New species of grayling <Emphasis Type="Italic">Thymallus tugarinae</Emphasis> sp. nova (Thymallidae) from the Amur River Basin

Data on a new species, low Amur grayling Thymallus tugarinae sp. nova, inhabiting tributaries of the lower and middle current of the Amur River, are presented. This species has been earlier equated with the Amur grayling T. grubii, described by Dybowski (1869) from the rivers Onon and Ingoda (the Upper Amur Basin). The new species differs from other representatives of the genus in the body coloration, the pattern on the upper fin, and certain morphological characters. On most of the Amur Basin, the grayling from the Lower Amur is sympatric with T. grubii and in its tributary Bureya River, also with the Bureya grayling T. burejensis. Individuals with intermediate traits are unknown, pointing to reproductive isolation. These data are supported by the results of molecular-genetic analysis (Froufe et al., 2003, 2005; Knizhin et al., 2004).     

A comparative analysis of two Amur grayling species from the <Emphasis Type="Italic">Thymallus</Emphasis> Genus (Salmoniformes; Thymallidae) according to a number of osteological and morphological features in their zone of sympatry

The results of the comparison of the Lower Amur grayling Thymallus tugarinae and the yellowspotted grayling T. flavomaculatus that were collected in the zone of their sympatry in the middle reaches of the Anuy River (the Lower Amur basin) for a number of osteological and morphological features are provided. The work was based on the analysis of X-ray images and a number of plastic features. Considerable differences were detected between the two species in the numbers of the bone elements of the axial skeleton. The differences in the number and topography of certain bone elements correlate with the morphological features of these species. The comparison results for certain features do not correspond with the literature data.     

Distribution,abundance, and size structure of Amur kaluga <Emphasis Type="Italic">Acipenser dauricus</Emphasis> and Amur sturgeon <Emphasis Type="Italic">A. schrenckii</Emphasis> in the Lower Amur and Amur Estuary

Distribution, population structure, and abundance of Amur kaluga Acipenser dauricus and Amur sturgeon A. schrenckii in the Lower Amur and Amur Estuary have been considered based on the materials of two surveys performed in 2011. Both species occur along almost the entire length of the Lower Amur and in major part of the Amur Estuary. The density of their aggregations has significantly decreased in most regions of the river if compared to the 1960s. In the Amur Estuary, A. dauricus and A. schrenckii are most abundant in freshwater and light salted water bodies of its western part. In 2011, the abundance and biomass of A. dauricus and A. schrenckii in the Lower Amur and Amur Estuary was 345000 specimens and 7110 tons and 289000 specimens and 1946 tons, respectively.     

On the diversity of fishes in mountain lakes of the Amur basin

Results of the study of 11 lakes situated in the mountainous part of the Amur River basin are reported. Six fish species, namely, blunt-snouted lenok Brachymystax tumensis, Baikal-Lena grayling Thymallus baicalolenensis, Siberian stone loach Barbatula toni, Lagowski’s minnow Rhynchocypris lagowskii, Czekanowski’s minnow Rh. czekanowskii, and Amur sculpin Cottus szanaga, were found in five lakes. Four species were found in one lake (Lake Pereval’noe, basin of the Amgun’ River), and two species were found in each of the remaining lakes. Lenok and Amur sculpin were the most common species. The fauna of Lake Okonon (basin of the river Zeya) was the most specific and did not have analogs among the lake faunas; Czekanowski’s minnow and Baikal black grayling were found in this lake. The lenok ecotype that formed in the mountain lakes differed from the river lenok in some regards. The potential pathways of formation and protection of mountain lake ichthyocenoses of the Amur basin are discussed.     

A new species of grayling <Emphasis Type="Italic">Thymallus svetovidovi</Emphasis> sp. nova (Thymallidae) from the Yenisei basin and its position in the genus <Emphasis Type="Italic">Thymallus</Emphasis>

The Upper Yenisei grayling Thymallus svetovidovi sp. nova that inhabits the headwaters of the Yenisei River in Mongolia is described. From the other representatives of the genus Thymallus, the species differs in the elements of body coloration, dorsal fin pattern, some morphometric characters, and genetic characteristics. Besides this species, most of the Yenisei basin is inhabited by Baikal grayling T. baicalensis Dyb., and its low reaches, by the Arctic grayling T. arcticus (Pall.).     

