Phylogeography of the dugong (Dugong dugon) based on historical samples identifies vulnerable Indian Ocean populations
Autoři:
Stephanie Plön aff001; Vibha Thakur aff002; Leslee Parr aff003; Shane D. Lavery aff002
Působiště autorů:
African Earth Observation Network (AEON)- Earth Stewardship Science Research Institute (ESSRI), Nelson Mandela University, Port Elizabeth, South Africa
aff001; School of Biological Sciences, University of Auckland, Auckland, New Zealand
aff002; Department of Biological Sciences, San José State University, San José, California, United States of America
aff003; Institute of Marine Science, University of Auckland, Auckland, New Zealand
aff004
Vyšlo v časopise:
PLoS ONE 14(9)
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pone.0219350
Souhrn
We investigated the phylogeography of the dugong (Dugong dugon) across its original range using museum material from 14 natural history museum and university collections. The mitochondrial DNA control region was successfully amplified from samples of bone or tooth powder from 162 individuals. These samples range from 1827 to 1996 and span the historical distribution range of the dugong. We were able to successfully amplify overlapping fragments of the D-loop region of the mitochondrial DNA (mtDNA) resulting in sequences of a 355 bp fragment for 162 individuals for the final analyses. This included a new sequence (189 bp) from a previously unidentified piece of skin of the extinct Steller’s sea cow (Hydrodamalis gigas), as an outgroup. The resulting dugong sequences match those from previous studies of dugongs from Australia and Indonesia, but revealed several new and divergent mtDNA lineages in the Indian Ocean. One mtDNA lineage includes most specimens from the Western Indian Ocean, with another distinct lineage isolated to nearby Madagascar and Comores. There is little geographic structuring detectable among other populations in the Western Indian Ocean and all populations from that region appear to have historically contained comparatively low levels of genetic diversity. The genetic diversity of several Indian Ocean samples collected after 1950 was lower than that of the samples collected earlier from similar locations, a result coincident with the anecdotal reductions in population size. The new lineages and potential loss of diversity highlight the particular conservation importance and vulnerability of dugong populations in the Western Indian Ocean.
Klíčová slova:
Biology and life sciences – Genetics – DNA – Population genetics – Phylogeography – Conservation genetics – Biochemistry – Nucleic acids – Forms of DNA – Mitochondrial DNA – Biogeography – Evolutionary biology – Population biology – Ecology – Ecological metrics – Species diversity – Conservation biology – Ecology and environmental sciences – Conservation science – Earth sciences – Geography – Marine and aquatic sciences – Bodies of water – Oceans – Indian Ocean – Research and analysis methods – Database and informatics methods – Bioinformatics – Sequence analysis – Sequence alignment – People and places – Geographical locations – Africa – Madagascar
Zdroje
1. Marsh H, Sobtzick S. Dugong dugon. 2015 Contract No.: e.T6909A43792211.
2. Marsh H, Penrose H, Eros C, Hughes J. The dugong (Dugong dugon) status report and action plans for countries and territories in its range. UNEP, 2002.
3. Parr L, Santos FR, Waycott M, Vianna JA, McDonald B, Caballero S, et al. Sirenian genetics and demography. In: Hines E, Reynolds J III, Mignucci-Giannoni A, Aragones L, Marmontel M, editors. Sirenian Conservation: Issues and Strategies in Developing Countries. Gainesville, Florida: University Press of Florida; 2012. p. 326pp.
4. Marsh H, O'Shea TJ, Reynolds JEI. Ecology and Conservation of the Sirenia- Dugongs and Manatees. Ecology and Conservation of the Sirenia- Dugongs and Manatees. Cambridge, UK.: Cambridge University Press 2011. p. 536.
5. Anonymous. Towards a Western Indian Ocean dugong strategy- the status of dugongs in the Western Indian Ocean and priority conservation actions. Dar es Salaam, Tanzania: UNEP, WWF, IUCN, WCS, 2004.
