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.

True foxes (genus: Vulpes) are small to medium-sized canids that inhabit diverse environments through-out Europe, Asia, Africa and North America. 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). This near universal distribution is made possible by special adaptations to the environment they live in. Whilst some foxes such as the Arctic fox (V. lagopus) are very specialized to their environment, others such as the Red fox (V. vulpes) can be found in many different habitats and are considered to be generalists. While morphological and physiological adaptations have, for the most part, been well studies in foxes, our current understanding of the underlying genetics is still very poor. Moreover, their near universal distribution, recent divergence (about 2-5 million years for most species), their close relationship to a model organism (the dog) and their reasonably sized genome (about 2.4Gb) make them prime candidates to study genomic adaptation of mammals to different environments. In this project, we focus on adaption to a variety of extreme environments, such as the Arctic, deserts and high-altitude. Interestingly, adaptation to extreme desert environments evolved independently at least twice in True foxes, once in the ancestor of the Blanfords (V. cana) and the Fennec fox (V. zerda), and more recently in the Rueppells fox (V. rueppellii). In order to investigate genomic adaptation to live in extreme environments we sequenced the genomes of six True fox species (Arctic fox, Red fox, Rueppells fox, Blanfords fox, Tibetan fox and Kit fox). Preliminary scans for positive selection showed that 10 genes are under selection only in the two desert foxes, which could indicate convergent evolution. Beside genes important in DNA replication (such as POLD1, DNA polymerase), development, cell cycle regulation, we identified a gene (ADORA1, Adenosine receptor A1), which has important function kidney, mucus secretion in the airway and inflammatory response. ADORA1 is an interesting candidate for adaptation to life in hot and arid desert environments, since it effects organs critical for life in these environments.