Mitochondrial DNA short tandem repeats unveil hidden population structuring and migration routes of an endangered marine turtle

Abstract

The assessment of the composition and dynamics of endangered populations is crucial for management and conservation, and appropriate genetic markers are critical. The genetic structuring of the Mediterranean green turtle (Chelonia mydas) populations and the origin of the stranded animals found along the Israeli coast was investigated using new highly polymorphic short tandem repeat (STR) markers. The structuring of nesting populations was studied using pairwise genetic distances and a principal coordinates analysis (PCoA). The contribution of the different nesting populations to the stranded sample was assessed by using a mixed‐stock analysis. A clear population genetic structure, not detected before, has been revealed. The four nesting populations are genetically well differentiated, and thus should be considered as different management units. The populations from Turkey and Israel showed higher resemblance, despite residing at opposite ends of the Mediterranean distribution. The Turkish nesting population is the main source of the stranded turtles sampled along the Israeli shore, confirming that individuals from this population migrate from north to south along the eastern shore of the Mediterranean, as previously shown by telemetry studies. The use of a highly polymorphic haplotyping method enabled the detection of a clear genetic structuring of the green turtle populations in the eastern Mediterranean Sea that was not revealed in previous studies, demonstrating the importance of marker selection in population genetics. The analysis of the genetic composition of the stranded turtles allowed us to investigate the migration patterns from nesting to foraging areas, supporting previous satellite‐tracking and stable‐isotope results. These results will help to delineate conservation management units for the species in the Mediterranean, and reveal connectivity among beaches and mixed aggregations.

Population-specific signatures of intra-individual mitochondrial DNA heteroplasmy and their potential evolutionary advantages

“…Our results demonstrate that, by analysing only a small number of families, we have recovered 11 out of 16 haplotypes previously reported for the whole population of Israel 30 . Furthermore, considering a previous comprehensive study in nesting females in the Mediterranean and that all our samples are from Israel, we have reported 25 new haplotypes for the Israeli population.…”

“…Consequently, most phylogenetic and phylogeographic studies have ignored the minor haplotypes indicated by additional peaks, Table 1. Samples were grouped according to the clusters detected in www.nature.com/scientificreports www.nature.com/scientificreports/ or at most reported it but did not use them for subsequent analysis 28,30 . Using HTS, we were able to investigate the whole population of mtDNA molecules composing an individual's haplotypic profile by analyzing the repeat region of the mtDNA D-loop of green sea turtles.…”

“…This region is not under strong selective pressure (but see 31 for coding regions) and thus, it would allow us to improve our understanding of the mode of inheritance and evolutionary mechanisms of this molecule. We could follow the occurrence of mutations in the D-loop, the rarer SNPs 32 as well as the more frequently occurring changes in the mtSTR short tandem repeats region 28,30 . Larger circles represent mature oocytes before fertilization and establishing the next generation of the population.…”

“…This includes 2 haplotypes previously thought as "orphans" (i.e., haplotypes found only in foraging areas but not in any putative nesting population of origin). The presence of orphan haplotypes is one of the shortcomings of accurate mixed stock analysis 30 . Using HTS we were able to show that these haplotypes can be present in low frequencies in heteroplasmic individuals and thus enhancing the power of mixed stock analysis.…”

“…Shamblin et al 29 used the same repetitive region to study green turtles from Brazil and detected population structure between two islands once thought to be one population. Although the use of the mtSTR region has greatly improved the resolution of sea turtles breeding stocks, all studies so far have used Sanger sequencing to define haplotypes and heteroplasmy has been reported as anecdotal without further consideration to the posterior analyses [28][29][30] . Sanger sequencing only allows the confidently distinct use of a maximum of two haplotypes within one individual with no esteem of its relative frequencies, consequently underestimating the number of mtSTR haplotypes within an individual.…”