Marine turtle mitogenome phylogenetics and evolution Sebastián Duchene a , Amy Frey a , Alonzo Alfaro-Núñez b , Peter H. Dutton a , M. Thomas P. Gilbert b , Phillip A. Morin a,⇑ a Protected Resources Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 9801 La Jolla Shores Dr., La Jolla, CA 92037, USA b Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark article info Article history: Received 7 March 2012 Revised 11 June 2012 Accepted 13 June 2012 Available online xxxx Keywords: Sea turtle Molecular clock Mitogenome Molecular adaptive evolution Mitochondrial phylogenetics abstract The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp’s ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single mem- ber of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae. Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D- Loop sequences have shown considerable structuring in species with broad geographic distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all sea turtles, and reveal phy- logeographic patterns within globally-distributed species. Although there was clear concordance between phylogenies and geographic origin of samples in most taxa, we found evidence of more recent dispersal events in the loggerhead and olive ridley turtles, suggesting more recent migrations (<1 Myr) in these species. Overall, our results demonstrate the complexity of sea-turtle diversity, and indicate the need for further research in phylogeography and molecular evolution. Published by Elsevier Inc. 1. Introduction The sea turtles comprise seven extant species grouped into two families: Dermochelidae, with the leatherback (Dermochelys coria- cea) as the single extant species, and Cheloniidae, with six species: hawksbill, Kemp’s ridley, olive ridley, loggerhead, green, and flat- back turtles (Eretmochelys imbricata, Lepidochelys kempii, L. oliva- cea, Caretta caretta, Chelonia mydas, and Natator depressus, respectively). Their phylogenetic placement has been somewhat debated, with different molecular data sets supporting different groupings within Cheloniidae. The placement of N. depressus has been particularly problematic, with different data supporting it as the sister taxon either to a clade comprising the genera Eretm- ochelys, Caretta, and Lepidochelys (Dutton et al., 1996; Iverson et al., 2007), or to Chelonia only (Naro-Maciel et al., 2008). Most sea turtles (except L. kempii and N. depressus) have a pan- tropical distribution across a wide latitudinal range from Canada to South Africa, Southern Argentina and Chile (Hirth et al., 1997). Ge- netic studies based on the mitochondrial D-Loop of C. mydas (Enca- lada et al., 1996), D. coriacea (Dutton et al., 1999), and L. olivacea (Bowen et al., 1991; Karl and Bowen, 1999) suggest differentiation of Indo-Pacific and Atlantic groups. This implies that South and Central America and the Isthmus of Panama represents a stronger geographic barrier to gene flow than do colder waters in the south- ern tip of Africa (Avise et al., 1992; Dutton et al., 1999), at least in these three species. Recent advances in DNA sequencing technologies have made more molecular markers available for turtle phylogenetics. Previ- ous studies have used as many as 14 nuclear markers across se- lected turtle lineages (including freshwater and terrestrial turtles; Barley et al., 2010), and five nuclear and two mitochondrial markers in marine turtles (Naro-Maciel et al., 2008). However, in terms of mitochondrial phylogenetics, only cytochrome b (Cytb) (Bowen et al., 1993), D-Loop, ND4 (Dutton et al., 1996) and 12S and 16S (Naro-Maciel et al., 2008) regions have been used, produc- ing highly supported trees for contrasting topologies (see Naro- Maciel et al., 2008). In other vertebrate groups, complete mitogenomes have demonstrated an increase in phylogenetic performance in terms of branch support and divergence-time estimation relative to 1055-7903/$ - see front matter Published by Elsevier Inc. http://dx.doi.org/10.1016/j.ympev.2012.06.010 ⇑ Corresponding author. E-mail addresses: garzonsebastian@hotmail.com (S. Duchene), amy.frey@noaa. gov (A. Frey), alonzoalfaro@gmail.com (A. Alfaro-Núñez), peter.dutton@noaa.gov (P.H. Dutton), mtpgilbert@gmail.com (M. Thomas P. Gilbert), phillip.morin@noaa. gov (P.A. Morin). Molecular Phylogenetics and Evolution xxx (2012) xxx–xxx Contents lists available at SciVerse ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Please cite this article in press as: Duchene, S., et al. Marine turtle mitogenome phylogenetics and evolution. Mol. Phylogenet. Evol. (2012), http:// dx.doi.org/10.1016/j.ympev.2012.06.010