Publications by authors named "Cuizhang Fu"

26 Publications

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Complete mitochondrial genome of (Cypriniformes: Gobionidae).

Authors:
Qi An Cuizhang Fu

Mitochondrial DNA B Resour 2021 1;6(8):2227-2228. Epub 2021 Aug 1.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China.

Mitochondrial genomes of two individuals of Tachanovsky's gudgeon have been determined on the basis of Sanger dideoxy sequencing. The gene compositions of two genomes contain 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region with the same length 16,614 bp. The phylogenetic tree reveals that the monotypic genus is a sister group of the subfamily Gobioninae within the family Gobionidae.
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http://dx.doi.org/10.1080/23802359.2021.1944385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8330723PMC
August 2021

Two mitochondrial genomes of freshwater gudgeons in the genus (Cypriniformes: Gobionidae).

Mitochondrial DNA B Resour 2020 Jul 30;5(3):3054-3055. Epub 2020 Jul 30.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China.

Two complete mitochondrial genomes of and are assembled, and they have the same length with slightly high A + T contents (54.88% and 56.57%) in base compositions. Results in the reconstructed phylogeny show that the genus is a monophyletic group, and it is a sister taxon of the genus .
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http://dx.doi.org/10.1080/23802359.2020.1797569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7782080PMC
July 2020

Three mitochondrial genomes of fishes (Cypriniformes: Gobionidae).

Mitochondrial DNA B Resour 2020 Jul 29;5(3):3046-3047. Epub 2020 Jul 29.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China.

New mitochondrial genomes of , , and have the length of 16,605, 16,606, and 16,609 bp with A + T bias. Inferred phylogeny shows that occupies basal position. and + are sister groups, and they together are a sister taxa of .
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http://dx.doi.org/10.1080/23802359.2020.1797553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7783098PMC
July 2020

Three mitochondrial genomes of freshwater fishes in the genus (Cypriniformes: Gobionidae).

Mitochondrial DNA B Resour 2020 Nov 20;5(3):3779-3781. Epub 2020 Nov 20.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, PR China.

Mitochondrial genomes of , , and have been determined using Sanger sequencing (GenBank Accession No. MT767745-MT767747). The three mitochondrial genomes consist of 13 protein-coding genes, two genes, 22 genes, and one control region with the length of 16,605, 16,611, and 16,607 bp. Phylogenetic analysis of the three species showed that is nested within a fully supported terminal clade with , and is a sister group of , , and . is positioned in a clade with and .
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http://dx.doi.org/10.1080/23802359.2020.1835583DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7703701PMC
November 2020

Three complete mitochondrial genomes of freshwater fishes in the genus (Cypriniformes: Gobionidae).

Mitochondrial DNA B Resour 2019 Jul 10;4(2):2179-2180. Epub 2019 Jul 10.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China.

has been misidentified as in China for a long time. In this study, we determined three mitochondrial genomes of and such that these data should contribute to molecular identifications of the two species. The size of new mitochondrial genomes was 16,609 or 16,599 bp with A + T bias of 55.7-56.5% in the base compositions. Our reconstructed phylogeny showed that and formed a sister taxon relationship, and they together were a monophyletic group.
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http://dx.doi.org/10.1080/23802359.2019.1623728DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7687625PMC
July 2019

Four complete mitochondrial genomes of fishes (Cypriniformes: Gobionidae).

Mitochondrial DNA B Resour 2019 Jul 10;4(2):2175-2176. Epub 2019 Jul 10.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China.

In this study, we determined complete mitochondrial genomes of , , , and so that these data could contribute to reconstruct interspecific phylogenetic relationships within the genus . The four mitochondrial genomes showed A + T bias (55.2-57.0%) of base compositions with the length from 16,594 to 16,608 bp. Phylogenetic relationships among fishes and their close relatives showed that the genus was a monophyletic group and it could be divided into two major groups.
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http://dx.doi.org/10.1080/23802359.2019.1623126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7687549PMC
July 2019

Two complete mitochondrial genomes of fishes (Cypriniformes: Gobionidae).

Mitochondrial DNA B Resour 2019 Jul 10;4(2):2173-2174. Epub 2019 Jul 10.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China.