6. Cockcroft VG, Guissamulo A, Findlay K. Dugongs (Dugong dugon) of the Bazaruto Archipelago, Mozambique. 2008.
7. Marshall CD, Al Ansi M, Dupont J, Warren C, Al Shaikh I, Cullen J. Large dugong (Dugong dugon) aggregations persist in coastal Qatar. Marine Mammal Science. 2018. Epub doi: 10.1111/mms.12497
8. Al-Abdulrazzak D, Pauly D. Reconstructing historical baselines for the Persian/Arabian Gulf Dugong, Dugong dugon (Mammalia: Sirena). Zoology in the Middle East. 2017;63(2):95–102. Epub doi: 10.1080/09397140.2017.1315853
9. Cleguer C, Garrigue C, Fuentes MMPB, Everingham Y, Hagihara R, Hamann M, et al. Drivers of change in the relative abundance of dugongs in New Caledonia. Wildlife Research. 2017;44:365–76. Epub http://dx.doi.org/10.1071/WR16133.
10. Hagihara R, Jones RE, Sobtzick S, Cleguer C, Garrigue C, Mars H. Compensating for geographic variation in detection probability with water depth improves abundance estimates of coastal marine megafauna. PLOS One. 2018;13(1):e0191476. Epub doi.org/10.1371/journal.pone.0191476. doi: 10.1371/journal.pone.0191476 29370216
11. Moritz C. Strategies to protect biological diversity and the evolutionary processes that sustain it. Syst Biol. 2002;51(2):238–54. doi: 10.1080/10635150252899752 12028731
12. Sheppard JK, Preen AR, Marsh H, Lawler I, Whiting SD, Jones R. Movement heterogeneity of dugongs, Dugong dugon (Müller), over large spatial scales. Journal of Experimental Marine Biology and Ecology. 2006;334:64–83.
13. Hobbs J-PA, Frisch AJ, Hender J, Gilligan JJ. Long-distance oceanic movement of a solitary dugong (Dugong dugon) to the Cocos (Keeling) Islands. Aquatic Mammals. 2007;33(2):175–8.
14. Blair D. Dugong genetic report- Final research report for the Australian Marine Mammal Centre. 2012.
15. Blair D, McMahon A, McDonald B, Tikel D, Waycott M, Marsh H. Pleistocene sea level fluctuations and the phylogeography of the dugong in Australian waters. Marine Mammal Science. 2014;30(1):104–21. Epub doi: 10.1111/mms.12022
16. McDonald B. Population genetics of the dugong around Australia: Implications of gene flow and migration. Townsville, Australia: James Cook University; 2005.
17. Seddon JM, Ovenden JR, Sneath HL, Broderick D, Dudgeon CL, Lanyon JM. Fine scale population structure of dugongs (Dugong dugon) implies low gene flow along the southern Queensland coastline. Conservation Genetics. 2014;15:1381–92. Epub doi: 10.1007/s10592-014-0624-x
18. Cope RC, Pollett PK, Lanyon JM, Seddon JM. Indirect detection of genetic dispersal (movement and breeding events) through pedigree analysis of dugong populations in southern Queensland, Australia. Biological Conservation. 2015;181:91–101.
19. Palmer D. Genetic characterization of Thailand Dugongs, implications for conservation. San José, CA, USA: San José State University; 2004.
20. Herrmann B, Hummel S. Ancient DNA-Recovery and analysis of genetic material from palaeontological, archaeological, museum, medical and forensic specimens. New York: Springer Verlag; 1994. 290 p.
21. Herrmann B, Hummel S. Introduction. In: Herrmann B, Hummel S, editors. Ancient DNA. New York: Springer-Verlag; 1994. p. 1–12.
22. Nielsen H, Engberg J, Thuesen I. DNA from arctic human burials. In: Herrmann B, Hummel S, editors. Ancient DNA. New York: Springer-Verlag; 1994. p. 122–40.
23. Marshall TC, Sunnucks P, Spalton JA, Greth A, Pemberton JM. Use of genetic data for conservation management: the case of the Arabian oryx. Animal Conservation. 1999;2:269–78.
24. Banks SC, Hoyle SD, Horsup A, Sunnucks P, Taylor AC. Demographic monitoring of an entire species (the northern hairy-nosed wombat, Lasiorhinus krefftii) by genetic analysis of non-invasively collected material. Conservation Genetics. 2003;6:101–7.
