Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): A proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses

Mayden, Richard L.; He, Shunping

doi:10.1016/j.ympev.2012.09.024

Cited by 18 publications

(18 citation statements)

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“…The recovery of a monophyletic subfamily Oxygastrinae corroborates the conclusions of Tang et al (2013), which were logical extensions of earlier works that had recognized a similar grouping under different names (e.g., Nikolskii 1954;Bănărescu 1967;Gosline 1978;Cavender & Coburn 1992), as well as many recent molecular studies that all pointed to an ill-defined group of fishes with uncertain affinities to other cyprinid families (e.g., He et al 2004;Saitoh et al 2006Saitoh et al , 2011Kong et al 2007aKong et al , b, 2008Rüber et al 2007;Wang et al 2007a;Mayden et al 2008;Fang et al 2009;Tang et al 2010Tang et al , 2011Tao et al 2010Tao et al , 2013. For more information on the nomenclatural rationale for the recognition of Oxygastrinae as the family-group name for this clade see Tang et al (2013), who detailed the various names that apply to the group and provided a partial synonymy for Oxygastrinae Bleeker 1860.…”

Section: Discussionsupporting

confidence: 86%

“…Numerous molecular studies have touched upon this group in one way or another (e.g., He et al 2001He et al , 2004He et al , 2008Wang et al 2002Wang et al , 2004Wang et al , 2007aWang et al , 2008Liu & Chen, 2003;Saitoh et al 2006Saitoh et al , 2011Kong et al 2007aKong et al , b, 2008Rüber et al 2007;Li et al 2009;Mayden et al 2008Mayden et al , 2009Fang et al 2009;Bufalino & Mayden 2010;Mayden & Chen, 2010;Tang et al 2010Tang et al , 2013Tao et al 2010Tao et al , 2013Liao et al 2011a). Liu and Chen (2003: figs.…”

Section: Introductionmentioning

confidence: 99%

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Limits and phylogenetic relationships of East Asian fishes in the subfamily Oxygastrinae (Teleostei: Cypriniformes: Cyprinidae)

Tang¹,

Agnew²,

Hirt³

et al. 2013

Zootaxa

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The cyprinid subfamily Oxygastrinae is composed of a diverse group of fishes that has been taxonomically and phylogenetically problematic. Their great variation in appearance, life histories, and trophic diversity resulted in uncertainty regarding their relationships, which led to their historical classification across many disparate subfamilies. The phylogenetic relationships of Oxygastrinae are resolved based on sequence data from four loci: cytochrome b, cytochrome c oxidase I, opsin, and recombination activating gene 1. A combined data matrix consisting of 4114 bp for 144 taxa was compiled and analyzed using maximum likelihood and parsimony optimality criteria. The subfamily Oxygastrinae is recovered as a monophyletic group that includes Ancherythroculter, Aphyocypris, Candidia, Chanodichthys, Ctenopharyngodon, Culter, Distoechodon, Elopichthys, Hainania, Hemiculter, Hemiculterella, Hemigrammocypris, Hypophthalmichthys, Ischikauia, Macrochirichthys, Megalobrama, Metzia, Mylopharyngodon, Nicholsicypris, Nipponocypris, Ochetobius, Opsariichthys, Oxygaster, Parabramis, Parachela, Paralaubuca, Pararasbora, Parazacco, Plagiognathops, Pseudobrama, Pseudohemiculter, Pseudolaubuca, Sinibrama, Squaliobarbus, Toxabramis, Xenocyprioides, Xenocypris, Yaoshanicus, and Zacco. Of these genera, the following were found to be monophyletic: Aphyocypris, Distoechodon, Hypophthalmichthys, Nipponocypris, Opsariichthys, Parachela, Paralaubuca, Plagiognathops, Xenocyprioides, and Xenocypris. The following genera were not monophyletic: Metzia, Hemiculter, Toxabramis, Ancherythroculter, Chanodichthys, Culter, Megalobrama. The remainder are either monotypic or were represented by only a single species. Four genera not examined in this study are provisionally classified in Oxygastrinae: Anabarilius, Longiculter, Pogobrama, and Rasborichthys.

