A SUMMARY OF SEA TURTLE GENETIC STUDIES IN THE INDIAN OCEAN AND SOUTHEAST

ANDREA D. PHILLOTT AND RUVANI N.N. GAMAGE

Biological Sciences, Asian University for Women, Chittagong, Bangladesh

#andrea.phillott@auw.edu.bd

Download article as PDF

Our summary has compiled available information about genetics of nesting and in-water sea turtle populations in the Indian Ocean and Southeast Asia so that others interested in this field of research might easily identify areas requiring further investigation. We have also identified studies with contradictory results that would benefit from additional investigation. Study outcomes have been presented without distinguishing among samples from different tissues or fluids, which included blood, skin, muscle, liver, eggshell, and egg albumen, as it was not anticipated that this would be an influential factor on the results.

Genetic Structure of Nesting Sea Turtle Populations In The Indian Ocean And Southeast Asia

Understanding the genetic structure of nesting populations is important to identify populations of conservation importance, determine population connectivity, and define management units within species (reviewed by Jensen et al., 2013a). Haplotypes known for nesting populations of green (Table 1 and 2), olive ridley (Table 3), hawksbill (Table 4 and 5), loggerhead (Table 6), leatherback (Table 7), and flatback (Table 8) sea turtles are presented below. Earlier studies utilised short (~380bp) mtDNA sequences but new mtDNA D-loop primers yield long (~800bp) sequences which improve resolution of stock structure and identify additional management units; it is recommended all future mtDNA studies utilise the longer sequences (see Abreu-Grobois et al., 2006; Shamblin et al., 2012). Studies such as Dutton et al. (2013) and Jensen et al. (2013b) have re-analysed shorter sequences and published additional haplotypes. New sequences should be designated a number according to guidelines at SWFC (2014) and ACCSTR (2014) and submitted to GenBank (www.ncbi. nim.nih.gov). The forthcoming manuscripts about green sea turtle haplotypes by Jensen et al. (see table 1) and hawksbill sea turtle haplotypes by FitzSimmons et al. (see Table 4) should resolve problems in understanding haplotypes for these species and understanding the relationship between previous sequence designations. It is hoped that future work can utilise longer sequences and potentially re-analyse samples collected previously, especially those still to be allocated a sequence number.

There is a lack of samples both by region (northwest Indian Ocean, eastern Africa, Bangladesh, Sri Lanka) and species (leatherback, loggerhead, olive ridley and flatback sea turtles) which could be addressed by collaboration between researchers in the appropriate region and those at labs with the capacity to conduct molecular genetics. As FitzSimmons (2014) explains in the preceding paper of this issue of IOTN, greater resolution of population stock structure in the Indian Ocean will inform more effective management plans and conservation efforts of the genetically diverse sea turtle populations in the Indian Ocean and Southeast Asia.

20-3-01

20-3-02 20-3-03 20-3-04 20-3-05 20-3-06 20-3-07 20-3-08 20-3-09 20-3-10

Genetic Structure of Feeding Ground Sea Turtle Populations in the Indian Ocean And Southeast Asia

Haplotypes known for feeding ground populations of loggerhead (Table 9), green (Table 10 and 11) and hawksbill (Table 12 and 13) sea turtles are presented below. There are no known haplotypes of foraging olive ridley, leatherback or flatback sea turtles in the Indian Ocean. As for nesting populations, new mtDNA D-loop primers yield long (~800bp) sequences should be utilised in future studies and new sequences should be submitted to GenBank (www.ncbi.nim.nih. gov) and numbered according to sequences at SWFC (2014) and ACCSTR (2014).

20-3-11 20-3-12 20-3-14 20-3-15

Genetic Diversity Among Sea Turtle Nesting Beaches In The Indian Ocean And Southeast Asia

Genetic diversity has been described among nesting olive ridley sea turtles in India (Shanker et al., 2011) and Australia (Jensen et al., 2013b); hawksbill turtle populations in the Persian Gulf (Mostafavi et al., 2011; Zolgharnein et al., 2011; Tabib et al., 2011, 2014; Nezhad et al., 2012, 2013); and, green turtle populations in Thailand (Kittiwattanawong et al., 2003), Malaysia (Joseph, 2013, 2014), Sri Lanka (Ekanayake et al. (2012), and the Mozambique channel (Bourjea et al., 2007). The population genetics of hawksbill turtles in the Persian Gulf have been summarized in Table 14 due to contradictory results that may be the result of different methodologies among studies. The importance of understanding genetic diversity among nesting populations has been reviewed by FitzSimmons and Limpus (2014).

