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 multiple rounds of sequencing and numerous tissue types. Furthermore, I use methods developed in Chapter 2 to generate two high quality SNP datasets suitable for the two xiv principle array-based genotyping platforms. Chapter 4 presents an R package containing user-friendly functions to facilitate the genomic analysis of inbreeding in the wild. In the next three chapters I delve a level deeper to provide diverse biological insights at multiple levels of organisation. In Chapter 5, a recessive loss-of-function mutation in the melanocortin 1 receptor was identified as the underlying cause for coat colouration in the Antarctic fur seal. However, no association between the hypopigmented genotype and multilocus-heterozygosity was discovered implying that there is no difference in inbreeding between blonde and wild-type individuals. In Chapter 6, I present a refined genome assembly for the Antarctic fur seal together with a high-density dataset of genome-wide SNP markers which I use to uncover rapid linkage disequilibrium decay, global population structure and variation in inbreeding. In Chapter 7, I reconstructed the demographic history of the Antarctic fur seal and provide evidence for a severe decline in population size during the time of peak sealing. In Chapter 8, I bring together methods and data developed throughout my dissertation to generate the first high density SNP chip for the Antarctic fur seal. Finally, Chapter 9 steps back from the fur seal system and considers how next-generation sequencing has revolutionised marine mammal research in general, and highlights the future promise of genomics for the study of wild populations. In summary, my dissertation shows how the successive development of a broad range of genomic resources can provide novel insights into a number of ecological and evolutionary phenomena. In particular, through uncovering variation in individual inbreeding coefficients my work suggests that previously reported heterozygosity-fitness correlations and the ongoing fur seal population decline may well be driven by inbreeding depression. In addition, my research contributes to a growing body of evidence indicating that inbreeding is likely to be more prevalent in wild populations than previously thought. Furthermore, although the Antarctic fur seal was heavily exploited by 18th and 19th century sealers, my results indicate that individuals are likely to have survived at multiple locations across the species range and in much higher numbers than historical records would suggest. This highlights the importance of relict populations for species recovery and indicates that only very severe and long-lasting bottlenecks will negatively impact population recovery, genetic diversity and adaptive potential. Ultimately however, the genomic resources developed during this dissertation provide a solid foundation for future work in the Antarctic fur seal and will be critical for understanding the species’ capacity to respond to a rapidly changing Antarctic environment