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

Descriptions of two new species of the botiid genus Leptobotia Bleeker, 1870 (Teleostei: Cypriniformes) from South China

Two new species of Leptobotia are here described as L. rotundilobus from the Xin'an-Jiang of the upper Qiantang-Jiang basin in both Anhui and Zhejiang Provinces and the Cao'e-Jiang in Zhejiang Province, and L. paucipinna from the Qing-Jiang of the middle Chang-Jiang basin in Hubei Province, South China. Both have a plain brown body as found in L. bellacauda Bohlen & Šlechtová, 2016, L. microphthalma Fu & Ye, 1983, L. posterodorsalis Chen & Lan, 1992 and L. tientainensis (Wu, 1930). The two new species are distinct from these species in vertebral counts, further from L. posterodorsalis in vent placement and further from the other three species in pectoral-fin length. Both differ in caudal-fin coloration and shape, and dorsal-fin location and coloration, and also in internal morphology. Their validity is confirmed by their own monophyly recovered in a phylogenetic analysis based on the mitochondrial cyt b and COI genes.

Characterization of the Complete Mitochondrial Genome of the Elongate Loach and Its Phylogenetic Implications in Cobitidae

The elongate loach is an endemic fish in China. Previous studies have provided some insights into the mitochondrial genome composition and the phylogenetic relationships of the elongate loach inferred using protein-coding genes (PCGs), yet detailed information about it remains limited. Therefore, in this study we sequenced the complete mitochondrial genome of the elongate loach and analyzed its structural characteristics. The PCGs and mitochondrial genome were used for selective stress analysis and genomic comparative analysis. The complete mitochondrial genome of the elongate loach, together with those of 35 Cyprinidae species, was used to infer the phylogenetic relationships of the Cobitidae family through maximum likelihood (ML) reconstruction. The results showed that the genome sequence has a full length of 16,591 bp, which includes 13 PCGs, 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 2 non-coding regions (CR D-loop and light chain sub-chain replication origin OL). Overall, the elongate loach shared the same gene arrangement and composition of the mitochondrial genes with other teleost fishes. The Ka/Ks ratios of all mitochondrial PCGs were less than 1, indicating that all of the PCGs were evolving under purifying selection. Genome comparison analyses showed a significant sequence homology of species of Leptobotia. A significant identity between L. elongata and the other five Leptobotia species was observed in the visualization result, except for L. mantschurica, which lacked the tRNA-Arg gene and had a shorter tRNA-Asp gene. The phylogenetic tree revealed that the Cobitidae species examined here can be grouped into two clades, with the elongate loach forming a sister relationship with L. microphthalma. This study could provide additional inferences for a better understanding of the phylogenetic relationships among Cobitidae species.

Species of Garra (Cyprinidae: Labeoninae) in the Salween River basin with description of an enigmatic new species from the Ataran River drainage of Thailand and Myanmar

Garra panitvongi, new species, is described from the Ataran River drainage, Salween River basin, of southeastern Myanmar and western Thailand. It is the sixth species of Garra known from the Salween River basin and is readily distinguished from all congeners by the red-orange color of the body and caudal fin, and a pointed proboscis with a blue stripe on each side from the anterior margin of the orbit to the tip of the proboscis and with the stripes forming a V-shape. Garra panitvongi is known in the aquarium trade as the Redtail Garra. Descriptive information is provided on poorly known species of Garra in the Salween River basin, and Garra nujiangensis is transferred to Ageneiogarra.

Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes

All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits, including the characteristic loss of eyes. To understand whether such phenotypic convergence shares similar genomic bases, here we investigated genome-wide evolutionary signatures of cavefish phenotypes by comparing whole-genome sequences of three pairs of cavefishes and their surface fish relatives. Notably, we newly sequenced and generated a whole-genome assembly of the Chinese cavefish Triplophysa rosa. Our comparative analyses revealed several shared features of cavefish genome evolution. Cavefishes had lower mutation rates than their surface fish relatives. In contrast, the ratio of nonsynonymous to synonymous substitutions (ω) was significantly elevated in cavefishes compared to in surface fishes, consistent with the relaxation of purifying selection. In addition, cavefish genomes had an increased mutational load, including mutations that alter protein hydrophobicity profiles, which were considered harmful. Interestingly, however, we found no overlap in positively selected genes among different cavefish lineages, indicating that the phenotypic convergence in cavefishes was not caused by positive selection of the same sets of genes. Analyses of previously identified candidate genes associated with cave phenotypes supported this conclusion. Genes belonging to the lipid metabolism functional ontology were under relaxed purifying selection in all cavefish genomes, which may be associated with the nutrient-poor habitat of cavefishes. Our work reveals previously uncharacterized patterns of cavefish genome evolution and provides comparative insights into the evolution of cave-associated phenotypic traits.

A new species of Homatula (Teleostei, Cobitoidea, Nemacheilidae) from the Pearl River drainage, Yunnan, China

Based on morphological and molecular analysis of Homatula species distributed in the Nanpanjiang River in Yunnan, China, we described a new species, Homatula robustasp. nov. It differs from its congeners by a combination of the following characters: naked and robust body with well-developed crests (caudal peduncle depth as a percentage of its length: 70.5–78.5%); lateral line complete; median notch on lower jaw; median gap on lower lip; three pairs of short barbels, with maxillary barbels extending posteriorly to anterior edge of eyes; branched dorsal-fin rays 8½; and vertebrae 37–39. It can further be distinguished from H. nanpanjiangensis by several differences of the caudal skeleton such as the number of hypural elements, the presence of epurale and the shape of neural and haemal spines. Phylogenetic analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene indicated that the new species represents an independent lineage. It is separated from other Homatula species by a minimum of 5.3% Kimura-2-parameter distance in the COI gene. Furthermore, we confirmed that Homatula wenshanensis should be a member of Homatula based on both skeleton and molecular evidence.

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. However, the results revealed more than 20% of undescribed species within the ingroup and showed that species do not cluster according to the presently recognised genera. At least one of the genetic clades shows signs of an eastward range expansion during the second half of Miocene from north India via Myanmar into Laos, western China, and western Thailand. We conclude that the approach of picking monophyletic lineages to study biodiversity, systematics, and evolutionary history helps to open the door to large animal families.

A review of the Cypriniform tribe Yunnanilini Prokofiev, 2010 from China, with an emphasis on five genera based on morphologies and complete mitochondrial genomes of some species

The loach tribe Yunnanilini from China is reviewed here using morphological characters and complete mitochondrial genomes of select species. Molecular data suggest that the tribe Yunnanilini is not monophyletic and can be divided into three clades. Species of the Yunnanilus nigromaculatus group form an independent genus and are placed in Eonemachilus. In the phylogenetic tree, Y. jinxiensis clusters with Paranemachilus genilepis, and Y. pulcherrimus clusters with Micronemacheilus cruciatus, indicating that Y. jinxiensis and Y. pulcherrimus belong to Paranemachilus and Micronemacheilus, respectively. Based on morphological data, Y. bailianensis and Y. longibarbatus are placed in Heminoemacheilus, while Y. jinxiensis and Y. pulcherrimus, are placed in Paranemachilus and Micronemacheilus, respectively. Yunnanilus niulanensis and Y. qujinensis are treated as junior synonyms of Eonemachilus caohaiensis. Eonemachilus, Micronemacheilus, and Yunnanilus are show short separation between anterior and posterior nostrils. The genera can be distinguished from each other by mouth structure, lateral line and cephalic lateral-line canals, and papillae on median part of both lips. The anterior and posterior nostrils of Heminoemacheilus and Paranemachilus are closely set. Paranemachilus and Micronemacheilus are distinguished by cheeks covered with scales and lips with papillae, respectively. Our phylogenetic tree and morphological characters support Traccatichthys as a valid genus, which can be distinguished from Micronemacheilus by anterior and posterior nostrils closely set (vs. clearly separated). Four species are placed in Traccatichthys.