Freshwater fishes in the genus include two species, and . In this study, we determined complete mitochondrial genomes of and to clarify their phylogenetic positions. The two mitochondrial genomes showed similar gene arrangements, codon use, gene overlaps or gene intervals with the length of 16,596 bp and 16,598 bp. Our phylogeny revealed that and were nested within fishes. The findings indicate that is a junior synonym of .
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http://dx.doi.org/10.1080/23802359.2019.1623116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7687540PMC
July 2019

Ten fish mitogenomes of the tribe Gobionini (Cypriniformes: Cyprinidae: Gobioninae).

Mitochondrial DNA B Resour 2018 Jul 27;3(2):803-804. Epub 2018 Jul 27.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Shanghai Institute of Eco-Chongming (SIEC), Fudan University, Shanghai, China.

Freshwater fishes of the subfamily Gobioninae (Cypriniformes: Cyprinidae) are composed of three major clades, the tribes Gobionini and Sarcocheilichthyini, and a - group. In this study, we determined ten complete fish mitogenomes from eight of all twelve genera in the tribe Gobionini. The ten mitogenomes displayed similar patterns in gene arrangements, codon use and gene overlaps with the length of 16,605-16,617 bp and base compositions slightly A + T bias of 56.1-58.0%. Our phylogeny of the tribe Gobionini revealed that the genera , , and were monophyletic, and other genera , , and were paraphyletic or polyphyletic. The findings indicate that the genera classifications of Gobionini are needed to be further confirmed.
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http://dx.doi.org/10.1080/23802359.2018.1467236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7800260PMC
July 2018

Multilocus resolution of Mugilidae phylogeny (Teleostei: Mugiliformes): Implications for the family's taxonomy.

Mol Phylogenet Evol 2016 Mar 29;96:161-177. Epub 2015 Dec 29.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai 200433, China. Electronic address:

The interrelationships among mugilids (Mugiliformes: Mugilidae) remain highly debated. Using a mitochondrial gene-based phylogeny as criterion, a revised classification with 25 genera in the Mugilidae has recently been proposed. However, phylogenetic relationships of major mitochondrial lineages remain unresolved and to gain a general acceptance the classification requires confirmation based on multilocus evidence and diagnostic morphological characters. Here, we construct a species-tree using twelve nuclear and three mitochondrial loci and infer the evolution of 71 morphological characters. Our multilocus phylogeny does not agree with previous morphology-based hypotheses for the relationships within Mugilidae, confirms the revised classification with 25 genera and further resolves their phylogenetic relationships. Using the well-resolved multilocus phylogeny as the criterion, we reclassify Mugilidae genera into three new subfamilies (Myxinae, Rhinomugilinae, and Cheloninae) and one new, recombined, subfamily (Mugilinae). The Rhinomugilinae subfamily is further divided into four tribes. The revised classification of Mugilidae is supported by morpho-anatomical synapomorphies or a combination of characters. These characters are used to erect a key to the subfamilies and genera.
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http://dx.doi.org/10.1016/j.ympev.2015.12.010DOI Listing
March 2016

Four complete mitochondrial genomes of the genera Candidia, Opsariichthys, and Zacco (Cypriniformes: Cyprinidae).

Mitochondrial DNA A DNA Mapp Seq Anal 2016 11 5;27(6):4613-4614. Epub 2015 Nov 5.

a Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University , Shanghai , China.

Members of Candidia, Nipponcrysis, Parazacco, Opsariichthys, and Zacco are a group of East Asian freshwater fishes, and these five genera form a monophyletic group within the subfamily Oxygastrinae (Cypriniformes: Cyprinidae). In this study, we first determined complete mitogenomes of Candidia pingtungensis, Opsariichthys acutipinnis, O. chengtui, and Zacco acanthogenys. The four mitogenomes with the length of 16 611-16 615 bp displayed the same patterns in gene arrangements and the use of start and stop codons for protein-coding genes. Our phylogeny divided Candidia, Nipponcrysis, Parazacco, Opsariichthys, and Zacco into two major groups that the former three genera consisted of a group and the latter two genera formed another group. The phylogeny also revealed that C. pingtungensis was nested within Nipponcrysis. Our findings indicate that the taxonomy status of Candidia and Nipponcrysis is still needed to be confirmed.
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http://dx.doi.org/10.3109/19401736.2015.1101582DOI Listing
November 2016

Phylogeographical analysis of a cold-temperate freshwater fish, the Amur sleeper (Perccottus glenii) in the Amur and Liaohe River basins of Northeast Asia.

