Marine Biology

, Volume 156, Issue 7, pp 1507–1515 | Cite as

Genetic evidence for the existence of cryptic species in an endangered clam Coelomactra antiquata

  • Lingfeng Kong
  • Qi LiEmail author
Original Paper


Coelomactra antiquata is a commercially important bivalve species, but has been suffering from severe population decline due to over-exploitation and the deterioration of environmental conditions. Previous genetic survey of C. antiquata conducted with allozymes combined with morphology revealed high levels of genetic differentiation between northern and southern populations which suggests a cryptic species might exist in C. antiquata. To test this hypothesis, amplified fragment length polymorphisms (AFLPs) and 16S rRNA gene sequence were used to re-evaluate the spatial genetic structure of six populations of C. antiquata along the coast of China. Both genetic markers display a sharp genetic break between the four northern populations (northern lineage) and two southern population (southern lineage). Large numbers of private alleles (AFLP) were found within the northern or southern populations and a deep divergence of about 6.5% in 16S rRNA gene sequence between the northern and southern lineages suggests the occurrence of potential cryptic or sibling species of C. antiquata. Applying previously published rates of mutation, divergence between the two lineages is estimated to have occurred approximately 3 million years ago and may be due to allopatric isolation during the middle Pliocene times. While no genetic differentiation was found within the northern or southern populations in both AFLP and 16S mtDNA markers, the results indicate that the northern and southern lineage should be managed separately and any translocation between the two areas should be avoided.


Amplify Fragment Length Polymorphism Cryptic Species Amplify Fragment Length Polymorphism Marker Neighbor Join Southern Population 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We would like to thank to Mr. Zhaoxing Qiu from Shandong Mariculture Research Institute, and Mr. Jianxin Zhu from Yellow Sea Fisheries Research Institute, for providing the samples of C. antiquata. Dr. Changdong Liu provided technical assistance with map drawing. The editor and two anonymous reviewers gave insightful comments on the manuscript. The study was supported by the grants from National High Technology Research and Development Program (2006AA10A409) and “111 Project” by Ministry of Education of China (B08049).


  1. Avise JC (1998) Conservation genetics in the marine realm. J Hered 89:377–382. doi: CrossRefGoogle Scholar
  2. Bandelt HJ, Forster P, Sykes BC, Richards MB (1995) Mitochondrial portraits of human populations using median networks. Genetics 141:743–753PubMedPubMedCentralGoogle Scholar
  3. Bandelt HJ, Macaulay V, Richards M (2000) Median networks: speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA. Mol Phylogenet Evol 16:8–28. doi: CrossRefGoogle Scholar
  4. Barber PH, Palumbi SR, Erdmann MV, Moosa MK (2000) Biogeography—a marine Wallace’s line? Nature 406:692–693. doi: CrossRefGoogle Scholar
  5. Barber PH, Palumbi SR, Erdmann MV, Moosa MK (2002) Sharp genetic breaks among populations of Haptosquilla pulchella (Stomatopoda) indicate limits to larval transport: patterns, causes, and consequences. Mol Ecol 11:659–674. doi: CrossRefGoogle Scholar
  6. Bensch S, Akesson M (2005) Ten years of AFLP in ecology and evolution: why so few animals? Mol Ecol 14:2899–2914. doi: CrossRefGoogle Scholar