Phylogenetic analysis and osteological comparison of the cave-dwelling spined loach, Bibarba parvoculus (Cypriniformes: Cobitidae), and its surface congener

Bibarba parvoculus, a depigmented and small-eyed, spined loach, is endemic to a karst cave in southern China. Both mitochondrial Cytb and nuclear RAG1 gene analyses indicate that B. parvoculus and its only surface congener, B. bibarba, form the basal-most lineage in the so-called Northern Clade of Cobitidae. Genetic divergence for Cytb is 10.3 % between B. parvoculus and B. bibarba. A duplication of the lamina circularis on the second and third pectoral rays occurs in male Bibarba species. The osteology of the two species is illustrated and compared using X-ray microtomography. Bibarba parvoculus has higher vertebral counts, a broader anterior part of the frontal bone at the orbital region and decreased sexual dimorphism when compared with B. bibarba. The coracoid, mesocoracoid and scapula are stouter in males of both species, but the three bones are autogenous in B. parvoculus, while fused with the cleithrum in B. bibarba. Specific differentiation of B. parvoculus is corroborated by both molecular and morphological evidence. The split between the two species is estimated to have occurred in the Early Miocene.

The mitogenome of freshwater loach Homatula laxiclathra (Teleostei: Nemacheilidae) with phylogenetic analysis of Nemacheilidae

The complete mitogenome can provide valuable genetic information to reconstruct relationships between species. In this study, we sequenced a stone loach, Homatula laxiclathra (Teleostei: Nemacheilidae), which is found in the northern region of the Qinling Mountains in China. The size of the H. laxiclathra mitogenome is 16,570 bp, which contains 37 typical mitochondrial genes including 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a control region (D-loop) with a total AT content of 55.8%. This is similar to other Nemacheilidae sequences published in GenBank. Furthermore, a mito-phylogenomic analysis of 46 Nemacheilidae species places H. laxiclathra in a robust monophyletic Homatula cluster with other Homatula species. Our results contribute toward a better understanding of a true phylogeny of these species based on large-scale taxonomic samplings as well as to help grasp the evolution of fish mitogenomes.

Exploring taxonomic diversity and biogeography of the family Nemacheilinae (Cypriniformes)

Nemacheilidae, in the superfamily Cobitoidea, is comprised of many of morphologically similar fish species that occur in Eurasian water bodies. This large group shows inconsistencies between traditional morphological taxonomy and molecular phylogenetic data. We used mitochondrial genomes, recombinase-activating gene proteins 1 (RAG1) and the mitochondrial cytochrome c oxidase I gene (COI) to study the phylogenetic relationships among Nemacheilidae species using Bayesian inference and maximum likelihood approaches. Phylogenetic analyses based on mitogenomes provided support for two clades (I and II). The mitogenomes, RAG1, and COI results indicated that several species and genera were not consistent with the traditional morphological subdivisions. The two clades inferred from mitogenomes showed clear geographical patterns. The Tibetan Plateau, Hengduan Mountains, and the Iran Plateau may act as a barrier dividing the clades. The estimated timing of clades separation (36.05 million years ago) coincides with the first uplift of the Tibetan Plateau. We conclude that the geological history of the Tibetan Plateau played a role in the diversification and distribution of the Nemacheilidae taxa. These results provided a phylogenetic framework for future studies of this complex group.

