A central theme in ecology is to understand the distribution and abundance of organisms and the factors influencing these patterns. This thesis investigated the taxonomic identity and biogeography of blood parasites, Amblyomma ticks and gastro-intestinal helminths of Galápagos tortoise, Chelonoidis spp. Blood parasite and ticks were assessed for co-phylogeographic patterns with their tortoise host. The patterns of helminths diversity was examined and whether factor such as host colonization history and local ecology determine their distribution and community composition. Microscope and phylogenetic analysis of 18S rDNA identified the blood parasite as a haemogregarine of the genus Hepatozoon. It was represented by just two haplotypes restricted to the northern volcanoes of Isabela. Thirty-seven tortoise blood samples yielded the same haemogregarine haplotype for Alcedo and Wolf volcanoes, unique to Chelonoidis spp. The only tortoise that was haemogregarine positive from Darwin yielded a different haplotype, related to haemogregarines reported from Galápagos land iguanas. Molecular analysis of the COI gene of Amblyomma ticks revealed 3 different species, one infesting tortoises of Alcedo and Wolf volcanoes, one in tortoises of Santiago and one of tortoises from Pinzón. Galápagos tortoise ticks from Alcedo and Wolf has been described before as A. unsingeri, while tortoise ticks from Santiago and Pinzón have been described as belonging to A. pilosum. The restricted distribution of tortoise haemogregarines impeded testing them for co-phylogeographic patterns. Ticks showed no agreement with the phylogeography of their tortoise host. Coprological and metabarcoding methods revealed the presence of Platyhelminths, Acanthocephala, and Nematoda. Metabarcoding however, exceeded the traditional method in sensitivity for parasite detection and identification. At least seven families of Nematoda were identified with most taxa widespread across the Galápagos archipelago suggesting little effect of host colonisation for the common taxa in their distribution. At least three genera were found only on one or two islands suggesting their potential local acquisition or exclusion. These results are relevant for understanding the diversity and ecology of Chelonoidis spp. parasites, the management andconservation of this reptile and as a model for other wild species.

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Understanding the degree of connectivity among populations, forming migratory links and evaluating factors that influence reproductive fitness is fundamental for the successful management of migratory species of conservation concern. In this thesis I focus on a regionally important rookery of green turtles (Chelonia mydas) at Alagadi beach in northern Cyprus that has been intensively studied since 1992. I employ high resolution genetic markers with different modes of inheritance to reveal fine scale population structuring among four rookeries within a 200 km stretch of shoreline. The relative importance of four foraging areas and the annual contribution from each site to the breeding cohort are evaluated using the stable isotope ratios of the turtles calibrated by satellite telemetry. The stable isotope ratios of the turtles reveal that a previous undisclosed foraging site at Lake Bardawil in Egypt is critical for the population recovery of the Alagadi rookery. The temporal consistency of stable isotope ratios reaffirm that green turtles exhibit high fidelity to foraging sites allowing the evaluation of foraging area effects on reproductive traits to be evaluated over multiple seasons. I investigate the population sub-structuring of the Alagadi nesting aggregation grouped by the foraging area used. The absence of genetic structure supported the Learning Migration Goal Theory and provided evidence that the significant among site phenotypic variability in the body size of recruits, the length of interbreeding intervals and the date that the first nest of the season was made is a result of foraging areas effects. No significant among site phenotypic variability was found for the size or number of clutches laid. Among site variability in interbreeding intervals resulted in substantial variation in the reproductive potential of individuals due to assumed differences in resource availability and environmental factors. The multilocus genotypes generated for 243 nesting females were employed to reconstruct the first wild marine turtle pedigree using a full-likelihood sib-ship reconstruction approach. This revealed that the effective contribution to the next generation was unequal and allowed a minimum age to maturity to be estimated from parent – offspring assignations. However, sample size constraints prevented accurate estimates for the narrow-sense heritability of the five morphological and life-history traits from the quantitative genetic analysis. The multifaceted approach taken here to unravel the cryptic life-history of marine turtles emphasises the importance of long-term individual-based monitoring and the data generated can be employed to advise conservation strategy for this critically endangered regional management unit.

Climate change threatens to disrupt biological systems around the globe, sparking debate over natural capacity for adaptation in a fragmented landscape. Marine turtles are evolutionarily ancient and have survived millions of years of prehistoric climate change, but are threatened by the rapidity of modern warming and a history of severe overexploitation that has left most populations depleted. This thesis explores a nesting aggregation of the green turtle (Chelonia mydas) in northern Cyprus, where a longitudinal programme of both intensive and extensive monitoring enables insight into individual and population level parameters and processes. Nesting on the two coastlines covered by this project is in the early stages of recovery, possibly in response to exhaustive nest protection efforts over the last twenty years. Saturation tagging at one key site allows us to confirm that recruitment of new breeders is an important driver of this trend, and that average clutch frequency has remained stable around three nests per female per year, validating nest-count derived abundance estimates at a regional scale. Concern has been raised, however, regarding recent changes in fishing practices which are impacting the local juvenile neritic phase, which may have a lagged effect on the recovery of this nesting population. A collaborative tracking effort including all other countries with major nesting in the Mediterranean allows us to identify major foraging grounds for this species, with two hotspots accounting for >50% of tracked individuals, as well as coastal and pelagic seasonal corridors of high use. Bycatch levels and mortality rates for turtles in these key areas are largely unknown and should be prioritised for investigation. Hatchling sex ratios from the main study beach are extremely female-biased (estimated 97% female for the twenty year period 1993-2012). A 1oC rise in average incubation temperatures threatens near complete hatchling feminisation on this beach, whilst a 2oC rise could reduce hatch success to less than 50%. Thermal effects on hatchling morphometrics are evident, with a 1oC rise in temperature reducing average length, width and weight by 1%, 2% and 3% respectively. More favourable incubation conditions were found early in the season, in deeper nests laid by larger females, and on beaches of lighter sand. In contrast, adult sex ratios at the main site are male-biased, posing questions regarding sex-specific survival rates and optimal hatchling sex ratios. A phenological shift towards earlier nesting is demonstrated for the first time in this species, and could potentially ameliorate warming effects. Carry-over climate forcing effects from the foraging ground influence the breeding frequency of individuals, driving population level responses in annual magnitude of nesting. This work emphasises the utility and necessity of long-term individual-based monitoring programmes in elucidating population trends and climate responses in iteroparous species with non-annual breeding.