Publication Cover
Mitochondrial DNA
The Journal of DNA Mapping, Sequencing, and Analysis
Volume 23, 2012 - Issue 1
404
Views
19
CrossRef citations to date
0
Altmetric
Full Length Research Papers

The complete mitochondrial genome of the loggerhead turtle Caretta caretta (Testudines: Cheloniidae): Genome description and phylogenetic considerations

, , , , , , , , , & show all
Pages 1-12 | Received 09 Sep 2011, Accepted 26 Oct 2011, Published online: 01 Feb 2012

References

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403–410.
  • Amer SA, Kumazawa Y. 2009. Complete sequence of the mitochondrial genome of the endangered Nile soft-shelled turtle Trionyx triunguis. Egypt J Exp Biol (Zool). 5:43–50.
  • Avise JC. 1994. Molecular markers, natural history and evolution. London: Chapman and Hall.
  • Avise JC. 2007. Conservation genetics of marine turtles—ten years later. In: Hewitt D, Fulbright T. editors. Frontiers in wildlife science: Linking ecological theory and management application. Boca Raton, FL: CRC Press295–314.
  • Avise JC, Bowen BW. 1994. Investigating sea turtle migration using DNA markers. Curr Opin Genet Dev. 4:882–886.
  • Baldwin R, Hughes GR, Prionce RIT. 2003. Loggerhead turtles in the Indian Ocean. In: Bolten AB, Witherington BE. editors. Loggerhead sea turtles. Washington, DC: Smithsonian Books218–232.
  • Barley AJ, Spinks PQ, Thomson RC, Shaffer HB. 2010. Fourteen nuclear genes provide phylogenetic resolution for difficult nodes in the turtle tree of life. Mol Phylogenet Evol. 55:1189–1194.
  • Bolten AB, Bjorndal KA, Martins HR, Dellinger T, Biscoito MJ, Encalada SE, Bowen BW. 1998. Transatlantic developmental migrations of loggerhead sea turtles demonstrated by mtDNA sequence analysis. Ecol Appl. 8:1–7.
  • Boore JL. 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27:1767–1780.
  • Bowen BW, Abreu-Grobois FA, Balazs GH, Kamezaki N, Limpus CJ, Ferl RJ. 1995. Trans-Pacific migrations of the loggerhead turtle (Caretta caretta) demonstrated with mitochondrial DNA markers. Proc Natl Acad Sci USA. 92:3731–3734.
  • Bowen BW, Avise JC, Richardson JI, Meylan AB, Margaritoulis D, Hopkins-Murphy SR. Loggerhead turtles (Caretta caretta) in the Northwestern Atlantic Ocean and Mediterranean sea. Cons Biol. 1993a; 7:834–844.
  • Bowen BW, Bass AL, Chow S-M, Bostrom M, Bjorndal KA, Bolten AB, Okuyama T, Bolker BM, Epperly S, Lacasella E, Shaver D, Dodd M, Hopkins-Murphy SR, Musick JA, Swingle M, Rankin-Baransky K, Teas W, Witzell WN, Dutton PH. 2004. Natal homing in juvenile loggerhead turtles (Caretta caretta). Mol Ecol. 13:3797–3808.
  • Bowen BW, Bass AL, Soares L, Toonen RJ. 2005. Conservation implications of complex population structure: Lessons from the loggerhead turtle (Caretta caretta). Mol Ecol. 14:2389–2402.
  • Bowen BW, Karl SA. 2007. Population genetics and phylogeography of sea turtles. Mol Ecol. 16:4886–4907.
  • Bowen BW, Nelson WS, Avise JC. A molecular phylogeny for marine turtles: Trait mapping, rate assessment, and conservation relevance. Proc Natl Acad Sci USA. 1993b; 90:5574–5577.
  • Boyle MC, FitzSimmons NN, Limpus CJ, Kelez S, Velez-Zuazo X, Waycott M. 2009. Evidence for transoceanic migrations by loggerhead sea turtles in the southern Pacific Ocean. Proc R Soc B. 276:1993–1999.
  • Broderick AC, Glen F, Godely BJ, Hays GC. 2002. Estimating the number of green and loggerhead turtles nesting annually in the Mediterranean. Oryx. 36:227–235.
  • Broughton RE, Milam JE, Roe BA. 2001. The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA. Genome Res. 11:1958–1967.
