A multi-gene dataset reveals a tropical New World origin and Early Miocene diversification of croakers (Perciformes: Sciaenidae)

Lo, Pei-Chun; Liu, Shuhui; Chao, Ning Labbish; Nunoo, F.K.E.; Mok, Hin‐Kiu; Chen, Wei‐Jen

doi:10.1016/j.ympev.2015.03.025

Cited by 69 publications

(92 citation statements)

References 75 publications

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“…As the phylogenetic tree showed, all nodes were strongly supported with high value of posterior probability (Figure 1). The result shows that P. pawak was placed as sister to the silver croaker P. argentata of the same genus, which is consistent to the croaker phylogenetic results using combined mitochondrial and nuclear genomes (Lo et al 2015).…”

supporting

confidence: 84%

Complete mitochondrial genome and the phylogenetic position of the Pawak croaker Pennahia pawak (Perciformes: Sciaenidae)

Lin

Guo

Liu

2017

Mitochondrial DNA Part B

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In this study, the complete mitogenome of the Pawak croaker Pennahia pawak was first determined. This mitogenome is 16,408 bp in length, and consists of 37 genes with the typical gene order and direction of transcription in vertebrates. The overall nucleotide composition is: 27.7% A, 29.5% C, 15.9% G, and 26.9% T. Sizes of the 22 tRNA genes range from 66 to 75 bp. One start codons (ATG) and two stop codons (AGA and TAA/TA/T) were detected in 13 protein-coding genes. In the Bayesian tree based on the complete mitogenomes of 17 species (including P. pawak ) from the family Sciaenidae, all nodes were strongly supported. The phylogenetic results suggested that P. pawak has the closest relationship to the silver croaker P. argentata , a species from the same genus.

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supporting

confidence: 84%

Complete mitochondrial genome and the phylogenetic position of the Pawak croaker Pennahia pawak (Perciformes: Sciaenidae)

Lin

Guo

Liu

2017

Mitochondrial DNA Part B

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“…It proved that using the mitogenome for phylogenetic analysis is more convincing than using single gene or multiple genes. Pennahia macrocephalus was placed as sister to the silver croaker P. argentata, a species from the same genus, which is consistent to the croaker phylogenetic results using combined mitochondrial and nuclear genomes (Lo et al 2015).…”

supporting

confidence: 79%

Complete mitochondrial genome and the phylogenetic position of the bighead pennah croaker Pennahia macrocephalus (Perciformes: Sciaenidae)

Guo

Liu

Lin

et al. 2016

Mitochondrial DNA Part B

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“…Recently, Lo et al [24] reconstructed the first comprehensive phylogeny of global sciaenids with rigorous taxonomic and molecular character sampling (6619 bp from two mitochondrial and four nuclear genes for 93 taxa). The constructed phylogeny was subsequently used as a framework to examine their origin and historical biogeography.…”

Section: Introductionmentioning

confidence: 99%

“…The constructed phylogeny was subsequently used as a framework to examine their origin and historical biogeography. They found that the Sciaenidae first originated and diversified in the tropical American waters in the Late Oligocene and dispersed outward in the Early Miocene, hypothesizing that the ancestor of the Indo-West Pacific endemic sciaenid genera underwent a single invasion event to the Indo-West Pacific (IWP) that evolved to form a diversified clade that today contains approximately 91 species [10, 24]. However, knowledge of the taxonomy and phylogeny of the sciaenids within this IWP clade is still limited due to lack of a thorough survey of all taxa.…”

Section: Introductionmentioning

confidence: 99%

Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade

Liu

Nor

et al. 2017

PLoS ONE

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The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene—Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa. In this study, we used DNA-based approaches to investigate the evolutionary relationships, to explore the species diversity, and to elucidate the taxonomic status of sciaenid species/genera within the Indo-West Pacific clade. Three datasets were herein built for the above objectives: the combined dataset (248 samples from 45 currently recognized species) from one nuclear gene (RAG1) and one mitochondrial gene (COI); the dataset with only RAG1 gene sequences (245 samples from 44 currently recognized species); and the dataset with only COI gene sequences (308 samples from 51 currently recognized species). The latter was primarily used for our biodiversity exploration with two different species delimitation methods (Automatic Barcode Gap Discovery, ABGD and Generalized Mixed Yule Coalescent, GMYC). The results were further evaluated with help of four supplementary criteria for species delimitation (genetic similarity, monophyly inferred from individual gene and combined data trees, geographic distribution, and morphology). Our final results confirmed the validity of 32 currently recognized species and identified several potential new species waiting for formal descriptions. We also reexamined the taxonomic status of the genera, Larimichthys, Nibea, Protonibea and Megalonibea, and suggested a revision of Nibea and proposed a new genus Pseudolarimichthys.

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A multi-gene dataset reveals a tropical New World origin and Early Miocene diversification of croakers (Perciformes: Sciaenidae)

Cited by 69 publications

References 75 publications

Complete mitochondrial genome and the phylogenetic position of the Pawak croaker Pennahia pawak (Perciformes: Sciaenidae)

Complete mitochondrial genome and the phylogenetic position of the Pawak croaker Pennahia pawak (Perciformes: Sciaenidae)

Complete mitochondrial genome and the phylogenetic position of the bighead pennah croaker Pennahia macrocephalus (Perciformes: Sciaenidae)

Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade

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