai valley during glacial periods. The Volga River divides the species into two major groups (western and eastern), both with a high level of haplotype diversity. The genetic variability indices are almost twofold higher in the western clade. The results ​​of neutrality and isolation by distance tests support a relatively recent range expansion of the eastern clade. In overall, the observed structure of genetic diversity supports the hypothesis on the European origin of S. pygmaeus with the center of species origin on the territory of Caucasian geographic region. The division of little ground squirrels into western and eastern phylogenetic lineages probably occurred under the influence of fluctuations of the Caspian Sea level, due to the formation of temporary migration corridors during the regression periods.

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.

Long-tailed ground squirrel (Urocitellus undulatus) is a polytypic species with a wide distribution from the Tien Shan to the Amur River region. Previously, considerable genetic differentiation between eastern and western populations of this species was demonstrated. Moreover, the greatest differences were observed in the western part of the range located in Central Asia, the region that was subjected to repeated glaciations in the past and represents one of the centers of the ground squirrel secondary diversification. The analysis of polymorphism of the mitochondrial DNA control region was carried out on long-tailed ground squirrels living in the northern part of Central Asia, on the territory of the Altai Mountains (45 individuals from 23 localities). The presence of two genetically differentiated (7.7% differences) and geographically separated lineages (western and eastern) was revealed. The data obtained disprove the hypothesis on unidirectional, from west to east, colonization of the Altai Mountains after the end of the last glacial maximum and show the two pathways of the ground squirrel colonization of the Altai, from both western and eastern refugia.

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%.

The radiation of Palearctic green toads (Bufotes) holds great potential to evaluate the role of hybridization in phylogeography at multiple stages along the speciation continuum. With fifteen species representing three ploidy levels, this model system is particularly attractive to examine the causes and consequences of allopolyploidization, a prevalent yet enigmatic pathway towards hybrid speciation. Despite substantial efforts, the evolutionary history of this species complex remains largely blurred by the lack of consistency among the corresponding literature. To get a fresh, comprehensive view on Bufotes phylogeography, here we combined genome-wide multilocus analyses (RAD-seq) with an extensive compilation of mitochondrial, genome size, niche modelling, distribution and phenotypic (bioacoustics, morphometrics, toxin composition) datasets, representing hundreds of populations throughout Eurasia. We provide a fully resolved nuclear phylogeny for Bufotes and highlight exceptional cyto-nuclear discordances characteristic of complete mtDNA replacement (in 20% of species), mitochondrial surfing during post-glacial expansions, and the formation of homoploid hybrid populations. Moreover, we traced the origin of several allopolyploids down to species level, showing that all were exclusively fathered by the West Himalayan B. latastii but mothered by several diploid forms inhabiting Central Asian lowlands, an asymmetry consistent with hypotheses on mate choice and Dobzhansky-Muller incompatibilities. Their intermediate call phenotypes potentially allowed for rapid reproductive isolation, while toxin compositions converged towards the ecologically-closest parent. Across the radiation, we pinpoint a stepwise progression of reproductive isolation through time, with a threshold below which hybridizability is irrespective of divergence (15My). Finally, we clarified the taxonomy of Bufotes (including genetic analyses of type series) and formally described two new species, B. cypriensis sp. nov. (endemic to Cyprus) and B. perrini sp. nov. (endemic to Central Asia). Embracing the genomic age, our framework marks the advent of a new exciting era for evolutionary research in these iconic amphibians. ispartof: MOLECULAR PHYLOGENETICS AND EVOLUTION vol:141 ispartof: location:United States status: published

[EN] Large African barbs of the genus Labeobarbus constitute a hexaploid lineage (2n = 150). This group is widely distributed in African freshwaters, and exhibits profound phenotypic variation that could be a prerequisite for adaptive radiation. Using morphological, molecular, and stable isotope analyses, we investigated whether an adaptive radiation has occurred in a riverine assemblage of the Labeobarbus gananensis complex. This complex is composed of six phenotypically distinct sympatric forms inhabiting the Genale River (Ethiopian highlands, East Africa) in the Juba and Wabe¿Shebelle drainages (Indian Ocean basin). Of the six forms, five were divergent in their mouth morphology, corresponding to generalised, lipped, scraping (two forms), and large¿mouthed phenotypes. One form had no mouth specialisation, but differed from the others in body shape (short and deep body; short form). Stable isotope analysis revealed differences in 15N among these forms, representing different foraging strategies (omnivorous, scraping, and piscivorous). Phylogenetic analysis of two mitochondrial DNA markers confirmed the monophyly of L. gananensis, suggesting an intra¿riverine radiation. However, the Genale assemblage appears to have originated through a combination of allopatric and sympatric events. Some of the specialised forms within the Juba and Wabe¿Shebelle drainage originated independently from the local generalised forms in three different river regions. Each of these cases could be considered as a small species flock composed of two or three sympatric forms. Our study shows that adaptive radiation in rivers can be enhanced by a combination of sympatric speciation and temporal geographic isolation, leading to local sympatric speciation followed by migration.

