DNA barcoding of Nilssonia congeners corroborates existence of wild N. nigricans in northeast India

Abstract

DNA barcode data of soft-shell turtles is limited in global DNA database while it is completely lacking for the highly debated species Nilssonia nigricans. We employed DNA barcoding technique to discriminate the species cluster for Nilssonia congeners, especially for the highly debated N. nigricans from different localities of northeast India. Sampling across the region included a few live specimens from wild, market sold carcass specimens, and a few dry carapaces meant for home decoration purpose. The generated sequences (621 bp of mtCOI) of dry carapaces showed 99–100% homology with the generated sequences of morphologically identified N. nigricans. The COI barcode sequences of N. nigricans (n = 12) showed 3.8% mean genetic divergence with N. hurum (n = 3), 10% with N. gangetica (n = 4), and 9.2% with N. formosa (GenBank sequences). Similarly, the mtCytb sequences of the dry carapace and live specimens of N. nigricans were 99–100% homologous with the conspecific database sequences and formed specific clusters. The inferred Neighbor-Joining (NJ), Maximum Likelihood (ML), and Bayesian (BA) phylogeny based on partial mtCOI gene efficiently discriminated all the congeners of Nilssonia into specific clusters and, therefore, it was helpful to detect the existence of N. nigricans.