Other Molecular Genetics Studies In The Indian Ocean And Southeast Asia

The use of microsatellite markers to understand paternity and mating systems in sea turtles is reviewed by Jensen et al. (2013a), and studies on paternity of sea turtle nesting populations in the region are summarised in Table 15.

DNA barcoding can be used for species identification, such as during forensic investigation of the species of turtle eggs or meat for commercial sale. Elmeer et al. (2011) has sequenced the cytochrome c oxidase subunit I (COI or cox1) gene from mitochondrial DNA of green turtles in Qatar for use in DNA barcoding. In a different type of forensic DNA analysis, 57 items made from tortoiseshell that had been confiscated by the US Fish and Wildlife Service identified 16 haplotypes, 94% of which were of Indo-Pacific origin (Shattuck, 2011).

20-3-16 20-3-17

Literature cited:

Abreu-Grobois A, J. Horrocks, A. Formia, P. Dutton, R. LeRoux, X. Velez-Zuazo, L. Soares & P. Meylan. 2006. New mtDNA d-loop primers which work for a variety of marine turtle species may increase the resolution of mixed stock analyses. In: Frick M, Panagopoulou A, Rees AF, Williams K (eds). Book of abstracts from the 26th annual symposium on sea turtle biology and conservation. International Sea Turtle Society, Athens. Pp. 179.

ACCSTR. 2014. mtDNA Sequences. Accessed at http://accstr.ufl. edu/resources/mtdna-sequences/ on 26th July 2014.

Al-Mohanna S.Y., A.S.Y. Al-Zaidan & P. George. 2013. Green turtles (Chelonia mydas) of the north-western Arabian Gulf, Kuwait: The need for conservation. Aquatic Conservation: Marine and Freshwater Ecosystems 24: 166-178.

Al-Mohanna S.Y. & P. George. 2010. Assessment of the origin of a loggerhead turtle, Caretta caretta, found in Kuwait waters, using mitochondrial DNA. Zoology in the Middle East 49: 39-44.

Alansari A.S. Unpubl. Genetic Diversity of Green Turtles in Oman. http://lifesciencedb.jp/ddbj/ff_list.cgi?max_num=all&project_ id=483585&type=plain. Accessed on 6th August 2014.

Arshaad W.M. & S.A.S.A. Kadir. 2008. Regional analysis on stock identification of green and hawksbill turtles in the Southeast Asian region. The Third Technical Consultation Meeting Research for Stock Enhancement of Sea Turtles (Japanese Trust Fund IV Program), 15-17 October 2008.

Arshaad W.M., N. Azliana, S.A.S.A. Kadir, & M. Katoh. 2013. Identification of natal origin sea turtles at Brunei Bay/Lawas foraging habitats. Regional Meeting on Conservation and Management of Sea Turtle Foraging Habitats in Southeast Asian Waters, 22-24 October 2013, AnCasa Hotel and Spa Kula Lumpar.

Bourjea J., S. Lapegue, L. Gagnevin, D. Broderick, J.A. Mortimer, S. Ciccione, D. Roos, C. Taquet & H. Grizel. 2007. Phylogeography of the green turtle, Chelonia mydas, in the Southwest Indian Ocean. Molecular Ecology 11: 1-21.

Bowen B.W., A.M. Clark, F.A. Abreu-Grobois, A. Chaves, H.A. Reichart & R.J. Ferl. 1998. Global phylogeography of the ridley sea turtles (Lepidochelys spp.) as inferred from mitochondrial DNA sequences. Genetica 101: 179-189.

Broderick D., H. Johanson, S. Lavery, J.A. Mortimer, J. Miller & C. Moritz. 1998. Genetic Assessment of Western and Central Indian Ocean Marine Turtle Stocks: Final Report to the Department of Environment, Republic of Seychelles Government. Department of Zoology, University of Queensland, Australia.

Dethmers K.E., D. Broderick, C. Moritz, N.N. FitzSimmons, C.J. Limpus, S. Lavery, S. Whiting, M. Guinea, R.I.T. Prince & R. Kennett. 2006. The genetic structure of Australasian green turtles (Chelonia mydas): exploring the geographical scale of genetic exchange. Molecular Ecology 15: 3931-3941.

Dethmers K.E.M., M.P. Jensen, N.N. FitzSimmons, D. Broderick, C.J. Limpus & C. Moritz. 2010. Migration of green turtles from Australasian feeding grounds inferred from genetic analyses. Marine and Freshwater Research 61: 1376-1387.

Dutton P.H., B.W. Bowen, D.W. Owens, A. Barragan & S.K. Davis. 1999. Global phylogeography of the leatherback turtle (Dermochelys coriacea). Journal of Zoology, London 248: 397-409.