Genetic legacy of tertiary climatic change: a case study of two freshwater loaches, Schistura fasciolata and Pseudogastromyzon myersi, in Hong Kong

The high biodiversity and strong population structure of freshwater fauna has often been attributed to historical geological and climatic alterations. The impact of these historical changes on obligate freshwater species on a small geographical scale has not been well understood due to the lack of fine-scale comparative phylogeographic studies. Strong population structure has been reported in a goby and a caridean shrimp in Hong Kong, a small but highly developed city in South China, but the common drivers of population differentiation in freshwater fauna in this region remain unclear. This study examined the fine-scale phylogeographic patterns of two freshwater loaches, Schistura fasciolata and Pseudogastromyzon myersi in Hong Kong, using sequence data of mitochondrial control region and two nuclear markers (interphotoreceptor retinoid binding protein gene 2 and ribosomal protein S13 gene). Results show that they exhibit pronounced population structure as supported by high and significant Φ_ST. Phylogenetic analyses based on the control region reveal six and three distinct lineages in S. fasciolata and P. myersi, respectively. Phylogeographic structure of both species generally follows the paleodrainage pattern, though P. myersi shows a shallower structure on the Mainland, perhaps due to their higher mobility. Most of these lineages diverged during the Pliocene and Late Pleistocene, a period with marked sea-level fluctuations. In a broader context, this suggests that sea-level fluctuation played an important role in shaping even the fine-scale population structure of freshwater fish in South China, implying that the genetic diversity of this fauna may be higher than expected.

Evolution and phylogenetic application of the MC1R gene in the Cobitoidea (Teleostei: Cypriniformes)

Fish of the superfamily Cobitoidea sensu stricto (namely loaches) exhibit extremely high diversity of color patterns, but so far little is known about their evolutionary mechanism. Melanocortin 1 receptor gene (MC1R) plays an important role during the synthesis of melanin and formation of animal body color patterns. In this study, we amplified and sequenced the partial MC1R gene for 44 loach individuals representing 31 species of four families. Phylogenetic analyses yielded a topology congruent with previous studies using multiple nuclear loci, showing that each of the four families was monophyletic with sister relationships of Botiidae+ (Cobitidae+(Balitoridae+Nemacheilidae)). Gene evolutionary analyses indicated that MC1R in loaches was under purifying selection pressure, with various sites having different dN/dS values. Both Botiidae and Cobitidae had lower dN/dS values than those of background lineages, suggesting their evolution might be strongly affected by purifying selection pressure. For Balitoridae and Nemacheilidae, both had larger dN/dS values than those of background lineages, suggesting they had a faster evolutionary rate under more relaxed selection pressure. Consequently, we inferred that the relatively stable color patterns in Botiidae and Cobitidae might result from the strong purifying selection pressure on the MC1R gene, whereas the complicated and diverse color patterns in Balitoridae and Nemacheilidae might be associated with the relaxed selection pressure. Given the easy experimental procedure for the partial MC1R gene and its excellent performance in reconstructing phylogeny, we suggest this gene could be used as a good molecular marker for the phylogenetic study of fish species.

The complete mitochondrial genome sequence of Vanmanenia stenosoma (Teleostei: Gastromyzontidae)

Vanmanenia stenosoma belongs to the order Cypriniformes, and it is a typical torrent loach in China. In this study, we successfully determined the complete mitochondrial genome sequence of V. stenosoma (type species of Vanmanenia), which is 16,560 base pairs (bp) and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a putative control region. The genome has the same gene order as that found in other species of the family Gastromyzontidae. This suggests those genera share a common ancestral mitogenome. Nevertheless, phylogenetic reconstructions did not support the monophyly of the genus Vanmanenia.

The Gastric Phenotype in the Cypriniform Loaches: A Case of Reinvention?

