Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei: Cypriniformes)

Li, Junbing; Wang, Xuzhen; Kong, Xianghui; Zhao, Kai; He, Shunping; Mayden, Richard L.

doi:10.1016/j.ympev.2007.09.012

Cited by 61 publications

(57 citation statements)

References 78 publications

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“…The resolution of Discogobio and Ptychidio in the subfamily Cyprininae is consistent with Chu (1935) and Bȃnȃrescu and Nalbant (1965), as well as more recent studies (e.g. Kong et al, 2007;Wang et al, 2007;Li et al, 2008;Tang et al, 2009;Yang and Mayden, 2010;Zheng et al, 2010). Although Luciocyprinus was not examined, its treatment in the literature (e.g.…”

Section: Discussionsupporting

confidence: 84%

“…Bȃnȃrescu and Nalbant disagreed with Lin (1933) on the placement of Ptychidio and Discogobio, removing both genera from Gobioninae to Cyprininae, hypothesizing that they are closely related to Garra. This affiliation with Garra and/ or other labeonins within the subfamily Cyprininae has been corroborated by several recent molecular studies (Kong et al, 2007;Wang et al, 2007;Li et al, 2008;Tang et al, 2009;Yang and Mayden, 2010;Zheng et al, 2010). Bȃnȃrescu and Nalbant reported the presence of an encapsulated air bladder in Microphysogobio, a genus not examined by Ramaswami (1955), which they thought was more closely related to Pseudogobio and Abbottina, genera with free swim bladders, than Saurogobio, a genus with an encapsulated swim bladder.…”

Section: Taxonomic Historymentioning

confidence: 52%

“…He et al (2008) did not find much resolution within Cyprinidae which extended to an inability to identify the gobionine sister group, but they did recover a monophyletic Gobioninae that included Gobiobotiinae. Li et al (2008) found Gobio and Gobiobotia sister to Leuciscinae. Mayden et al (2009) presented several different topologies, almost all of which found Gobioninae to be monophyletic, but with the sister group varying between Acheilognathinae and Leuciscinae.…”

Section: Molecular Systematicsmentioning

confidence: 99%

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Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae)

Tang

Agnew

Chen

et al. 2011

Molecular Phylogenetics and Evolution

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Section: Discussionsupporting

confidence: 84%

Section: Taxonomic Historymentioning

confidence: 52%

Section: Molecular Systematicsmentioning

confidence: 99%

See 1 more Smart Citation

Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae)

Tang

Agnew

Chen

et al. 2011

Molecular Phylogenetics and Evolution

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“…However, the morphological grouping of the schizothoracins had been challenged by recent molecular evidences (Li et al, 2008;Yang et al, 2015a;Yonezawa et al, 2014). The present phylogeny revealed two independent origins of these Tibetan Plateau endemic polyploid cyprinids, migrating independently of each other to the Tibetan Plateau and adapted to high altitude (Yonezawa et al, 2014).…”

Section: Biogeographic Patterns and Ploidy Levels In The Cyprininaementioning

confidence: 74%

Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau

Wang

Gan

et al. 2016

Sci. China Life Sci.

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Origin and diversification of the Tibetan polyploid cyprinids (schizothoracins) may help us to explore relationships between diversification of the cyprinids and the Tibetan Plateau uplift. Cyprininae phylogeny was analyzed using mitochondrial and nuclear DNA sequences to trace origins of polyploidy and diversifications of schizothoracins. Ancestral states reconstruction for ploidy levels indicated that the Cyprininae was diploid origin and the schizothoracin clades tetraploid origins. There were two diversification rate shifts along with diversification of the cyprinine fishes in response to the Tibetan uplift. The unusual diversification shifts were located to branches subtending the clades of Tibetan polyploid cyprinids. Our analyses suggested that (i) phylogeny of Cyprininae recovered two independent origins of the Tibetan polyploidy schizothoracins; (ii) diversifications of the schizothoracins were closely related to the Neogene uplift of the Tibetan plateau in the following ways: the relatively ancient Late Oligocene-Middle Miocene adaptive radiation may be associated with the uplift of the southern Tibet and Himalaya; the Middle Miocene-Early Pleistocene lineage-specific diversification broadly coincident with major phase of the Neogene Tibetan uplift; and the most recent Pleistocene diversification shift in Schizothorax closely coincident with the successive Kunlun-Huanghe and Gonghe movements of the Tibetan uplift and the glaciation-induced climate oscillations on the plateau.Cyprininae, polyploid, schizothoracins, the Tibetan Plateau, diversifications Citation:Wang, X., Gan, X., Li J., Chen, Y., and He, S. (2016). Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau.

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“…Among these species, 16 species represent the cave and surface species of the genus Sinocyclocheilus. In the light of the molecular phylogenetic relationships with Cyprininae (Li et al 2008a), the other four cyprinid species (Danio rerio, Carassius auratus, Cyprinus carpio, and Procypris rabaudi) were assigned to the outgroup taxa, as listed in Table 1. Muscle or fin tissues used for DNA extraction in this study were preserved in 95% ethanol.…”

Section: Samplesmentioning

confidence: 99%

Distinct Evolutionary Patterns Between Two Duplicated Color Vision Genes Within Cyprinid Fishes

Gan

2009

J Mol Evol

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We investigated the molecular evolution of duplicated color vision genes (LWS-1 and SWS2) within cyprinid fish, focusing on the most cavefish-rich genusSinocyclocheilus. Maximum likelihood-based codon substitution approaches were used to analyze the evolution of vision genes. We found that the duplicated color vision genes had unequal evolutionary rates, which may lead to a related function divergence. Divergence of LWS-1 was strongly influenced by positive selection causing an accelerated rate of substitution in the proportion of pocketforming residues. The SWS2 pigment experienced divergent selection between lineages, and no positively selected site was found. A duplicate copy of LWS-1 of some cyprinine species had become a pseudogene, but all SWS2 sequences remained intact in the regions examined in the cyprinid fishes examined in this study. The pseudogenization events did not occur randomly in the two copies of LWS-1 within Sinocyclocheilus species. Some cave species of Sinocyclocheilus with numerous morphological specializations that seem to be highly adapted for caves, retain both intact copies of color vision genes in their genome. We found some novel amino acid substitutions at key sites, which might represent interesting target sites for future mutagenesis experiments. Our data add to the increasing evidence that duplicate genes experience lower selective constraints and in some cases positive selection following gene duplication. Some of these observations are unexpected and may provide insights into the effect of caves on the evolution of color vision genes in fishes.

show abstract

Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei: Cypriniformes)

Cited by 61 publications

References 78 publications

Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae)

Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae)

Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau

Distinct Evolutionary Patterns Between Two Duplicated Color Vision Genes Within Cyprinid Fishes

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