Qiongying Tang

Mitochondrial capture and incomplete lineage sorting in the diversification of balitorine loaches (Cypriniformes, Balitoridae) revealed by mitochondrial and nuclear genes

Tang, Q.‐Y., Liu, S.‐Q., Yu, D., Liu, H.‐Z. & Danley, P.D. (2012) Mitochondrial capture and incomplete lineage sorting in the diversification of balitorine loaches (Cypriniformes, Balitoridae) revealed by mitochondrial and nuclear genes. —Zoologica Scripta, 41, 233–247.

The complete mitogenome sequence of a cave loach Triplophysa rosa (Teleostei, Balitoridae, Nemacheilinae)

China is very rich in cavefishes and some detailed studies on their taxonomy and biology have been carried out, but many other aspects such as genetics and evolution need further investigation. Here, we sequenced the complete mitogenome sequence of the Rose Blind Plateau Loach, Triplophysa rosa, and combined with other 27 ostariophysan complete mitogenome sequences, the phylogenetic position of T. rosa was estimated. The 16,585 bp mitogenome of T. rosa was a typical vertebrate mitochondrial genome containing 13 protein-coding, 2 rRNA, 22 tRNA genes, and 1 control region (CR). The CR of T. rosa was characterized by one termination-associated sequence and seven conserved sequence blocks (CSB-B, D, E, F, and CSB I, II, III). Phylogenetic analyses showed that T. rosa belongs to the subfamily Nemacheilinae and formed a sister-group relationship with the genus Barbatula. Further analyses based on the concatenated mitochondrial cyt b and D-loop sequences showed that T. rosa clustered with other Triplophysa species, and it was located in the basal position within the genus. In addition, the molecular clock estimations showed that T. rosa might have diverged from other Triplophysa species at about 48.3 million years ago during the rapid uplift period of the Qinghai-Tibetan Plateau.

Phylogenetic relationships of the Cobitoidea (Teleostei: Cypriniformes) inferred from mitochondrial and nuclear genes with analyses of gene evolution

The superfamily Cobitoidea of the order Cypriniformes is a diverse group of fishes, inhabiting freshwater ecosystems across Eurasia and North Africa. The phylogenetic relationships of this well-corroborated natural group and diverse clade are critical to not only informing scientific communities of the phylogeny of the order Cypriniformes, the worlds largest freshwater fish order, but are key to every area of comparative biology examining the evolution of traits, functional structures, and breeding behaviors to their biogeographic histories, speciation, anagenetic divergence, and divergence time estimates. In the present study, two mitochondrial gene sequences (COI, ND4+5) and four single-copy nuclear gene segments (RH1, RAG1, EGR2B, IRBP) were used to infer the phylogenetic relationships of the Cobitoidea as reconstructed from maximum likelihood (ML) and partitioned Bayesian Analysis (BA). Analyses of the combined mitochondrial/nuclear gene datasets revealed five strongly supported monophyletic Cobitoidea families and their sister-group relationships: Botiidae+(Vaillantellidae+(Cobitidae+(Nemacheilidae+Balitoridae))). These recovered relationships are in agreement with previous systematic studies on the order Cypriniformes and/or those focusing on the superfamily Cobitoidea. Using these relationships, our analyses revealed pattern lineage- or ecological-group-specific evolution of these genes for the Cobitoidea. These observations and results corroborate the hypothesis that these group-specific-ancestral ecological characters have contributed in the diversification and/or adaptations within these groups. Positive selections were detected in RH1 of nemacheilids and in RAG1 of nemacheilids and genus Vaillantella, which indicated that evolution of RH1 (related to eyes optic sense) and RAG1 (related to immunity) genes appeared to be important for the diversification of these groups. The balitorid lineage (those species inhabiting fast-flowing riverine habitats) had, as compared with other cobitoid lineages, significantly different dN/dS, dN and dS values for ND4 and IRBP genes. These significant differences are usually indicative of weaker selection pressure, and lineage-specific evolution on genes along the balitorid lineage. Furthermore, within Cobitoidea, excluding balitorids, species living in subtropics had significantly higher dN/dS values in RAG1 and IRBP genes than those living in temperate and tropical zones. Among tropical cobitoids, genes COI, ND5, EGR2B, IRBP and RH1, had a significantly higher mean dS value than those species in subtropical and temperate groups. These findings suggest that the evolution of these genes could also be ecological-group-specific and may have played an important role in the adaptive evolution and diversification of these groups. Thus, we hypothesize that the genes included in the present study were actively involved in lineage- and/or ecological-group-specific evolutionary processes of the highly diverse Cobitoidea. These two evolutionary patterns, both subject to further testing, are hypothesized as integral in the diversification with this major clade of the worlds most diverse group of freshwater fishes.