Zoolog Sci 2014 Oct;31(10):671-9

1 Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Institute of Biodiversity Science, Fudan University, Shanghai 200433, China.

The Amur sleeper Perccottus glenii (Perciformes, Gobioidei, Odontobutidae) is well known as an invasive fish in the river basins of Eastern and Central Europe, but its genetic background is unavailable across its native habitats in northeast Asia. In this study, we used the mitochondrial cytochrome b gene by sampling 19 populations of P. glenii across its native distributional areas of Liaohe and Amur River basins to explore its evolutionary history. Phylogenetic analyses identified three major clades within P. glenii, among which Clade A and Clade B were co-distributed in the Liaohe and Amur River basins, and Clade C was restricted to the latter. Molecular dating showed that the splits of Clades A, B and C have happened in the late Early-early Middle Pleistocene and the most recent common ancestors of these clades have been presented in the late Middle-early Late Pleistocene. The P. glenii showed very high levels of genetic structure among populations (ΦST = 0.801), probably due to the characters of its life histories with very limited dispersal ability. The admixture of different clades in some populations of P. glenii probably reflects historical secondary contact. These findings indicate that Pleistocene climatic oscillation and river capture were major determinants for genetic variations and evolutionary history of the P. glenii.
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http://dx.doi.org/10.2108/zs130046DOI Listing
October 2014

Complete mitochondrial genome of the Easten hulafish, Trachinops taeniatus (Perciformes: Plesiopidae).

Mitochondrial DNA 2015 27;26(5):742-3. Epub 2014 Jan 27.

a Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering , and Institute of Biodiversity Science, Fudan University , Shanghai , China.

The first complete mitochondrial genome (mitogenome) of Plesiopidae (Teleostei: Perciformes) was determined using the Eastern hulafish Trachinops taeniatus as a representative species of the family. The mitogenome was 16,821 bp in length, including 13 typical vertebrate protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region. The gene arrangement was similar to other fishes except for the reversal position of tRNA(Ala) and tRNA(Asn). The overall base composition was 27.4% for A, 27.5% for C, 27.4% for T and 17.7% for G. This mitogenome should contribute to resolving phylogenetic position of Plesiopidae.
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http://dx.doi.org/10.3109/19401736.2013.845767DOI Listing
June 2016

Complete mitochondrial genomes of two brown frogs, Rana dybowskii and Rana cf. chensinensis (Anura: Ranidae).

Mitochondrial DNA A DNA Mapp Seq Anal 2016 22;27(1):155-6. Epub 2014 Jan 22.

b Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering , and Institute of Biodiversity Science, Fudan University , Shanghai , China.

We first determined complete mitochondrial genomes of Rana dybowskii and Rana cf. chensinensis (Anura: Ranidae). The mitogenomic lengths of R. dybowskii and R. cf. chensinensis were 18,864 and 18,808 bp, respectively. The two mitogenomes have similar gene compositions including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region. Rana dybowskii and R. cf. chensinensis mitogenomes displayed same gene order arrangements and similar base compositions with an A + T bias. Mitogenomic data of the two species contributed to provide molecular marker for their conservative genetics and clarified their phylogenetic position under mitogenome-based phylogeny of the genus Rana.
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http://dx.doi.org/10.3109/19401736.2013.878921DOI Listing
September 2016

Complete mitochondrial genome of a brown frog, Rana kunyuensis (Anura: Ranidae).

Mitochondrial DNA A DNA Mapp Seq Anal 2016 17;27(1):34-5. Epub 2014 Jan 17.

b Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering , and Institute of Biodiversity Science, Fudan University , Shanghai , China.

The first complete mitochondrial genome (mitogenome) of Rana sensu stricto (sensu Frost, 2013) was determined using Rana kunyuensis as a representative species. The mitogenome was 22,255 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and duplicated control regions. The mitogenome of R. kunyuensis showed novel gene order arrangement with a translocation of tRNA(Leu)((CUN)) and ND5 in comparison with published anuran mitogenomes to date. This mitogenome should contribute to understand the evolution of anuran mitochondrial gene order arrangements.
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http://dx.doi.org/10.3109/19401736.2013.869681DOI Listing
September 2016

Complete mitochondrial genome of a freshwater snail, Semisulcospira libertina (Cerithioidea: Semisulcospiridae).

