Geographic patterns of genetic variation in a broadly distributed marine vertebrate: new insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences

PLoS One. 2014 Jan 23;9(1):e85956. doi: 10.1371/journal.pone.0085956. eCollection 2014.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Atlantic Ocean
  • Conservation of Natural Resources
  • DNA, Mitochondrial / genetics*
  • Female
  • Genetic Variation*
  • Genetics, Population
  • Haplotypes
  • Indian Ocean
  • Mediterranean Sea
  • Mitochondria / genetics
  • Molecular Sequence Data
  • Phylogeny
  • Phylogeography
  • Sequence Analysis, DNA
  • Turtles / genetics*

Substances

  • DNA, Mitochondrial

Grants and funding

The NOAA-Fisheries Service and The Ocean Foundation funded travel for convening the Atlantic-Mediterranean Loggerhead Genetics Working Group meetings and laboratory analysis. The National Research Foundation Thuthuka Grant and Nelson Mandela Metropolitan University funded fieldwork in South Africa. Stipend support was provided to Brian Shamblin was by the National Research Council to lead data analysis and manuscript preparation at the NOAA-Southwest Fisheries Science Center. Funding support for Kelly Stewart was partially provided by the National Research Council at the Southwest Fisheries Science Center and also by the Lenfest Ocean Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.