DNA Barcoding Reveals Cryptic Diversity within Commercially Exploited Indo-Malay Carangidae (Teleosteii: Perciformes)
Open Access
- 29 November 2012
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 7 (11), e49623
- https://doi.org/10.1371/journal.pone.0049623
Abstract
DNA barcodes, typically focusing on the cytochrome oxidase I gene (COI) in many animals, have been used widely as a species-identification tool. The ability of DNA barcoding to distinguish species from a range of taxa and to reveal cryptic species has been well documented. Despite the wealth of DNA barcode data for fish from many temperate regions, there are relatively few available from the Southeast Asian region. Here, we target the marine fish Family Carangidae, one of the most commercially-important families from the Indo-Malay Archipelago (IMA), to produce an initial reference DNA barcode library. Here, a 652 bp region of COI was sequenced for 723 individuals from 36 putative species of Family Carangidae distributed within IMA waters. Within the newly-generated dataset, three described species exhibited conspecific divergences up to ten times greater (4.32–4.82%) than mean estimates (0.24–0.39%), indicating a discrepancy with assigned morphological taxonomic identification, and the existence of cryptic species. Variability of the mitochondrial DNA COI region was compared within and among species to evaluate the COI region's suitability for species identification. The trend in range of mean K2P distances observed was generally in accordance with expectations based on taxonomic hierarchy: 0% to 4.82% between individuals within species, 0% to 16.4% between species within genera, and 8.64% to 25.39% between genera within families. The average Kimura 2-parameter (K2P) distance between individuals, between species within genera, and between genera within family were 0.37%, 10.53% and 16.56%, respectively. All described species formed monophyletic clusters in the Neighbour-joining phylogenetic tree, although three species representing complexes of six potential cryptic species were detected in Indo-Malay Carangidae; Atule mate, Selar crumenophthalmus and Seriolina nigrofasciata. This study confirms that COI is an effective tool for species identification of Carangidae from the IMA. There were moderate levels of cryptic diversity among putative species within the central IMA. However, to explain the hypothesis of species richness in the IMA, it is necessary to sample the whole family across their broad geographic range. Such insights are helpful not only to document mechanisms driving diversification and recruitment in Carangidae, but also to provide a scientific framework for management strategies and conservation of commercially-important fisheries resources.Keywords
This publication has 48 references indexed in Scilit:
- MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model SpaceSystematic Biology, 2012
- DNA barcoding Indian marine fishesMolecular Ecology Resources, 2010
- A Rapid Bootstrap Algorithm for the RAxML Web ServersSystematic Biology, 2008
- Patterns of biodiversity and endemism on Indo-West Pacific coral reefsProceedings of the National Academy of Sciences of the United States of America, 2008
- Identifying Canadian Freshwater Fishes through DNA BarcodesPLOS ONE, 2008
- Mapping the spawning grounds of North Sea cod ( Gadus morhua ) by direct and indirect meansProceedings Of The Royal Society B-Biological Sciences, 2008
- bold: The Barcode of Life Data System (http://www.barcodinglife.org)Molecular Ecology Notes, 2007
- DNA Barcoding: Error Rates Based on Comprehensive SamplingPLoS Biology, 2005
- Identification of Birds through DNA BarcodesPLoS Biology, 2004
- A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequencesJournal of Molecular Evolution, 1980