Mitochondrial DNA 2015 10;26(6):897-8. Epub 2014 Jan 10.

a Center for Watershed Ecology, Institute of Life Science and Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University , Nanchang , China and.

The first complete mitochondrial genome (mitogenome) of Cerithioidea (Gastropoda: Caenogastropoda) was determined using a freshwater snail Semisulcospira libertina (Cerithioidea: Semisulcospiridae) as a representative species of the superfamily. The mitogenome was 15,432 bp in length, including 13 typical invertebrate protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The overall base composition was 31.4% for A, 17.8% for C, 34.8% for T and 16.0% for G with a A+T bias. The mitogenome of S. libertina displayed novel gene order arrangement compared with published Caenogastropoda mitogenomes to date. This mitogenome contributed in resolving phylogenetic position and interrelationships of Cerithioidea.
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http://dx.doi.org/10.3109/19401736.2013.861449DOI Listing
March 2016

Complete mitochondrial genome of Pseudorasbora elongata (Cypriniformes: Cyprinidae).

Mitochondrial DNA 2015 Apr 11;26(2):250-1. Epub 2013 Sep 11.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University , Shanghai , China and.

Phylogenetic placement of Pseudorasbora elongate remains unresolved. We determined the first complete mitochondrial genome of P. elongate that its mitogenome data should contribute to clarify the systematics of Pseudorasbora fishes. The mitogenome was 16,607 bp in length, including 13 typical protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region. The overall base composition of the heavy strain was 31.1% for A, 24.8% for C, 28.2% for T and 15.9% for G, with the A + T bias of 59.3%.
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http://dx.doi.org/10.3109/19401736.2013.823184DOI Listing
April 2015

Complete mitochondrial genome of Southern Smiler, Opistognathus jacksoniensis (Perciformes: Opistognathidae).

Mitochondrial DNA 2014 Feb 10;25(1):48-9. Epub 2013 Jul 10.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University , Shanghai , China.

The first complete mitochondrial genome (mitogenome) of Opistognathidae (Teleostei: Perciformes) has been determined using the Southern Smiler, Opistognathus jacksoniensis, as a representative species of the family. This mitogenome was 16,650 bp in length, including 13 typical vertebrate protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA genes and 1 control region. All genes were encoded on the heavy strain except for ND6 and eight tRNA genes. The overall base composition of the heavy strain was 27.4% for A, 30.2% for C, 25.7% for T and 16.7% for G. The mitogenome data of O. jacksoniensis should contribute to clarify phylogenetic position of Opistognathidae under mitogenome-based phylogenetic reconstruction of perciform fishes.
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http://dx.doi.org/10.3109/19401736.2013.782019DOI Listing
February 2014

Complete mitochondrial genome of Rhynchocypris cf. lagowskii (Cypriniformes: Cyprinidae).

Mitochondrial DNA 2014 Oct 8;25(5):379-80. Epub 2013 Jul 8.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Institute of Biodiversity Science, Fudan University , Shanghai 200433 , China.

Rhynchocypris lagowskii sensu lato (Cypriniformes: Cyprinidae) has been revealed as a species complex including two species, i.e. R. lagowskii sensu stricto and a cryptic species R. cf. lagowskii. We determined the first complete mitochondrial genome (mitogenome) of R. cf. lagowskii by comparing with a published mitogenome of R. lagowskii sensu stricto. The two species displayed similar pattern of mitochondrial gene arrangements and similar base compositions of the heavy strain with a bias in the A+T content. There were the nucleotide sequence similarity of 91.8% for mitogenomes and pairwise p-distance of 6.9% for COI genes between R. cf. lagowskii and R. lagowskii sensu stricto and these results supported the two species as different species.
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http://dx.doi.org/10.3109/19401736.2013.809432DOI Listing
October 2014

Complete mitochondrial genome of Phoxinus tumensis (Cypriniformes: Cyprinidae).

Mitochondrial DNA 2014 Oct 2;25(5):368-9. Epub 2013 Jul 2.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Institute of Biodiversity Science, Fudan University , Shanghai , China.