  7. Benzie JAH (1999) Major genetic differences between crown-of-thorns starfish (Acanthaster planci) populations in the Indian and Pacific Oceans. Evol Int J Org Evol 53:1782–1795. doi: Google Scholar
  8. Borsa P (2002) Allozyme, mitochondrial-DNA, and morphometric variability indicate cryptic species of anchovy (Engraulis encrasicolus). Biol J Linn Soc Lond 75:261–269. doi: Google Scholar
  9. Bowen BW, Nelson WS, Avise JC (1993) A molecular phylogeny for marine turtles: trait mapping, rate assessment, and conservation relevance. Proc Natl Acad Sci USA 90:5574–5577. doi: CrossRefGoogle Scholar
  10. Colborn J, Crabtree RE, Shaklee JB, Pfeiler E, Bowen BW (2001) The evolutionary enigma of bonefishes (Albula spp.): cryptic species and ancient separations in a globally distributed shorefish. Evol Int J Org Evol 55:807–820. doi:[0807:TEEOBA]2.0.CO;2 CrossRefGoogle Scholar
  11. Collin R (2000) Phylogeny of the Crepidula plana (Gastropoda: Calyptraeidae) cryptic species complex in North America. Can J Zool 78:1500–1514. doi: CrossRefGoogle Scholar
  12. Dawson MN, Jacobs DK (2001) Molecular evidence for cryptic species of Aurelia aurita (Cnidaria, Scyphozoa). Biol Bull 200:92–96. doi: CrossRefGoogle Scholar
  13. de Vargas C, Norris R, Zaninetti L, Gibb SW, Pawlowski J (1999) Molecular evidence of cryptic speciation in planktonic foraminifers and their relation to oceanic provinces. Proc Natl Acad Sci USA 96:2864–2868. doi: CrossRefGoogle Scholar
  14. Derycke S, Remerie T, Vierstraete A, Backeljau T, Vanfleteren J, Vincx M, Moens T (2005) Mitochondrial DNA variation and cryptic speciation within the free-living marine nematode Pellioditis marina. Mar Ecol Prog Ser 300:91–103. doi: CrossRefGoogle Scholar
  15. Etter RJ, Rex MA, Chase MC, Quattro JM (1999) A genetic dimension to deep-sea biodiversity. Deep Sea Res Part I Oceanogr Res Pap 46:1095–1099. doi: CrossRefGoogle Scholar
  16. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491PubMedPubMedCentralGoogle Scholar
  17. Excoffier L, Laval G, Schneider S (2005) Arlequin version 3.0: an integrated software package for population genetics data analysis. Evol Bioinformatics 1:47–50CrossRefGoogle Scholar
  18. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evol Int J Org Evol 39:783–791. doi: CrossRefGoogle Scholar
  19. Felsenstein J (2005) PHYLIP (phylogeny inference package) version 3.65. Department of Genome Sciences, University of Washington, SeattleGoogle Scholar
  20. Goetze E (2003) Cryptic speciation on the high seas; global phylogenetics of the copepod family Eucalanidae. Proc R Soc B Biol Sci 270:2321–2331. doi: CrossRefGoogle Scholar
  21. Haq BU, Hardenbol J, Vail PR (1987) Chronology of fluctuating sea levels since the Triassic. Science 235:1156–1167. doi: CrossRefGoogle Scholar
  22. Hebert PDN, Ratnasingham S, deWaard JR (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc B Biol Sci 270:S96–S99. doi: CrossRefGoogle Scholar
  23. Hewitt G (2000) The genetic legacy of the Quaternary ice ages. Nature 405:907–913. doi: CrossRefGoogle Scholar
  24. Hoare K, Goldson AJ, Giannasi N, Hughes RN (2001) Molecular phylogeography of the cosmopolitan bryozoan Celleporella hyalina: cryptic speciation? Mol Phylogenet Evol 18:488–492. doi: CrossRefGoogle Scholar
  25. Holsinger KE, Lewis PO, Dey DK (2002) A Bayesian approach to inferring population structure from dominant markers. Mol Ecol 11:1157–1164. doi: CrossRefGoogle Scholar
