Sea turtle conservation: genetics and genomics for a better management

Abstract

Conservation actions aim to preserve and recover animal and plant species using in-situ or ex- situ strategies. The first, aims to protect and sustain populations in their natural habitat, the second are implemented when local populations are extinct or are about to be. Conservation genetics can provide important insights into the dynamics of endangered populations facilitating their management. This thesis uses traditional markers and new generation sequencing to improve conservation management of the loggerhead (Caretta caretta) and the green turtle (Chelonia mydas). In the first 2 chapters we used microsatellites and mtDNA to assess the outcome of a reintroduction program of green turtles in the Cayman Islands and the status of the reintroduced wild population. We found that 90% of adult wild females and 80% of wild F1 hatchlings were related to the captive population, proving the program successful. This relatedness did affect negatively the fitness of the wild population. Moreover, we found that after only one generation, genetic differentiation between the populations was significant. Our results suggest that assisted colonisation is a viable solution to the global decline of biodiversity. The third chapter explores the potential of 2b-RAD methodology in the field of non-model species population genomics and provides guidelines to optimise protocol and decision making using 2b-RAD. We discovered that, given the big genome size of the loggerhead turtle, a selective-base ligation should be used to obtain an overall depth of coverage of 20x and make the study cost-effective. The fourth chapter studies the population structure and local adaptation of 9 Eastern Mediterranean loggerhead turtle rookeries using 2b- RAD genomic sequencing. We found a high level of population structure and no overlapping among rookeries. Bayesian clustering indicated our individuals to be grouped in nine genetic clusters, which correspond to the distribution found in the PCoA. We found that atmospheric temperature and geographic location of the rookery have a significant impact on population structure, as outlier loci were found associated with these predictors. These results aim to use fine scale genetic information of the Eastern Mediterranean Sea to inform and improve conservation management of loggerhead turtle rookeries.