Molecular phylogenetic analysis of tropical freshwater mussels (Mollusca: Bivalvia: Unionoida) resolves the position of Coelatura and supports a monophyletic Unionidae

Molecular Phylogenetics and Evolution

Volumn 61, Issue 2, 2011, Pages 504-514

  Whelan, Nathan V ^a   Geneva, Anthony J ^b,c   Graf, Daniel L ^a,b  

^a UNIVERSITY OF ALABAMA   (United States)

^b ACADEMY OF NATURAL SCIENCES OF DREXEL UNIVERSITY   (United States)

^c UNIVERSITY OF ROCHESTER   (United States)

Author keywords

28S; COI; Freshwater mussel; Phylogeny; Unionidae

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; CELL NUCLEUS; CLASSIFICATION; DNA SEQUENCE; GENETICS; PHYLOGENY; STATISTICAL MODEL; UNIONIDAE;

ANIMALS; BAYES THEOREM; CELL NUCLEUS; DNA, MITOCHONDRIAL; LIKELIHOOD FUNCTIONS; PHYLOGENY; SEQUENCE ANALYSIS, DNA; UNIONIDAE;

BIVALVIA; CAELATURA; MOLLUSCA; UNIONIDAE; UNIONOIDA;

EID: 80052749776     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2011.07.016     Document Type: Article

References (74)

