Re-examination of Population Structure and Phylogeography of Hawksbill Turtles in the Wider Caribbean Using Longer mtDNA Sequences

Abstract

Management of the critically endangered hawksbill turtle in the Wider Caribbean (WC) has been hampered by knowledge gaps regarding stock structure. We carried out a comprehensive stock structure re-assessment of 11 WC hawksbill rookeries using longer mtDNA sequences, larger sample sizes (N = 647), and additional rookeries compared to previous surveys. Additional variation detected by 740 bp sequences between populations allowed us to differentiate populations such as Barbados-Windward and Guadeloupe (F (st) = 0.683, P < 0.05) that appeared genetically indistinguishable based on shorter 380 bp sequences. POWSIM analysis showed that longer sequences improved power to detect population structure and that when N < 30, increasing the variation detected was as effective in increasing power as increasing sample size. Geographic patterns of genetic variation suggest a model of periodic long-distance colonization coupled with region-wide dispersal and subsequent secondary contact within the WC. Mismatch analysis results for individual clades suggest a general population expansion in the WC following a historic bottleneck about 100 000-300 000 years ago. We estimated an effective female population size (N (ef)) of 6000-9000 for the WC, similar to the current estimated numbers of breeding females, highlighting the importance of these regional rookeries to maintaining genetic diversity in hawksbills. Our results provide a basis for standardizing future work to 740 bp sequence reads and establish a more complete baseline for determining stock boundaries in this migratory marine species. Finally, our findings illustrate the value of maintaining an archive of specimens for re-analysis as new markers become available.

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“…Products were then separated on an ABI 3100 or 3730 DNA analyzer with Genescan Rox500 fluorescent size standard (PE Applied Biosystems). Additionally, we amplified and sequenced the mtDNA control region using the primers H950g and LCM15382 (Abreu-Grobois et al 2006) under PCR conditions described by LeRoux et al (2012) for at least 1 sample from each of the 141 nests and all of the nesting females. MtDNA sequences were aligned and assigned haplotypes using Seqscape v2.5 (PE Applied Biosystems).…”

Predicting connectivity of green turtles at Palmyra Atoll, central Pacific: a focus on mtDNA and dispersal modelling

“…DNA extractions were performed using a DNeasy kit following the manufacturer's instructions (Qiagen Inc.). Primers LCM15382 and H950 were used to amplify an approximately 857 bp fragment of the mtDNA control region and two tRNAs [48]. Standard conditions and negative controls were used, and sequencing was carried out in both directions [39,47].…”

Advances in the Application of Genetics in Marine Turtle Biology and Conservation

“…In cases where there is not extensive haplotype sharing among rookeries, the extended control region sequence can effectively identify natal origin of foraging turtles (LeRoux et al, 2012). However, when overlaps in control region haplotypes among rookeries are prevalent, the addition of other mtDNA markers or complete mitogenomic sequencing can help resolve uncertainties (Shamblin et al, 2012a).…”