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Section: Discussionsupporting

confidence: 86%

Section: Introductionmentioning

confidence: 99%

Limits and phylogenetic relationships of East Asian fishes in the subfamily Oxygastrinae (Teleostei: Cypriniformes: Cyprinidae)

Tang¹,

Agnew²,

Hirt³

et al. 2013

Zootaxa

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“…Placement of these families has varied across different studies [1, 4, 7, 69, 70] and here we obtain sister relationships between Acheilognathidae + Gobionidae and Tanichthyidae + Leuciscidae, with Xenocyprididae sister to all four of these families (Fig. 2).…”

Section: Discussionsupporting

confidence: 59%

Resolving Cypriniformes relationships using an anchored enrichment approach

et al. 2016

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BackgroundCypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288 bp, average locus length of 1011 bp).ResultsConcatenation analysis establishes a robust tree with 97 % of nodes at 100 % bootstrap support. Species tree analysis was highly congruent with the concatenation analysis with only two major differences: monophyly of Cobitoidei and placement of Danionidae.ConclusionsMost major clades obtained in prior molecular studies were validated as monophyletic, and we provide robust resolution for the relationships among these clades for the first time. These relationships can be used as a framework for addressing a variety of evolutionary questions (e.g. phylogeography, polyploidization, diversification, trait evolution, comparative genomics) for which Cypriniformes is ideally suited.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0819-5) contains supplementary material, which is available to authorized users.

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“…(3) The oldest known Mylopharyngodon fossil ( Mylopharyngodon wui ), paleomagnetically dated to 12.5 Mya [50], is known from the middle Miocene of China. Ctenopharyngodon idella is the sister group of Mylopharyngodon piceusi [51], [52], and we assumed that the MRCA of Mylopharyngodon and its sister group was at least 12.5 Mya (log (mean) = “0.5” log (stdev) = “1.0” offset = “12.5”). (4) The oldest fossil similar to Myxocyprinus asiaticus ( Plesiomyxocyprinus arratiae ) was recorded from the early to middle Eocene in China (37.2–40.4 Mya; [46], [53]).…”

Section: Methodsmentioning

confidence: 99%

Molecular Phylogeny and Biogeography of Percocypris (Cyprinidae, Teleostei)

Yang

Chen

2013

PLoS ONE

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Fierce predatory freshwater fishes, the species of Percocypris (Cyprinidae, Teleostei) inhabit large rivers or lakes, and have a specific distribution pattern. Only a single species or subspecies occurs in each large-scale drainage basin of the Southeastern Tibetan Plateau. In this study, the molecular phylogenetic relationships for all but one of the described subspecies/species of Percocypris were investigated based on three mitochondrial genes (16S; COI; Cyt b) and one nuclear marker (Rag2). The results of Maximum Likelihood and Bayesian Inference analyses show that Percocypris is a strongly supported monophyletic group and that it is the sister group of Schizothorax. Combined with analyses of morphological characters, our results suggest that Percocypris needs to be reclassified, and we propose that six species be recognized, with corresponding distributions in five main drainages (including one lake). In addition, based on the results of the estimation of divergence times and ancestral drainages, we hypothesize that Percocypris likely originated in the early Miocene from a paleo-connected drainage system containing the contemporary main drainages of the Southeastern Tibetan Plateau. This study suggests that vicariance (due to the uplift of the Tibetan Plateau modifying the large-scale morphologies of drainage basins in the Southeastern Tibetan Plateau) has played an important role in the speciation of the genus. Furthermore, external morphological characters (such as the length of the fins) and an internal trait (the position of pterygiophore) appear to be correlated with different habitats in rivers and the lake.

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Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): A proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses

Cited by 18 publications

References 69 publications

Limits and phylogenetic relationships of East Asian fishes in the subfamily Oxygastrinae (Teleostei: Cypriniformes: Cyprinidae)

Limits and phylogenetic relationships of East Asian fishes in the subfamily Oxygastrinae (Teleostei: Cypriniformes: Cyprinidae)

Resolving Cypriniformes relationships using an anchored enrichment approach

Molecular Phylogeny and Biogeography of Percocypris (Cyprinidae, Teleostei)

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