Genome Adaptation in Arctic and desert Foxes (genus: Vulpes)

True foxes (genus: Vulpes) are small to medium-sized canids that inhabit diverse environments through-out the Holarctic, South East Asia, South Africa and Northern Africa. Their habitats include the extreme cold of the Arctic, the dry and hot deserts of Northern Africa and Arabia, urban areas, high altitude and even the marine (they follow Polar bears onto the ice). While their morphological or physiological adaptations have, for the most part, been well studied, not much is know about the underlying genetic changes. Their near universal distribution, recent divergence (less than 2-5 Myrs for most species) and their reasonably sized genome (about 2.4Gb) make them prime candidates to study genomic adaptation of mammals to different environments. A major aim of my project is to study genomic adaptations to life in cold Arctic, as well as hot desert environments. To do so, I plan to sequence the genomes of the closely related Arctic fox (Vulpes lagopus) and the Rueppells fox (V. ruepelli) using de-novo assembly and the genomes of the Blanfords (V. cana) and the Fennec fox (V. zerda) using reference based mapping. While the Arctic fox is specialized to the cold and arid conditions of the Arctic, the latter three are adapted to a life in hot and arid desert environments. Desert adaptations evolved independently at least twice in canids, once in the ancestor of the Blanfords and the Fennec fox, and more recently in the Rueppells fox. Thus, sequencing of those genomes would allow me to investigate whether the two independent adaptation events affected the same genes or genomic regions. Comparisons between fox and to other mammal genomes, such as wolf, dog, tiger, human, etc., allow for the detection of gene or protein domain enrichment or depletion in the fox family as well as the detection of positively selected genes. The function of these genes or gene families can then be determined using databases of known gene functions. A comparative approach using high quality genomes also allows for the study of copy number variants, non-coding and SNP data. By including further fox species this project can be easily expanded to other environments.

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