Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis

Imoto, Junichi; Saitoh, Kenji; Sasaki, Takeshi; Yonezawa, Takahiro; Adachi, Jun; Kartavtsev, Yuri; Miya, Masaki; Nishida, Mutsumi; Hanzawa, Naoto

doi:10.1016/j.gene.2012.10.019

Cited by 100 publications

(80 citation statements)

References 85 publications

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“…In contrast to our findings, a much older separation of ∼37.1 Mya during the Eocene was estimated by Imoto et al . () between North American and Eurasian sister species of cyprinids (Cypriniformes: Cyprinidae: Leuciscinae). They used mitogenome data and a relaxed molecular clock adapted from fossil calibrations employed by Saitoh et al .…”

Section: Discussionmentioning

confidence: 97%

Phylogenetic and biogeographical relationships of theSanderpikeperches (Percidae: Perciformes): patterns across North America and Eurasia

Haponski

Stepien

2013

Biol J Linn Soc Lond

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North America and Eurasia share several closely related taxa that diverged either from the breakup of the Laurasian supercontinent or later closures of land bridges. Their modern population structures were shaped in Pleistocene glacial refugia and via later expansion patterns, which are continuing. The pikeperch genus Sander contains five species – two in North America (S. canadensis and S. vitreus) and three in Eurasia (S. lucioperca, S. marinus, and S. volgensis) – whose evolutionary relationships and relative genetic diversities were previously unresolved, despite their fishery importance. This is the first analysis to include the enigmatic and rare sea pikeperch S. marinus, nuclear DNA sequences, and multiple mitochondrial DNA regions. Bayesian and maximum‐likelihood trees from three mitochondrial and three nuclear gene regions support the hypothesis that Sander diverged from its sister group Romanichthys/Zingel ∼24.6 Mya. North American and Eurasian Sander then differentiated ∼20.8 Mya, with the former diverging ∼15.4 Mya, congruent with North American fossils dating to ∼16.3–13.6 Mya. Modern Eurasian species date to ∼13.8 Mya, with S. volgensis being basal and comprising the sister group to S. lucioperca and S. marinus, which diverged ∼9.1 Mya. Genetic diversities of the North American species are higher than those in Eurasia, suggesting fewer Pleistocene glaciation bottlenecks. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110, 156–179.

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Section: Discussionmentioning

confidence: 97%

Phylogenetic and biogeographical relationships of theSanderpikeperches (Percidae: Perciformes): patterns across North America and Eurasia

Haponski

Stepien

2013

Biol J Linn Soc Lond

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“…Leuciscidae has long been supported as monophyletic across many studies [1, 3, 19, 24–29, 31, 32, 72, 73] but relationships among the genera within have had differing results. Clades have been resolved in multiple studies and include: (1) far eastern phoxinins (Eurasian), (2) open posterior myodome (OPM), (3) creek chub – plagopterin (CC-P), (4) western North America (WNA), and (5) leuciscin (European) [4, 13, 24, 26, 28, 34, 74–81]. Our results also obtained the five major clades within Leuciscidae (Fig.…”

Section: Discussionmentioning

confidence: 99%

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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“…The specific primers were designed based on the alignments of the relatively conserved regions of Phoxinus oxycephalus (GenBank accession nos. : NC_027273; Sui, Liang, & He, and NC_018818; Imoto et al, ), and the specific primer sequences are shown in Table . PCR amplification was performed in a 20 μl reaction volume containing about 10 μl Premix Taq, 1 μl template, 7 μl ddH 2 O, and 1 μl each primer.…”

Section: Methodsmentioning

confidence: 99%

The complete mitochondrial genome of Rhynchocypris oxycephalus (Teleostei: Cyprinidae) and its phylogenetic implications

Zhang

Cheng

2019

Ecology and Evolution

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Rhynchocypris oxycephalus (Teleostei: Cyprinidae) is a typical small cold water fish, which is distributed widely and mainly inhabits in East Asia. Here, we sequenced and determined the complete mitochondrial genome of R. oxycephalus and studied its phylogenetic implication. R. oxycephalus mitogenome is 16,609 bp in length (GenBank accession no.: MH885043), and it contains 13 protein‐coding genes (PCGs), two rRNA genes, 22 tRNA genes, and two noncoding regions (the control region and the putative origin of light‐strand replication). 12 PCGs started with ATG, while COI used GTG as the start codon. The secondary structure of tRNA‐Ser (AGN) lacks the dihydrouracil (DHU) arm. The control region is 943bp in length, with a termination‐associated sequence, six conserved sequence blocks (CSB‐1, CSB‐2, CSB‐3, CSB‐D, CSB‐E, CSB‐F), and a repetitive sequence. Phylogenetic analysis was performed with maximum likelihood and Bayesian methods based on the concatenated nucleotide sequence of 13 PCGs and the complete sequence without control region, and the result revealed that the relationship between R. oxycephalus and R. percnurus is closest, while the relationship with R. kumgangensis is farthest. The genus Rhynchocypris is revealed as a polyphyletic group, and R. kumgangensis had distant relationship with other Rhynchocypris species. In addition, COI and ND2 genes are considered as the fittest DNA barcoding gene in genus Rhynchocypris . This work provides additional molecular information for studying R. oxycephalus conservation genetics and evolutionary relationships.

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Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis

Cited by 100 publications

References 85 publications

Phylogenetic and biogeographical relationships of theSanderpikeperches (Percidae: Perciformes): patterns across North America and Eurasia

Phylogenetic and biogeographical relationships of theSanderpikeperches (Percidae: Perciformes): patterns across North America and Eurasia

Resolving Cypriniformes relationships using an anchored enrichment approach

The complete mitochondrial genome of Rhynchocypris oxycephalus (Teleostei: Cyprinidae) and its phylogenetic implications

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