DNA Barcoding Reveals High Cryptic Diversity of the Freshwater Halfbeak Genus Hemirhamphodon from Sundaland

Abstract

DNA barcoding of the cytochrome oxidase subunit I (COI) gene was utilized to assess the species diversity of the freshwater halfbeak genus Hemirhamphodon. A total of 201 individuals from 46 locations in Peninsular Malaysia, north Borneo (Sarawak) and Sumatra were successfully amplified for 616 base pairs of the COI gene revealing 231 variable and 213 parsimony informative sites. COI gene trees showed that most recognized species form monophyletic clades with high bootstrap support. Pairwise within species comparisons exhibited a wide range of intraspecific diversity from 0.0% to 14.8%, suggesting presence of cryptic diversity. This finding was further supported by barcode gap analysis, ABGD and the constructed COI gene trees. In particular, H. pogonognathus from Kelantan (northeast Peninsular Malaysia) diverged from the other H. pogonognathus groups with distances ranging from 7.8 to 11.8%, exceeding the nearest neighbor taxon. High intraspecific diversity was also observed in H. byssus and H. kuekanthali, but of a lower magnitude. This study also provides insights into endemism and phylogeographic structuring, and limited support for the Paleo-drainage divergence hypothesis as a driver of speciation in the genus Hemirhamphodon.

Exploring hidden diversity in Southeast Asia’s Dermogenys spp. (Beloniformes: Zenarchopteridae) through DNA barcoding

“…Even though DNA barcoding is a very effective tool for the systematics and validation of numerous freshwater fish taxa 32 , 34 , 70 , 75 , this approach leans heavily on the work of classical taxonomists, including the primary documentation of species and distributions, and ongoing work in validating and describing new OTUs. Morphological identification is likely to remain a fundamental approach for taxonomic identifications in most instances, and where DNA barcodes find no match in the barcode libraries, morphology remains the first port of call to validate a specimen’s identity 76 .…”

Molecular systematics of threadfin breams and relatives (Teleostei, Nemipteridae)

“…; Lim et al . ). Primers used to amplify and sequence the gene loci targeted in this study are listed in Table S2, and the laboratory protocols have been outlined in our previous studies (see, e.g., Lo et al .…”

“…Two nuclear genes (Rhodopsin [RH], recombination activating protein 1 [RAG1]) and one mitochondrial gene (cytochrome oxidase subunit I [COI]) were used in this study as molecular markers. These genes were selected for their ability to provide valuable phylogenetic information and to delimit the species [COI] based on previous studies investigating fish systematics (Chen et al 2003(Chen et al , 2008(Chen et al , 2014L opez et al 2004;Ward et al 2005;Durand et al 2012;Santini et al 2014;Lo et al 2015;Roxo et al 2015;Lim et al 2016). Primers used to amplify and sequence the gene loci targeted in this study are listed in Table S2, and the laboratory protocols have been outlined in our previous studies (see, e.g., Lo et al 2015).…”

Review: Progress and potential of DNA barcoding for species identification of fish species

“…However, traditional taxonomy fails to discriminate some species due to several conditions, for example, species that having various external body colorations especially when specimens are not fresh (Sriwattanarothai et al 2010), museum preserved species (Hebert et al 2013) and samples showing phenotypic plasticity (Weigand et al 2011). Unlike the traditional taxonomy, DNA barcoding gives information on cryptic (Lim et al 2016;Thiriet et al 2016) and sibling species (Blanco-Bercial et al 2014;Shao'e-Sun et al 2016). This identification technique fully supports the improvement of animal classification as well as helps to sort out any ambiguity at the species level.…”