Global climate change will severely decrease potential distribution of the East Asian coldwater fish Rhynchocypris oxycephalus (Actinopterygii, Cyprinidae)

Global climate change has been suggested to cause decrease of distribution area of many species. However, this has not been tested for East Asian inland coldwater fish. Chinese minnow (Rhynchocypris oxycephalus) is a small typical coldwater fish, which is endemic to East Asia and generally inhabits stream headwaters. Due to its occurrence in temperate south China, there is growing concern about its future fate in the face of global warming. In this study, we employed maximum entropy approach to analyze how distribution of this species would be impacted by future climate change. We collected data of 310 independent distribution points and 20 environmental variables, and conducted modeling under three general circulation models assuming two gas emission scenarios for 2020s, 2050s, and 2080s. The results showed that the Min temperature of coldest month was the most important climatic variable for potential distribution of the Chinese minnow. Modeling predicted geographical distribution of the Chinese minnow would shrink over time and become much more limited in all the situations especially in South-eastern China, and there would be little suitable habitat left in this region by 2080s. Our results confirm that climate change clearly poses a severe threat to the Chinese minnow, and we suggest that conservation efforts should focus on lower temperature areas within the current range, because these areas will remain relatively cool and may be still suitable for the Chinese minnow even under the most drastic climate change scenarios.

The complete mitochondrial genome sequence of Triplophysa bleekeri (Teleostei, Balitoridae, Nemacheilinae).

The genus Triplophysa (plateau loach) is a highly diverse group in the family Balitoridae with 133 valid species, and they play an important role in zoogeographic study of the Qinghai-Tibet Plateau. In this study, we sequenced the complete mitochondrial genome of a Triplophysa species, Triplophysa bleekeri. Combined with the complete mitogenome sequences of other 10 balitorids, the phylogenetic position of T. bleekeri was estimated. The mitochondrial genome of T. bleekeri is similar to those of the typical vertebrates, 16,568 bp in length, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 non-coding control region (D-loop). In the D-loop region, two pair of motifs, “TACAT” and its reverted and complemented sequence “ATGTA”, can be found in the domain of termination-associated sequence; six conserved sequences (CSB-F, CSB-E, CSB-D, and CSB I–III) can be identified by searching some conserved motifs. Phylogenetic analyses showed that the three Triplophysa species clustered together, with T. bleekeri sister to Triplophysa stoliczkai. The two genera Triplophysa and Barbatula formed a sister-group relationship, the genus Lefua located in the intermediate position, and the genus Schistura was in the basal position in the subfamily Nemacheilinae. Further investigations with more Triplophysa species included need to be performed to better understand the evolutionary history of this intriguing genus.

Geological events and Pliocene climate fluctuations explain the phylogeographical pattern of the cold water fish Rhynchocypris oxycephalus (Cypriniformes: Cyprinidae) in China

BackgroundRhynchocypris oxycephalus is a cold water fish with a wide geographic distribution including the relatively warm temperate regions of southern China. It also occurs in second- and third-step geomorphic areas in China. Previous studies have postulated that high-altitude populations of R. oxycephalus in southern China are Quaternary glacial relics. In this study, we used the mitochondrial gene Cytb and the nuclear gene RAG2 to investigate the species phylogeographical patterns and to test two biogeographic hypotheses: (1) that divergence between lineages supports the three-step model and (2) climatic fluctuations during the Quaternary resulted in the present distribution in southern China.ResultsPhylogenetic analysis detected three major matrilines (A, B, and C); with matrilines B and C being further subdivided into two submatrilines. Based on genetic distances and morphological differences, matriline A potentially represents a cryptic subspecies. The geographic division between matrilines B and C coincided with the division of the second and third geomorphic steps in China, suggesting a historical vicariance event. Pliocene climatic fluctuations might have facilitated the southwards dispersal of R. oxycephalus in matriline C, with the subsequent warming resulting in its split into submatrilines C1 and C2, leaving submatriline C2 as a relic in southern China.ConclusionsOur study demonstrates that geological events (three steps orogenesis) and climate fluctuations during the Pliocene were important factors in shaping phylogeographical patterns in R. oxycephalus. Notably, no genetic diversity was detected in several populations, all of which possessed unique genotypes. This indicates the uniqueness of local populations and calls for a special conservation plan for the whole species at the population level.