Abstract The taxonomy and systematics of Phoxinus (Cypriniformes: Cyprinidae) is still not well-resolved. In this study, we determined the first complete mitochondrial genome (mitogenome) of Phoxinus tumensis. The mitogenome was 17,050 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region. All genes were encoded on the heavy strain except for ND6 and eight tRNA genes. The overall base composition of the heavy strain was 27.9% for A, 25.5% for C, 28.4% for T and 18.2% for G. The control region was revealed to contain tandem repeats. The mitogenome data of P. tumensis should contribute to clarify the systematics of Phoxinus fishes.
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http://dx.doi.org/10.3109/19401736.2013.803096DOI Listing
October 2014

Genus-level taxonomic changes implied by the mitochondrial phylogeny of grey mullets (Teleostei: Mugilidae).

C R Biol 2012 Oct-Nov;335(10-11):687-97. Epub 2012 Oct 15.

Institut de recherche pour le développement (IRD), UMR 5119 ECOSYM, bâtiment 24, Cc.093, université Montpellier 2, place E.-Bataillon, 34095 Montpellier cedex 5, France.

A comprehensive mitochondrial phylogeny of the family Mugilidae (Durand et al., Mol. Phylogenet. Evol. 64 (2012) 73-92) demonstrated the polyphyly or paraphyly of a proportion of the 20 genera in the family. Based on these results, here we propose a revised classification with 25 genera, including 15 genera currently recognized as valid (Agonostomus, Aldrichetta, Cestraeus, Chaenomugil, Chelon, Crenimugil, Ellochelon, Joturus, Mugil, Myxus, Neomyxus, Oedalechilus, Rhinomugil, Sicamugil and Trachystoma), 7 resurrected genera [Dajaus (for Agonostomus monticola), Gracilimugil (for Liza argentea), Minimugil (for Sicamugil cascasia), Osteomugil (for several species currently under Moolgarda and Valamugil, including M. cunnesius, M. engeli, M. perusii, and V. robustus), Planiliza (for Indo-Pacific Chelon spp., Indo-Pacific Liza spp., and Paramugil parmatus), Plicomugil (for Oedalechilus labiosus), and Squalomugil (for Rhinomugil nasutus)] and 3 new genera: Neochelon gen. nov. (for Liza falcipinnis), Parachelon gen. nov. (for L. grandisquamis) and Pseudomyxus gen. nov. (for Myxus capensis). Genus Chelon was shown to include exclusively Chelon spp. and Liza spp. from the Atlantic and the Mediterranean, and Liza spp. species endemic to eastern southern Africa. Genus Crenimugil should now include C. crenilabis, Moolgarda seheli and V. buchanani. Genus names Liza, Moolgarda, Paramugil, Valamugil and Xenomugil should be abandoned because they are no longer valid. Further genetic evidence is required to confirm or infirm the validity of the genus Paracrenimugil Senou 1988. The mitochondrial phylogeny of the 25 genera from the present revision is the following: [(Sicamugil, (Minimugil, Rhinomugil)); Trachystoma; ((Myxus, Neomyxus), (Cestraeus, Chaenomugil, (Agonostomus, Dajaus, Joturus), Mugil)); (Aldrichetta, Gracilimugil); Neochelon gen. nov.; (Pseudomyxus gen. nov., (Chelon, Oedalechilus, Planiliza, Parachelon gen. nov.)); ((Squalomugil, (Ellochelon, Plicomugil)), (Crenimugil, Osteomugil))]. Agonostomus monticola and several species with large distribution ranges (including Moolgarda seheli, Mugil cephalus and M. curema) consist of separate lineages whose geographic distribution suggests they are cryptic species, thus warranting further taxonomic work in the Mugilidae at the infra-generic level.
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http://dx.doi.org/10.1016/j.crvi.2012.09.005DOI Listing
May 2013

A multilocus phylogeny of Asian noodlefishes Salangidae (Teleostei: Osmeriformes) with a revised classification of the family.

Mol Phylogenet Evol 2012 Mar 8;62(3):848-55. Epub 2011 Dec 8.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai 200433, China.

