title: Causes and consequences of genetic diversity in pinnipeds
Creators: name: Stoffel, M
Publisher: name: Liverpool John Moores University
Year: 2021

description: The rise of empirical population genetics and more recently the genomic revolution have given us the tools to explore completely new questions in ecology and evolution. Based on only a single temporal sample of individuals, genetics now allows us to glimpse into the demographic history of a species and gain insights into its population dynamics during the last glacial period or the impact of recent bottlenecks caused by human exploitation. Measuring genetic variation is also key to exploring the forces shaping phenotypic variation, which are well understood for some traits but are completely unknown for many others. Among the latter are chemical and bacterial phenotypes, which are so complex in themselves that it is not clear how they are determined by an animals' genotype. Nevertheless, a better knowledge of the interconnectivity between animal genetics, chemicals and microbiota has the potential to drastically change our understanding of ecological and evolutionary processes. However, very few studies have bridged the gap between population genetics, chemical ecology and microbiology in wild populations. Pinnipeds are an extraordinary group of marine mammals for exploring such wide-ranging questions. From the tropical waters of the Central Pacific to the wild seas of the Southern Ocean, pinnipeds inhabit nearly every marine environment in the world. They show a remarkable variety of life-history adaptations where chemical communication and host-microbe interactions play a potentially critical role, such as the flawless mother-pup recognition in fur seals or the sex-specific feeding strategies in Northern elephant seals. Pinnipeds also differ greatly in their recent demographic histories, as large-scale commercial exploitation by 18th and 19th century sealers brought many species to the edge of extinction, while others remained largely untouched. In my dissertation, I elucidate the origins of genetic variation among pinnipeds using demographic inference, but I also explore some of the more unknown consequences of genetic variation: chemical and microbial phenotypes, and their potential functions. Lastly, inspired by the open science movement, I developed three scientific packages in R which emerged from the analyses in this dissertation. My thesis is divided into the following chapters: In chapter 1, I give an overview of the historical context and main questions of this dissertation and describe the pinnipeds as a study system. In chapter 2, I present a comparative genetic analysis of the demographic consequences of commercial exploitation. We found that around one-third of all pinnipeds underwent severe genetic bottlenecks and that these were mediated by both ecology and life-history. Moreover, genetic diversity seems to be largely determined by contemporary population size and reduced only by very severe bottlenecks. Chapter 3 presents the first genomic investigation into the demographic history of the Northern elephant seal. Using a novel genome sequence and restriction-site associated DNA sequencing, we infer both an extreme recent bottleneck and a likely post-glacial expansion of the species. In chapter 4, we characterise the chemical basis of olfactory mother-offspring recognition in Antarctic fur seals. The skin chemical profiles were surprisingly diverse, with chemical compounds differing between populations and mother-offspring pairs and correlating with heterozygosity and genetic relatedness. Chapter 5 explores the development of gut microbiota in young Northern elephant seals. Using a diet-controlled setting, we show that gut microbiota of young seals are already highly complex and change radically within only a few weeks. Furthermore, we show that gut microbiota are highly sex-specific and linked to genotype in males but not in females. In chapter 6, we describe GCalignR, an R package for aligning gas chromatography data across many individuals for field studies in animal ecology and evolution. Chapter 7 presents inbreedR, an R package for analysing inbreeding and inbreeding depression using genetic and genomic markers. The rptR package described in chapter 8 quantifies intra-class coefficients or repeatabilities for Gaussian and non-Gaussian traits in a mixed model framework. Lastly, chapter 9 puts the findings of this thesis in a broader context, discusses its limitation with respect to the neutral theory of molecular evolution and the complexities of assigning function to chemical compounds and microbes in wild organisms and outlines future directions. To summarise, my dissertation provides novel insights into how recent and historical demography shaped the genetic makeup of contemporary populations, thereby contributing to the old riddle of the determinants of genetic diversity. Moreover, I show that individual genetic variability shapes complex chemical signatures and gut microbial communities in the wild and explore the potential mechanisms by which these could be intertwined with pinniped ecology and evolution. Lastly, I hope that both the openly available and documented analytical pipelines as well as the R packages that have emerged from this dissertation will help to facilitate scientific progress and replicability.