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

Liu, Siqing; Mayden, Richard L.; Zhang, Jiabo; Yu, Dan; Tang, Qisheng; Deng, Xin; Liu, Huanzhang

doi:10.1016/j.gene.2012.07.040

Cited by 43 publications

(52 citation statements)

References 69 publications

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“…Morphological variation is often inconsistent with the proposed molecular phylogenetic relationships (Liu et al, ; Prokofiev, ; Sgouros, ; Tang, Liu, Mayden, & Xiong, ; Zhu, ). For example, Schistura species do not display monophyly but instead show polyphyly (Liu et al, ; Nalbant & Bianco, ; Sgouros, ; Tang et al, ). Several Homatula species exhibit either paraphyly or polyphyly (Min, Chen, Yang, Winterbottom, & Mayden, ).…”

Section: Introductionmentioning

confidence: 99%

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

Chen

Yang

et al. 2019

Ecology and Evolution

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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.

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Section: Introductionmentioning

confidence: 99%

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

Chen

Yang

et al. 2019

Ecology and Evolution

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“…Molecular data included sequences from the type locality of P. zonalternans and from several localities near the type locality of P. phuketensis. Schistura fasciolata (JN177233- Liu et al 2012) and Nemacheilus pallidus (MF289074; UF 176446) were used as an outgroup.…”

Section: Resultsmentioning

confidence: 99%

A revision of the Paracanthocobitis zonalternans (Cypriniformes: Nemacheilidae) species complex with descriptions of three new species

Singer

Pfeiffer

Page

2017

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1,005

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The Paracanthocobitis zonalternans species complex is revised based on analysis of morphological and molecular data. Three new species, P. nigrolineata, P. marmorata, and P. triangula are described, and P. phuketensis is removed from synonymy. All species are described morphologically, geographic ranges are delimited, and relationships are discussed for those for which molecular data (cytochrome c oxidase subunit 1 -COI) are available. In view of the morphological similarities of some of the species, a surprising result of this study was the moderately large genetic distances among species. Uncorrected COI p-distances between geographic clades of P. zonalternans ranged from 7.6-9.3%, suggesting that the species are reproductively isolated from one another even though morphological changes are minor. Paracanthocobitis phuketensis, distributed in several rivers draining to the Gulf of Thailand and to the Andaman Sea, shows considerable intraspecific variation that should be explored in detail for historical and ecological explanations. Cobitis chlorosoma McClelland, 1839 from Assam, India, is a synonym of P. botia, not P. zonalternans.

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“…Moreover, on the basis of morphological data, earlier models proposed that the botids were within the same family as the cobitids, and the nemacheilids were within the Balitoridae [13]. However, the phylogeny of the Cobitoidea has been revised more recently using DNA data [22, 24, 69, 70, 71, 72, 73]. Through the use of the mitochondrial DNA genes cytochrome b and control region, and the nuclear recombination activating gene 1 (RAG-1), the Nemacheilidae and Balitoridae have been reassigned as separate sister families, and the Botiidae and Cobitidae are now recognised as different families.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2016

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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.

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

Cited by 43 publications

References 69 publications

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

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

A revision of the Paracanthocobitis zonalternans (Cypriniformes: Nemacheilidae) species complex with descriptions of three new species

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

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