Polymorphism in mitochondrial coding regions of mediterranean loggerhead turtles: Evolutionary relevance and structural effects

We sequenced coding portions (1.6 kb) of the mtDNA in 170 loggerhead (Caretta caretta) turtles sampled in the central Mediterranean. The sequences spanned the entire ND1 and ND3 genes, the tRNAGly and tRNAArg, plus the 3′ and 5′ termini of COXIII and ND4L genes, respectively. Based on our sequencing results and published complete mitogenomes, we constructed a maximumparsimonyphylogeny of C. carettamatrilines that shedsnew light on the evolutionary relationships within the collection of lineages found in the Mediterranean and so far recognized by Dloop haplotypes only. We show that the new variants are useful to understand the ancestry of extant haplotypes, to improve genetically based studies on the philopatry and migratory behavior of the species, and for conservation purposes. In order to better understandthe biological significance of the observed variation, we addressed intraspecific nonsynonymous substitutions in the context of the three-dimensional modeled structures of ND1 and ND3. The positions of variant amino acids within the folded subunits are consistent with a coadaptation with the restructuring of membrane thickness, fluidity, and lipid composition, a wellknown responsemechanism to thermal conditions.Thepatternof amino acid substitutions departs from neutrality, suggesting local adaptation and/or polymorphism-based local selection.