Species with large geographic distributions present a challenge for phylogeographic studies due to the logistic difficulties of obtaining adequate samples. Daphnia O.F. Müller (Anomopoda: Daphniidae) is a model genus for evolutionary biology and ecology, but many regions such as the remote areas of Siberia, remain poorly studied. Here we examined genetic polymorphism in the ribosomal 12S and the protein-coding ND2 mitochondrial genes of three closely related taxa of the Daphnia (Daphnia) longispina complex, namely D. galeata Sars, D. longispina O.F. Müller and D. dentifera Forbes. We estimated the phylogenetic relationships among these taxa based on a concatenated alignment of these two genes. Using sequences from the present study and those available in GenBank, we investigated the geographic distributions of the mitochondrial haplotypes of these species and proposed an evolutionary scenario for each taxon. Network structures, haplotype distribution patterns, and FST values indicated significant differences in the evolutionary history of the examined species. Our analysis of D. galeata populations confirmed its recent and fast expansion, without a previous phase of a strong population disconnection. In contrast, the high haplotype diversity in D. dentifera and D. longispina could be explained by the survival of different phylogroups in several glacial refugia located in different geographic regions. For all studied species, maximum haplotype diversity was recorded in the remote regions of Siberia-lakes of the Yenisei River and Transbaikalia. Our study is an important step in our understanding of the evolutionary history of the Daphnia longispina group and provides further evidence of the biogeographic significance of Siberia for freshwater taxa.

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.

Here, we present the complete mitochondrial genome of the Blotched snake, Elaphe sauromates (Pallas, 1814). Mitogenome complete sequence is 17,187 bp long and consists of 13 protein-coding genes (P...

Here, we present complete mitochondrial genome of the four-lined snake, Elaphe quatuorlineata (Bonnaterre, 1790) and its comparison with closely related E. sauromates (Pallas, 1814). The complete sequence of the mitogenome is 17,183 bp long and consists of 13 protein-coding genes, two rRNA and 22 tRNA genes, and two control regions. It possesses the same gene order as other mitogenomes of Elaphe spp. and the base composition is as follows: 35.0% (A), 26.7% (C), 25.6% (T), and 12.7% (G), with an A + T bias (60.6%). The presented mitogenome will provide new data for phylogenetic analysis within phylogenetically close western Palearctic species of the genus Elaphe.

The genus Rutilus is a widely distributed lineage of cyprinids and ranges from West Europe to East Siberia. Although matrilineal phylogeny and phylogeography of western species were already studied, roaches from remaining part of the range were not examined. Phylogenetic analysis based on cytochrome b sequences detected the following three major phylogenetic clades: (i) R. frisii, (ii) R. rutilus s. str., and (iii) group of six Ponto–Caspian taxa: R. caspicus, R. heckelii, R. rutilus aralensis, R. rutilus lacustris, R. schelkovnikovi, and R. stoumboudae. Our results suggest that these “species” within Ponto–Caspian clade could be a single species (R. lacustris by priority of description). The Ponto–Caspian clade is most widely distributed among others and covers the freshwaters from the Aegean Sea basin to Laptev Sea tributaries. Both R. rutilus s. str. and Ponto–Caspian clades sympatrically occur in Black Sea and Caspian Sea basins, Azov Sea itself, and even in drainage of White Sea. The vastest zone of contact (approximately 1700 km) was detected in the Volga basin. The spatial pattern of haplotype diversity and the shape of haplotype network argued for multiple refugia in Ponto–Caspian region as well as a rapid post-glacial colonization of Volga River and Siberia.

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.

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%.