Conservation biology and genomics of a flagship endangered species: the Mauritian pink pigeon Nesoenas mayeri

The reduction of natural populations is a major conservation problem and the main cause of increased extinction risk. I investigated conservation issues that limit the growth of the pink pigeon population, including infection with Trichomonas gallinae, biased sex ratios and the reduction in both reproductive fitness and life history traits. In particular, I examined the association between these issues in the pink pigeon and genome-wide genetic variation using 45,841 single nucleotide polymorphisms (SNPs) generated using restriction site associated DNA sequencing (RAD-seq). The average observed and expected heterozygosity (Ho and He respectively) were low, at 0.27 and 0.28 respectively. Rapid genetic loss has increased inbreeding depression in the population. The effective population size was found to be particularly small in one subpopulation, Ile aux Aigrettes. Examining genome-wide heterozygosity for both immune and non-immune genes between males and females showed that males have a higher level of gene variation than females, which may explain the male-biased sex ratio in fledglings that this study found to be significant. A significant negative association was found between genome-wide heterozygosity and infection with Trichomonas gallinae. The longevity and body weight of adult birds and fledgling success showed a significant positive relationship with the level of genome-wide heterozygosity. Reproductive success, in terms of the number of nests, eggs laid and hatched young that died before fledging, did not show any significant relationship with the level of genome-wide heterozygosity. However, using genome-wide association studies (GWAS), this study identified a genomic region close to the progesterone receptor gene (PRG) that potential affects egg-laying in the pink pigeon. The findings of this thesis suggest an association between the problems limiting the growth of the pink pigeon population and a reduction in genome-wide variation, suggesting that the pink pigeon may be entering a vortex that may drive the species to extinction and thus emphasising the urgent need for conservation management to avoid its extinction