Molecular Phylogeny and Conservation Priorities of the Subfamily Acheilognathinae (Teleostei: Cyprinidae)

It is increasingly accepted that conservation work should consider the evolutionary history of target species. Fishes in the subfamily Acheilognathinae, family Cyprinidae, are, with the exception of three species exclusively distributed in Europe, restricted to Asia and show a distinct spawning behavior in laying their eggs in gill chambers of freshwater mussels. At present, many of the 70 species recognized in this group are facing with serious population decline in China and Japan, and their phylogenetic relationships are not well resolved. In the present study, based on mtDNA cyt b and 12S rRNA gene sequences, we reconstructed a more detailed species-level phylogenetic tree of this group, and assessed species conservation priorities based on their evolutionary distinctiveness. Molecular phylogenetic analyses showed that the Acheilognathinae contains two major clades: Acheilognathus clade and Tanakia-Rhodeus clade. Based on this phylogenetic result, conservation priority analyses were conducted using ED (evolutionary distinctiveness)/HED (heightened evolutionary distinctiveness), and EDGE (evolutionary distinctiveness and global endangeredness)/HEDGE (heightened evolutionary distinctiveness and global endangeredness) methods. The results suggested that T. himantegus, T. lanceolata, A. gracilis, A. imberbis, T. tanago, and A. longipinnis should be ranked as the top-priority species for conservation. According to our results, we also discussed the current conservation efforts of the bitterling fishes and gave suggestions for future work.

The complete mitochondrial genome sequence of Sinogastromyzon sichangensis (Cypriniformes, Balitoridae).

Abstract Sinogastromyzon sichangensis, belonging to the family Balitoridae in Cypriniformes, is endemic to the Upper Yangtze River and the Qing River. In this study, the complete mitochondrial genome of S. sichangensis was sequenced with its structure analyzed. The mitochondrial genome of S. sichangensis is similar to those of the typical vertebrates, 16,567 bp in length, including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and one non-coding control region (D-loop). The D-loop of S. sichangensis was characterized by one termination-associated sequence and seven conserved sequence blocks (CSB-F, CSB-E, CSB-D, CSB-B and CSB I-III). The mitogenome sequence of S. sichangensis could contribute to estimate the phylogenetic relationship of the Balitoridae. Further investigations with more Sinogastromyzon species and other balitorid fishes included should be performed to better understand the evolutionary history of this unique group of fishes which can successfully adapt to mountain torrents.

Phylogenetic relationships among Cobitoidea based on mitochondrial ND4 and ND5 gene sequences

In the present study, we cloned and sequenced 10 new ND4 and ND5 gene sequences of Cobitoidea. These sequences were used to reconstruct phylogenetic relationships together with those of 15 other species downloaded from GenBank. The results showed that the length of ND4 gene sequence was 1 380-1 387 bp with ATG as starting codon and incomplete termination signal as terminated codon; the length of ND5 gene sequence was 1 821-1 839 bp with ATG as starting codon and TAA or TAG as terminated codon; three tRNA genes coding tRNAs that carry hisidine, serine and leucine respectively, were inserted between ND4 and ND5 genes. A, T, C and G accounted for 30.4%, 27.3%, 14.2% and 28.1% in ND4/ND5 gene (including intervening three tRNA genes). The content of A+T (57.7%) is higher than that of G+C (42.3%). The estimated Ti/Tv ratio was 1.586. With Danio rerio and Cyprinus carpio as outgroups, the phylogenetic relationships of Cobitoidea were analyzed using maximum parsimony (MP) method, maximum likelihood (ML) method and Bayesian analyses (BI). Results of all the three methods indicated that Cobitinae, Nemacheilinae, Botiinae, Balitoridae and Vaillantellidae were all monophyletic respectively, and their interrelationships were: (Vaillantellidae + (Botiinae + (Cobitinae + (Nemacheilinae + Balitoridae)))), which was consistent with the previous studies based on the whole mitogenome and some nuclear genes sequences (eg. RAG1 gene). However, the present results differ from those based upon other mtDNA genes sequences (e.g. the cyt b and D-loop showed that Nemacheilinae grouped with Cobitinae forming sister-group, then they clustered with Balitoridae). The difference could be due to the phylogenetic information carried by different length sequence: Longer sequences carry more information and result in more reliable phylogenetic trees.

Acheilognathus striatus (Family: Cyprinidae), a new bitterling species from the lower Yangtze River, China

A new species of bitterling, Acheilognathus striatus sp. nov., is described on the basis of 57 specimens collected from the lower Yangtze River in Jiangxi Province, China. It can be distinguished from all congeners by the following combined characters: a pair of relatively long barbels, slightly longer than half of eye diameter; dorsal fin with three simple and 8–9 branched fin rays, anal fin with three simple and 7–8 branched fin rays; a black longitudinal stripe on body from the base of caudal peduncle, distinctly reaching anteriorly to the vertical line from the origin of dorsal fin, broader in males than in females; a scale distance between the longitudinal stripe and lateral line below the origin of dorsal fin; dorsal and anal fin margined with black band in males.