Dutton P.H., C. Hitipeuw, M. Zein, S.R. Benson, G. Petro, J. Pita, V. Rei, Al. Ambio & J. Bakarbessy. 2007. Status and genetic structure of nesting populations of leatherback turtles (Dermochelys coriacea) in the western Pacific. Chelonian Conservation and Biology 6: 47-53.

Dutton P.H., S.E. Roden, K.R. Stewart, E. LaCasella, M. Tiwari, A. Formia, J.C. Thomé, S.R. Livingstone, S. Eckert, D. Chacon- Chaverri, P. Rivalan & P. Allman. 2013. Population stock structure of leatherback turtles (Dermochelys coriacea) in the Atlantic revealed using mtDNA and microsatellite markers. Conservation Genetics 14: 625-636.

Ekanayake, E.M.L., T. Kapurusinghe, M.M. Saman, D.S. Rathnakumara, P.Samaraweera, K.B. Ranawana & R.S. Rajakaruna. 2012. Genetic diversity of green turtle population nesting at Kosgoda turtle rookery, Sri Lanka. Proceedings of the Jaffna International Research Conference 176.

Ekanayake, E.M.L., T. Kapurusinghe, M.M. Saman, D.S. Rathnakumara, P.Samaraweera, K.B. Ranawana & R.S. Rajakaruna. 2013. Paterbity of green turtle (Chelonia mydas) clutches laid at Kosgoda, Sri Lanka. Herpetological Conservation and Biology 8: 27-36.

Elmeer K., P. McCormick & A. Almalki. 2011. Sequencing of

cytochrome C oxidase subunit I gene of mitochondrial DNA from Chelonia mydas in Qatar. Journal of American Science 7: 783-788.

FitzSimmons N.N. & C.J. Limpus. 2014. Marine turtle genetic stocks of the Indo-Pacific: Identifying boundaries and knowledge gaps. Indian Ocean Turtle Newsletter 20: 2-18.

Formia A., B.J. Godley, J.-F. Dontaine & M.W. Bruford. 2006. Mitochondrial DNA diversity and phylogeography of endangered green turtle (Chelonia mydas) populations in Africa. Conservation Genetics 7: 353-369.

Jensen M.P., N.N. FitzSimmons & P.H. Dutton. 2013a. Molecular genetics of sea turtles. In: The Biology of Sea Turtles Volume III (eds. Wyneken, J., KJ. Lohmann & J.A. Musick). CRC Press: Boca Raton LA, USA.

Jensen M.P., C.J. Limpus, S.D. Whiting, M. Guinea., R.I.T. Prince, K.E.M. Dethmers, I.B.W. Adnyana, R. Kennett & N.N. FitzSimmons. 2013b. Defining olive ridley turtle Lepidochelys olivacea management units in Australia and assessing the potential impacts of mortality in ghost nets. Endangered Species Research 21: 241-253.

Joseph J. 2013. Population genetics of green turtles (Chelonia mydas) in Malaysia based on mitochondrial DNA sequences. In: Proceedings of the Thirtieth Annual Symposium on Sea Turtle Biology and Conservation (comps. Blumenthal, J., A. Panagopoulou & A.F. Rees). NOAA Technical Memorandum NMFS-SEFSC-640: 177p.

Joseph J. 2013. Population genetics of green turtles (Chelonia mydas) in Malaysia based on mitochondrial DNA sequences. In: Proceedings of the Thirtieth Annual Symposium on Sea Turtle Biology and Conservation (comps. Blumenthal, J., A. Panagopoulou & A.F. Rees). NOAA Technical Memorandum NMFS-SEFSC-640: 177p.

Joseph J. 2014. Population genetics of green turtles (Chelonia mydas) in Malaysia based on mitochondrial DNA sequences. http://iconferences.seaturtle.org/preview.shtml?event_ id=17&abstract_id=3500. Accessed on 16th June 2014.

Joseph J. and C.Y. Kuen. 2012. Determination of natal origins of Juvenile green turtles foraging at Sipadann waters, Sabah, Malaysia. In: Proceedings of the Thirty-first Annual Symposium

on Sea Turtle Biology and Conservation (comps. Jones, T.T. & B.P. Wallace). NOAA Technical Memorandum NOAA NMFS- SEFSC-631: 322p.

Joseph J. and C.Y. Kuen. 2014. Determination of natal origins of juvenile green turtles foraging at Sipadann waters, Sabah, Malaysia. http://iconferences.seaturtle.org/preview.shtml?event_ id=18&abstract_id=3942. Accessed on 16th June 2014.

