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.     

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.     

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.     

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.     

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.     

Characterization of invasive fish species in a river transposition region: evolutionary chromosome studies in the genus <Emphasis Type="Italic">Hoplias</Emphasis> (Characiformes,Erythrinidae)

Karyotypic analyses were performed in fishes from the genus Hoplias (H. malabaricus and H. lacerdae groups) from the São Francisco River basin (Brazil), in an impacted region by a river transposition which altered the local ecology and fish fauna. The karyotypes were investigated using chromosomal markers obtained from classic and molecular cytogenetics (Giemsa, CMA₃ and DAPI staining, C-banding, Ag-NORs, and FISH with 18S rDNA, 5S rDNA and 5SHindIII satellite DNA probes). Two karyotypic forms were found for the H. malabaricus group—karyomorph F, corresponding to the native form from the São Francisco River basin, and karyomorph A, corresponding to the invading form from the Upper Paraná River basin. Specimens from the H. lacerdae group exhibited striking chromosome differences in relation to the H. malabaricus group, thereby enabling good cytotaxonomic characterization and inferences regarding the karyotype evolution of these groups.     

Comments on the Mond Scraper, <Emphasis Type="Italic">Capoeta mandica</Emphasis> (Teleostei: Cyprinidae): Re-Description,Molecular Systematics and Distribution Modeling

Capoeta mandica was originally described as C. barroisi mandica from Mond River, Persian Gulf basin, based on morphological characters and later was considered as a distinct species based on a few small specimens. However, there is still controversial debate about its systematic position and morphological characters. To resolve the issue, new collected specimens from Iranian drainage basins examined morphologically and molecularly. Results revealed that C. mandica is a distinct taxon in the Capoeta trutta group. This taxon confirms the zoogeographical separation of the Persis basin (southern Iran) by the rise in post-Pleistocene sea level, isolating rivers from the Tigris-Euphrates and western basins.     

New host species and new distribution areas of <Emphasis Type="Italic">Salmincola lavaretus</Emphasis> (Copepoda: Lernaeopodidae): A parasite of coregonid fishes of Siberia

Data on the infestation of certain fish species by the parasitic copepod Salmincola lavaretus are presented for the first time. The infested fish species included Bauntovsky whitefish (Coregonus baunti), an endemic species from the Maloye and Bolshoye Kapylyushi lakes; Siberian whitefish (C. pidschian) and Siberian cisco (C. sardinella) from Bolshoye Kapylyushi Lake and Baunt Lake, which belong to the Tsypo-Tsypikan lake system (the Lena River basin, Transbaikalia); and Teletsky whitefish (C. lavaretus natio smitti) from Teletskoe Lake (the Ob River basin). Previously, S. lavaretus had been described as a parasite of Baikal omul (C. migratorius) and Baikal whitefish (C. baicalensis) from Baikal. The taxons of S. longimanus complex (S. longimanus, S. l. sibirica, S. svetlanovi, and S. lavaretus)—parasites of nasal fossae of grayling and coregonid fishes—were registered in the lakes of the Lake Baikal basin (Lake Baikal and Khovsgol Lake), the Lena River, the Yenisei and the Ob rivers (the largest rivers of the Arctic zoogeographic province), and the Kobdo River (the Western Mongolian province). It was assumed that S. longimanus complex is more widely distributed in the water bodies of the Arctic zoogeographic province of the Palearctic.     

Continued feeding on <Emphasis Type="Italic">Diporeia</Emphasis> by deepwater sculpin in Lake Huron

Monitoring changes in diets of fish is essential to understanding how food web dynamics respond to changes in native prey abundances. In the Great Lakes, Diporeia, a benthic macroinvertebrate and primary food of native benthivores, declined following the introduction of invasive Dreissena mussels and these changes were reflected in fish diets. We examined the diets of deepwater sculpin Myoxocephalus thompsonii collected in bottom trawls during 2010–2014 in the main basin of Lake Huron, and compared these results to an earlier diet study (2003–2005) to assess if their diets have continued to change after a prolonged period of Dreissena mussel invasion and declined Diporeia densities. Diporeia, Mysis, Bythotrephes, and Chironomidae were consumed regularly and other diet items included ostracods, copepods, sphaerid clams, and fish eggs. The prey-specific index of relative importance calculated for each prey group indicated that Mysis importance increased at shallow (≤55 m) and mid (64–73 m) depths, while Diporeia importance increased offshore (≥82 m). The average number of Diporeia consumed per fish increased by 10.0% and Mysis decreased by 7.5%, while the frequency of occurrence of Diporeia and Mysis remained comparable between time periods. The weight of adult deepwater sculpin (80 mm and 100 mm TL bins) increased between time periods; however, the change in weight was only significant for the 80 mm TL group (p?<?0.01). Given the historical importance of Diporeia in the Great Lakes, the examination of deepwater sculpin diets provides unique insight into the trophic dynamics of the benthic community in Lake Huron.     

