A molecular phylogeny of the marine mussel genus Perna (Bivalvia: Mytilidae) based on nuclear (ITS1&2) and mitochondrial (COI) DNA sequences

Molecular Phylogenetics and Evolution

Volumn 44, Issue 2, 2007, Pages 685-698

  Wood, Ann R ^a   Apte, Smita ^a   MacAvoy, Elizabeth S ^a   Gardner, Jonathan P A ^a  

^a VICTORIA UNIVERSITY OF WELLINGTON   (New Zealand)

Author keywords

Bivalves; COI; Internal transcribed spacer; ITS; Mussels; Perna; Ribosomal RNA

Indexed keywords

CYTOCHROME C OXIDASE; DNA; RIBOSOMAL SPACER DNA;

ANIMAL; ARTICLE; BIVALVE; CELL NUCLEUS; CLASSIFICATION; GENETICS; MITOCHONDRION; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE; PHYLOGENY;

ANIMALS; BASE SEQUENCE; BIVALVIA; CELL NUCLEUS; DATABASES, NUCLEIC ACID; DNA; DNA, RIBOSOMAL SPACER; ELECTRON TRANSPORT COMPLEX IV; MITOCHONDRIA; PHYLOGENY;

BIVALVIA; MYTILIDAE; PERNA; PERNA CANALICULUS; PERNA PERNA; PERNA VIRIDIS;

EID: 34447257385     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2006.12.019     Document Type: Article

References (101)