Distribution of Masu Salmon <Emphasis Type="Italic">Oncorhynchus masou</Emphasis> (Salmonidae) in Amur River Basin

The presented data on the distribution of the masu salmon Oncorhynchus masou in the Amur River Basin are collected in 1976–2015. In the analyzed region the species’ spawning range includes the lower part of the Amur River basin from the rivers flowing into the Amur estuary to the basins of the Anyui and Amgun’ Rivers in their middle courses. The information on the catch of a masu salmon specimen in the Khor River Basin (approximately 1300 km from the Amur River mouth) in 2015 is presented. It is assumed that the total Amur population does not exceed several thousand of adult anadromous fish.     

Finding of Amur sculpin <Emphasis Type="Italic">Mesocottus haitej</Emphasis> and <Emphasis Type="Italic">Cottus szanaga</Emphasis> (Cottidae) in Tugur River basin (Khabarovsk krai,Russia)

The first official finding of the Amur sculpin Mesocottus haitej and Cottus szanaga is reported for the basin of Tugur River (Shantarsky zoogeographical region). Previously, these species were known for this region from the literature only.     

New species of <Emphasis Type="Italic">Jakutoproductus</Emphasis> from the Lower Permian of Verkhoyansk Region

Two new brachiopod species of Jakutoproductus, J. lenensis sp. nov. and J. talchanensis sp. nov., are described. J. lenensis occurs in the upper part of the J. verkhoyanicus Zone of the Khorokytian Horizon (Asselian–Sakmarian deposits) of the lower reaches of the Lena River and in the Sobolokh-Mayan and Allara-Khadaryn’ya river basins. J. talchanensis is identified from the Khorokytian Horizon of the Talchan River (Baraiy River basin). A new subzone, the J. lenensis Subzone, is proposed for the upper part of the J. verkhoyanicus Zone of the Khorokytian Horizon of the Verkhoyansk Region.     

Morphological characteristics and intraspecific structure of <Emphasis Type="Italic">Triplophysa orientalis</Emphasis> (Balitoridae: Nemacheilinae)

The morphology and intraspecific structure of Triplophysa orientalis inhabiting the inland basins of Tsaidam (northeastern edge of the Tibetan Plateau) and the basin of the upper reach of the Huang He River in China were studied. Significant morphological differences between the populations from the inland basins and the Huang He River were revealed; the latter were distinguished as a separate subspecies T. o. hwanghoensis subsp. n. Intermediate character of some traits of the new subspecies between the nominative subspecies and T. hutjertjuensis was found; as a result, the status of the latter was reduced to the subspecies level. The synonymy of T. o. elongata with the nominative subspecies was confirmed. The differences between T. orientalis and T. obscura—morphologically poorly distinguishable species, sympatric in the basin of the upper reach of the Huang He River—were defined more exactly.     

First finding of loach (Cobitidae: <Emphasis Type="Italic">Misgurnus</Emphasis>) in the lower Miocene deposits of Western Siberia

The first finding of a fossil loach of the genus Misgurnus from the Lower Miocene deposits of Western Siberia is described. The fossil form is extremely close to the modern M. mohoity from the Amur River basin. It is the actual proof of the hypothesis of latitudinal community of the Eurasian Neogene ichthyofauna.     

Redescription and systematic position of nominal loach species <Emphasis Type="Italic">Nemacheilus compressirostris</Emphasis> and <Emphasis Type="Italic">N. sibiricus</Emphasis> (Nemacheilidae)

Type specimens of nominal species Nemacheilus compressirostris Warpachowsky, 1897, and N. sibiricus Gratzianov, 1907, from the upper Ob River basin were redescribed, and lectotypes for both species were selected. Although some traits were not preserved well enough, it was established that both names should be classified with Barbatula cf. toni, corresponding to the “snub-nosed” morphotype fide Prokofiev (2007). None of the names are suitable for designation of the morph “tigris” fide Gundrizer (1975) and Prokofiev (2007). A comparison table of diagnostic traits of the genus Barbatula from the Asian part of the range was compiled.     

