Revision of the Schistura cincticauda species group (Teleostei, Nemacheilidae) using molecular and morphological markers.

To approach the taxonomy of large and complex animal groups it is of advantage to focus on species groups with shared derived character state. We investigate the composition, morphological characteristics and relationships of and within the Schistura cincticauda species group, whose members are small freshwater fishes that inhabit streams and rivers in eastern Myanmar and western and southern Thailand. A phylogenetic analysis using molecular genetic markers demonstrated the monophyly of this group; a combined genetic and morphological analysis revealed the inclusion of at least twelve species.

Sequence capture: Obsolete or irreplaceable? A thorough validation across phylogenetic distances and its applicability to hybrids and allopolyploids.

As whole-genome sequencing has become pervasive, some have suggested that reduced genomic representation approaches, for example, sequence capture, are becoming obsolete. In the present study, we argue that these techniques still provide excellent tools in terms of price and quality of data as well as in their ability to provide markers with specific features, as required, for example, in phylogenomics. A potential drawback of the wide-scale application of reduced representation approaches could be their drop in efficiency with increasing phylogenetic distance from the reference species.

Using Species Groups to Approach the Large and Taxonomically Unresolved Freshwater Fish Family Nemacheilidae (Teleostei: Cypriniformes).

Large animal families with unresolved taxonomy are notoriously difficult to handle with respect to their biodiversity, systematics, and evolutionary history. We approach a large and taxonomically unresolved family of freshwater fishes (Nemacheilidae, >600 species) by proposing, on the basis of morphologic data, a species group within the family and study its phylogeny with conclusions regarding its diversity, taxonomy, and biogeographic history. Phylogenetic analyses of two mitochondrial and three nuclear genes of 139 specimens, representing about 46 species (17 candidate species from the proposed species-group, plus 29 comparative species), revealed that the proposed species group does not form a distinct monophyletic lineage, but that the candidate and comparative species mixed in three different lineages.

One northward, one southward: Contrasting biogeographical history in two benthic freshwater fish genera across Southeast Asia (Teleostei: Cobitoidea: Nemacheilus, Pangio).

Southeast Asia is one of the world's biodiversity hotspots, and the high level of diversity and endemism was reached by colonisation events as well as internal diversification. We investigate the phylogenetic relationships and biogeographic history of the loach genus Nemacheilus, which is widely distributed and common across freshwaters of Southeast Asia. In addition we present the ancestral range reconstruction of the related loach genus Pangio that commonly occurs in the same region as Nemacheilus.

Resolving an unnoticed diversity within the Schistura robertsi species complex (Teleostei: Nemacheilidae) using molecules and morphology.

The Schistura robertsi species complex is a group of freshwater fish inhabiting streams in southeast Myanmar as well as in western and southern Thailand. In southern Thailand, the distribution exceeds the biogeographically important 'Surat Thani - Krabi line'. The complex is believed to include five described and one undescribed species, but monophyly and systematics of the group have never been studied explicitly.

Taxonomic Diversity Not Associated with Gross Karyotype Differentiation: The Case of Bighead Carps, Genus (Teleostei, Cypriniformes, Xenocyprididae).

The bighead carps of the genus ( and ) are important aquaculture species. They were subjected to extensive multidisciplinary research, but with cytogenetics confined to conventional protocols only. Here, we employed Giemsa-/C-/CMA- stainings and chromosomal mapping of multigene families and telomeric repeats.

Sea water shaping the freshwater biota: Hidden diversity and biogeographic history in the Paracanthocobitis zonalternans species complex (Teleostei: Nemacheilidae) in western Southeast Asia.

Western Southeast Asia is hosting one of the world's most diverse faunas, and one of the reasons for this huge diversity is the complex geologic past of the area, increasing the frequency of isolation and expansion events over evolutionary time scale. As an example case, the present study reveals the phylogeny and biogeographic history of the Paracanthocobitis zonalternans species complex, small benthic freshwater fish (Teleostei: Nemacheilidae) that are commonly occurring across western Southeast Asia (from central Myanmar through western and southern Thailand to northern Malaysia). The group is particularly interesting since it occurs in three biogeographic subdivisions (Indian, Indochinese, Malay/Sundaic) and across all of the major biogeographic barriers in the region.

