Tracking the southern river terrapin (Batagur affinis) through environmental DNA: prospects and challenges

Abstract

Environmental DNA detection has emerged as a powerful tool to monitor aquatic species without the need for capture or visual identification and is particularly useful for rare or elusive species. Our objective was to develop an eDNA approach for detecting the southern river terrapin (Batagur affinis) in Malaysia. We designed species-specific primers for a fragment of B. affinis mtDNA and evaluated their effectiveness in silico, in vitro and in situ. The primers amplified 110 bp of the cytochrome b mtDNA sequence of B. affinis from aquarium water samples housing nine juvenile B. affinis. We also successfully detected B. affinis eDNA from river samples taken from a site where turtles were known to be in the vicinity. Prospects and challenges of using an eDNA approach to help determine the distribution of B. affinis, essential information for an effective conservation plan, are discussed.

Keywords:

• Batagur affinis
• critically endangered species
• distribution
• ecology
• environmental DNA
• genetic population
• Kemaman
• Malaysia
• molecular marker
• southern river terrapin
• species monitoring
• turtle

Acknowledgements

We are grateful to Cheah Men How and Natasha Serrao for assistance in the field and helpful comments and edits to an earlier version of this manuscript. We thank Jedsada Sukantamala, Wazel B. Mahad, Wan F. A. Jusoh and WWF-Malaysia staff for assistance in the field.

Disclosure statement

The authors report no conflicts of interest.

Additional information

Funding

This study was supported by the Turtle Conservation Fund (awarded 2016) and the University of Nottingham Malaysia Small Grant Scheme (awarded 2015).