Evolutionary genomics of the thriving red fox

Scientific background and motivation: Conservation genomics has emerged as a major research area, using genomes to understand population decline and extinction. Despite large numbers of conservation genomics studies of a variety of organisms, we lack a general understanding of how the evolutionary histories of struggling and successful species differ. The motivating argument behind this project is that the second part of the equation is missing-we are not studying the thriving species to any substantial degree. To identify the factors that sets successful species apart from less successful ones, we need to study the full spectrum of species success.

Few if any species represent the other side of the spectrum better than the red fox (Vulpes vulpes), which is a species that is doing exceptionally well. It is the land mammal with the largest natural distribution and occupies a wide range of habitats, from the deserts of Arabia to the tundra of the North American arctic, and even thrives in urban environments.

The project will use whole-genome sequencing of previously collected red fox DNA samples from across the globe, and perform population genetics analyses to address questions on their diversity and evolutionary history, including:
- Is the success of the fox driven by genetic adaptation-do the genomes of foxes living in different environments display evidence of local adaptation, including through local gene flow from other fox species?
- What is the time depth of genetic diversification in the species-did foxes in different parts of the world diverge genetically a long time ago, or is current diversity the result of recent expansion?
- What factors best explain the shape of genetic relationships-Ice Age climate changes, mountains, deserts, human societies, deliberate human translocation?

Methodology: Many studies in evolutionary genetics have been limited to low-resolution assays, e.g microsatellites and mitochondria. The higher resolution offered by whole genome sequencing has primarily been enjoyed by studies of humans and agricultural organisms. It's high time the full power of genomics is unleashed on the natural world too, which is why we propose to use whole genome sequencing. There have also been substantial analytical advances in the last decade, including methods based on f-statistics, and coalescent-based tools such as PSMC and MSMC, which will be central tools in the project. In the wake of whole genomes and new methods, a more nuanced view of ancestry and the complexity of the evolutionary past is emerging in human population genomics, and in this project we aim to bring these new ways of thinking about evolution and genetic diversity into ecological genomics too.