Divergent Evolution of Symbiotic Bacteria: Rhizobia of the Relic Legume <Emphasis Type="Italic">Vavilovia formosa</Emphasis> Form an Isolated Group within <Emphasis Type="Italic">Rhizobium leguminosarum</Emphasis> bv. <Emphasis Type="Italic">viciae</Emphasis>

Comparative sequence analysis of symbiotic genes (nodA, nodC, nodD, nifH), which are elements of accessory component of the rhizobial genome, demonstrated that the strains of Rhizobium leguminosarum bv. viciae, isolated from the nodules of a relic legume, Vavilovia formosa, the closest relative of hypothetical common ancestor of the tribe Fabeae, represented a group separated from the strains of R. leguminosarum bv. viciae, isolated from other representatives of this tribe (Vicia, Lathyrus, Pisum, Lens). No isolation was observed relative to the genes representing the core component of the rhizobial genome (16S rDNA, ITS, glnII) or relative to host specificity of the rhizobia. The data obtained suggest that sequence divergence of symbiotic genes marks the initial stage of sympatric speciation, which can be classified as the isolation of the relic “vaviloviae” symbiotype, a possible evolutionary precursor of the “viciae” biotype.     

Relationships within <Emphasis Type="Italic">Capitotricha bicolor</Emphasis> (Lachnaceae,Ascomycota) as inferred from ITS rDNA sequences,including some notes on the <Emphasis Type="Italic">Brunnipila</Emphasis> and <Emphasis Type="Italic">Erioscyphella</Emphasis> clades

DNA sequences of Capitotricha bicolor from Quercus, Fagus sylvatica, Alnus alnobetula, and Nothofagus, and C. rubi from Rubus idaeus were obtained from apothecia to establish whether specimens from different hosts belong to separate species. The obtained ITS1–5.8S–ITS2 rDNA sequences were examined with Bayesian and parsimony phylogenetic analyses. Intra- and interspecific variation was also investigated based on molecular distances in the ITS region. The phylogenetic analyses supported the specific distinctness of Capitotricha rubi and the Capitotricha from Nothofagus, but also suggest specific distinctness between samples from Quercus, Fagus, and Alnus. The interspecific distances were larger than intraspecific distances for all examined units. The smallest distance was found between the “Alnus alnobetula” and “Fagus sylvatica” units. Two new sequences of Brunnipila are published. Capitotricha, Lachnum, and Erioscyphella are compared to each other based on hair and excipulum characteristics.     

Revision of the genus <Emphasis Type="Italic">Melamphaes</Emphasis> (Melamphaidae): 6. oligo-raker species: <Emphasis Type="Italic">M. papavereus,M. simus,M. hubbsi</Emphasis>

Three oligo-raker species (≤19 rakers on the first gill arch) of the genus Melamphaes have been considered. A new species, M. papavereus, out of the group “M. typhlops” has been described from the Bay of Bengal of the Indian Ocean. M. simus and M. hubbsi out of the group “M. simus” have been revised. M. simus inhabits all oceans between 40° N and 40° S. M. hubbsi has been known from single specimens caught in the central part of the South Atlantic between 11° and 19° S.     

Genome-wide identification and expression analysis of the molecular chaperone binding protein <Emphasis Type="Italic">BiP</Emphasis> genes in <Emphasis Type="Italic">Citrus</Emphasis>

Here, we report for the first time the genome-wide identification and expression analysis of the molecular chaperone BiP genes in Citrus. Six genes encoding the conserved protein domain family GPR78/BiP/KAR2 were identified in the genome of Citrus sinensis and C. clementina. Two of them, named here as CsBiP1 and CsBiP2, were classified as true BiPs based on their deduced amino acid sequences. Alignment of the deduced amino acid sequences of CsBiP1 and CsBiP2 with BiP homologs from soybean and Arabidopsis showed that they contain all the conserved functional motifs of BiPs. Analysis of the promoter region of CsBiPs revealed the existence of cis-acting regulatory sequences involved in abiotic, heat-shock, and endoplasmic reticulum (ER) stress responses. Publicly available RNA-seq data indicated that CsBiP1 is abundantly expressed in leaf, flower, fruit, and callus, whereas CsBiP2 expression is rarely detected in any tissues under normal conditions. Comparative quantitative real-time PCR (qPCR) analysis of expression of these genes between C. sinensis grafted on the drought-tolerant “Rangpur” lime (C. limonia) and -sensitive “Flying Dragon” trifoliate orange (Poncirus trifoliata) rootstocks showed that CsBiP1 was upregulated by drought stress on the former but downregulated on the latter, whereas the CsBiP2 mRNA levels were downregulated on drought-stressed “Flying Dragon,” but remained constant on “Rangpur.” CsBiP2 upregulation was only observed in C. sinensis seedlings subjected to osmotic and cold treatments. Taken together, these results indicate the existence of two highly conserved BiP genes in Citrus that are differentially regulated in the different tissues and in response to abiotic stresses.     