  26. Hudson RR, Turelli M (2003) Stochasticity overrules the “three-times rule”: genetic drift, genetic draft, and coalescence times for nuclear loci versus mitochondrial DNA. Evol Int J Org Evol 57:182–190. doi: Google Scholar
  27. Jozefowicz CJ, Foighil DO (1998) Phylogenetic analysis of southern hemisphere flat oysters based on partial mitochondrial 16S rDNA gene sequences. Mol Phylogenet Evol 10:426–435. doi: CrossRefGoogle Scholar
  28. Kirkendale LA, Meyer CP (2004) Phylogeography of the Patelloida profunda group (Gastropoda: Lottidae): diversification in a dispersal-driven marine system. Mol Ecol 13:2749–2762. doi: CrossRefGoogle Scholar
  29. Kitaura J, Nishida M, Wada K (2002) Genetic and behavioral diversity in the Macrophthalmus japonicus species complex (Crustacea: Brachyura: Ocypodidae). Mar Biol (Berl) 140:1–8. doi: CrossRefGoogle Scholar
  30. Knowlton N (1993) Sibling species in the sea. Annu Rev Ecol Syst 24:189–216. doi: CrossRefGoogle Scholar
  31. Knowlton N (2000) Molecular genetic analyses of species boundaries in the sea. Hydrobiologia 420:73–90. doi: CrossRefGoogle Scholar
  32. Knowlton N, Weigt LA (1998) New dates and new rates for divergence across the Isthmus of Panama. Proc R Soc B Biol Sci 265:2257–2263. doi: CrossRefGoogle Scholar
  33. Kong L, Li Q, Qiu Z (2007) Genetic and morphological differentiation in the clam Coelomactra antiquata (Bivalvia: Veneroida) along the coast of China. J Exp Mar Biol Ecol 343:110–117. doi: CrossRefGoogle Scholar
  34. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163. doi: CrossRefGoogle Scholar
  35. Lapegue S, Boutet I, Leitao A, Heurtebise S, Garcia P, Thiriot-Quievreux C, Boudry P (2002) Trans-Atlantic distribution of a mangrove oyster species revealed by 16S mtDNA and karyological analyses. Biol Bull 202:232–242. doi: CrossRefGoogle Scholar
  36. Lee CE (2000) Global phylogeography of a cryptic copepod species complex and reproductive isolation between genetically proximate “populations”. Evol Int J Org Evol 54:2014–2027. doi: CrossRefGoogle Scholar
  37. Lee T, Foighil DO (2004) Hidden Floridian biodiversity: mitochondrial and nuclear gene trees reveal four cryptic species within the scorched mussel, Brachidontes exustus, species complex. Mol Ecol 13:3527–3542. doi: CrossRefGoogle Scholar
  38. Li Q, Park C, Kijima A (2002) Isolation and characterization of microsatellite loci in the Pacific abalone, Haliotis discus hannai. J Shellfish Res 21:811–815Google Scholar
  39. Liu DJ, Xie KE (2003) Reproductive biology of Coelomactra antiquata. Chin J Zool 38:10–15 (in Chinese)Google Scholar
  40. Liu H, Zhu JX, Sun HL, Fang JG, Gao RC, Dong SL (2006) The clam, Xishi tongue Coelomactra antiquata (Spengler), a promising new candidate for aquaculture in China. Aquaculture 255:402–409. doi: CrossRefGoogle Scholar
  41. Liu JX, Gao TX, Wu SF, Zhang YP (2007) Pleistocene isolation in the Northwestern Pacific marginal seas and limited dispersal in a marine fish, Chelon haematocheilus (Temminck and Schlegel, 1845). Mol Ecol 16:275–288. doi: CrossRefGoogle Scholar
  42. Mathews LM (2006) Cryptic biodiversity and phylogeographical patterns in a snapping shrimp species complex. Mol Ecol 15:4049–4063. doi: CrossRefGoogle Scholar
  43. Meng XP, Cheng HL, Dong ZG (2005) The study status and prospect of Coelomactra antiquata in China. J Hebei Norm Univ Sci Technol 19:71–75 (in Chinese)Google Scholar
  44. Miller MP (1997) Tools for population genetic analysis (TFPGA) 1.3: a Windows program for the analysis of allozyme and molecular population genetic data. Available from