1. Agard J., Kishore R., and Bayne B. Perna viridis (Linnaeus, 1758): first record of the Indo-Pacific green mussel (Mollusca: Bivalvia) in the Caribbean. Caribbean Mar. Stud. 3 (1993) 59-60
2. Ahmed M. Chromosomes of two species of the marine mussel Perna (Mytilidae: Pelecypoda). Boletin del Instituto Oceanográfico, Universidad de Oriente, Venezuela 13 (1974) 17-22
3. Alfaro M.E., Zoller S., and Lutzoni F. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov Chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20 (2003) 255-266
4. Appukuttan, K.K., Nair, T.P., 1980. Fishery and biology of the brown mussel, Perna indica Kuriakose and Nair. In: Coastal Aquaculture: Mussel Farming. Progress and Prospects. Central Marine Fisheries Research Institute Bulletin 29, Cochin, India, pp. 5-9.
5. Appukuttan K.K., Nair T.P., and Thomas K.T. Spat settlement of brown mussel Perna indica Kuriakose and Nair in the southwest coast of India. J. Mar. Biol. Assoc. India 31 (1989) 266-275
6. Apte S., and Gardner J.P.A. Population genetic subdivision in the New Zealand greenshell mussel (Perna canaliculus) inferred from single-strand conformation polymorphism analysis of mitochondrial DNA. Mol. Ecol. 11 (2002) 1617-1628
7. Beckley L.E. Primary settlement of Perna perna (L.) on littoral seaweeds on St Croix Island. S. Afr. J. Zool. 14 (1979) 171-174
8. Benson A.J., Marelli D.C., Frischer M.E., Danforth J.M., and Williams J.D. Establishment of the green mussel, Perna viridis (Linnaeus 1758) (Mollusca: Mytilidae) on the west coast of Florida. J. Shellfish Res. 20 (2001) 21-29
9. Beu A.G. Marine Mollusca of oxygen isotope stages of the last 2 million years in New Zealand. Part 1: revised generic positions and recognition of warm-water and cool-water migrants. J. R. Soc. N. Z. 34 (2004) 111-265
10. Brandley M.C., Schmitz A., and Reeder T.W. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst. Biol. 54 (2005) 373-390
11. Buchanan, S.J., 1994. The settlement behaviour and recruitment of Perna canaliculus, M.Sc. Thesis, University of Auckland, Auckland, New Zealand.
12. Charleston M.A. Spectrum: spectral analysis of phylogenetic data. Bioinformatics 14 (1998) 98-99
13. Cheung S.G. Population dynamics and energy budgets of greenlipped mussel, Perna viridis (Linneaus), in a polluted harbour. J. Exp. Mar. Biol. Ecol. 168 (1993) 1-24
14. Crisp M.D., and Cook L.G. Do early branching lineages signify ancestral traits?. Trends Ecol. Evol. 20 (2005) 122-128
15. Cunningham C.W. Can three incongruence tests predict when data should be combined?. Mol. Biol. Evol. 14 (1997) 733-740
16. Cunningham C.W. Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods. Syst. Biol. 46 (1997) 464-478
17. del Rio C.J. Tertiary marine molluscan assemblages of eastern Patagonia (Argentina); a biostratigraphic analysis. J. Paleontol. 78 (2004) 1097-1122
18. DeVries T.J. Oligocene deposition and Cenozoic sequence boundaries in the Pisco Basin (Peru). J. S. Am. Earth Sci. 11 (1998) 217-231
19. Donald K.M., Kennedy M., and Spencer H.G. Cladogenesis as the result of long-distance rafting events in south Pacific topshells (Gastropoda, Trochidae). Evolution 59 (2005) 1701-1711
20. Eriksson T. r8s Bootstrap Kit (2003), Stockholm University, Stockholm, Sweden
21. Farris J.S., Källersjö M., Kluge A.G., and Bult C. Constructing a significance test for incongruence. Syst. Biol. 44 (1995) 570-572
22. Fleming C.A. Marwick's illustrations of New Zealand shells with a checklist of New Zealand Cenozoic mollusca. NZ Dept. Scientific & Industrial Research Bulletin 173 (1966) 456
23. Fleming C.A. The Geological History of New Zealand and its Life (1979), Auckland University Press, New Zealand 141 pages
24. Folmer O., Black M., Hoeh W., Lutz R., and Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3 (1994) 294-299
25. Gosling E.M. Bivalve Molluscs: Biology, Ecology and Culture (2003), Fishing News Books, Blackwell Science 443 pages
26. Griffiths C.L., and Branch G.M. The exploitation of coastal invertebrates and seaweeds in South Africa: historical trends, ecological impacts and implications for management. Trans. R. Soc. S. Afr. 52 (1997) 121-148
