Fitness & major histocompatibility complex diversity of two bottlenose dolphin populations

Low genetic diversity diminishes the potential to adapt to change and thus reduces individual fitness as well as population viability. Therefore, it is crucial to identify genetic variation that affects fitness and population viability. Until recently, the search for the genetic basis of fitness variation, and the related field of conservation genetics, have mostly relied on neutral genetic markers, such as mitochondrial DNA and microsatellites. However, ecological and evolutionary processes relevant to fitness can only be inferred by non-neutral genes, such as those of the major histocompatibility complex (MHC). In this thesis I examined the interplay between demographic parameters, fitness and MHC genetic diversity of two West Australian populations of bottlenose dolphins (Tursiops cf aduncus): a large population (N ≈ 3000), in Shark Bay (SB) and a much smaller population (N ≈ 250) off Bunbury (BB). With collaborators, I assessed demographic parameters, characterized MHC variation, and investigated the relationship between fitness and MHC diversity. In chapter 2, our demographic analysis showed that the SB population, which is comparatively unimpacted by human activity, was much larger and displayed greater reproductive output than the urban BB population. Reproductive rates of the SB population showed large temporal fluctuations. In chapter 3, using a combination of Sanger and next-generation Illumina MiSeq sequencing, we identified a large variety of MHC sequence variants. We also classified MHC supertypes, variants which encode particular antigen binding sites with differing physiochemical properties. These MHC supertypes may serve as an improved marker for biologically relevant genetic variation. Transcription of some of the MHC sequence variants was confirmed in both populations. Chapter 4 shows that the larger SB population displayed greater MHC diversity—nucleotide diversity and a novel measure of ‘supertype diversity’—than the BB population. The SB populat