The stomach, which is characterized by acid peptic digestion in vertebrates, has been lost secondarily multiple times in the evolution of the teleost fishes. The Cypriniformes are largely seen as an agastric order; however, within the superfamily Cobitoidea, the closely related sister groups Nemacheilidae and Balitoridae have been identified as gastric families. The presence of these most recently diverged gastric families in an otherwise agastric clade indicates that either multiple (>2–3) loss events occurred with the Cyprinidae, Catostomidae and Cobitidae, or that gastric reinvention arose in a recent ancestor of the Nemacheilidae/Balitoridae sister clade. In the present study, the foregut regions of Cobitidae, Nemacheilidae/Balitoridae and the ancestral Botiidae family members were examined for the presence of gastric glands and gastric proton pump (Atp4a) α subunit expression by histology and immunohistochemistry respectively. Atp4a gene expression was assessed by reverse transcriptase-polymerase chain reaction (RT-PCR). Gastric glands expressing apical H⁺/K⁺-ATPase α subunit and isolated partial sequences of atp4a, identified using degenerate primers showing clear orthology to other vertebrate atp4a sequences, were detected in representative species from Nemacheilidae/ Balitoridae and Botiidae, but not Cobitidae (Misgurnus anguillicaudatus). In summary, we provide evidence for an uninterrupted gastric evolutionary lineage in the Cobitoidea, making it highly improbable that the stomach was reinvented in the Nemacheilidae/Balitoridae clade consistent with Dollo’s principle. These results also indicate that the gastric trait may be present elsewhere in the Cobitoidea.

Mitogenomic perspectives on the origin of Tibetan loaches and their adaptation to high altitude

Tibetan loaches are the largest group of Tibetan fishes and are well adapted to the Tibetan Plateau. To investigate the origin of Tibetan loaches and their adaptations to the Tibetan Plateau, we determined 32 complete mitochondrial genomes that included 29 Tibetan loach species, two Barbatula species and Schistura longus. By combining these newly determined sequences with other previously published mitochondrial genomes, we assembled a large mitogenomic data set (11,433 bp) of 96 species in the superfamily Cobitoidea, to investigate the phylogenetic status of the genus Triplophysa. The resulting phylogeny strongly supported that the genus Triplophysa forms a monophyletic group within Nemacheilidae. Our molecular dating time suggests that the lineage leading to the Tibetan loaches and other loaches diverged approximately 23.5 Ma, which falls within the period of recent major uplifts of the Tibetan Plateau in the Early Miocene. Selection analyses revealed that the mitochondrial protein-coding genes of Tibetan loaches have larger ratios of nonsynonymous to synonymous substitutions than do those of non-Tibetan loaches, indicating that Tibetan loaches accumulated more nonsynonymous mutations than non-Tibetan loaches and exhibited rapid evolution. Two positively selected sites were identified in the ATP8 and ND1 genes.

The complete mitochondrial genome of Claea dabryi (Teleostei, Nemachilinae, Claea)

Claea dabryi is a small bottom-dwelling fish that is endemic to the upper stream of the Yangtze River. In this study, we successfully sequenced the first mitochondrial genome of C. dabryi. The mitogenome is 16 569 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region (D-loop). Most of the genes are encoded on the heavy strand, except for eight tRNAs (tRNA^Gln, tRNA^Ala, tRNA^Asn, tRNA^Cys, tRNA^Tyr, tRNA^Ser, tRNA^Glu, and tRNA^Pro) and ND6 gene. In this paper, we utilized 12 protein-coding genes of C. dabryi and other 11 closely species to construct the species phylogenetic tree to verify the accuracy of C. dabryi.

MITOSCISSOR: A Useful Tool for Auto-Assembly of Mitogenomic Datasets in the Evolutionary Analysis of Fishes

