Cryptic diversity in the pen shell Atrina pectinata (Bivalvia: Pinnidae): High divergence and hybridization revealed by molecular and morphological data

Molecular Ecology

Volumn 20, Issue 20, 2011, Pages 4332-4345

  Liu, Jun ^a   Li, Qi ^a   Kong, Lingfeng ^a   Zheng, Xiaodong ^a  

^a OCEAN UNIVERSITY OF CHINA   (China)

Author keywords

Atrina pectinata; cryptic species; hybridization; internal transcribed spacer; introgression; species delimitation

Indexed keywords

INTERNAL TRANSCRIBED SPACER; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; ATRINA PECTINATA; BIVALVE; CHINA; CRYPTIC SPECIES; GENETICS; HYBRIDIZATION; INTROGRESSION; JAPAN; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPECIES DELIMITATION; SPECIES DIFFERENTIATION;

ATRINA PECTINATA; CRYPTIC SPECIES; HYBRIDIZATION; INTERNAL TRANSCRIBED SPACER; INTROGRESSION; SPECIES DELIMITATION;

ANIMALS; BIVALVIA; CHINA; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETIC SPECIATION; HYBRIDIZATION, GENETIC; JAPAN; MOLECULAR SEQUENCE DATA; PHYLOGENY;

ANIMALIA; ATRINA PECTINATA; BIVALVIA; PINNIDAE;

EID: 80053946143     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2011.05275.x     Document Type: Article

References (71)

