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
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 di�erence
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
coe�cients mywork 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.
Authors: Humble, Emily
1 April, 2018