1. Appleton C.C. The Unionacea (Mollusca, Lamellibranchiata) of South-Central Africa. Ann. South Afr. Mus. 1979, 77:151-174.
2. Araujo R., Toledo C., Machordom A. Redescription of Unio gibbus Spengler, 1793, a west Palearctic freshwater mussel with hookless glochidia. Malacologia 2009, 51:131-141.
3. Barnhart M.C., Haag W.R., Roston W.R. Adaptations to host infection and larval parasitism in Unionoida. J. North Am. Benthol. Soc. 2008, 27:370-394.
4. Bergsten J. A review of long-branch attraction. Cladistics 2005, 21:163-193.
5. Bieler, R., Carter, J.G., Coan, E.V., 2010. Classification of bivalve families. In: Bouchet, P., Rocroi, J.-P. (Eds.), Nomenclator of Bivalve Familes. Malacologia, pp. 113-133.
6. Bogan A.E., Hoeh W.R. On becoming cemented: evolutionary relationships among the genera in the freshwater bivalve family Etheriidae (Bivalvia: Unionoida). The Evolutionary Biology of the Bivalvia. Geological Society, London, Special Publications 2000, vol. 177:159-168. The Geological Society of London, London.
7. Brandt R.A. The non-marine aquatic Mollusca of Thailand. Archiv Molluskenkd. 1974, 105:1-423.
8. Bremer K. Branch support and tree stability. Cladistics 1995, 10:295-304.
9. Cadotte M.W., Davies T.J. Rarest of the rare: advances in combining evolutionary distinctiveness and scarcity to inform conservation at biogeographical scales. Divers. Distrib. 2010, 16:376-385.
10. Cadotte M.W., Davies T.J., Regetz J., Kembel S.W., Cleland E., Oakley T.H. Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history. Ecol. Lett. 2010, 13:96-105.
11. Clarke K.R., Warwick R.M. A taxonomic distinctiveness index and its statistical properties. J. Appl. Ecol. 1998, 35:523-531.
12. Crisp M.D., Trewick S.A., Cook L.G. Hypothesis testing in biogeography. Trends Ecol. Evol. 2011, 26:66-72.
13. Cummings K.S., Graf D.L. Mollusca: Bivalvia. Ecology and Classification of North American Freshwater Invertebrates 2009, 309-384. Academic Press, Elsevier, New York. third ed. J.H. Thorp, A.P. Covich (Eds.).
14. Efron B., Halloran E., Holmes S. Bootstrap confidence levels for phylogenetic trees. Proc. Natl. Acad. Sci. USA 1996, 93.
15. Farris J.S., Källersjö M., Kluge A.G., Bult C. Testing significance of incongruence. Cladistics 1995, 10:315-319.
16. Felsenstein J. Inferring Phylogenies 2003, Sinauer Associates, Sunderland, Massachusetts.
17. Folmer O., Black M., Hoeh W., Lutz R., Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 1994, 3:294-299.
18. Giribet G., Wheeler W. On bivalve phylogeny: a high-level analysis of the Bivalvia (Mollusca) based on combined morphology and DNA sequences data. Invertebr. Biol. 2002, 121:271-324.
19. Graf D.L. Molecular phylogenetic analysis of two problematic freshwater mussel genera (Unio and Gonidea) and a re-evaluation of the classification of Nearctic Unionidae (Bivalvia: Palaeoheterodonta: Unionoida). J. Mollus. Stud. 2002, 68:65-71.
20. Graf D.L., Cummings K.S. Palaeoheterodont diversity (Mollusca: Trigonioida+Unionoida): what we know and what we wish we knew about freshwater mussel evolution. Zool. J. Linn. Soc. - London 2006, 148:343-394.
21. Graf D.L., Cummings K.S. Freshwater mussels (Mollusca: Bivalvia: Unionoida) of Angola, with description of a new species, Mutela wistarmorrisi. Proc. Acad. Nat. Sci. Phila. 2006, 155:163-194.
22. Graf D.L., Cummings K.S. Review of the systematics and global diversity of freshwater mussel species (Bivalvia: Unionoida). J. Mollus. Stud. 2007, 73:291-314.
23. Graf D.L., Cummings K.S. Preliminary review of the freshwater mussels (Mollusca: Bivalvia: Unionoida) of northern Africa, with an emphasis on the Nile. J. Egypt. Ger. Soc. Zool. 2007, 53D:89-118.
24. Graf D.L., Cummings K.S. Actual and alleged freshwater mussels (Mollusca: Bivalvia: Unionoida) from Madagascar and the Mascarenes, with description of a new genus Germainaia. Proc. Acad. Nat. Sci. Phila. 2009, 158:221-238.
25. Graf D.L., Cummings K.S. Comments on the value of COI for family-level freshwater mussel systematics: a reply to Hoeh, Bogan, Heard & Chapman. Malacologia 2010, 52:191-197.