1. Allendorf FW, Leary RF, Spruell P, Wenburg JK, (2001) The problems with hybrids: setting conservation guidelines. Trends in Ecology and Evolution, 16, 613-622. (Pubitemid 32947021)
2. Avise JC, (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge.
3. Ballard JWO, Whitlock MC, (2004) The incomplete natural history of mitochondria. Molecular Ecology, 13, 729-744. (Pubitemid 38390584)
4. Bickford D, Lohman DJ, Sodhi NS, et al. (2006) Cryptic species as a window on diversity and conservation. Trends in Ecology and Evolution, 22, 148-155.
5. Bolnick DI, Fitzpatrick BM, (2007) Sympatric speciation: models and empirical evidence. Annual Review of Ecology, Evolution and Systematics, 38, 459-487.
6. Borchsenius F, (2009) FastGap 1.2. Department of Biological Sciences. University of Aarhus, Denmark. Available at.
7. Chan KMA, Levin SA, (2005) Leaky prezygotic isolation and porous genomes: rapid introgression of maternally inherited DNA. Evolution, 59, 720-729. (Pubitemid 40589284)
8. Chen G, Hare MP, (2008) Cryptic ecological diversification of a planktonic estuarine copepod, Acartia tonsa. Molecular Ecology, 17, 1451-1468. (Pubitemid 351347638)
9. Chen J, Li Q, Kong LF, Zheng XD, Yu RH, (2010) COI-based DNA barcoding in Tapetinae species (Mollusca, Bivalvia, Veneridae) along the coast of China. Zoological Research, 31, 345-352.
10. De Queiroz K, (2007) Species concepts and species delimitation. Systematic Biology, 56, 879-886. (Pubitemid 350129638)
11. Dowling TE, Secor CL, (1997) The role of hybridization and introgression in the diversification of animals. Annual Review Ecology and Systematics, 28, 593-619. (Pubitemid 28012305)
12. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792-1797. (Pubitemid 38832724)
13. FAO (1998) FAO species identification guide for fishery purpose. The living marine resources of the Western Central Pacific. Volume 1. Seaweeds, Corals, Bivalves and Gastropods.
14. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R, (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3, 294-299.
15. Funk DJ, Omland KE, (2003) Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution and Systematics, 34, 397-423. (Pubitemid 38171425)
16. Galtier N, Nabholz B, Glémin S, Hurst GDD, (2009) Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Molecular Ecology, 18, 4541-4550.
17. Guindon S, Gascuel O, (2003) A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Systematic Biology, 52, 696-704. (Pubitemid 37365050)
18. Harper FM, Hart MW, (2007) Morphological and phylogenetic evidence for hybridization and introgression in a sea star secondary contact zone. Invertebrate Biology, 126, 373-384. (Pubitemid 350260867)
19. Hebert PDN, Cywinska A, Ball SL, deWaard JR, (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B, Biological Sciences, 270, 313-321. (Pubitemid 36228536)
20. Hedgecock D, Li G, Banks MA, Kain Z, (1999) Occurrence of the Kumamoto oyster Crassostrea sikamea in the Ariake Sea, Japan. Marine Biology, 133, 65-68. (Pubitemid 29085419)
21. Hellberg ME, Vacquier VD, (1999) Rapid evolution of fertilization selectivity and lysin cDNA sequences in teguline gastropods. Molecular Biology Evolution, 16, 839-848. (Pubitemid 29260837)
22. Hillis DM, Dixon MT, (1991) Ribosomal DNA: molecular evolution and phylogenetic inference. Quarterly Review of Biology, 66, 411-453.
23. Hsieh C, Chen CS, Chiu TS, (2005) Composition and abundance of copepods and ichthyoplankton in Taiwan Strait (western North Pacific) are influenced by seasonal monsoons. Marine and Freshwater Research, 56, 153-161. (Pubitemid 40728164)
24. Hutchinson GE, (1957) Concluding remarks. Cold Spring Harbor Symposium on Quantitative Biology, 22, 415-427.
25. Hwang JS, Wong CK, (2005) The China Coastal Current as a driving force for transporting Calanus sinicus (Copepoda: Calanoida) from its population centers to waters off Taiwan and Hong Kong during the winter northeast monsoon period. Journal of Plankton Research, 27, 205-210. (Pubitemid 40307292)
26. Imbrie J, Berger A, Boyle EA, et al. (1993) On the structure and origin of major glaciation cycles 2. The 100,000-year cycle. Paleoceanography, 8, 699-735.
27. Johnson SB, Warén A, Vrijenhoek RC, (2008) DNA barcoding of Lepetodrilus limpets reveals cryptic species. Journal of Shellfish Research, 27, 43-51. (Pubitemid 351544021)
28. Knowles LL, Carstens BC, (2007) Delimiting species without monophyletic gene trees. Systematic Biology, 56, 887-895. (Pubitemid 350129639)
29. Knowlton N, (1993) Sibling species in the sea. Annual Review of Ecology and Systematics, 24, 189-216.
30. Knowlton N, (2000) Molecular genetic analyses of species boundaries in the sea. Hybrobiologia, 420, 73-90. (Pubitemid 30308653)
31. Laegdsgaard P, Johnson C, (2001) Why do juvenile fish utilize mangrove habitats? Journal of Experimental Marine Biology and Ecology, 257, 229-253. (Pubitemid 32220668)
32. Lam K, Morton B, (2003) Mitochondrial DNA and morphological identification of a new species of Crassostrea (Bivalvia: Ostreidae) cultured for centuries in the Pearl River Delta, Hong Kong, China. Aquaculture, 228, 1-13. (Pubitemid 37436152)
33. Lambeck K, Esat TM, Potter EK, (2002) Links between climate and sea levels for the past three million years. Nature, 419, 199-206. (Pubitemid 35025452)
34. Lee T, Foighil DO', (2004) Hidden Floridian biodiversity: mitochondrial and nuclear gene trees reveal four cryptic species within the scorched mussel, Brachidontes exusturs, species complex. Molecular Ecology, 13, 3527-3542. (Pubitemid 39428764)
35. Lessios HA, Pearse JS, (1996) Hybridization and introgression between Indo-Pacific species of Diadema. Marine Biology, 126, 715-723.
