Genetic diversity and phylogenetic analysis of blackbuck (Antilope cervicapra) in southern India.

Blackbuck (Antilope cervicapra) is a threatened species endemic to the Indian subcontinent. Many populations of blackbuck are found in southern India. Populations of blackbuck are negatively affected in many places for various reasons, such as habitat destruction and poaching. Their range decreased sharply during the 20th century. There is very limited information available on the population dynamics of blackbuck in southern India. For the phylogenetic and genetic diversity analyses of blackbuck populations among different distribution ranges in southern India, we sequenced mt DNA of cytochrome b (Cyt b) for 120, cytochrome c oxidase subunit-1 (COI) for 137 and the control region (CR) for 137 fecal pellets from eleven different locations in southern India. We analyzed the genetic structure of three mitochondrial markers, the CR, Cyt b and the COI region, separately and in a combined dataset. The haplotype diversity and nucleotide diversity of CR were 0.969 and 0.047, respectively, and were higher than those of Cyt b and COI. A Bayesian phylogeny and an MJ network based on the CR and combined dataset (105 sequences) signified several distinct haplotype clusters within blackbuck, whereas no clusters were identified with the Cyt b and COI phylogenetic analyses. The analysis of molecular variance of the combined data set revealed 52.46% genetic variation within the population. Mismatch distribution analysis revealed that blackbuck populations underwent complex changes with analysis of the combined dataset in each population and analysis of each marker separately in the overall population. The results provide evidence that blackbuck in different geographic locations has a distinct population structure due to habitat fragmentation after the formation of the Western and Eastern Ghats.

DNA barcode approaches to reveal interspecies genetic variation of Indian ungulates.

In the past two decades, identification of species from noninvasive sampling has turned out to be an important tool for wildlife conservation. In this study a total 93 specimens representing 22 species of ungulates were analyzed from partial sequences of mtDNA COI and Cytb genes. All the species showed unique clades, and sequences divergence within species was between 0.01-3.9% in COI and 0.01-13.7 in Cytb, whereas divergence between species ranged from 2.2 to 29.5% in COI and 2.3 to 28.8% in Cytb. Highest intraspecific divergence was observed within the Ovis aries in COI and Porcula salvania in Cytb. Bayesian (BA) phylogeny analysis of both genes combined distinguishes all the studied species as monophyletic criteria. The Indian rhinoceros (Rhinoceros unicornis) exhibited closer relation to horse (Equus caballus). No barcode gap was observed between species in COI. This study demonstrates that even short fragments of COI and Cytb generated from fecal pellets can efficiently identify the Indian ungulates, thus demonstrating its high potential for use in wildlife conservation activities.