26. Graf D.L., Ó Foighil D. The evolution of brooding characters among the freshwater pearly mussels (Bivalvia: Unionoidea) of North America. J. Mollus. Stud. 2000, 66:157-170.
27. Graf D.L., Ó Foighil D. Molecular phylogenetic analysis of 28S rDNA supports a Gondwanan origin for Australasian Hyriidae (Mollusca: Bivalvia: Unionoida). Vie Milieu 2000, 50:245-254.
28. Heard W.H., Vail V.A. The systematic position of Unio caffer (Pelecypoda: Unionoida: Unionidae). Zool. Afr. 1976, 11:45-58.
29. Hillis D.M., Bull J.J. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 1993, 42:182-192.
30. Hoeh W.R., Black M.B., Gustafson R.G., Bogan A.E., Lutz R.A., Vrijenhoek R.C. Testing alternative hypotheses of Neotrigonia (Bivalvia: Trigonioida) phylogenetic relationships using cytochrome c oxidase subunit I DNA sequences. Malacologia 1998, 40:267-278.
31. Hoeh W.R., Bogan A.E., Heard W.H. A phylogenetic perspective on the evolution of morphological and reproductive characteristics in the Unionoida. Ecology and Evolution of the Freshwater Mussels Unionoida. Ecological Studies 2001, vol. 145:257-280. Springer-Verlag, Berlin.
32. Hoeh W.R., Bogan A.E., Cummings K.S., Guttman S.I. Evolutionary relationships among the higher taxa of freshwater mussels (Bivalvia: Unionoida): inferences on phylogeny and character evolution from analyses of DNA sequence data. Malacological Rev 2002, 31/32:123-141.
33. Hoeh W.R., Bogan A.E., Heard W.H., Chapman E.G. Palaeoheterodont phylogeny, character evolution and phylogenetic classification: a reflection on methods of analysis. Malacologia 2009, 51:307-317.
34. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
35. ICZN International Code of Zoological Nomenclature 1999, International Trust for Zoological Nomenclature, London. fourth ed.
36. Khalloufi N., Toledo C., Machordom A., Boumaïza M., Araujo R. The unionids of Tunisia: taxonomy, phylogenetic relationships, with redescription of Unio ravoisieri Deshayes, 1847, U. durieui Deshayes, 1847. J. Mollus. Stud. 1847, 77:103-115.
37. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., Higgins D.G. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
38. Littlewood D.T.J. Molecular phylogenetics of cupper oysters based on partial 28S rRNA gene sequences. Mol. Phylogenet. Evol. 1994, 3:221-229.
39. Lydeard C., Mulvey M., Davis G.M. Molecular systematics and evolution of reproductive traits in North American freshwater unionacean mussels (Mollusca: Bivalvia) as inferred from 16S rRNA gene sequences. Philos. Trans. Roy. Soc. B 1996, 351:1593-1603.
40. Lydeard C., Cowie R.H., Ponder W., Bogan A.E., Bouchet P., Clark S.A., Cummings K.S., Frest T.J., Gargominy O., Herbert D.G., Hershler R., Perez K.E., Roth B., Seddon M., Strong E.E., Thompson F.G. The global decline of nonmarine mollusks. Bioscience 2004, 54:321-330.
41. Maddison, W.P., Maddison, D.R., 2010. Mesquite: a Modular System for Evolutionary Analysis. Version. 2.73. http://www.mesquiteproject.org.
42. Mandahl-Barth G. Studies on African Freshwater Bivalves 1988, Danish Bilharziasis Laboratory, Charlottenlund.
43. Miller, M.A., Holder, M.T., Vos, R., Midford, P.E., Liebowitz, T., Chan, L., Hoover, P., Warnow, T., 2011. The CIPRES Portals. CIPRES 2009-08-04. http://www.phylo.org/sub_sections/portal.
44. Okusu A., Schwabe E., Eernisse D.J., Giribet G. Towards a phylogeny of chitons (Mollusca, Polyplacophora) based on combined analysis of five molecular loci. Org. Divers. Evol. 2003, 3:281-302.
45. Ortmann A.E. The systematic position of the unionid-genus Parreysia. Nautilus 1910, 23:139-142.
46. Ortmann A.E. The anatomy of two African nayades, Unio caffer and Spatha wahlbergi. Nautilus 1918, 31:75-78.
47. Pain T., Woodward F.R. A monograph of the African bivalves of the genera Brazzaea Bourguignat, Mweruella Haas, Prisodontopsis Tomlin and Pseudospatha Simpson. Rev. Zool. Bot. Afr. 1968, 77:190-220.
48. Park J.-K., Ó Foighil D. Sphaeriid and corbiculid clams represent separate heterodont bivalve radiations into freshwater environments. Mol. Phylogenet. Evol. 2000, 14:75-88.