Kittiwattanawong K., S. Mananasup, M. Kinoshita & K. Nakayama. 2003. No genetic divergence between green turtle Chelonia mydas nesting populations from the Andaman Sea and the Gulf of Thailand. In: Proceedings of the 4th SEASTAR2000 Workshop: 15-19.

Kuen C.Y. & J. Joseph. 2012. Genetics investigation of green turtle (Chelonia mydas) carcasses from the 2007 poaching incident in Sabah waters. In: Proceedings of the Thirty-first Annual Symposium on Sea Turtle Biology and Conservation (comps. Jones, T.T. & B.P. Wallace). NOAA Technical Memorandum NOAA NMFS-SEFSC-631: 322p.

Kuen C.Y. & J. Joseph. 2014. Genetics investigation of green turtle (Chelonia mydas) carcasses from the 2007 poaching incident in Sabah waters. http://iconferences.seaturtle.org/preview. shtml?event_id=18&abstract_id=3930. Accessed on 16th June 2014.

Kuen C.Y. & J. Joseph. 2011. Harvesting of sea turtles at feeding grounds in Malaysia: whose turtles’ stock will be affected? In: Proceedings of Universiti Malaysia Terengganu 10th International Annual Symposium on Sustainability Science and Management (UMTAS) 2011, Kuala Terengganu, Malaysia 1: 511-515.

Kuen C.Y. & J. Joseph. 2013. Using DNA to determine the origin of green and hawksbill turtles from the feeding grounds of Malaysian waters. In: Proceedings of the Thirtieth Annual Symposium on Sea Turtle Biology and Conservation (comps. Blumenthal, J., A. Panagopoulou & A.F. Rees). NOAA Technical Memorandum NMFS-SEFSC-640: 177p.

Mobaraki A., N. FitzSimmons & M. Jensen. 2014. Reproduction and genetic study of hawksbill sea turtles in Iran. In: 34th Annual Symposium on Sea Turtle Biology and Conservation, New Orleans, Louisiana, USA, 10-17 April 2014. http://iconferences. seaturtle.org/preview.shtml?event_id=17&abstract_id=3359. Accessed on 16th June 2014.

July 2014

33

Indian Ocean Turtle Newsletter No. 20

34

Moritz C., D. Broderick, K. Dethmers, N. FitzSimmons & C. Limpus. 2002. Population genetics of Southeast Asian and western Pacific green turtles, Chelonia mydas. Final Report to UNEP/ CMS. http://www.environment.gov.au/resource/population- genetics-Southeast-asian-and-western-pacific-green-turtles- chelonia-mydas. Accessed on 6th June 2014.

Mortimer J. A. & D. Broderick. 1999. Population genetic structure and developmental migrations of sea turtles in the Chagos Archipelago and adjacent regions inferred from mtDNA sequence variation. Ecology of the Chagos Archipelago, Linnean Society Occasional Publications.

Mostafavi P.G., S. Shahnavaz, M. Noroozi, M.R. Fatemi, M.H. Shahhosseiny & A. Mahvari. 2011. Population genetic of Eretmochelys imbricata in two islands in the northern part of the Persian Gulf using microsatellite markers. International Journal of Marine Science and Engineering 1:69-73.

Nezhad S.R.K., E. Modheji & H. Zolgharnein. 2012. Polymorphism analysis of mitochondrial DNA control region of hawksbill turtles (Eretmochelys imbricata) in the Persian Gulf. Journal of Fisheries and Aquatic Sciences 7: 339-345.

Nezhad S.R.K., E. Modheji & H. Zolgharnein. 2013. Polymorphism analysis of mitochondrial DNA control region of hawksbill turtles (Eretmochelys imbricata) in the Persian Gulf. Indian Journal of Geo Marine Sciences 42: 300-303.

Okayama T., R. Doaz-Fernandez, Y. Baba, M. Halim, O. Abe, N. Azeno & H. Koike. 1999. Genetic diversity of the hawksbill turtle in the Indo-Pacific and Caribbean Regions. Chelonian Conservation and Biology 3: 312-317.

Pacioni C., S. Trocini, M. Heithaus, D. Burkholder, J. Thomson, K. Warren & M. Krützen 2013. Preliminary assessment of the genetic profile of the Western Australian loggerhead turtle population using mitochondrial DNA. In: Proceedings of the First Western Australian Marine Turtle Symposium (comps. Prince, R.I.T., S. Whiting, H. Raudino, A. Vitenbergs & K. Pendoley). 28–29th August 2012. Science Division, Department of Parks and Wildlife, Perth, Western Australia. Pp. 65.

