Mitochondrial DNA diversity and phylogeography of endangered green turtle (Chelonia mydas) populations in Africa

We analysed the genetic structure of seven nesting sites of the endangered green turtle (Chelonia mydas) in Africa using mitochondrial DNA control region sequences. Tissue samples were collected from 188 nesting females at six sites in West Africa and one in the Indian Ocean. A 488 bp fragment of the control region revealed 14 different haplotypes, 10 of which are previously undescribed. The most common haplotype (CM8) was observed in 157 individuals. All other haplotypes were closely related, except two divergent lineages: CM38, removed by four substitutions, and the three Indian Ocean haplotypes, distinguished by 31 substitutions. Significant differences in haplotype and nucleotide diversity were observed between Atlantic rookeries and among ocean basins. Analysis of molecular variance revealed high levels of differentiation between the Atlantic and the Indian Ocean populations but a much shallower Atlantic substructuring. Green turtle population genetic structure is thought to have been shaped by a dynamic succession of extinction and recolonisation of rookeries, by natal homing and occasional breakdown in nest-site fidelity. Mismatch distributions of pairwise differences between haplotypes at each rookery were found to be consistent with recent population expansion. We argue that demographic histories can be explained by scenarios at several temporal scales, including geological events, sea level fluctuations and more recent patterns of exploitation. We discuss management and conservation implications of our results for these threatened populations, identifying two ESUs (one in the Atlantic and one in the Indian ocean) and three MUs within the Atlantic.