Conservation Genetics

, Volume 13, Issue 1, pp 99–115 | Cite as

Pleistocene isolation, secondary introgression and restricted contemporary gene flow in the pig-eye shark, Carcharhinus amboinensis across northern Australia

  • B. J. Tillett
  • M. G. Meekan
  • D. Broderick
  • I. C. Field
  • G. Cliff
  • J. R. Ovenden
Research Article


We examine the structure and phylogeography of the pig-eye shark (Carcharhinus amboinensis) common in shallow coastal environments in northern Australia using two types of genetic markers, two mitochondrial (control region and NADH hydrogenase 4) and two nuclear (microsatellite and Rag 1) DNA. Two populations were defined within northern Australia on the basis of mitochondrial DNA evidence, but this result was not supported by nuclear microsatellite or Rag 1 markers. One possibility for this structure might be sex-specific behaviours such as female philopatry, although we argue it is doubtful that sufficient time has elapsed for any potential signatures from this behaviour to be expressed in nuclear markers. It is more likely that the observed pattern represents ancient populations repeatedly isolated and connected during episodic sea level changes during the Pleistocene epoch, until current day with restricted contemporary gene flow maintaining population genetic structure. Our results show the need for an understanding of both the history and ecology of a species in order to interpret patterns in genetic structure.


Pleistocene Secondary introgression Predator Carcharhinus spp. Genetic structure North Australia 



Funded by Tropical Rivers and Coastal Knowledge Research Hub, Charles Darwin University, Darwin and the Molecular Fisheries Laboratory, Department of Employment, Economic Development and Innovation, Queensland Government. Sampling was undertaken with the kind support of fishermen; Wildlife Resources Inc; Kakadu National Park; Fishing and Fisheries Research, Centre James Cook University; Department of Fisheries—Western Australia, Fish for the Future, RSK Environment LTD/University of Bangor and the Department of Resources—Fisheries, Northern Territory. We also thank R. Street and J. Morgan for their technical expertise and Bioscience North Australia for their support.

Supplementary material

10592_2011_268_MOESM1_ESM.pdf (67 kb)
Supplementary material 2 (PDF 67 kb)
10592_2011_268_MOESM2_ESM.pdf (129 kb)
Supplementary material 3 (PDF 128 kb)