25. Comstock KE, Ostrander EA, Wasser SK. Amplifying nuclear and mitochondrial DNA from African elephant ivory: a tool for monitoring the ivory trade. Conservation Biology 2003;17(6):1840–3.
26. Abercrombie DL, Clarke SC, Shivji MS. Global-scale genetic identification of hammerhead sharks: Application to assessment of the international fin trade and law enforcement. Conservation Genetics 2005;6:775–88.
27. Johnson JA, Watson RT, Mindell DP. Prioritizing species conservation: does the Cape Verde kite exist? Proceedings of the Royal Society, B Series. 2005;272:1365–71.
28. Shivji MS, Chapman DD, Pikitch EK, Raymond PW. Genetic profiling reveals illegal international trade in fins of the great white shark, Carcharodon carcharias. Conservation Genetics 2005;6:1035–39.
29. Wasser SK, Clark WJ, Drori O, Kisamo ES, Mailand C, Mutayoba B, et al. Combating the illegal trade in African elephant ivory with DNA forensics. Conservation Biology 2008;22(4):1065–71. doi: 10.1111/j.1523-1739.2008.01012.x 18786100
30. Dalebout ML, Ross GJB, Baker AJ, Anderson RC, Best PB, Cockcroft VG, et al. Appearance, distribution, and genetic distinctiveness of Longman's beaked whale, Indopacetus pacificus. Marine Mammal Science. 2003;19(3):421–61.
31. Dalebout ML, Van Helden A, Van Waerebeek K, Baker CS. Molecular genetic identification of southern hemisphere beaked whales (Cetacea: Ziphiidae). Molecular Ecology. 1998;7:687–94. 9640649
32. Pichler FB, Dalebout ML, Baker CS. Non-destructive DNA extraction from sperm whale teeth and scrimshaw. Molecular Ecology Notes. 2001;1:106–11.
33. Pichler FB, Dawson SM, Slooten E, Baker CS. Geographic isolation of Hector's dolphin populations described by mitochondrial DNA sequence. Conservation Biology. 1998;12(3):676–82.
34. Pichler FB, Baker CS. Loss of genetic diversity in the endemic Hector's dolphin due to fisheries-related mortality. Proceedings of the Royal Society, London B. 2000;267:97–102.
35. Plön S. The status and natural history of pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales off Southern Africa [PhD]. Grahamstown, South Africa: Rhodes University; 2004.
36. Dalebout ML, Mead JG, Baker CS, Baker AN, van Helden AL. A new species of beaked whale Mesoplodon perrini sp. n. (Cetacea: Ziphiidae) discovered through phylogenetic analyses of mitochondrial DNA sequences. Marine Mammal Science. 2002;18(3):577–608.
37. Wada S, Oishi M, Yamada TK. A newly discovered species of living baleen whale. Nature. 2003;426:278–81. doi: 10.1038/nature02103 14628049
38. Pimper LE, Remis MI, Goodall RNP, Baker CS. Teeth and bones as sources of DNA for genetic diversity and esex identification of Commerson's dolphins (Cephalorhynchus commersonii). Aquatic Mammals. 2009;35(5):330–3.
39. Foote AD, Hofreiter M, Morin PA. Ancient DNA from marine mammals: studying long-lived species over ecological and evolutionary timescales. Annals of Anatomy. 2011;194(1):112–20. doi: 10.1016/j.aanat.2011.04.010 21652193
40. Frankham R, Ballou JD, Briscoe DA. Introduction to Conservation Genetics. 2nd Edition ed. Cambridge: Cambridge University Press; 2009. 618pp. p.
41. Bonde RK, McGuire PM, Hunter ME. A review of the key genetic tools to assist imperiled species conservation: analyzing West Indian manatee populations. Journal of Marine Animals and their Ecology. 2012;5(1):8–19.
42. Baker EA. Deep sequencing approaches to dugong (Dugong dugon) population genetics and diet 2013.
43. Werle E, Schneider C, Renner M, Volker M, Fiehn W. Convenient single-step, one tube purification of PCR products for direct sequencing. Nucleic Acids Res 1994;22(20):4354–5. doi: 10.1093/nar/22.20.4354 7937169
44. Drummond AJ, Ashton B, Cheung M, Heled J, Kearse M, Moir R, et al. Geneious. Available from http://www.geneious.com.; 2009.
