Stickleback phylogenies resolved: Evidence from mitochondrial genomes and 11 nuclear genes

Kawahara, Ryouka; Miya, Masaki; Mabuchi, Kohji; Near, Thomas J.; Nishida, Mutsumi

doi:10.1016/j.ympev.2008.10.014

Cited by 63 publications

(80 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The origin of L-strand (O L ) was detected in the cluster of five tRNA genes, with being located between tRNA Asn and tRNA Cys . The gene arrangement of three mitogenomes was identical to those observed in other Pungitius species (Kawahara et al 2009;Hwang et al 2012aHwang et al , 2012bGuo et al 2016aGuo et al , 2016bShikano et al 2016aShikano et al , 2016b). The evolutionary relationship among P. kaibarae lineages and the phylogenetic placement of this complex within genus Pungitius were inferred based on 13 protein-coding and 2 rRNA genes using BEAST2 (Bouckaert et al 2014) implemented following the parameter setting and time calibration described in Wang et al (2015).…”

supporting

confidence: 73%

The complete mitochondrial genomes of three geographical lineages in short ninespine stickleback (Pungitius kaibarae) complex and their phylogenetic implication

Bae

Lee

Jeon

et al. 2017

Mitochondrial DNA Part B

View full text Add to dashboard Cite

show abstract

supporting

confidence: 73%

The complete mitochondrial genomes of three geographical lineages in short ninespine stickleback (Pungitius kaibarae) complex and their phylogenetic implication

Bae

Lee

Jeon

et al. 2017

Mitochondrial DNA Part B

View full text Add to dashboard Cite

show abstract

“…KT989571) and consisted of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a control region. The order and direction of these genes are identical to those of other Gasterosteidae species including Pungitius fishes (Miya et al 2001;Kawahara et al 2009;Hwang et al 2012aHwang et al ,2012b. Of the 13 protein-coding genes, 4 (ND2, COII, ND4 and Cytb) showed an incomplete stop codon.…”

mentioning

confidence: 77%

“…It is an important model species in evolutionary biology, genetics and behavioural research ( € Ostlund-Nilsson et al 2007;Meril€ a 2013). Pungitius pungitius has been the focus of many population genetic and phylogeographic studies using mitochondrial gene fragments (e.g., Aldenhoven et al 2010;Shikano et al 2010;Bae & Suk 2015;Wang et al 2015), but until now, only a partial assembly of the whole mitochondrial genome has been available from one individual originating from Hokkaido, Japan (Kawahara et al 2009). …”

mentioning

confidence: 99%

Complete mitochondrial genome of the nine-spined stickleback Pungitius pungitius (Gasterosteiformes, Gasterosteidae)

Guo

Toli

Merilä

2016

Mitochondrial DNA Part B

View full text Add to dashboard Cite

The complete mitochondrial genome of the nine-spined stickleback Pungitius pungitius was obtained with Illumina sequencing of genomic DNA. The assembled mitogenome sequence was 16 582 bp long, and the gene number, order and contents were identical to those of other sequenced Pungitius mitogenomes. The complete mitogenome of P. pungitius from its European range can provide an important template for further phylogenetic and population genetic studies of the Pungitius species complex.

show abstract

“…DNA extraction, amplification protocols and primers basically followed previous studies (Mabuchi et al 2006;Kawahara et al 2009). Two mitochondrial and two nuclear DNA fragments were sequenced: ca.…”

Section: Molecular Analysesmentioning

confidence: 99%

Revision of the systematics of the cardinalfishes (Percomorpha: Apogonidae) based on molecular analyses and comparative reevaluation of morphological characters

Mabuchi¹,

Fraser²,

Song³

et al. 2014

Zootaxa

Self Cite

View full text Add to dashboard Cite

Molecular analyses were conducted based on 120 of the estimated 358 species of the family Apogonidae with 33 of 40 genera and subgenera, using three gobioids and one kurtid as collective outgroups. Species of Amioides, Apogon, Apogonichthyoides, Apogonichthys, Archamia, Astrapogon, Brephamia, Cercamia, Cheilodipterus, Fibramia n. gen., Foa, Fowleria, Glossamia, Gymnapogon, Jaydia, Lachneratus, Nectamia, Ostorhinchus, Paroncheilus, Phaeoptyx, Pristiapogon, Pristicon, Pseudamia, Pterapogon, Rhabdamia, Siphamia, Sphaeramia, Taeniamia, Verulux, Vincentia, Yarica, Zapogon and Zoramia were present in the molecular analyses; species of Bentuviaichthys, Holapogon, Lepidamia, Neamia, Paxton, Pseudamiops and Quinca were absent from the analyses. Maximum-likelihood (ML), Bayesian (BA), and Maximum parsimony (MP) analyses based on two mitochondrial (12S rRNA-tRNAVal-16S rRNA, ca. 1500 bp; COI, ca. 1500 bp) and two nuclear DNA (RAG1, ca. 1300 bp; ENC1, ca. 800 bp) fragments reproduced two basal clades within the monophyletic family: one including a single species, Amioides polyacanthus, and the other comprising species of Pseudamia. All the other apogonid species formed a large well-established monophyletic group, in which almost identical 12 major clades were reproduced, with phylogenetic positions of four species (Glossamia aprion, Ostorhinchus margaritophorus, Pterapogon kauderni, and Vincentia novaehollandiae) left unsettled. Apogon sensu lato and recent Ostorhinchus (excepting O. margaritophorus) were divided into six and three major clades, respectively. Each of the recognized clades in the family was then evaluated for morphological characters to identify synapomorphies. Based on the results of the molecular analyses and the reevaluation of morphological characters, four subfamilies were proposed within the family: Apogoninae (including most of the species in the family), Amioidinae new subfamily (including Amioides, and based on morphology, Holapogon), Paxtoninae new subfamily (including Paxton, based only on morphology) and Pseudamiinae (including Pseudamia). Within the largest subfamily Apogoninae, twelve new tribes were proposed based on the 12 molecular clades and associated morphology: Apogonichthyini, Apogonini (mainly including species of Apogon sensu stricto), Archamiini, Cheilodipterini, Gymnapogonini, Ostorhinchini (including striped species of recent Ostorhinchus), Pristiapogonini, Rhabdamiini, Sphaeramiini (mainly including barred species of traditional Ostorhinchus, such as Apogonichthyoides, Jaydia and Nectamia), Siphamiini, Veruluxini, and Zoramiini. Two additional tribes are proposed based only on morphology: Glossamiini and Lepidamiini. For each of the 14 tribes, morphological characters were described. One new genus, Fibramia, type species Apogon thermalis, recently in Ostorhinchus, was described supported by morphology and molecular trees. A key to all genera is provided and all valid and uncertain status species are allocated to tribes and genera.

show abstract

Stickleback phylogenies resolved: Evidence from mitochondrial genomes and 11 nuclear genes

Cited by 63 publications

References 24 publications

The complete mitochondrial genomes of three geographical lineages in short ninespine stickleback (Pungitius kaibarae) complex and their phylogenetic implication

The complete mitochondrial genomes of three geographical lineages in short ninespine stickleback (Pungitius kaibarae) complex and their phylogenetic implication

Complete mitochondrial genome of the nine-spined stickleback Pungitius pungitius (Gasterosteiformes, Gasterosteidae)

Revision of the systematics of the cardinalfishes (Percomorpha: Apogonidae) based on molecular analyses and comparative reevaluation of morphological characters

Contact Info

Product

Resources

About