  • Carreras C, Pascual M, Cardona L, Aguilar A, Margaritoulis D, Rees A, Turkozan O, Levy Y, Gasith A, Aureggi M, Khalil M. The genetic structure of the loggerhead sea turtle (Caretta caretta) in the Mediterranean as revealed by nuclear and mitochondrial DNA and its conservation implications. Conserv Genet. 2006a; 8:761–775.
  • Carreras C, Pont S, Maffucci F, Pascual M, Barceló A, Bentivegna F, Cardona L, Alegre F, SanFélix M, Fernández G, Aguilar A. Genetic structuring of immature loggerhead sea turtles (Caretta caretta) in the Mediterranean Sea reflects water circulation patterns. Mar Biol. 2006b; 149:1269–1279.
  • Curole AP, Kocher TD. 1999. Mitogenomics: Digging deeper with complete mitochondrial genomes. Trends Ecol Evol. 14:394–398.
  • Dodd CKJr. 1988. Synopsis of the biological data on the loggerhead sea turtle Caretta caretta (Linnaeus, 1758). US Fish Wildl Serv Biol Rep. 88:1–110.
  • Dutton PH, Bowen BW, Owens DW, Barragan A, Davis SK. 1999. Global phylogeography of the leatherback turtle (Dermochelys coriacea). J Zool (Lond). 248:397–409.
  • Dutton PH, Davis SK, Guerra T, Owens D. 1996. Molecular phylogeny for marine turtles based on sequences of the ND4-leucine tRNA and control regions of mitochondrial DNA. Mol Phylogenet Evol. 5:511–521.
  • Ehrhart LM, Bagley DA, Redfoot WE. 2003. Loggerhead turtles in the Atlantic Ocean: Geographic distribution, abundance and population status. In: Bolten AB, Witherington BE. editors. Loggerhead sea turtles. Washington, DC: Smithsonian Books157–174.
  • Gaffney ES. 1975. Phylogeny of the chelydrid turtles: A study of shared derived characters in the skull. Fieldiana Geol. 33:157–178.
  • Garman S. 1880. On certain species of Chelonioidae. Bull Mus Comp Zool. 6:123–126.
  • Groombridge B. 1990. Marine turtles in the Mediterranean: Distribution, population status, conservation. Nat Environ Ser (Counc Eur). 48:1–98.
  • Hatase H, Kinoshita M, Bando T, Kamezaki N, Sato K, Matsuzawa Y, Goto K, Omuta K, Nakashima Y, Takeshita H, Sakamoto W. 2002. Population structure of loggerhead turtles, Caretta caretta, nesting in Japan: Bottlenecks on the Pacific population. Mar Biol. 141:299–305.
  • Hatase H, Omuta K, Tsukamoto K. 2007. Bottom or midwater: Alternative foraging behaviours in adult female loggerhead sea turtles. J Zool (Lond). 273:46–55.
  • Hawkes LA, Broderick AC, Coyne MS, Godfrey MH, Lopez-Jurado L-F, Lopez-Suarez P, Merino SE, Varo-Cruz N, Godley BJ. 2006. Phenotypically linked dichotomy in sea turtle foraging requires multiple conservation approaches. Curr Biol. 16:990–995.
  • Inoue JG, Miya M, Katsumi T, Nishida M. 2003. Evolution of the deep-sea gulper eel mitochondrial genomes: Large-scale gene rearrangements originated within the eels. Mol Biol Evol. 20:1917–1924.
  • IUCN 2011. IUCN Red List of Threatened Species. Version 2011.2. Available at: http://www.iucnredlist.org. Accessed on 14 November 2011.
  • Janke A, Arnason U. 1997. The complete mitochondrial genome of Alligator mississippiensis and the separation between recent archosauria (birds and crocodiles). Mol Biol Evol. 14:1266–1272.
  • Janke A, Erpenbeck D, Nilsson M, Arnason U. 2001. The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): Implications for amniote phylogeny. Proc R Soc Lond, B, Biol Sci. 268:623–631.
  • Jung S-O, Lee Y-M, Kartavtsev Y, Park I-S, Kim DS, Lee J-S. 2006. The complete mitochondrial genome of the Korean soft-shelled turtle Pelodiscus sinensis (Testudines, Trionychidae). DNA Sequence. 17:471–483.
  • Kumazawa Y, Nishida M. 1999. Complete mitochondrial DNA Sequences of the green turtle and blue-tailed mole skink: Statistical evidence for Archosaurian affinity of turtles. Mol Biol Evol. 16:784–792.