  1. Arevalo E, Davis SK, Sites JW (1994) Mitochondrial-DNA sequence divergence and phylogenetic-relationships among 8 chromosome races of the Sceloporus grammicus complex (Phrynosomatidae) in central Mexico. Syst Biol 43:387–418Google Scholar
  2. Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC (1987) Intraspecific phylogeography—the mitochondrial DNA bridge bewteen population-genetics and systematics. Annu Rev Ecol Syst 18:489–522Google Scholar
  3. Carlson JK, Ribera MM, Conrath CL, Heupel MR, Burgess GH (2010) Habitat use and movement patterns of bull sharks, Carcharhinus leucas determined using po-up satellite archival tags. J Fish Biol 77:661–675PubMedGoogle Scholar
  4. Chapman DD, Babcock EA, Gruber SH, Dibattista JD, Franks BR, Kessel SA, Guttridge T, Pikitch EK, Feldheim KA (2009) Long-term natal site-fidelity by immature lemon sharks (Negaprion brevirostris) at a subtropical island. Mol Ecol 18:3500–3507PubMedCrossRefGoogle Scholar
  5. Chenoweth SF, Hughes JM, Keenan CP, Lavery S (1998) When oceans meet: a teleost shows secondary intergradation at an Indian-Pacific interface. Proceedings of the Royal Society of London Series B-Biological Sciences, vol 265, pp 415–420Google Scholar
  6. Clement M, Possada D, Crandall K (2000) TCS: a computer program to estimate genealogies. Mol Ecol 9:1657–1660Google Scholar
  7. Cliff G, Dudley J (1991) Sharks caught in the protective nets off Natal, South Africa. 5. The Java Shark Carcharhinus amboinensis (Müller and Henle). S Afr J Mar Sci 11:443–453CrossRefGoogle Scholar
  8. Cornuet JM, Luikart G (1997) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequence data. Genetics 144:2001–2014Google Scholar
  9. Drummond AJ, Ashton B, Cheung M, Heled J, Kearse M, Moir R, Stones-Harves S, Thrierer T, Wilson A (2009) Geneious v4.65Google Scholar
  10. Duncan KM, Martin AP, Bowen BW, De Couet HG (2006) Global phylogeography of the scalloped hammerhead shark (Sphyrna lewini). Mol Ecol 15:2239–2251PubMedCrossRefGoogle Scholar
  11. Estoup A, Largiader CR, Perrot E, Chourrout D (1996) Rapid one-tube DNA extraction for reliable PCR detection of fish polymorphic markers and transgenes. Mol Mar Biol Biotechnol 5:295–298Google Scholar
  12. Excoffier L, Laval G, Schneider S (2005) Arlequin ver 3.0. An integrated software package for population genetics data analysis. Evol Bioinformat Online 1:47–50Google Scholar
  13. Feildheim KA, Gruber SH, Ashley MV (2002) The breeding biology of lemon shark at a tropical nursery lagoon. In: Proceedings of the royal society biolgical sciences, London, pp 1655–1661Google Scholar
  14. Feldheim KA, Gruber SH, Ashley MV (2004) Reconstruction of parental microsatellite genotypes reveals female polyandry and philopatry in the lemon shark, Negaprion brevirostris. Evolution 58:2332–2342PubMedGoogle Scholar
  15. Field IC, Meekan MG, Buckworth RC, Bradshaw CJA (2009) Protein mining the world’s oceans: Australasia as an example of illegal expansion-and-displacement fishing. Fish Fish 10:323–328Google Scholar
  16. Frankham R, Ballou JD, Briscoe DA (2002) Introduction to the conservation genetics. Cambridge University Press, CambridgeGoogle Scholar
  17. Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915–925PubMedGoogle Scholar
  18. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755PubMedCrossRefGoogle Scholar
  19. Inoue JG, Miya M, Tsukamoto K, Nishida M (2001) A mitogenomic perspective on the basal teleostean phylogeny: resolving higher-level relationships with longer DNA sequences. Mol Phylogenet Evol 20:275–285PubMedCrossRefGoogle Scholar
  20. IUCN (2010) Red list of threatened species. Version 2010.3Google Scholar
  21. Jensen JL, Bohonak AJ, Kelley ST (2005) Isolation by distance, web service. BMC Genet 6:1–6CrossRefGoogle Scholar
  22. Keeney DB, Heupel MR, Hueter RE, Heist EJ (2005) Microsatellite and mitochondrial DNA analyses of the genetic structure of blacktip shark (Carcharhinus limbatus) nurseries in the northwestern Atlantic, Gulf of Mexico, and Caribbean Sea. Mol Ecol 14:1911–1923PubMedCrossRefGoogle Scholar
  23. Kuhnt W, Holbourn A, Hall R, Zuvela M, Kase R (2004) Neogene history of the Indonesian throughflow. In: Clift P, Kuhnt W, Wang P, Hayes D (eds.) Continent–ocean interactions within East Asian Marginal Seas, pp 299–320Google Scholar
  24. Kumar S, Dudley J, Nei M, Tamura K (2008) MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Bioinformatics 9:299–306PubMedGoogle Scholar
  25. Last PR, Stevens JD (2009) Sharks and rays of Australia. CSIRO, VictoriaGoogle Scholar
  26. Lukoschek V, Waycott M, Marsh H (2007) Phylogeography of the olive sea snake, Aipysurus laevis (Hydrophiinae) indicates Pleistocene range expansion around northern Australia but low contemporary gene flow. Mol Ecol 16:3406–3422PubMedCrossRefGoogle Scholar
  27. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
  28. Northern Territory Government (2009) Fishery status reports 2008. Department of Resources, DarwinGoogle Scholar