A group of small and transparent Asian noodlefishes (Osmeriformes: Salangidae) are commercially important fishery species, however, interrelationships among these fishes remain unresolved in previous studies using mitochondrial markers. We re-examine phylogenetic relationships of Salangidae by including complete taxon sampling, based on seven nuclear loci and one mitochondrial gene using a multilocus coalescence-based species-tree method. Our results show a well-resolved phylogeny of Salangidae that does not agree with previous hypotheses. The topology test suggests that our hypothesis represents the most likely phylogeny. Using the inferred species-tree as criterion, we recombine the rank of subfamilies and genera in the Salangidae, and erect a new genus Neosalangichthys. Our revised classification of Salangidae is well supported by reinterpreting previously proposed diagnostic characters. Finally, re-defined synapomorphic characters are used to erect a key to the genera of Salangidae.
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http://dx.doi.org/10.1016/j.ympev.2011.11.031DOI Listing
March 2012

Biogeographical consequences of Cenozoic tectonic events within East Asian margins: a case study of Hynobius biogeography.

PLoS One 2011 28;6(6):e21506. Epub 2011 Jun 28.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Institute of Biodiversity Science, Fudan University, Shanghai, China.

Few studies have explored the role of Cenozoic tectonic evolution in shaping patterns and processes of extant animal distributions within East Asian margins. We select Hynobius salamanders (Amphibia: Hynobiidae) as a model to examine biogeographical consequences of Cenozoic tectonic events within East Asian margins. First, we use GenBank molecular data to reconstruct phylogenetic interrelationships of Hynobius by bayesian and maximum likelihood analyses. Second, we estimate the divergence time using the bayesian relaxed clock approach and infer dispersal/vicariance histories under the 'dispersal-extinction-cladogenesis' model. Finally, we test whether evolutionary history and biogeographical processes of Hynobius should coincide with the predictions of two major hypotheses (the 'vicariance'/'out of southwestern Japan' hypothesis). The resulting phylogeny confirmed Hynobius as a monophyletic group, which could be divided into nine major clades associated with six geographical areas. Our results show that: (1) the most recent common ancestor of Hynobius was distributed in southwestern Japan and Hokkaido Island, (2) a sister taxon relationship between Hynobius retardatus and all remaining species was the results of a vicariance event between Hokkaido Island and southwestern Japan in the Middle Eocene, (3) ancestral Hynobius in southwestern Japan dispersed into the Taiwan Island, central China, 'Korean Peninsula and northeastern China' as well as northeastern Honshu during the Late Eocene-Late Miocene. Our findings suggest that Cenozoic tectonic evolution plays an important role in shaping disjunctive distributions of extant Hynobius within East Asian margins.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021506PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125272PMC
December 2011

Phylogenetic position of the enigmatic Lepidogalaxias salamandroides with comment on the orders of lower euteleostean fishes.

Mol Phylogenet Evol 2010 Nov 30;57(2):932-6. Epub 2010 Jul 30.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Institute of Biodiversity Science, Fudan University, Shanghai 200433, China.

This study examines phylogenetic placement of the enigmatic Western Australian Lepidogalaxias, and extends previous studies by including eight new taxa to enable re-examination phylogenetic relationships of lower euteleostean fishes at the ordinal level, based on mitochondrial genomes from 39 ingroup taxa and 17 outgroups. Our results suggest that Lepidogalaxias occupies a basal position among all euteleosts, in contrast with earlier hypotheses that variously suggested a closer relationship to esocid fishes, or to the galaxiid Lovettia. In addition our evidence shows that Osmeriformes should be restricted Retropinnidae, Osmeridae, Plecoglossidae and Salangidae. This reduced Osmeriformes is supported in our results as the sister group of Stomiiformes. Galaxiidae, which is often closely linked to Osmeriformes, emerges as sister group of a combined Osmeriformes, Stomiiformes, Salmoniformes, Esociformes and Argentiformes, and we give Galaxiiformes the rank of order to include all remaining galaxioid fishes (Galaxias and allied taxa, Aplochiton and Lovettia). Our results also support a sister group relationship between Salmoniformes and Esociformes, which are together the sister group of Argentiniformes.
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http://dx.doi.org/10.1016/j.ympev.2010.07.016DOI Listing
November 2010

Cryptic species and historical biogeography of eel gobies (Gobioidei: Odontamblyopus) along the northwestern Pacific coast.

Zoolog Sci 2010 Jan;27(1):8-13

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Institute of Biodiversity Science, Fudan University, Shanghai, China.