The Taxonomic Status and Intraspecific Differentiation of the Black Sea Horse Mackerel, <Emphasis Type="Italic">Trachurus mediterraneus ponticus</Emphasis> (Aleev, 1956) (Carangidae)

The taxonomic status of the horse mackerel, Trachurus mediterraneus ponticus (Aleev, 1956), which inhabits the Black Sea, has been clarified based on the analysis of variation in the nucleotide sequence of the mtDNA cytochrome b (Cyt-b) locus. A comparison of this species with the horse mackerel from the Mediterranean basin and the World Ocean has shown that the Black Sea horse mackerel is neither an independent species nor a subspecies and can only be qualified as the species Trachurus mediterraneus (Steindachner, 1868) distributed throughout the Mediterranean Sea basin. A hypothesis has been made about the possible cause of the origin and existence of two forms, “large” and “small”, of the horse mackerel. By using the technique of calculating ontogenetic trajectories, it has been found that these are two morpho-ecological forms, whose differentiation is most likely determined by the type of feeding.     

Evolution and systematics of Green Bush-crickets (Orthoptera: Tettigoniidae: <Emphasis Type="Italic">Tettigonia</Emphasis>) in the Western Palaearctic: testing concordance between molecular,acoustic, and morphological data

The genus Tettigonia includes 26 species distributed in the Palaearctic region. Though the Green Bush-crickets are widespread in Europe and common in a variety of habitats throughout the Palaearctic ecozone, the genus is still in need of scientific attention due to the presence of a multitude of poorly explored taxa. In the present study, we sought to clarify the evolutionary relationships of Green Bush-crickets and the composition of taxa occurring in the Western Palaearctic. Based on populations from 24 disjunct localities, the phylogeny of the group was estimated using sequences of the cytochrome oxidase subunit I (COI) and the internal transcribed spacers 1 and 2 (ITS1 and ITS2). Morphological and acoustic variation documented for the examined populations and taxa was interpreted in the context of phylogenetic relationships inferred from our genetic analyses. The trees generated in the present study supported the existence of three main lineages: “A”—composed of all sampled populations of Tettigonia viridissima and the Tettigonia vaucheriana complex, “B”—comprising Tettigonia caudata, Tettigonia uvarovi, and the Tettigonia armeniaca complex, and “C”—consisting of Tettigonia cantans. The present study provides the first phylogenetic foundation for reviewing the systematics of Tettigonia (currently classified mostly according to morphological characteristics), proposing seven new synonymies.     

High-throughput sequencing of <Emphasis Type="Italic">Prunus ferganensis</Emphasis> indicates that it is a geographical population of <Emphasis Type="Italic">P. persica</Emphasis>

Peach belongs to the genus Prunus, which includes Prunus persica and its relative species, P. mira, P. davidiana, P. kansuensis, and P. ferganensis. Of these, P. ferganensis have been classified as a species, subspecies, or geographical population of P. persica. To explore the genetic difference between P. ferganensis and P. persica, high-throughput sequencing was used in different peach accessions belonging to different species. First, low-depth sequencing data of peach accessions belonging to four categories revealed that similarity between P. ferganensis and P. persica was similar to that between P. persica accessions from different geographical populations. Then, to further detect the genomic variation in P. ferganensis, the P. ferganensis accession “Xinjiang Pan Tao 1” and the P. persica accession “Xia Miao 1” were sequenced with high depth, and sequence reads were assembled. The results showed that the collinearity of “Xinjiang Pan Tao 1” with the reference genome “Lovell” was higher than that of “Xia Miao 1” and “Lovell” peach. Additionally, the number of genetic variants, including single nucleotide polymorphisms (SNPs), structural variations (SVs), and the specific genes annotated from unmapped sequence in “Xia Miao 1” was higher than that in “Xinjiang Pan Tao 1” peach. The data showed that there was a close distance between “Xinjiang Pan Tao 1” (P. ferganensis) and reference genome which belong to P. persica, comparing “Xia Miao 1” (P. persica) and reference ones. The results accompany with phylogenetic tree and structure analysis confirmed that P. ferganensis should be considered as a geographic population of P. persica rather than a subspecies or a distinct species. Furthermore, gene ontology analysis was performed using the gene comprising large-effect variation to understand the phenotypic difference between two accessions. The result revealed that the pathways of gene function affected by SVs but SNPs and insertion-deletions markedly differed between the two peach accessions.