  • Laurent L, Casale P, Bradai MN, Godley BJ, Gerosa G, Broderick AC, Schroth W, Schierwater B, Levy AM, Freggi D, Abd el-Mawla EM, Hadoud DA, Gomati HE, Domingo M, Hadjichristophorou M, Kornaraky L, Demirayak F, Gautier CH. 1998. Molecular resolution of marine turtle stock composition in fishery bycatch: A case study in the Mediterranean. Mol Ecol. 7:1529–1542.
  • Lee PLM. 2008. Molecular ecology of marine turtles: New approaches and future directions. J Exp Mar Biol Ecol. 356:25–42.
  • Lee J-S, Miya M, Lee Y-S, Kim CG, Park E-H, Aoki Y, Nishida M. 2001. The complete DNA sequence of the mitochondrial genome of the self-fertilizing fish Rivulus marmoratus (Cyprinodontiformes, Rivulidae) and the first finding of duplication of control region in fish. Gene. 280:1–7.
  • Limpus CJ, Gyuris E, Miller JD. 1988. Reassessment of the taxonomic status of the marine turtle genus Natator Mc Culloch, 1908, with a redescription of the genus and species. Trans R Soc South Aust. 112:1–9.
  • Mindell DP, Sorenson MD, Dimcheff DE, Hasegawa M, Ast JC, Yuri T. 1999. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Syst Biol. 48:138–152.
  • Miya M, Nishida M. 1999. Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei: Stomiiformers): First example of transfer RNA gene rearragenements in bony fishes. Mar Biotechnol. 1:416–426.
  • Monzón-Argüello C, López-Jurado LF, Rico C, Marco A, López P, Hays GC, Lee PLM. 2010. Evidence from genetic and Lagrangian drifter data for transatlantic transport of small juvenile green turtles. J Biogeogr. 37:1752–1766.
  • Moore MK, Bemiss JA, Rice SM, Quattro JM, Woodley CM. 2003. Use of restriction fragment length polymorphisms to identify sea turtle eggs and cooked meats to species. Conserv Genet. 4:95–103.
  • Mueller RL, Boore JL. 2005. Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders. Mol Biol Evol. 22:2104–2112.
  • Naro-Maciel E, Le M, FitzSimmons NN, Amato G. 2008. Evolutionary relationships of marine turtles: A molecular phylogeny based on nuclear and mitochondrial genes. Mol Phylogenet Evol. 49:659–662.
  • Naro-Maciel E, Reid B, Fitzsimmons NN, Le M, Desalle R, Amato G. 2010. DNA barcodes for globally threatened marine turtles: A registry approach to documenting biodiversity. Mol Ecol Resour. 10:252–263.
  • Nei M. 1987. Molecular evolutionary genetics. New York: Columbia University Press.
  • Nesbø CL, Arab MO, Jakobsen KS. 1998. Heteroplasmy, length and sequence variation in the mtDNA control regions of three Percid fish species (Perca fluviatilis, Acerina cernua, Stizostedion lucioperca). Genetics. 148:1907–1919.
  • Nikolaidis N, Scouras ZG. 1996. The Drosophila montium subgroup species. Phylogenetic relationships based on mitochondrial DNA analysis. Genome. 39:874–883.
  • Nylander JAA, Wilgenbusch JC, Warren DL, Swofford DL. 2008. AWTY (are we there yet?): A system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics. 24:581–583.
  • Ojala D, Montoya J, Attardi G. 1981. tRNA punctuation model of RNA processing in human mitochondria. Nature. 290:470–474.
  • Palkovacs EP, Gerlach J, Caccone A. 2002. The evolutionary origin of Indian Ocean tortoises (Dipsochelys). Mol Phylogenet Evol. 24:216–227.
  • Parham JF, Feldman CR, Boore JL. The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): Description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNA. BMC Evol Biol. 2006a; 6:11–21.
  • Parham JF, Macey JR, Papenfuss TJ, Feldman CR, Türkzan O, Polymeni R, Boore J. The phylogeny of Mediterranean tortoises and their close relatives based on complete mitochondrial genome sequences from museum specimens. Mol Phylogenet Evol. 2006b; 38:50–64.