49. Posada D. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
50. Potter P.E., Szatmari P. Global Miocene tectonics and the modern world. Earth-Sci. Rev. 2009, 96:279-295.
51. Prashad B. XIX. Studies on the anatomy of Indian Mollusca. 3. The soft parts of some Indian Unionidae. Rec. Indian Mus. 1919, 16:289-296.
52. Prashad B. XVII. Studies on the anatomy of Indian Mollusca. 2. The marsupium and glochidium of some Unionidae and on the Indian species hitherto assigned to the genus Nodularia. Rec. Indian Mus. 1919, 15:143-148.
53. Prozorova L.A., Sayenko E.M., Bogatov V.V., Wu M., Liu Y.-Y. Bivalves of the Yangtze River drainage. Bull. Russ. Far East Mala. Soc. 2005, 9:46-58.
54. Phylogeny and Conservation 2005, Cambridge University Press, Cambridge. A. Purvis, J.L. Gittleman, T. Brooks (Eds.).
55. Roe K.J., Hoeh W.R. Systematics of freshwater mussels (Bivalvia: Unionoida). Molecular Systematics and Phylogeography of Mollusks. Smithsonian Series in Comparative Evolutionary Biology 2003, 91-122. Smithsonian Books, Washington. C. Lydeard, D.R. Lindberg (Eds.).
56. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
57. Scotese C.R., Gahahan L.M., Larson R.L. Plate tectonic reconstructions of the Cretaceous and Cenozoic ocean basins. Tectonophysics 1988, 155:27-48.
58. Simone, L.R.L., 2006. Land and Freshwater Molluscs of Brazil. EGB, Fapesp, São Paulo.
59. Sleem S.H., Ali T.G. Application of RAPD-PCR in taxonomy of certain freshwater bivalves of genus Caelatura. Glob. J. Mol. Sci. 2008, 3:27-31.
60. Sorenson, M.D., Franzosa, E.A., 2007. TreeRot, Version 3. Boston University, Boston, MA.
61. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
62. Strayer D.L. Challenges for freshwater invertebrate conservation. J. North Am. Benthol. Soc. 2006, 25:271-287.
63. Strayer D.L., Dudgeon D. Freshwater biodiversity conservation: recent progress and future challenges. J. North Am. Benthol. Soc. 2010, 29:344-358.
64. Strayer D.L., Hunter D.C., Smith L.C., Borg C.K. Distribution, abundance, and roles of freshwater clams (Bivalvia, Unionidae) in the freshwater tidal Hudson River. Freshwater Biol. 1994, 31:239-248.
65. Subba Rao, N.V., 1989. Handbook Freshwater Molluscs of India. Zoological Survey of India, Calcutta.
66. Swofford, D.L., 2002. PAUP*. Phylogenetic Analysis using Parsimony (* and Other Methods). Version 4b10. Sinauer Associates, Sunderland, Massachusetts.
67. Swofford D.L., Olsen G.J., Waddell P.J., Hillis D.M. Phylogenetic inference. Molecular Systematics 1996, 407-514. Sinauer Associates, Inc., Sunderland, Massachusetts. second ed. D.M. Hillis, C. Moritz, B.K. Mable (Eds.).
68. Van Damme D., Pickford M. The Late Cenozoic bivalves of the Albertine Basin (Uganda-Congo). Geo-Pal Uganda 2010, 2:1-121.
69. Van Damme D., Van Bocxlaer B. Freshwater molluscs of the Nile Basin, past and present. The Nile: Origin, Environments, Limnology and Human Use 2009, 585-629. Springer Science+Business Media B.V. H.J. Dumont (Ed.).
70. Vaughn C.C., Gido K.B., Spooner D.E. Ecosystem processes performed by unionid mussels in stream mesocosms: species roles and effects of abundance. Hydrobiologia 2004, 527:35-47.
71. Wächtler K., Mansur M.C.D., Richter T. Larval types and early postlarval biology in Naiads (Unionoida). Ecology and Evolution of the Freshwater Mussels Unionoida 2001, 93-125. Springer-Verlag, Berlin. G. Bauer, K. Wächtler (Eds.).
72. Walker J.M., Curole J.P., Wade D.E., Chapman E.G., Bogan A.E., Watters G.T., Hoeh W.R. Taxonomic distribution and phylogenetic utility of gender-associated mitochondrial genomes in the Unionoida (Bivalvia). Malacologia 2006, 48:265-282.
73. Wilgenbusch, J.C., Warren, D.L., Swofford, D.L., 2004. AWTY: a System for Graphical Exploration of MCMC Convergence in Bayesian Phylogenetic Inference. http://www.ceb.csit.fsu.edu/awty.
74. Xia X., Xie Z., Salemi M., Chen L., Wang Y. An index of substitution saturation and its application. Mol. Phylogenet. Evol. 2003, 26:1-7.