27. Hanyu K., and Sekiguchi H. Perna mussels introduced into Ise and Mikawa bays, central Japan. Sessile Organisms 17 (2000) 1-11
28. Hayden B.J. What do we know about greenshell mussel spat? Part I. Seafood New Zealand 2 (1994) 45-47
29. Hellberg M.E., and Vacquier V.D. Rapid evolution of fertilization selectivity and lysin cDNA sequences in teguline gastropods. Mol. Biol. Evol. 16 (1999) 839-848
30. Helmuth B., Veit R.R., and Holbertson R. Long-distance dispersal of a subantarctic brooding bivalve (Gaimardia trapesina) by kelp-rafting. Mar. Biol. 120 (1994) 421-426
31. Hendy M.D., and Penny D. Spectral analysis of phylogenetic data. J. Classif. 10 (1993) 5-24
32. Hickman R.W. Potential for the use of stranded seed mussels in mussel farming. Aquaculture 9 (1976) 287-293
33. Hickman R.W. Allometry and growth of the green-lipped mussel Perna canaliculus in New Zealand. Mar. Biol. 51 (1979) 311-327
34. Hickman R.W. Perna canaliculus (Gmelin) in New Zealand. In: Menzel W. (Ed). Estuarine and Marine Bivalve Mollusc Culture (1991), CRC Press, Boca Raton, FL 326-333
35. Hicks, D.W., 2001. Two invasive mussels in the genus Perna in the Gulf of Mexico. In: Virtual Proceedings for the "State of the Bay" Symposium V, January 31-February 2, 2001, Texas Natural Resource Conservation Commission, Austin, Texas, USA, pp. 159-170.
36. Hicks D.W., and Tunnell J.W. Invasion of the south Texas coast by the edible brown mussel Perna perna (Linnaeus, 1758). The Veliger 36 (1993) 92-94
37. Hillis D.M., and Bull J.J. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42 (1993) 182-192
38. Holland B.S. Invasion without a bottleneck: microsatellite variation in natural and invasive populations of the brown mussel Perna perna (L.). Mar. Biotechnol. 3 (2001) 407-415
39. Holland B.S., Gallagher D.S., Hicks D.W., and Davis S.K. Cytotaxonomic verification of a non-indigenous marine mussel in the Gulf of Mexico. The Veliger 42 (1999) 280-282
40. Huang, Z.G., Lee, S.Y., Mak, P.M.S., 1983. The distribution and population structure of Perna viridis (Bivalvia: Mytilacea) in Hong Kong waters. In: Morton, B., Dudgeon, D. (Eds.), Proceedings of the Second International Workshop on the Malacofauna of Hong Kong and Southern China. Hong Kong University Press, pp. 465-471.
41. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
42. Huelsenbeck J.P., Larget B., Miller R.E., and Ronquist F. Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 51 (2002) 673-688
43. Huelsenbeck J.P., Larget B., and Alfaro M. Bayesian phylogenetic model selection using reversible jump Markov Chain Monte Carlo. Mol. Biol. Evol. 21 (2004) 1123-1133
44. Ingrao D.A., Mikklesen P.M., and Hicks D.W. Another introduced marine mollusc in the Gulf of Mexico: the Indo-Pacific green mussel, Perna viridis, in Tampa Bay, Florida. J. Shellfish Res. 20 (2001) 13-19
45. Jacobi C.M., Rosenberg C., and Vianna-Morgante A.M. The karyotype of the brown mussel, Perna perna (L.) (Bivalvia: Mytilidae). Rev. Bras. Genet. 30 (1990) 669-673
46. Jeffs A.G., Holland R.C., Hooker S.H., and Hayden B.J. Overview and bibliography of research on the greenshell mussel, Perna canaliculus, from New Zealand waters. J. Shellfish Res. 18 (1999) 347-360
47. Kass R.E., and Raftery A.E. Bayes factors. J. Am. Stat. Assoc. 90 (1995) 773-795
48. Kuriakose, P.S., 1980. Mussels (Mytilidae: Genus Perna) of the Indian coast. In: Coastal Aquaculture: Mussel Farming. Progress and Prospects. Central Marine Fisheries Research Institute Bulletin 29, Cochin, India, pp. 1-5.
49. Kuriakose P.S., and Nair N.B. The genus Perna along the coasts of India with the description of a new species Perna indica. Aquat. Biol. 1 (1976) 25-36
50. Lee M.S.Y. Uninformative characters and apparent conflict between molecules and morphology. Mol. Biol. Evol. 18 (2001) 676-680
51. Libertini A., Boato A., Panozzo M., and Fogato V. Karyotype and genome size in some species of Mytilidae (Bivalvia, Mollusca). La Kromosomo II 82 (1996) 2819-2827
52. Marko P.B. Fossil calibration of molecular clocks and the divergence times of geminate species pairs separated by the Isthmus of Panama. Mol. Biol. Evol. 19 (2002) 2005-2021