45. Bandelt HJ, Forster P, Rohl A. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 1999;16:37–48. doi: 10.1093/oxfordjournals.molbev.a026036 10331250
46. Excoffier L, Lischer HEL. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources. 2010;10:564–7. doi: 10.1111/j.1755-0998.2010.02847.x 21565059
47. Bowen BW, Gaither MR, DiBattista JD, Iacchei M, Andrews KR, Grant WS, et al. Comparative phylogeography of the ocean planet. Proceedings of the National Academy of Sciences of the United States of America. 2016;113:7962–9. doi: 10.1073/pnas.1602404113 27432963
48. Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. 2001;29:1165–88.
49. Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C- H, Xie D, et al. BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. PLoS Computational Biology. 2014;10:e1003537. doi: 10.1371/journal.pcbi.1003537 24722319
50. Bouckaert RR, Drummond AJ. bModelTest: Bayesian phylogenetic site model averaging and model comparison. BMC Evol Biol. 2017;17:42. doi: 10.1186/s12862-017-0890-6 28166715
51. Parr LA, Duffield DA. Interspecific comparison of mitochondrial DNA variation among extant species of Sirenians. In: Pfeiffer CJ, Nachtigall PE, editors. Molecular and Cell Biology of Marine Mammals. Malabar, Florida, USA: Krieger Publishing Company; 2002. p. 152–8.
52. Heled J, Drummond AJ. Bayesian inference of population size history from multiple loci. BMC Evol Biol. 2008;8:289. doi: 10.1186/1471-2148-8-289 18947398
53. Peakall R, Smouse PE. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics. 2012;28:2537–9. doi: 10.1093/bioinformatics/bts460 22820204
54. Springer MS, Signore AV, Paijmans JLA, Vélez-Juarbe J, Domning DP, Bauer CE, et al. Interordinal gene capture, the phylogenetic position of Steller’s sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia Molecular Phylogenetics and Evolution. 2015;91:178–93.
55. Moritz C. Defining 'evolutionarily significant units' for conservation. TREE. 1994;9:373–5. doi: 10.1016/0169-5347(94)90057-4 21236896
56. Amaral AR, Smith BD, Mansur RM, Brownell RL, Rosenbaum HC. Oceanographic drivers of population differentiation in Indo-Pacific bottlenose (Tursiops aduncus) and humpback (Sousa spp.) dolphins of the northern Bay of Bengal. Conservation Genetics. 2017;18:371–81.
57. Tikel D. Using a genetic approach to optimise dugong (Dugong dugon) conservation management. Townsville, Queensland, Australia: James Cook University; 1997.
58. Vianna JA, Bonde RK, Caballero S, Giraldo JP, Lima RP, Clark A, et al. Phylogeography, phylogeny and hybridization in trichechid sirenians: implications for manatee conservation. Molecular Ecology. 2006;15:433–47. doi: 10.1111/j.1365-294X.2005.02771.x 16448411
59. Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, et al. Time-dependent rates of molecular evolution. Molecular Ecology. 2011;20:3087–101. doi: 10.1111/j.1365-294X.2011.05178.x 21740474
60. Grant WS. Problems and cautions with sequence mismatch analysis and Bayesian skyline plots to infer historical demography. Journal of Heredity. 2015:333–46. Epub doi: 10.1093/jhered/esv020 25926628
61. Eckert CG, Samis KE, Lougheed SC. Genetic variation across species' geographical ranges: the central-marginal hypothesis and beyond. Molecular Ecology. 2008;17:1170–88. doi: 10.1111/j.1365-294X.2007.03659.x 18302683
62. Farhadi A, Jeffs AG, Farahmand H, Rejiniemon TS, Smith G, Lavery SD. Mechanisms of peripheral phylogeographic divergence in the Indo-Pacific: lessons from the spiny lobster Panulirus homarus. BMC Evol Biol. 2017;(17):195.
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