  45. Miller K, Alvarez B, Battershill C, Northcote P, Parthasarathy H (2001) Genetic, morphological, and chemical divergence in the sponge genus Latrunculia (Porifera: Demospongiae) from New Zealand. Mar Biol (Berl) 139:235–250. doi: CrossRefGoogle Scholar
  46. Moore MS (1995) Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees. Evol Int J Org Evol 49:718–729. doi: Google Scholar
  47. Moritz C (2002) Strategies to protect biological diversity and the evolutionary processes that sustain it. Syst Biol 51:238–254. doi: CrossRefGoogle Scholar
  48. Mueller UG, Wolfenbarger LL (1999) AFLP genotyping and fingerprinting. Trends Ecol Evol 14:389–394. doi: CrossRefGoogle Scholar
  49. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590PubMedPubMedCentralGoogle Scholar
  50. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
  51. Palumbi SR (1994) Genetic divergence, reproductive isolation, and marine speciation. Annu Rev Ecol Syst 25:547–572. doi: CrossRefGoogle Scholar
  52. Palumbi SR (1996) Nucleic acids II: the polymerase chain reaction. In: Hillis D, Moritz C (eds) Molecular systematics. Sinauer, Sunderland, pp 205–247Google Scholar
  53. Palumbi SR, Grabowsky G, Duda T, Geyer L, Tachino N (1997) Speciation and population genetic structure in tropical Pacific Sea urchins. Evol Int J Org Evol 51:1506–1517. doi: CrossRefGoogle Scholar
  54. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295. doi: CrossRefGoogle Scholar
  55. Posada D, Buckley TR (2004) Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol 53:793–808. doi: CrossRefGoogle Scholar
  56. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817–818. doi: CrossRefGoogle Scholar
  57. Qi QZ, Gao RC, Qiu WR, Huang XQ (1995) The life history of Coelomactra antiquata. J Fujian Norm Univ 11:82–88 (in Chinese)Google Scholar
  58. Raymond M, Rousset F (1995) An exact test for population differentiation. Evol Int J Org Evol 49:1280–1283. doi: CrossRefGoogle Scholar
  59. Reid DG, Lal K, Mackenzie-Dodds J, Kaligis F, Littlewood DTJ, Williams ST (2006) Comparative phylogeography and species boundaries in Echinolittorina snails in the central Indo-West Pacific. J Biogeogr 33:990–1006. doi: CrossRefGoogle Scholar
  60. Rocha-Olivares A, Fleeger JW, Foltz DW (2001) Decoupling of molecular and morphological evolution in deep lineages of a meiobenthic harpacticoid copepod. Mol Biol Evol 18:1088–1102CrossRefGoogle Scholar
  61. Schizas NV, Street GT, Coull BC, Chandler GT, Quattro JM (1999) Molecular population structure of the marine benthic copepod Microarthridion littorale along the southeastern and Gulf coasts of the USA. Mar Biol (Berl) 135:399–405. doi: CrossRefGoogle Scholar
  62. Schneider JA, Foighil DO (1999) Phylogeny of giant clams (Cardiidae: Tridacninae) based on partial mitochondrial 16S rDNA gene sequences. Mol Phylogenet Evol 13:59–66. doi: CrossRefGoogle Scholar
  63. Shackleton NJ, Opdyke ND (1977) Oxygen isotope and palaeomagnetic evidence for early Northern Hemisphere glaciation. Nature 270:216–219. doi: CrossRefGoogle Scholar
  64. Slatkin M (1993) Isolation by distance in equilibrium and nonequilibrium populations. Evol Int J Org Evol 47:264–279. doi: CrossRefGoogle Scholar
  65. Sweijd NA, Bowie RCK, Evans BS, Lopata AL (2000) Molecular genetics and the management and conservation of marine organisms. Hydrobiologia 420:153–164. doi: CrossRefGoogle Scholar
