Genome scan for signatures of adaptive evolution in wild African goat (capra nubiana)

A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Life Sciences of the Nelson Mandela African Institution of Science and TechnologyNubian ibex (Capra nubiana) is a wild goat species inhabiting the Sahara and Arabia deserts. C. nubiana thrives well in its habitat which is characterized by intense solar radiation, high temperatures, little feed, and water supply. The genetic basis of C. nubiana adaptation to its environment remains unknown. Adaptive signatures of evolution in C. nubiana genome were investigated using comparative genomics approaches. Paired-end sequence reads of three C. nubiana individuals and other publicly available genome data were used for comparative genomic analysis. Positive selection signals were detected from sequence alignment by comparing the rates of synonymous versus non-synonymous substitutions (dN/dS) in orthologous protein-coding genes shared by C. nubiana and related species using CodeML program in PAML package. Copy number variations were detected from the sequence data using read-depth method, with the domestic goat genome data acting as the reference. Genes involved in the skin barrier and hair follicle development, such as ATP binding cassette subfamily A member 12 and UV stimulated scaffold protein A, were found to be positively selected, suggesting that C. nubiana has evolved adaptive mechanisms to cope with solar radiation and temperature extremes in its environment. Additionally, a DNA repair gene (UV stimulated scaffold protein A) was reported to be under strong selection signals, further supporting the assertion that C. nubiana has acquired adaptive mechanisms to deal with possible DNA damages induced by prolonged exposure to solar radiation. Similarly, duplications of viral response genes such as UL16 binding protein 3, Cluster of Differentiation 48, Natural Killer Group 2D ligand 1-like, Bactericidal/permeability-increasing fold containing family A, member 1, and Natural Killer Group 2D ligand 4-like were reported in C. nubiana, indicating that it has acquired adaptive strategies to cope with viral stressors in its environment. Additionally, xenobiotic compounds metabolism genes involved in biotransformation (Cytochrome P450 2D6, carboxylesterase 1 and cytochrome P450 family 2 subfamily B member 6), conjugation (UDP Glucuronosyltransferase-2B7 and Glutathione S transferase Mu 4), and transport (Multidrug resistance protein 4) of toxic compounds were found to be expanded in C. nubiana, suggesting possible adaptative mechanisms to desert diets that are affluent in toxic compounds. This work represents the first effort to understand the genomic of adaptations in C. nubiana, a wild African goat. The C. nubiana genomic information generated in this study is an important resource for researchers seeking to find genes of interest for breeding purposes among small ruminants of economic importance