  29. Ovenden JR, Street R, Broderick D (2006) New microsatellite loci for Carcharhinid sharks (Carcharhinus tilstoni and C-sorrah) and their cross-amplification in other shark species. Mol Ecol Notes 6:415–418CrossRefGoogle Scholar
  30. Ovenden JR, Kashiwagi T, Broderick D, Giles J, Salini J (2009) The extent of population genetic subdivision differs among four co-distributed shark species in the Indo-Australian archipelago. BMC Evol Biol 9:40PubMedCrossRefGoogle Scholar
  31. Pardini AT, Jones CS, Noble LR, Kreiser B, Malcolm H, Bruce BD, Stevens JD, Cliff G, Scholl MC, Francis M, Duffy CAJ, Martin AP (2001) Sex-biased dispersal of great white sharks. Nature 412:139PubMedCrossRefGoogle Scholar
  32. Peakall R, Smouse PE (2005) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295CrossRefGoogle Scholar
  33. Portnoy DS, Piercy AN, Musick JA, Burgess GH, Graves JE (2007) Genetic polyandry and sexual conflict in the sandbar shark, Carcharhinus plumbeus, in the western North Atlantic and Gulf of Mexico. Mol Ecol 16:187–197PubMedCrossRefGoogle Scholar
  34. Possada D, Crandall KA (1998) Modeltest: testing the model of DNA substitutions. Bioinformatics 14:817–818CrossRefGoogle Scholar
  35. Ramos-Onsins SE, Rozas J (2002) Statistical properties of new neutrality tests against population growth. Mol Biol Evol 19:2092–2100PubMedGoogle Scholar
  36. Reynolds J, Weir BS, Cockerham CC (1983) Estimation of the co-ancestry coefficient—basis for a short-term genetic distance. Genetics 105:767–779PubMedGoogle Scholar
  37. Rozen S, Skaletsky H (2000) Primer 3 on the WWW for general users and for biologist programmers. Methods Mol Methodol 132:365–386Google Scholar
  38. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234Google Scholar
  39. Schultz JK, Feldheim KA, Gruber SH, Ashley MV, McGovern TM, Bowen BW (2008) Global phylogeography and seascape genetics of the lemon sharks (genus Negaprion). Mol Ecol 17:5336–5348PubMedCrossRefGoogle Scholar
  40. Slatkin M (1991) Inbreeding coefficients and coalescence times. Genet Res 58:167–175PubMedCrossRefGoogle Scholar
  41. Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequences. Genetics 139:1463–1563Google Scholar
  42. Swofford DL (2000) PAUP* phylogenetic analysis using parsimon (*and other methods). Sinauer Associates, Sunderland, MAGoogle Scholar
  43. Tajima F (1983) Evolutionary relstionship of DNA sequences in finite populations. Genetics 123:585–595Google Scholar
  44. Tajima F (1996) The amount of DNA polymorphism maintained in a finite population when the neutral mutation rate varies among sites. Genetics 143:1457–1465PubMedGoogle Scholar
  45. Tillett BJ, Parry DL, Munksgaard NC, Meekan MJ, Field IC, Bradshaw CJA, Thorburn D (2011) Decoding fingerprints—elemental composition of vertebrae map ontogenetic habitat partitioning between two morphologically similar apex predators in northern Australia. Mar Ecol Prog Ser 434:133–142CrossRefGoogle Scholar
  46. Tillett BJ, Meekan MJ, Field I, Thorburn D, Ovenden J (in review) Evidence for reproductive philopatry in the bull shark, Carcharhinus leucas in northern Australia. J Fish BiolGoogle Scholar
  47. van Oosterhout C, Hutchinson WF, Wills PM, Siple P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538CrossRefGoogle Scholar
  48. Voris HK (2000) Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations. J Biogeogr 27:1153–1167CrossRefGoogle Scholar
  49. Walsh PS, Metzger DA, Higuchi R (1991) Chelex-100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10:506–513PubMedGoogle Scholar
  50. White WT, Last PR, Stevens JD, Yearsley GK, Fahmi, Dharmadi (2006) Economically important sharks and rays of Indonesia. CSIRO Publishing, CanberraGoogle Scholar
  51. Williams M, Cook E, van der Kaars S, Barrows T, Shulmeister J, Kershaw P (2009) Glacial and deglacial climatic patterns in Australia and surrounding regions from 35000 to 10000 years ago reconstructed from terrestrial and near-shore proxy data. Quat Sci Rev 28:2398–2419CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • B. J. Tillett
    • 1
    • 2
    • 3
    • 4
  • M. G. Meekan
    • 2
    • 6
  • D. Broderick
    • 4
  • I. C. Field
    • 1
    • 2
    • 7
  • G. Cliff
    • 5
  • J. R. Ovenden
    • 4
  1. 1.Research Institute for the Environment and LivelihoodsCharles Darwin UniversityCasuarina, DarwinAustralia
  2. 2.Australian Institute of Marine ScienceArafura Timor Research FacilityDarwinAustralia
  3. 3.Tropical Rivers and Coastal Knowledge Research HubCharles Darwin UniversityYularaAustralia
  4. 4.Molecular Fisheries Laboratory, Queensland Department of EmploymentEconomic Development and InnovationSt LuciaAustralia
  5. 5.KwaZulu-Natal Sharks BoardUmhlangaSouth Africa
  6. 6.Australian Institute of Marine ScienceUWA Ocean Sciences Centre (MO96)CrawleyAustralia
  7. 7.Marine Mammal Research Group, Graduate School of The EnvironmentMacquarie UniversitySydneyAustralia

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