  • Peng QL, Nie LW, Pu YG. 2006. Complete mitochondrial genome of Chinese big-headed turtle, Platysternon megacephalum, with a novel gene organization in vertebrate mtDNA. Gene. 380:14–20.
  • Pissios P, Scouras ZG. 1993. Mitochondrial DNA evolution in the montium-species subgroup of Drosophila. Mol Biol Evol. 10:375–382.
  • Posada D, Crandall KA. 1998. Modeltest: Testing the model of DNA substitution. Bioinformatics. 14:817–818.
  • Randi E, Lucchini V. 1998. Organization and evolution of the mitochondrial DNA control region in the avian genus Alectoris. J Mol Evol. 47:449–462.
  • Ray DA, Densmore LD. 2002. The crocodilian mitochondrial control region: General structure, conserved sequences and evolutionary implications. J Exp Zool B. 294:334–345.
  • Reece JS, Ehrhart LM, Parkinson CL. 2006. Mixed stock analysis of juvenile loggerheads (Caretta caretta) in Indian River Lagoon, Florida: Implications for conservation planning. Conserv Genet. 7:345–352.
  • Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572–1574.
  • Russell DR, Beckenbach AT. 2008. Recoding of translation in turtle mitochondrial genomes: Programmed frameshift mutations and evidence of a modified genetic code. J Mol Evol. 67:682–695.
  • Sbisa E, Tanzariello F, Reyes A, Graziano P, Saccone C. 1997. Mammalian mitochondrial D-loop region structural analysis: Identification of new conserved sequences and their functional and evolutionary implications. Gene. 205:125–140.
  • Schofield G, Hobson VJ, Fossette S, Lilley MKS, Katselidis KA, Hays GC. 2010. Fidelity to foraging sites, consistency of migration routes and habitat modulation of home range by sea turtles. Divers Distrib. 16:840–853.
  • Shadel GS, Clayton DA. 1997. Mitochondrial DNA maintenance in vertebrates. Annu Rev Biochem. 66:409–435.
  • Swofford DL. 2003. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sunderland, MA: Sinauer Associates.
  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731–2739.
  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876–4882.
  • Turtle Taxonomy Working Group [Rhodin AGJ, van Dijk PP, Iverson JB, Shaffer HB]. 2010. Turtles of the World, 2010 update: Annotated checklist of taxonomy, synonymy, distribution, and conservation status. In: Rhodin AGJ, Pritchard PVH, van Dijk PP, Saumure RA, Buhlmann KA, Iverson JB, Mittermeier RA. editors. Conservation biology of freshwater turtles and tortoises: A compilation project of the IUCN/SSC Tortoise and Freshwater Turtle Specialist Group Chelonian Research Monographs No. 5, p. 000.85–000.164, doi: 10.3854/crm.5.000.checklist.v3.2010, http://www.iucn-tftsg.org/cbftt/.
  • van der Kuyl AC, Ballasina DLP, Dekker JT, Maas J, Willemsen RE, Goudsmit J. 2002. Phylogenetic relationships among the species of the genus Testudo (Testudines: Testudinidae) inferred from mitochondrial 12S rRNA gene sequences. Mol Phylogenet Evol. 22:174–183.
  • Vittas S, Drosopoulou E, Kappas I, Pantzartzi CN, Scouras ZG. 2011. The mitochondrial genome of the European catfish, Silurus glanis (Siluriformes, Siluridae). J Biol Res—Thessalon. 15:25–35.
  • Walberg MW, Clayton DA. 1981. Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA. Nucleic Acids Res. 9:5411–5421.
  • Wolstenholme DR. 1992. Animal mitochondrial DNA: Structure cursor for mitochondrial genomic rearrangement. Int Rev Cyt. 141:173–216.
  • Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J Mol Evol. 39:306–314.
  • Zardoya R, Meyer A. 1998. Complete mitochondrial genome suggests diapsid affinities of turtles. Proc Natl Acad Sci USA. 95:14226–14231.
  • Zhang L, Nie L, Cao C, Zhang Y. 2008. The complete mitochondrial genome of the Keeled box turtle Pyxidea mouhotii and phylogenetic analysis of major turtle groups. J Genet Genomics. 35:33–40.
  • Zuker M, Mathews DH, Turner DH. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide in RNA biochemistry and biotechnology. In: Barciszewski J, Clark BFC, editors RNA. editors. biochemistry and biotechnology. Dordrecht, the Netherlands: Kluwer Academic Publishers11–43.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.