Developing a genomic toolkit for the Antarctic fur seal: new insights into old questions

The genomic revolution has provided researchers with the opportunity to address broadreaching questions in ecology, evolution and conservation with greater power and precision than ever before. It is nowpossible to sequence genomes and produce high-resolution genomic marker datasets for practically any species for which high quality DNA can be collected. There are a vast and expanding number of ways in which to develop genomic resources, but the gold standard is to create a permanent and diverse toolkit, as this is likely to provide the greatest power for addressing outstanding and timely questions long into the future. The Antarctic fur seal (Arctocephalus gazella) is an important polar predator and arguably one of the most intensely monitored pinniped species in the world. During the 18th and 19th century it was the target of large-scale commercial exploitation and despite having rebounded, worsening environmental conditions in the South Atlantic have meant that many fur seal populations are in decline again. Nevertheless, the Antarctic fur seal is yet to benefit from the genomic revolution and as such, many fundamental aspects of its biology remain poorly understood. In my dissertation, I developed a permanent genomic toolkit for the Antarctic fur seal and used this to investigate a broad range of phenomena including inbreeding, population structure and demography. In the first chapters of my thesis, I lay the genomic and methodological foundation for many of the subsequent elements of my PhD. In Chapter 2, I present the first genome assembly for the Antarctic fur seal and use this to explore the genomic characteristics of 144 SNP probe sequences in order to optimize the development of a custom genotyping array. I found that probes mapping uniquely and completely to the fur seal genome were more likely to successfully validate, a pattern that holds up across a variety of species. In Chapter 3, I describe a hybrid transcriptome assembly comprising information from