Phillips K.P., T.H. Jorgensen, K.G. Jolliffe, S-M. Jolliffe, J. Henwood & D.S. Richardson. 2013. Reconstructing paternal genotypes to infer patterns of sperm storage and sexual selection

in the hawksbill turtle. Molecular Ecology 22: 2301-2312.

Pittard S.D. 2010. Genetic Population Structure of the Flatback Turtle (Natator depressus): A Nuclear and Mitochondrial DNA Analysis. Unpublished PhD Thesis submitted to University of Canberra. Pp. 116.

Roberts M. A., T.S. Schwartz & S.A. Karl. 2004. Global population genetic structure and male-mediated gene flow in the green sea turtle (Chelonia mydas): Analysis of microsatellite loci. Genetics Society of America 111: 1857-1870.

SFWSFC. 2014. Green turtle mtDNA sequences. https://swfsc. noaa.gov/textblock.aspx?Division=PRD&ParentMenuId=212& id=11212. Accessed on 26th July 2014.

Shamblin B.M., A.B. Bolten, K.A. Bjorndal, P.H. Dutton, J.T. Nielsen, F. A. Abreu-Grobois, K.J. Reich, B.E. Witherington, D.A. Bagley, L.M. Ehrhart, A.D. Tucker, D.S. Addison, A. Arenas, C. Johnson, R.R. Carthy, M.M. Lamont, M.G. Dodd, M.S. Gaines, E. LaCasella & C.J. Nairn. 2012. Expanded mitochondrial control region sequences increase resolution of stock structure among North Atlantic loggerhead turtle rookeries. Marine Ecology Progress Series 469: 145-160.

Shamblin B.M., A.B. Bolten, F.A. Abreu-Grobois, K.A. Bjorndal, L. Cardona, C. Carreras, M. Clusa, C. Monzón-Argüello. C.J. Nairn, J.T. Nielsen, R. Nel, L.S. Soares, K.R. Stewart. S.T. Vilaça. O. Türkozan, C. Yilmaz & P.H. Dutton. 2014. Geographic patterns of genetic variation in a broadly distributed marine vertebrate: New insights into loggerhead turtle stock structure form expanded mitochondrial DNA sequences. PLoS ONE 9: e85956.

Shanker K., B.C. Choudhury & R.K. Aggarwal. 2011. Conservation genetics of Marine Turtles on the Mainland Coast of India and Offshore Islands. Final Project Report. Wildlife Institute of India, Dehradun and Centre for Cellular and Molecular Biology, Hyderabad.

Shanker K., J. Ramadevi, B.C. Choudhury, L. Singh & R.K. Aggarwal. 2004. Phylogeography of olive ridley turtles (Lepidochelys olivacea) on the east coast of India: implications for conservation theory. Molecular Ecology 13: 1899-1909.

Shattuck E.G. 2011. Geographic origins of illegally harvested hawksbill sea turtle products. Unpublished Master of Science

Thesis submitted to Michigan State Unversity. http://etd.lib. msu.edu/islandora/object/etd%3A346/datastream/OBJ/view. Accessed on 6th June 2014.

Tabib M., H. Zolgharnein, M. Mohammadi, M.A. Salari-Aliabadi, A. Qasemi, S. Roshani, H. Rajabi-Maham & F. Frootan. 2011. mtDNA variation of the critically endangered hawksbill turtle (Eretmochelys imbricata) nesting on Iranian islands of the Persian Gulf. Genetics and Molecular Research 10: 1499-1503.

Tabib M., F. Frootan & M.A. Hesni. 2014. Genetic diversity and phylogeography of hawksbill turtle in the Persian Gulf. Journal of Biodiversity and Environmental Sciences 4: 51-57.

Vargas S.M., M.P. Jensen, A. Mobaraki, F.R Santos, D. Broderick, J. Mortimer, C. Limpus, S. Whiting & N.N. FitzSimmons. 2013. Phylogeography of the hawksbill turtle (Eretmochelys imbricata) from the Indo-Pacific Region. In: Proceedings of the Thirtieth Annual Symposium on Sea Turtle Biology and Conservation (Blumenthal, J., A. Panagopoulou & A.F. Rees). NOAA Technical Memorandum NMFS-SEFSC-640: 177p.

Zolgharnein H., M. Salari-Aliabadi, A.M. Forougmand & S. Roshani. 2011. Genetic population structure of hawksbill turtle (Eretmochelys imbricata) using microsatellite analysis. Iranian Journal of Biotechnology 9: 56-62.