DNA barcoding reveals overlooked marine fishes

Abstract

With more than 15 000 described marine species, fishes are a conspicuous, diverse and increasingly threatened component of marine life. It is generally accepted that most largebodied fishes have been described, but this conclusion presumes that current taxonomic systems are robust. DNA barcoding, the analysis of a standardized region of the cytochrome c oxidase 1 gene (COI), was used to examine patterns of sequence divergence between populations of 35 fish species from opposite sides of the Indian Ocean, chosen to represent differing lifestyles from inshore to offshore. A substantial proportion of inshore species showed deep divergences between populations from South African and Australian waters (mean = 5.10%), a pattern which also emerged in a few inshore/offshore species (mean = 0.84%), but not within strictly offshore species (mean = 0.26%). Such deep divergences, detected within certain inshore and inshore/offshore taxa, are typical of divergences between congeneric species rather than between populations of a single species, suggesting that current taxonomic systems substantially underestimate species diversity. We estimate that about one third of the 1000 fish species thought to bridge South African and Australian waters actually represent two taxa.

A DNA Sequence–Based Approach To the Identification of Shark and Ray Species and Its Implications for Global Elasmobranch Diversity and Parasitology

“…These results suggest that undescribed diversity exists among scalloped hammerheads, which may include sympatric species. This result is consistent with those of a number of previous authors who also reported genetic diversity within S. lewini (e.g., Abercrombie et al, 2005;Duncan et al, 2006;Quattro et al, 2006;Zemlak et al, 2009).…”

“…There has been much recent interest in exploring elasmobranch sequence variation using the barcode marker cytochrome oxidase 1 (COI) (e.g., Holmes et al, 2009;Moura et al, 2008;Toffoli et al, 2008;Ward et al, 2005Ward et al, , 2008Ward et al, , 2009Wong et al, 2009;Zemlak et al, 2009). While such barcode work will provide a useful parallel assessment of sequence variation, the fragment of COI used is both shorter (650 vs. 1044 bp) and more slowly evolving in chondrichthyans than is the NADH2 fragment (Moore et al, 2011).…”

Phylogenetic Analysis of the Darkfin Hind, Cephalopholis urodeta (Serranidae) Using Partial Mitochondrial CO1 Gene Sequences (Analisis Filogenetik Cephalopholis urodeta (Serranidae) Menggunakan Runutan Gen CO1 Mitokondria Parsial)

“…Molecular techniques can be a major tool for systematic ichthyology and may also be useful for biological fisheries to quickly solve problems about the taxonomic level of species and populations (Chow et al, 1993;Zemlak et al, 2009). The mithochondrial DNA segment that we use for the identification and phylogenetic analysis of blackfin hind (family Serranidae) is cytochrome c oxidase subunit 1 (CO1).…”

Adding nuclear rhodopsin data where mitochondrial COI indicates discrepancies – can this marker help to explain conflicts in cyprinids?

“…The second focus of this study is on labeonine cyprinid genera, where members of Crossocheilus, Hemigrammocapoeta, barcoding proved to be a powerful and reliable tool for discriminating a large range of species, including all major taxa of marine as well as freshwater fishes [e.g. 1,[5][6][7][8][9][10][11][12]. The tool has gained additional attention among biologists by having the potential to reveal cryptic diversity, especially given the enormous amount of data collected globally, which can easily be used to compare own sequence data on a regional scale.…”