Adaptation of <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis> to the Yangtze River basin

Background

Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms adapt to climate changes is a crucial biological question that is still largely unanswered. The plant Arabidopsis thaliana is an excellent system to study this fundamental question. Its origin is in the Iberian Peninsula and North Africa, but it has spread to the Far East, including the most south-eastern edge of its native habitats, the Yangtze River basin, where the climate is very different.

Results

We sequenced 118 A. thaliana strains from the region surrounding the Yangtze River basin. We found that the Yangtze River basin population is a unique population and diverged about 61,409 years ago, with gene flows occurring at two different time points, followed by a population dispersion into the Yangtze River basin in the last few thousands of years. Positive selection analyses revealed that biological regulation processes, such as flowering time, immune and defense response processes could be correlated with the adaptation event. In particular, we found that the flowering time gene SVP has contributed to A. thaliana adaptation to the Yangtze River basin based on genetic mapping.

Conclusions

A. thaliana adapted to the Yangtze River basin habitat by promoting the onset of flowering, a finding that sheds light on how a species can adapt to locales with very different climates.

     

Comparative karyology of species of the genera <Emphasis Type="Italic">Misgurnus</Emphasis> and <Emphasis Type="Italic">Cobitis</Emphasis> (Cobitidae) from the Amur River Basin in connection with their taxonomic relations and the evolution of karyotypes

Data are first provided on karyotypes of four species of Cobitidae from the Amur Basin: Misgurnus nikolskyi (2n = 50 = 10m + 4 sm + 36sta, NF = 64), Cobitis lutheri, (2n = 50 = 12m + 8sm + 30sta, NF = 70), C. choii (2n = 50 = 8m + 10sm + 8st + 24a, NF = 68), and C. melanoleuca (2n = 50 = 6m + 16sm + 28sta, NF = 72), and number of chromosomes in M. mohoity (2n = 50) and karyotypes of C. melanoleuca from the basin of the Don, Malyi and Bol’shoi Uzen rivers, and Selenga. These data are discussed in connection with problems of taxonomy of the studied genera, as well as the evolutionary relations of their karyotypes. On the basis of karyological differences between the populations of C. melanoleuca from different parts of the range, a new subspecies C. melanoleuca gladkovi subsp. nov. that inhabits waters of Europe is described.     

Redescription of <Emphasis Type="Italic">Cottus sibiricus</Emphasis> and an estimation of differences between this species and <Emphasis Type="Italic">Cottus dzungaricus</Emphasis> (Cottidae)

The type specimens of Cottus sibiricus and C. dzungaricus as well as individuals from the Olkha River (Yenisei River basin) are studied. The diagnostic features of C. sibiricus are established. Comparative morphological and molecular analysis of divergence between C. sibiricus and C. dzungaricus demonstrates that the differences lie within the limits of one polymorphous species. The rank of Dzungarian sculpin is lowered to the subspecies, C. sibiricus dzungaricus.     

Genetic structure of diploid-polyploid complex of spined loach genus <Emphasis Type="Italic">Cobitis</Emphasis> (<Emphasis Type="Italic">Cypriniformes,Cobitidae</Emphasis>) in the Lower Danube

The extremely high diversity of spined loach biotypes in the Lower Danube has been detected by biochemical genetic investigation and cytometric analysis of 358 specimens collected in the riverbed and shallow channels. Along with two diploid species (C. elongatoides and C. “tanaitica”), six hybrid forms were revealed, namely, diploid C. elongatoides-“tanaitica”; triploid C. 2 elongatoides-“tanaitica,” C. elongatoides-2 “tanaitica,” and C. 2 elongatoides-species-1; and tetraploid C. 3 elongatoides-“tanaitica” and C. elongatoides-species-2-2 “tanaitica.” In addition, specimens with recombinant genotypes were also found. In spite of the apomictic mode of reproduction, the polyploids did not possess clonal structure, but according to the level of polymorphism and the genotype distribution, they were isomorphous to parental diploid species. Thus, in contrast to the polyploidy in Cobitids of the Dnieper, which have appeared in the basin due to the expansion, the polyploids of the Lower Danube are autochthonous and were derived by crossing with local diploid species. The process is apparently proceeds without any limitations.     

