Conservation Genetics of the Critically Endangered Southern River Terrapin (Batagur affinis) in Malaysia: Genetic Diversity and Novel Subspecies Distribution Ranges

SIMPLE SUMMARY: A novel comprehensive population genetics study of two Batagur affinis subspecies in Malaysia is part of a conservation genetics effort aimed at long-term sustainability. As the conservation status of this species is critically endangered, we found only six different haplotypes from four study areas and low genetic diversity using D-loop markers. Nevertheless, using genetic markers, we revealed the presence of one of the Southern River terrapin subspecies (B. affinis edwardmolli) in Kedah, Malaysia. ABSTRACT: A population genetics study was carried out on the Southern River terrapin (Batagur affinis) from four places in Peninsular Malaysia: Pasir Gajah, Kemaman (KE), Terengganu; Bukit Pinang (BP), Kedah; Bota Kanan (BK), Perak; and Bukit Paloh, Kuala Berang (KB), Terengganu. The goal of this study is to identify genetic differences in two subspecies of B. affinis in Malaysia. No previous reports were available on the genetic diversity, phylogenetic relationships and matrilineal hereditary structure of these terrapin populations in Malaysia. The sequencing identified 46 single nucleotide polymorphisms that defined six mitochondrial haplotypes in the Southern River terrapins. Tajima’s D test and Fu’s Fs neutrality tests were performed to evaluate the signatures of recent historical demographic events. Based on the tests, the B. affinis edwardmolli was newly subspecies identified in the west coast–northern region of Kedah state. In addition, the B. affinis edwardmolli in Bukit Paloh, Kuala Berang (KB), Terengganu (Population 4), was shown to have a single maternal lineage compared to other populations. Low genetic diversity, but significant genetic differences, were detected among the studied Southern River terrapin populations.