Dynamics of tandemly repeated DNA sequences during evolution of diploid and tetraploid botiid loaches (Teleostei: Cobitoidea: Botiidae).

Polyploidization has played an important role in the evolution of vertebrates, particularly at the base of Teleostei-an enormously successful ray-finned fish group with additional genome doublings on lower taxonomic levels. The investigation of post-polyploid genome dynamics might provide important clues about the evolution and ecology of respective species and can help to decipher the role of polyploidy per se on speciation. Few studies have attempted to investigate the dynamics of repetitive DNA sequences in the post-polyploid genome using molecular cytogenetic tools in fishes, though recent efforts demonstrated their usefulness.

, a new species of loach (Teleostei: Botiidae) from Guilin, southern China.

Leptobotia micra, new species, is described from the upper Li River (Pearl River basin) around Guilin in Guangxi province, southern China. The new species is evidently the smallest species of Leptobotia, with females of 45‒46 mm SL bearing oocytes. It can be distinguished from all other species of Leptobotia by a combination of the following characters: no dark bars or dorsal saddles on body, a row of white dots along dorsal midline, 4+34 vertebrae, a predorsal distance of 58.

The complete mitochondrial transcript of the red tail loach as assembled from RNAseq (Teleostei: Botiidae).

Here, we present the first complete mitochondrial genome of the Red Tailed Loach (Teleostei: Botiidae) from Thailand, assembled from next-generation transcriptome sequencing data. The assembled transcript corresponds to the full length mitochondrial genome of , which measured 16,865 bp in length, and contained 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. A slight A + T bias was observed in the mitogenome of with an overall base composition of 32.

, a new species of loach from the lower Yangtze basin in China (Teleostei: Cypriniformes: Botiidae).

A new species, Leptobotia bellacauda is described from the lower Yangtze River basin. The new species is distinguished from all other species of Leptobotia by a combination of the following characters: body plain brown, prominent black bar in caudal fin, dorsal half of head dusky black, ventral half of head cream colour, eye well developed, lobes of caudal fin rounded, origin of pelvic fins beneath or anterior to dorsal-fin origin, and pectoral fin in adult males enlarged, with numerous tubercles.

A Ploidy Difference Represents an Impassable Barrier for Hybridisation in Animals. Is There an Exception among Botiid Loaches (Teleostei: Botiidae)?

One of the most efficient mechanisms to keep animal lineages separate is a difference in ploidy level (number of whole genome copies), since hybrid offspring from parents with different ploidy level are functionally sterile. In the freshwater fish family Botiidae, ploidy difference has been held responsible for the separation of its two subfamilies, the evolutionary tetraploid Botiinae and the diploid Leptobotiinae. Diploid and tetraploid species coexist in the upper Yangtze, the Pearl River and the Red River basins in China.

Molecular Evidence for Multiple Origins of the European Spined Loaches (Teleostei, Cobitidae).

We present a phylogenetic investigation of the Northern Clade, the major monophyletic clade within the freshwater fish family Cobitidae, one of the most prominent families of freshwater fishes found in Asian and European waters. Phylogenetic reconstructions based on the cytochrome b and RAG-1 genes show the genera Microcobitis, Sabanejewia, Koreocobitis and Kichulchoia as monophyletic groups. These reconstructions also show a Cobitis sensu lato and a Misgurnus sensu lato group.

Karyotype differentiation in 19 species of river loach fishes (Nemacheilidae, Teleostei): extensive variability associated with rDNA and heterochromatin distribution and its phylogenetic and ecological interpretation.

Background: Loaches of the family Nemacheilidae are one of the most speciose elements of Palearctic freshwater ichthyofauna and have undergone rapid ecological adaptations and colonizations. Their cytotaxonomy is largely unexplored; with the impact of cytogenetical changes on this evolutionary diversification still unknown. An extensive cytogenetical survey was performed in 19 nemacheilid species using both conventional (Giemsa staining, C- banding, Ag- and Chromomycin A3/DAPI stainings) and molecular (fluorescence in situ hybridization with 5S rDNA, 45S rDNA, and telomeric (TTAGGG)n probes) methods.