Preliminary data on the variability of three microsatellite loci in Pacific <Emphasis Type="Italic">Gadus macrocephalus</Emphasis> and Atlantic <Emphasis Type="Italic">G. morhua</Emphasis> cod (Gadidae)

Variability of microsatellite DNA loci Gmo3, Gmo34, and Gmo35 is studied in samples of Pacific cod Gadus macrocephalus and Atlantic cod G. morhua. The results show high values of identity of the samples within the North Pacific basin (0.9766–0.9924) and within the Northeast Atlantic basin (0.9580). Based on the pairwise assessment of genetic differentiation, the F _ST values are significantly different in all variants between the samples of Pacific and Atlantic cod (F _ST = 0.5235–0.6719, p < 0.001). Within the basins, the significant differences in the frequencies of main alleles are revealed in the loci Gmo3 and Gmo34 for the samples from the Pacific and Atlantic oceans, respectively.     

Phylogenetic and taxonomic assessment of the endangered Cumberland bean, <Emphasis Type="Italic">Villosa trabalis</Emphasis> and purple bean, <Emphasis Type="Italic">Villosa perpurpurea</Emphasis> (Bivalvia: Unionidae)

Inadequate understanding of the phylogeography, taxonomy, and historical distribution of two critically imperiled freshwater mussels, Cumberland bean, Villosa trabalis, and purple bean, Villosa perpurpurea, has hindered management and recovery actions related to population restoration within their extant ranges. For more than 100 years, the purple-to-pink nacre of V. perpurpurea and white nacre of V. trabalis have been the only defining phenotypic characteristics used to distinguish each species. Genetic samples were analyzed from 140 individuals collected from 10 streams located in Virginia, Tennessee, and Kentucky, representing all known extant populations of each species. A 784-bp section of the mitochondrial DNA ND1 region was sequenced to assess the phylogeography and taxonomic validity of these taxa. Results of our phylogenetic analyses showed 100 % Bayesian posterior support for two distinct clades, one occurring in the Cumberland River basin and the other in the Tennessee River basin, separated by a mean genetic distance of 4 %. Mean genetic distances between haplotypes within each clade was <1 %. Among individuals from the Cumberland River basin, the nacre of shells was white to bluish-white, but in the Tennessee River basin, nacre graded from white to pink to dark purple; thus, nacre color is a variable and inconsistent character in nominal V. trabalis and V. perpurpurea occurring in the Tennessee River basin. Our data suggest that these morphologically similar species do not co-occur, as was previously believed. Instead, we conclude that the two species most likely share a common ancestor, but became isolated within each basin and experienced allopatric speciation. Updates to nomenclature, taxonomic placement, and recovery plans for the investigated species are needed.     

Genome-wide identification and evolution of <Emphasis Type="Italic">TC1</Emphasis>/<Emphasis Type="Italic">Mariner</Emphasis> in the silkworm (<Emphasis Type="Italic">Bombyx mori</Emphasis>) genome

TC1/Mariner transposons belong to class II transposable elements (TEs) that use DNA-mediated “cut and paste” mechanism to transpose, and they have been identified in almost all organisms. Although silkworm (Bombyx mori) has a large amount of TC1/Mariner elements, the genome wide information of this superfamily in the silkworm is unknown. In this study, we have identified 2670 TC1/Mariner (Bmmar) elements in the silkworm genome. All the TEs were classified into 22 families by means of fgclust, a tool of repetitive sequence classification, seven of which was first reported in this study. Phylogenetic and structure analyses based on the catalytic domain (DDxD/E) of transposase sequences indicated that all members of TC1/Mariner were grouped into five subgroups: Mariner, Tc1, maT, DD40D and DD41D/E. Of these five subgroups, maT rather than Mariner possessed most members of TC1/Mariner (51.23%) in the silkworm genome. In particular, phylogenetic analysis and structure analysis revealed that Bmmar15 (DD40D) formed a new basal subgroup of TC1/Mariner element in insects, which was referred to as bmori. Furthermore, we concluded that DD40D appeared to intermediate between mariner and Tc1. Finally, we estimated the insertion time for each copy of TC1/Mariner in the silkworm and found that most of members were dramatically amplified during a period from 0 to 1 mya. Moreover, the detailed functional data analysis showed that Bmmar1, Bmmar6 and Bmmar9 had EST evidence and intact transposases. These implied that TC1/Mariner might have potential transpositional activity. In conclusion, this study provides some new insights into the landscape, origin and evolution of TC1/Mariner in the insect genomes.