10.1371/journal.pone.0176623
Pei-Chun Lo
Pei-Chun
Lo
Shu-Hui Liu
Shu-Hui
Liu
Siti Azizah Mohd Nor
Siti
Azizah Mohd Nor
Wei-Jen Chen
Wei-Jen
Chen
Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade
Public Library of Science
2017
ABGD
Indo-West Pacific clade
RAG
Generalized Mixed Yule Coalescent
GMYC
species delimitation methods
gene
dataset
COI
Automatic Barcode Gap Discovery
Indo-West Pacific
Indo-West Pacific sciaenid clade
taxonomic status
perciform fish families
2017-04-28 17:32:42
Dataset
https://plos.figshare.com/articles/dataset/Molecular_exploration_of_hidden_diversity_in_the_Indo-West_Pacific_sciaenid_clade/4951724
<div><p>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 (<i>RAG1</i>) and one mitochondrial gene (<i>COI</i>); the dataset with only <i>RAG1</i> gene sequences (245 samples from 44 currently recognized species); and the dataset with only <i>COI</i> 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, <i>Larimichthys</i>, <i>Nibea</i>, <i>Protonibea</i> and <i>Megalonibea</i>, and suggested a revision of <i>Nibea</i> and proposed a new genus <i>Pseudolarimichthys</i>.</p></div>