Phylogeny of the Southeast Asian freshwater fish genus Pangio (Cypriniformes; Cobitidae).

The genus Pangio is one of the most species-rich of the loach family Cobitidae and widespread across South and Southeast Asia. Its species diversity has never been studied under a clear phylogenetic approach, but four 'species-groups' were proposed according to the most obvious morphological characters. We present here phylogenetic analyses of the genus Pangio based on sequence data of the mitochondrial cytochrome b gene, the nuclear recombination-activating gene 1 (RAG 1) and a combined dataset of 109 specimens from 18 morphologically identified species across the whole distribution area of the genus.

Around or across the Carpathians: colonization model of the Danube basin inferred from genetic diversification of stone loach (Barbatula barbatula) populations.

Despite increasing information about postglacial recolonization of European freshwater systems, very little is known about pre-Pleistocene history. We used data on the recent distribution and phylogenetic relationships of stone loach mitochondrial lineages to reconstruct the initial colonization pattern of the Danube river system, one of the most important refuges for European freshwater ichthyofauna. Fine-scale phylogeography of the Danubian populations revealed five highly divergent lineages of pre-Pleistocene age and suggested the multiple origin of the Danubian stone loach.

Molecular phylogeny of the freshwater fish family Cobitidae (Cypriniformes: Teleostei): delimitation of genera, mitochondrial introgression and evolution of sexual dimorphism.

The family Cobitidae represents a characteristic element of the Eurasian ichthyofauna. Despite diverse features of sexual dimorphism, comparably few morphological characters have been utilized for taxonomic studies resulting in many unresolved puzzles. Here we present the phylogenetic relationships of Cobitidae as inferred from the mitochondrial cytochrome b gene and the nuclear gene RAG-1.

Across Siberia and over Europe: Phylogenetic relationships of the freshwater fish genus Rhodeus in Europe and the phylogenetic position of R. sericeus from the River Amur.

We present the phylogenetic relationships of the freshwater fish genus Rhodeus from 45 localities in Europe and three localities in the Amur basin using the mitochondrial cytochrome b sequence. The study aims to (1) test the colonisation history between Europe and East Asia and (2) to reconstruct the evolutionary history of Rhodeus in Europe. Our analyses revealed five monophyletic clades which correspond to four species: R.

Molecular phylogeny of the Southeast Asian freshwater fish family Botiidae (Teleostei: Cobitoidea) and the origin of polyploidy in their evolution.

The freshwater fish family Botiidae is represented by seven genera on the Indian subcontinent and in East and Southeast Asia and includes diploid as well as evolutionary tetraploid species. We present a phylogeny of Botiidae including 33 species representing all described genera using the mitochondrial cytochrome b and 12s rRNA genes to reconstruct the phylogenetic relationships among the genera and to estimate the number of polyploidisation events during their evolution. Our results show two major lineages, the subfamilies Leptobotiinae with the genera Leptobotia and Parabotia and Botiinae with the genera Botia, Chromobotia, Sinibotia, Syncrossus, and Yasuhikotakia.

The Alps as barrier to dispersal in cold-adapted freshwater fishes? Phylogeographic history and taxonomic status of the bullhead in the Adriatic freshwater drainage.

The freshwater faunas of the Italian peninsula are isolated from the rest of Europe by the geographic barrier of the Alps and consequently have developed many endemic forms and contain few non-endemic species. However, some 'non-endemics' may either represent recent invaders of the Adriatic basin or cryptic endemic species. To test these two hypotheses against each other, we studied the origin and phylogenetic relationships of bullheads, cold adapted freshwater fishes of the genus Cottus, from both sides of the Alps and Dinaric Mountains.

Cobitis ohridana and Barbatula zetensis in the River Moraca basin, Montenegro: distribution, habitat, population structure and conservation needs.

In this paper, we report on the distribution, habitat, population structure and conservation needs of Cobitis ohridana and Barbatula zetensis in the basin of the River Moraca in Montenegro. Our data show both species to be mainly distributed in the lower stretch of the main river and some tributaries in lowland habitats. Cobitis ohridana preferred more shallow water with a higher abundance of filamentous algae, while Barbatula zetensis was more numerous in slightly deeper water with more stones as a bottom substrate.