As a result of the development of rapid and efficient sequencing technologies, complete sequences of numerous mitochondrial genomes are now available. Mitochondrial genomes have been widely used to evaluate relationships between species in several fields, including evolutionary and population genetics, as well as in forensic identification and in the study of mitochondrial diseases in humans. However, the creation of mitochondrial genomes is extremely time consuming. In this paper, we present a new tool, MITOSCISSOR, which is a rapid method for parsing and formatting dozens of complete mitochondrial genome sequences. With the aid of MITOSCISSOR, complete mitochondrial genome sequences of 103 species from Tetraodontiformes (a difficult-to-classify order of fish) were easily parsed and formatted. It typically takes several days to produce similar results when relying upon manual editing. This tool could open the .gb file of Genbank directly and help us to use existing mitogenomic data. In the present study, we established the first clear and robust molecular phylogeny of 103 tetraodontiform fishes, a goal that has long eluded ichthyologists. MITOSCISSOR greatly increases the efficiency with which DNA data files can be parsed and annotated, and thus has the potential to greatly facilitate evolutionary analysis using mitogenomic data. This software is freely available for noncommercial users at http://www.filedropper.com/mitoscissor.

Bottom Feeding and Beyond: How the Premaxillary Protrusion of Cypriniforms Allowed for a Novel Kind of Suction Feeding

While much of the functional work on suction feeding has involved members of Acanthopterygii, an earlier cypriniform radiation led to over 3200 species filling nearly every freshwater trophic niche. Within the great majority of acanthomorph clades that have been investigated suction feeding and the underlying morphology responsible for the generation of rapid suction have been largely conserved. This conserved feeding-apparatus is often associated with increasing the force experienced by the prey item, thus making a strike on elusive prey more effective. Cypriniforms' trophic anatomy is comprised of a number of novelties used for benthic feeding, which characterized early members of this clade. The modified cypriniform structure of the oral jaws represents a situation in which a particular type of suction feeding allowed for probing the benthos with a more functionally maneuverable anatomy. Requisite evolutionary modifications included origin and elongation of a median kinethmoid, duplications of certain divisions of the muscles of the adductor mandibulae, and origin of a dorsal, intra-buccal muscular palatal organ used in winnowing detritus. The elongated kinethmoid (coupled with modified adductor muscles) allowed for a type of premaxillary protrusion that decoupled the upper and lower jaws, enabled premaxillary protrusions with a closed mouth, and facilitated benthic feeding by increasing functional flexibility. The resultant flow of fluid generated by cypriniforms is also quite flexible, with multiple instances of peak flow in a single feeding event. This greatly modified morphology allowed for a degree of kinematic maneuverability not seen within most acanthomorphs. Later cypriniform radiations into piscivorous, insectivorous, or planktivorous feeding guilds were associated with shortening of the kinethmoid and with simplified morphology of the adductor, likely involving an emphasis on ram feeding. Although this suite of morphological novelties seemingly originated within the context of benthic feeding, with minimal modifications these anatomical features were later coopted during radiations into different functional niches.

Paragyrodactylus variegatus n. sp. (Gyrodactylidae) from Homatula variegata (Dabry De Thiersant, 1874) (Nemacheilidae) in central China

Paragyrodactylus variegatus n. sp. (Monogenea: Gyrodactylidae) is described from the fins and body surface of Homatula variegata (Dabry de Thiersant, 1874) living in cold-water streams in the Qinling Mountains of central China. It represents the third known species in the genus, with all species parasitizing Asian river loaches (Cypriniformes: Nemacheilidae). The new species resembles most closely Paragyrodactylus iliensis Gvosdev and Martechov, 1953 , but is diagnosed by its marginal hooks being longer than 19 μm, a sickle longer than 4 μm, a sickle aperture shorter than the sickle distal width, and absence of a ventromedial indentation in the haptoral accessory hard part. Scanning electron microscopy reveals a central foramen in the haptoral accessory hard part, and small knob-like protuberances on the heel and toe of the marginal hook sickle. A partial 18S (448 bp) and complete ITS-1, 5.8S, and ITS-2 (1,139 bp) rDNA sequences are provided. A preliminary phylogenetic analysis based on the partial 18S gene, which included all sequenced genera of the Gyrodactylidae, suggests P. variegatus n. sp. is basal within Gyrodactylus sensu lato. It is proposed that the genus is a relict freshwater lineage parasitizing river loaches in the mountain plateaus of central Asia.