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

HongChiun Lim; Muchlisin Zainal Abidin; Chaidir Parlindungan Pulungan; Mark de Bruyn; Siti Azizah Mohd Nor

doi:10.1371/journal.pone.0163596

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

PLoS One. 2016 Sep 22;11(9):e0163596. doi: 10.1371/journal.pone.0163596. eCollection 2016.

Authors

HongChiun Lim^{1

2}, Muchlisin Zainal Abidin³, Chaidir Parlindungan Pulungan⁴, Mark de Bruyn^{5

6}, Siti Azizah Mohd Nor^{1

7}

Affiliations

¹ School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia.
² School of Biological Sciences, Faculty of Integrative Sciences and Technology, Quest International University Perak, Ipoh, Perak, Malaysia.
³ Department of Aquaculture, Faculty of Marine and Fisheries, Syiah Kuala University, Banda Aceh, Indonesia.
⁴ Department of Aquatic Resources Management, Faculty of Fisheries and Marine Science, Riau University, Pekanbaru, Indonesia.
⁵ School of Biological Sciences, Bangor University, Bangor, United Kingdom.
⁶ School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia.
⁷ Centre for Marine and Coastal Studies, Universiti Sains Malaysia, Penang, Malaysia.

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.

Grants and funding

This work was funded by Universiti Sains Malaysia, iRec project (1002/PBIOLOGI/910403). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.