53. Monirith I., Ueno D., Takahashi S., Nakata H., Sudaryanto A., Subramanian A., Karuppiah S., Ismail A., Muchtar M., Zheng J.S., Richardson B.J., Prudente M., Hue N.D., Tana T.S., Tkalin A.V., and Tanabe S. Asia-Pacific mussel watch: monitoring contamination of persistent organochlorine compounds in coastal waters of Asian countries. Mar. Pollut. Bull. 46 (2003) 281-300
54. Moore R.C. Treatise on Invertebrate Paleontology. Part N. Mollusca 6 (1969), The Geological Society of America, Inc., and The University of Kansas, Bivalvia
55. Morton B. The functional morphology of the organs of the mantle cavity of Perna viridis (Linnaeaus, 1758) (Bivaliva: Mytilacea). Am. Malacol. Bull. 5 (1987) 159-164
56. Narasimham, K.A., 1980. Fishery and biology of the green mussel, Perna viridis (Linnaeus). In: Coastal Aquaculture: Mussel Farming. Progress and Prospects. Central Marine Fisheries Research Institute Bulletin 29, Cochin, India, pp. 10-17.
57. Nichol, R., 1986. Analysis of midden from N44/215: hard times at Hahei? Pacific Anthropological Records 37. In: Anderson, A.J. (Ed.), Traditional Fishing in the Pacific: Ethnological and Archaeological Papers from the 15th Pacific Science Congress, pp. 179-198.
58. Nylander J.A.A., Ronquist F., Huelsenbeck J.P., and Nieves-Aldrey J.L. Bayesian phylogenetic analysis of combined data. Syst. Biol. 53 (2004) 47-67
59. O'Foighil D., Marshall B.A., Hilbish T.J., and Pino M.A. Trans-Pacific range extension by rafting is inferred for the flat oyster Ostrea chilensis. Biol. Bull. 196 (1999) 122-126
60. Parkington J. Coastal settlement between the mouths of the Berg and Olifants Rivers, Cape Province. S. Afr. Archaeol. Bull. 31 (1976) 127-140
61. Parulekar A.H., Dalal S.G., Ansari Z.A., and Harkantra S.N. Environmental physiology of raft-grown mussels in India. Aquaculture 29 (1982) 83-93
62. Phillips M.J., Delsuc F., and Penny D. Genome-scale phylogeny and the detection of systematic biases. Mol. Biol. Evol. 21 (2004) 1455-1458
63. Posada D., and Buckley T.R. Model selection and model averaging in phylogenetics: advantages of Akaike Information Criterion and Bayesian Approaches over likelihood ratio tests. Syst. Biol. 53 (2004) 793-808
64. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
65. Powell A.W.B. New Zealand Mollusca: Marine, Land and Freshwater Shells (1979), William Collins Publishers Ltd, Auckland, New Zealand 500 pages
66. Powell A.W.B., and Bartrum J.A. The Tertiary (Waitematan) molluscan fauna of Oneroa, Waiheke Island. Trans. R. Soc. N. Z. 60 (1929) 395-447
67. Power A.J., Walker R.L., Payne K., and Hurley D. First occurrence of the nonindigenous green mussel, Perna viridis (Linnaeus, 1758) in coastal Georgia, United States. J. Shellfish Res. 23 (2004) 741-744
68. Ramachandran N., Nair K.R., and Thomas K.T. Stock assessment of the brown mussel, Perna indica (Kuriakose and Nair) from the southwest coast of India. Indian J. Fish. 45 (1998) 437-439
69. Rawson P.D., and Hilbish T.J. Evolutionary relationships among the male and female mitochondrial DNA lineages in the Mytilus edulis species complex. Mol. Biol. Evol. 12 (1995) 893-901
70. Rich P.V. Preliminary report on the fossil avian remains from late tertiary sediments at Langebaanweg (Cape Province), South Africa. S. Afr. J. Sci. 76 (1980) 166-170
71. Robba, E., 1987. The final occlusion of Tethys: its bearing on Mediterranean benthic molluscs. In: McKenzie, K.G. (Ed.), Proceedings of the International Symposium on Shallow Tethys 2, pp. 405-426.
72. Ronquist F., and Huelsenbeck J.P. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
73. Ronquist, F., Huelsenbeck, J.P., van der Mark, P., 2005. MrBayes 3.1 Manual.
74. Sanderson, M.J., 2004. r8s, version 1.70 User's Manual, December 2004, available online at http://ginger.ucdavis.edu/r8s/.
75. Sanmartin I., and Ronquist F. Southern hemisphere biogeography inferred by event-based models: plant versus animal patterns. Syst. Biol. 53 (2004) 216-243