36. Li Q, Yu H, Yu RH, (2006) Genetic variability assessed by microsatellites in cultured populations of the Pacific oyster (Crassostrea gigas) in China. Aquaculture, 259, 95-102. (Pubitemid 44247082)
37. Liang XY, Lin HQ, Wu PR, Liu Y, (1986) Comparison on morphology of Pinnidae (Mollusca, Lamellibranchia) from Fujian coast. Tropic Oceanology, 5, 13-19.
38. 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 & Schlegel, 1845). Molecular Ecology, 16, 275-288.
39. Makino W, Tanabe AS, (2009) Extreme population genetic differentiation and secondary contact in the freshwater copepod Acanthodiaptomus pacificus in the Japanese Archipelago. Marine Biology, 18, 2699-2713.
40. Mallet J, (2006) Species concepts. In: Evolutionary Genetics: Concepts and Case Studies (eds, Fox CW, Wolf JB,). pp. 367-373, Oxford University Press, Oxford.
41. Marko PB, (2002) Fossil calibration of molecular clocks and the divergence times of geminate species pairs separated by the Isthmus of Panama. Molecular Biology Evolution, 19, 2005-2021. (Pubitemid 35388123)
42. Martin DP, Lemey P, Lott M, et al. (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics, 26, 2462-2463.
43. Mayr E, (1963) Animal Species and Evolution. Harvard University Press, Cambridge, Massachusetts.
44. Nielsen R, Wakeley J, (2001) Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics, 158, 885-896. (Pubitemid 32552323)
45. Palumbi SR, (1994) Genetic divergence, reproductive isolation, and marine speciation. Annual Review of Ecology and Systematics, 25, 547-572. (Pubitemid 24986131)
46. Posada D, (2008) jModelTest: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253-1256. (Pubitemid 351882013)
47. Qiao Yl, Lin Zj, (2007) The relationship between the main features of landform, the distribution of bottom sediment and fishery distribution. Transactions of Oceanology and Limnology, 12, 232-238.
48. Renoult JP, Geniez P, Bacquet P, Benoit L, Crochet PA, (2009) Morphology and nuclear markers reveal extensive mitochondrial introgressions in the Iberian Wall Lizard species complex. Molecular Ecology, 18, 4298-4315.
49. Ronquist F, Huelsenbeck JP, (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574. (Pubitemid 37038874)
50. Roques S, Sévigy JM, Bernatchez L, (2001) Evidence for broadscale introgressive hybridization between two redfish (genus Sebastes) in the North-west Atlantic: a rare marine example. Molecular Ecology, 10, 149-165. (Pubitemid 32097536)
51. Rosewater J, (1961) The family Pinnidae in the Indo-Pacific. Indo-Pacific Mollusca, 1, 175-226.
52. Ross KG, Gotzek D, Ascunce MS, Shoemaker DD, (2010) Species delimitation: a case study in a problematic ant taxon. Systematic Biology, 59, 162-184.
53. Simmons MP, Ochoterena H, (2000) Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology, 49, 369-381.
54. Swofford DL, (2003) PAUP: Phylogenetic Analysis using Parsimony (* and other Methods) Version 4. Sinauer Associates, Sunderland, Massachusetts.
55. Tamura K, Nei M, (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10, 512-526. (Pubitemid 23157236)
56. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596-1599. (Pubitemid 47236692)
57. Thompson JD, Gibson TJ, Plewniak F, Jaanmougin F, Higgins DG, (1997) The Clustal-X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 24, 4876-4882.
58. Tsang LM, Chan BKK, Ma Y, Chu KH, (2008) Genetic differentiation, hybridization and adaptive divergence in two subspecies of the acorn barnacle Tetraclita japonica in the northwestern Pacific. Molecular Ecology, 17, 4151-4163.
59. UNEP (2007) Mangrove demonstration sites in the South China Sea. UNEP/GEF/SCS Technical Publication No. 7. (Available at).
60. Wang ZR, (1964) Preliminary studies on Chinese Pinnidea. Studia Marina Sinica, 5, 131-141.
61. Wang ZR, (1997) Fauna Sinica: Phylum Mollusca, Order Mytiloida. Chinese Science Press, Peking (in Chinese).
62. Wang PX, (1999) Response of Western Pacific marginal seas to glacial cycles: paleoceanographic and sedimentological features. Marine Geology, 156, 5-39.
63. Wang MF, Yu XY, Yang ST, Gui JF, (2000) A comparative study on isozyme phenotypic divergence among four types of pen shell Atrina pectinata Linnaeus. Tropic Oceanology, 19, 45-50.
64. Winckworth R, (1929) Marine mollusca from south India and Ceylon. III: Pinna. With an index to the recent species of Pinna. Proceedings of the Malacological Society of London, 18, 276-297.
65. Xu JW, Chan TY, Tsang LM, Chu KH, (2009) Phylogeography of the mitten crab Eriocheir sensu stricto in East Asia: Pleistocence isolation, population expansion and secondary contact. Molecular Phylogenetics and Evolution, 52, 45-56.
66. Xue DX, Zhang T, Wang HY, Zheng XD, Meng FY, (2009) Comparative study on 28S rDNA and COI of scaly and non-scaly phenotypes in species of Atrina pectinata. Marine Sciences, 33, 88-91.
67. Yokogawa K, (1996) Genetic divergence in two forms of pen shell Atrina pectinata. Venus, 55, 25-39.
68. Yu XY, Wang MF, Li HW, Cai YY, (2000) Comparison on morphological difference inside species of pen shell Atrina pectinata. Tropic Oceanology, 19, 39-43.
69. Yu XY, Mao Y, Wang MF, Zhou L, Gui JF, (2004) Genetic heterogeneity analysis and RAPD markers detection among four forms of Atrina pectinata Linnaeus. Journal of Shellfish Research, 23, 165-171. (Pubitemid 38642251)
70. Zhao K, Duan ZY, Peng ZG, et al. (2009) The youngest split in sympatric schizothoracine fish (Cyprinidae) is shaped by ecological adaptations in a Tibetan Plateau glacier lake. Molecular Ecology, 18, 3616-3628.
71. Zhu WL, Wu GX, Bi LM, (2004) Palaeolimology and hydrocarbon potential in Beibu Gulf Basin of South China Sea. Oceanologia Etlimnologia Sinica, 35, 8-14.