Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (∼800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting comprehensive international cooperative data management and research in marine ecology.

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The Mediterranean green turtle regional management unit is one of the 17 management units of green turtles considered a global conservation priority. However, previous studies using different genetic markers revealed very little diversity and differentiation across populations due to the overdominance of one haplotype (CM-A13) in the Mediterranean. We, therefore, used a more informative marker, mitochondrial short tandem repeats (mtSTRs), in 431 samples collected along the eastern Mediterranean coasts of Turkey and Northern Cyprus. In addition, we added the mtSTR haplotypes of previous studies and reached a total of 980 samples covering 12 nesting beaches (almost 100% of the populations in the region). We identified 42 haplotypes, 4 of which were recorded for the first time in the region. The species has a genetic diversity in the region higher than previously thought, ranging from 0.54 (Sugözü, Turkey) to 0.934 (Israel) and with the most common haplotypes being 6-8-8-4 (26.5%), 6-8-5-4 (17.3%), and 6-8-6-4 (14.9%). The analysis of a more extensive data set of mtSTRs supported recognizing at least three management units in the Mediterranean. Furthermore, we used the new data to assess the origin of the turtles foraging in Israel. We determined that Samandağ (Turkey) was the population of origin of most of the individuals.Overall, we show that mtSTRs highly improve the resolution to detect population structuring and source for this species and region.