  66. Swofford DL (2003) PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4.0b10 Sinauer Associates, SunderlandGoogle Scholar
  67. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial-DNA in humans and chimpanzees. Mol Biol Evol 10:512–526Google Scholar
  68. Tarjuelo I, Posada D, Crandall KA, Pascual M, Turon X (2001) Cryptic species of Clavelina (Ascidiacea) in two different habitats: harbours and rocky littoral zones in the northwestern Mediterranean. Mar Biol (Berl) 139:455–462. doi: CrossRefGoogle Scholar
  69. Therriault TW, Docker MF, Orlova MI, Heath DD, MacIsaaca HJ (2004) Molecular resolution of the family Dreissenidae (Mollusca: Bivalvia) with emphasis on Ponto-Caspian species, including first report of Mytilopsis leucophaeata in the Black Sea basin. Mol Phylogenet Evol 30:479–489. doi: CrossRefGoogle Scholar
  70. Thompson AR, Thacker CE, Shaw EY (2005) Phylogeography of marine mutualists: parallel patterns of genetic structure between obligate goby and shrimp partners. Mol Ecol 14:3557–3572. doi: CrossRefGoogle Scholar
  71. Thorpe JP, Sole-Cava AM, Watts PC (2000) Exploited marine invertebrates: genetics and fisheries. Hydrobiologia 420:165–184. doi: CrossRefGoogle Scholar
  72. Tzeng TD, Yeh SY, Hui CF (2004) Population genetic structure of the kuruma prawn (Penaeus japonicus) in East Asia inferred from mitochondrial DNA sequences. ICES J Mar Sci 61:913–920. doi: CrossRefGoogle Scholar
  73. Vekemans X, Beauwens T, Lemaire M, Roldan-Ruiz I (2002) Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Mol Ecol 11:139–151. doi: CrossRefGoogle Scholar
  74. Vos P, Hogers R, Bleeker M, Reijans M, Vandelee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414. doi: CrossRefGoogle Scholar
  75. Wada K, Nishihira M, Furota T, Nojima S, Yamanishi R, Nishikawa T, Goshima S, Suzuki T, Kato M, Shimamura K, Fukuda H (1996) The present status of benthic organisms inhabiting the tidal flats in Japan. WWF Jpn Sci Rep 3:1–182Google Scholar
  76. Wang S, Xie Y (2005) China species red list, vol III. Invertebrates. Higher Education press, BeijingGoogle Scholar
  77. Wang CH, Li CH, Li SF (2008) Mitochondrial DNA-inferred population structure and demographic history of the mitten crab (Eriocheir sensu stricto) found along the coast of mainland China. Mol Ecol 17:3515–3527. doi: PubMedGoogle Scholar
  78. Ward RD, Woodwark M, Skibinski DOF (1994) A comparison of genetic diversity levels in marine, freshwater, and anadromous fishes. J Fish Biol 44:213–232. doi: CrossRefGoogle Scholar
  79. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evol Int J Org Evol 38:1358–1370. doi: Google Scholar
  80. Williams ST, Knowlton N, Weigt LA, Jara JA (2001) Evidence for three major clades within the snapping shrimp genus Alpheus inferred from nuclear and mitochondrial gene sequence data. Mol Phylogenet Evol 20:375–389. doi: CrossRefGoogle Scholar
  81. Wright JT, Zuccarello GC, Steinberg PD (2000) Genetic structure of the subtidal red alga Delisea pulchra. Mar Biol (Berl) 136:439–448. doi: CrossRefGoogle Scholar
  82. Wu JF, Zhang HH, Liang CY, Chen SW (2002) Resource and conservation strategy of Coelomactra antiquata in coast of Guangdong province, China. J Zhanjiang Ocean Univ 22:68–69 (in Chinese)Google Scholar
  83. Zhivotovsky LA (1999) Estimating population structure in diploids with multilocus dominant DNA markers. Mol Ecol 8:907–913. doi: CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  1. 1.Fisheries CollegeOcean University of ChinaQingdaoChina

Personalised recommendations