DNA barcoding using skin exuviates can improve identification and biodiversity studies of snakes

Abstract

Snakes represent a taxonomically underdeveloped group of animals in India with a lack of experts and incomplete taxonomic descriptions being the main deterrents to advances in this area. Molecular taxonomic approaches using DNA barcoding could aid in snake identification as well as studies of biodiversity. Here a non-invasive sampling method using DNA barcoding is tested using skin exuviates. Taxonomically authenticated samples were collected and tested for validation and comparisons to unknown snake exuviate samples. This approach was also used to construct the first comprehensive study targeting the snake species from Maharashtra state in India. A total of 92 skin exuviate samples were collected and tested for this study. Of these, 81 samples were successfully DNA barcoded and compared with unknown samples for assignment of taxonomic identity. Good quality DNA was obtained irrespective of age and quality of the exuviate material, and all unknown samples were successfully identified. A total of 23 species of snakes were identified, six of which were in the list of Endangered species (Red Data Book). Intra- and inter-specific distance values were also calculated, and these were sufficient to allow discrimination among species and between species without ambiguity in most cases. Two samples were suspected to represent cryptic species based on deep K2P divergence values (>3%), and one sample could be identified to the genus level only. Eleven samples failed to amplify COI sequences, suggesting the need for alternative PCR primer pairs. This study clearly documents how snake skin exuviates can be used for DNA barcoding, estimates of diversity and population genetic structuring in a noninvasive manner.

• DNA barcoding
• exuviate
• India
• snake taxonomy
• species

Acknowledgements

We express gratitude to the Siddharth zoo, Aurangabad and the Katraj Snake Park of Puna, India for providing authenticated snake exuviate samples. We also acknowledge our thanks the PHCDBS snake gene bank for supplying the tissues samples from their public collection for this study.

Declaration of interest

Authors of this manuscript declare that they do not have any conflict of interests regarding this work. This study was carried out using funding and facilities from the Paul Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad. Also, GDK was supported by the Department of Biotechnology, Government of India under CREST fellowship programme 2012–13.