Mitochondrial genome sequencing and applications for the conservation of endangered species: sea turtles as case studies

Mitochondrial DNA (mtDNA) is widely used in evolutionary and population genetic studies thanks to its small size, conserved structure, high mutation rate, lack of recombination and maternal inheritance. These features make mtDNA one of the main markers of choice to define population structure and demography and reconstruct phylogeographic patterns of dispersal and migration, particularly in sea turtles where life cycles are based on female-philopatry to nesting sites. For decades, parts of single-genes or non-coding sequences of mtDNA have been used as genetic markers to address questions on the life history of organism. With the advent of next generation sequencing techniques, the characterization of whole mtDNA, as well as whole nuclear genome sequences, has become more accessible. In this thesis, I developed wet and dry lab pipelines for whole mitogenome sequencing using biological samples collected from live or stranded individuals of three sea turtle species across different geographic areas. I compared mitogenome sequence data and information from single gene sequencing to study the population structure, demography and evolutionary history of loggerhead turtles (Caretta caretta), green turtles (Chelonia mydas) and hawksbill turtles (Eretmochelys imbricata). The mitogenome pipeline proved effective in generating medium–to-high coverage whole mitochondrial genomes for C. caretta from the Mediterranean Sea and globally, as well as C. mydas and E. imbricata sampled in the Gulf of Guinea, West Africa. In all case studies, mitogenomes resolved matrilineages more clearly than traditional markers, revealing numerous mitogenomic variants for each single, widely distributed mtDNA control region haplotype. Whole mitogenomes also helped clarify global-scale species phylogeography and provided insight into adaptive and non-neutral evolutionary processes that might have affected natural populations. Comparing the results of this thesis with previous studies based on single-gene markers, some discrepancies emerged, which helped explain divergent conclusions previously reported in the literature on the evolutionary history of sea turtle populations. These findings underscored the importance of using most informative markers (e.g. whole mitogenomes) for population and evolutionary genetic analyses. To fully leverage mitogenomics, it is crucial to implement efficient methodological pipelines, as demonstrated in this thesis. Moreover, clearly defined research questions are essential to optimize sampling strategies and ensure adequate sample sizes. At both local and global scales, whole mitogenomes, eventually integrated with broad single-gene datasets and nuclear sequences, hold significant potential to improve our understanding of population structure, ecology and evolution of sea turtles, while supporting the design of informed management and conservation strategies.