Cryptic species are common in gobioid fishes, as revealed by recent molecular studies. This study collected molecular and morphological data to delimit species boundaries and to reveal the historical biogeography of Odontamblyopus lacepedii sensu lato by sampling 87 specimens from 16 locations in the northwestern Pacific. Phylogenetic trees based on mitochondrial NADH dehydrogenase subunit 5 sequences identified three major clades. Clear morphological separations among these clades were detected by examining morphological characters used in taxonomic diagnosis. Therefore, these clades were delineated as three separate species: O. lacepedii sensu stricto (in the East China Sea, Yellow Sea, Gulf of Bohai, and Ariake Bay); O. sp. (in the southern East China Sea and southern Yellow Sea); and O. rebecca (in the Gulf of Tonkin, northern South China Sea, and southern East China Sea). Estimated divergence times were 0.61 +/- 0.15 Ma between O. lacepedii and O. sp., and 2.31+/-0.36 Ma between O. rebecca and O. lacepedii+O. sp. These findings indicate that isolation of marginal seas and habitat fragmentation during major falls in sea level in the late Pliocene and Pleistocene may have been responsible for genetic breaks among Odontamblyopus species in the northwestern Pacific.
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http://dx.doi.org/10.2108/zsj.27.8DOI Listing
January 2010

Species delimitation and historical biogeography in the genus Helice (Brachyura: Varunidae) in the northwestern Pacific.

Zoolog Sci 2009 Jul;26(7):467-75

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai 200433, China.

The genus Helice is comprised of four species, H. formosensis, H. latimera, H. tientsinensis, and H. tridens. A recent molecular analysis identified H. formosensis and H. tientsinensis as junior synonyms of H. latimera. We used three mitochondrial and two nuclear genes to further delineate species boundaries in Helice and to add to knowledge of the historical biogeography of the genus. The molecular data revealed deep divergences between the H. formosensis-latimera-tientsinensis complex and H. tridens. Clear genetic separations with incomplete lineage sorting and convincing morphological divergences were detected among H. formosensis, H. latimera, and H. tientsinensis, and a coalescence analysis revealed negligible gene flow among these species, except for weak unidirectional gene flow from H. formosensis to H. latimera. The estimated divergence time of 1.42-1.92 Ma between the H. formosensis-latimera-tientsinensis complex and H. tridens is consistent with the opening of the Tsushima/Korea Strait (1.71-1.52 Ma). The divergence time (approximately 22-730 ka) among H. formosensis, H. latimera, and H. tientsinensis indicates that the Taiwan Strait acted as a biogeographic barrier during major falls in sea level during the Pleistocene. Our findings indicate that H. formosensis, H. latimera, and H. tientsinensis are valid species, and that straits (Tokara Strait, Tsushima/Korea Strait, and Taiwan Strait), the Okinawa Trough, and currents (Kuroshio Current, Tsushima Current, and Taiwan Strait Warm Current) have acted as geographic barriers resulting in allopatric speciation among onshore marine animals in the northwestern Pacific.
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http://dx.doi.org/10.2108/zsj.26.467DOI Listing
July 2009

Phylogenetic relationships of salangid fishes (Osmeridae, Salanginae) with comments on phylogenetic placement of the salangids based on mitochondrial DNA sequences.

Mol Phylogenet Evol 2005 Apr 21;35(1):76-84. Epub 2005 Jan 21.

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai 200433, China.

We used partial DNA sequences of cytochrome b and 16S mitochondrial genes to determine the phylogenetic placement of salangid fishes and the generic relationships within the salangids. Our molecular data strongly support the monophyly of salangid fishes, the inclusion of salangids in the Osmeridae, and the sister group relationship between salangids and osmerids. Our analyses suggest that Plecoglossus can be separated from all the other salangids and osmerids. Mallotus and Hypomesus are clustered within Osmerinae, rather than allied with Salanginae. As regards the relationships within the salangids, our analyses are incongruent with all previous classification hypotheses. Our phylogenetic analyses support the sister group relationships between Protosalanx and Neosalanx, and between Salanx and Hemisalanx. More evidences show that Leucosoma is more closely related to the Salanx-Hemisalanx clade, while Salangichthys forms part of an unresolved basal polytomy.
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http://dx.doi.org/10.1016/j.ympev.2004.11.024DOI Listing
April 2005
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