The development of a widely available global database of DNA barcodes has been proposed as a species-identification tool for large taxonomic assemblages of animals. The approach has particular value in revealing cryptic species, which typically have high incidence in marine environments.
Despite the wealth of DNA barcode data for fish from many temperate regions, there are relatively few such data available for SE Asian waters.
In Chapter 2, an initial reference DNA barcode library was produced for the marine fish Family Carangidae, one of the most commercially-important families from the Indo-Malay Archipelago (IMA). Thirty-species of Family Carangidae were collected from the IMA to examine the accuracy of DNA barcoding concepts and protocols, such as ease of amplification of the barcode gene cytochrome coxidase I (COI), and implementation of the ‘barcoding gap’ concept for species delimitation. All described species formed monophyletic clusters in Neighbour-joining phylogenetic tree,
although three species representing complexes of six potential cryptic species were detected.
Within 723 individuals, three described species (Atule mate, Selar crumenophthalmus and Seriolina nigrofasciata) exhibited conspecific divergences up to ten time s 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 within the IMA. Additional conspecifics sequences available from other geographical regions
revealed the existence of several more complexes of potentially cryptic species outside the 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 information will contribute to the development of an integrated taxonomic framework, thus informing management strategies for subsequent conservation and management of Carangidae. Additionally, the results will provide greater understanding of recruitment, and processes driving species diversification in the IMA.
The effectiveness of molecular methods in detecting population structure of marine fish was examined in Chapter 3. Identification of population structure of fisheries stocks is important in the IMA because a large proportion of the IMA fisheries occur as mixed-stocks. Selar crumenophthalmus (pelagic),
Atule mate (moderately pelagic) and Selaroides leptolepis (demersal) are commercially-important Carangidae with contrasting habitat use. It is
unknown whether these three species in Malaysian waters form single respective stocks, or are genetically subdivided into distinct populations.
Population structure inferred from nuclear as well as mtDNA markers was lower in the pelagic (Selar crumenophthalmus) and moderately pelagic (Atule mate) species than in the demersal species, Selaroides leptolepis, which is consistent with the hypothesis that pelagic and/or moderately pelagic
species will display less genetic divergence compared to demersal species due to their potential to undertake long-distance migrations in oceanic waters. This chapter also examined population genetic structure of Indo-Malay
Atule mate with samples from Kuwait. All analyses showed significant
genetic differences between samples from these two localities. Within IMA itself, there were two mitochondrial lineages detected in Atule mate suggesting the existence of potential cryptic species. However, there were lack of genetic differentiation in Selar crumenophthalmusand Selaroides leptolepis. Such core information is required for their effective conservation and management since rates of harvesting have been reported as continuing to decline.
In Chapter 4, we focussed on a highly mobile pelagic species, Selar crumenophthalmus, to investigate its phylogeographic patterns and popula
tion genetic structuring within the IMA. It is important to know whether a population consists of one homogeneous population, or many discrete populations associated with different geographic areas. Samples were collected from six geographic regions; the South China Sea, Straits of
Malacca, Sulu Sea, Celebes Sea, Andaman Sea and the Bismarck Sea. Both mtDNA and nuclear DNA data showed low genetic differentiation among localities with low FSTv values indicating extensive gene flow within regions.
Such data can provide a better understanding of potential isolation mechanisms of pelagic marine species, as well as to assist fisheries managers in designing suitable management plans in designing suitable management plans in the IMA.