Genetic variability in an organism allows us to assess its ability to respond to changing environmental conditions or disease epidemics. Hence, preserving this genetic diversity is an essential aspect of conservation biology. Phylogenetic tools are often used to study this variation within and between groups and build strategies for management of Evolutionarily Significant Units. Population genetics, in addition, provides us information on the gene flow between populations, signatures of inbreeding and other aspects of their genetic condition. Studies in the past decade have brought up yet another angle of looking at biodiversity, in the form of the microbiome. Since microorganisms have a faster turnover than eukaryotic genes, the microbial diversity could potentially show signatures of change at much smaller time frames. For my PhD, I studied the variation in Antilope cervicapra or blackbuck across its range, both in terms of genetics of the animal and its gut microbial diversity.
The first chapter tries to clarify the phylogenetic position of Antilope cervicapra with respect to other antelope lineages. Both concatenated and coalescent based methods were used, on data from 12 nuclear markers, to resolve the phylogenetic relationships between multiple species of antelope belonging to the four genera, Gazella, Nanger, Eudorcas and Antilope. I find that both coalescent and concatenated based phylogenetic analyses consistently place A. cervicapra as sister to Gazella dorcas, thus making Gazella a paraphyletic group. Divergence dating using fossil calibrations and biogeographic analyses, show that the Antilope lineage diverged around ~2 mya and dispersed from the Saharo-Arabian realm into India, post the expansion of grasslands. Unlike the gazelle found in India, A. cervicapra was better suited to grasslands and semi-arid conditions and did not extend their range beyond the Indian subcontinent.
The second chapter looks at phylogeography and population genetics of A. cervicapra across its geographic range. Using both mitochondrial and microsatellite genetic information, I find that different markers shed light on different aspect of their evolutionary history. The blackbucks seem capable of travelling much longer distances than expected, although habitat fragmentation in recent times have probably restricted their movement, as seen by the lack of shared haplotypes between locations. Both microsatellite (nuclear) and mitochondrial data indicate that the population from the Eastern part of India is genetically distinct and the species as a whole shows signatures of having undergone a bottleneck and recent genetic expansion. Further the microsatellites indicate the presence of 3 genetic clusters in this species, pertaining to the Northern, Southern and Eastern regions of India. The study also indicates the most likely demographic scenario where an ancestral population separated into two groups that gave rise to the North and South clusters and the East population was derived from the South at a later time period.
In the third chapter, I compare the gut-microbiome of blackbucks from ten different locations, to understand what drives their alpha and beta diversity. Metagenome information from the V3-V4 region of 16S rRNA were used to delineate different taxonomic orders of gut bacterial communities, to determine whether host genetics or the host environment has a stronger influence in structuring gut microbial community. Results show that although distance to human settlement and precipitation affect species richness of gut microbes, the correlations between nucleotide diversity and Shannon and Simpson alpha diversities were significant. Further the pairwise dissimilarity between the gut microbial composition increases with both increasing geographical distance as well as pairwise microsatellite distance. This study sets a baseline for further research on how animal gut microbiomes associate with host genes and potentially influence fitness.
Largely, my thesis looks at diversity in an endemic ungulate from different angles and also tries to elucidate its taxonomic position among Antilopinae.