76. Segnini de Bravo M.I., Chung K.S., and Pérez J.E. Salinity and temperature tolerances of the green and brown mussels, Perna viridis and Perna perna (Bivalvia: Mytilidae). Rev. Biol. Trop. 5 (1998) 121-125
77. Shafee M.S. Reproduction of Perna picta (Mollusca: Bivalvia) from the Atlantic coast of Morocco. Mar. Ecol. Prog. Ser. 53 (1989) 235-245
78. Shafee M.S. Production estimate of a mussel population Perna picta (Born) on the Atlantic coast of Morocco. J. Exp. Mar. Biol. Ecol. 163 (1992) 183-197
79. Shull H.C., Perez-Losada M., Blair D., Sewell K., Sinclair E.A., Lawler S., Ponniah M., and Crandall K.A. Phylogeny and biogeography of the freshwater crayfish Euastacus (Decapoda: Parastacidae) based on nuclear and mitochondrial DNA. Mol. Phylog. Evol. 37 (2005) 249-263
80. Siddall S.E. A clarification of the genus Perna (Mytilidae). Bull. Mar. Sci. 30 (1980) 858-870
81. Simmons M.P., and Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49 (2000) 369-381
82. Skibinski D.O.F., Gallagher C., and Beynon C.M. Sex-limited mitochondrial DNA transmission in the marine mussel Mytilus edulis. Genetics 138 (1994) 801-809
83. Star B., Apte S., and Gardner J.P.A. Genetic structuring among populations of the greenshell mussel Perna canaliculus revealed by analysis of randomly amplified polymorphic DNA. Mar. Ecol. Prog. Ser. 249 (2003) 171-182
84. Stilwell J.D., and Zinsmeister W.J. Molluscan systematics and biostratigraphy: lower tertiary La Meseta formation, Seymour Island, Antarctic Peninsula. Antarct. Res. Ser. (1992) 55
85. Strugnell J., Norman M., Jackson J., Drummond A.J., and Cooper A. Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework. Mol. Phylog. Evol. 37 (2005) 426-441
86. Swadling P. The implications of shellfish exploitation for New Zealand Prehistory. Mankind 11 (1977) 11-18
87. * and Other Methods). Sinauer, Sunderland, MA.
88. Tamura K., and Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10 (1993) 512-526
89. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24 (1997) 4876-4882
90. Tomalin B.J., and Kyle R. Subsistence and recreational mussel (Perna perna) collecting in KwaZulu-Natal, South Africa: fishing mortality and precautionary management. S. Afr. J. Zool. 33 (1998) 12-22
91. Vakily, J.M., 1989. The biology and culture of mussels of the genus Perna. ICLARM Studies and Reviews 17. International Centre for Living Aquatic Resources Management, Manila, Philippines, and Deutsche Gesellschaft für Technische Zusammenarbeit (GTZ) GmbH, Eschborn, Germany, 63 pages.
92. Vrielynck B., Odin G.S., and Dercourt J. Miocene palaeogeography of the Tethys ocean: potential global correlations in the Mediterranean. In: Montanari A., Odin G.S., and Coccioni R. (Eds). Miocene Stratigraphy: An Integrated Approach (1997), Elsevier Science, Amsterdam 157-165
93. Wagstaff S.J., and Garnock-Jones P.J. Evolution and biogeography of the Hebe complex (Scrophulariaceae) inferred from ITS sequences. N. Z. J. Bot. 36 (1998) 425-437
94. Waters J.M., and Roy M.S. Out of Africa: the slow train to Australasia. Syst. Biol. 53 (2004) 18-24
95. White T., Bruns T., Lee S., and Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M.A., Gelfand D.H., Sninsky J.J., and White T.J. (Eds). PCR Protocols: A Guide to Methods and Applications (1990), Academic Press, San Diego, California 315-322
96. Xia X. Data analysis in molecular biology and evolution (2000), Kluwer Academic publishers, Boston 276 pages
97. Xia X., and Xie Z. DAMBE: Data analysis in molecular biology and evolution. J. Hered. 92 (2001) 371-373
98. Yang Z. On the best evolutionary rate for phylogenetic analysis. Syst. Biol. 47 (1998) 125-133
99. Yoshiyasu H., Ueda I., and Asahina K. Annual reproductive cycle of the green mussel Perna viridis (L.) at Enoshima Island, Sagami Bay, Japan. Sessile Organisms 21 (2004) 19-26
100. Young, N.D., Healy, J., 2003. GapCoder automates the use of indel characters in phylogenetic analysis. BMC Bioinformatics 4, 6, available at http://www.biomedcentral.com/1471-2105/4/6.
101. Zouros E., Ball A.O., Saavedra C., and Freeman K.R. An unusual type of mitochondrial DNA inheritance in the blue mussel Mytilus. Proc. Natl. Acad. Sci. USA 91 (1994) 7463-7467