Resolving tylenchid evolutionary relationships through multiple gene analysis derived from EST data

Molecular Phylogenetics and Evolution

Volumn 36, Issue 3, 2005, Pages 536-545

  Scholl, Elizabeth H ^a   Bird, David McK ^a  

^a NONE

Author keywords

Bayesian; Caenorhabditis elegans; COG; Cyst nematode; Orthologues; Root knot nematode

Indexed keywords

ANIMAL; ARTICLE; EXPRESSED SEQUENCE TAG; GENETIC SELECTION; GENETICS; MOLECULAR EVOLUTION; NEMATODE; PHYLOGENY;

ANIMALS; EVOLUTION, MOLECULAR; EXPRESSED SEQUENCE TAGS; PHYLOGENY; SELECTION (GENETICS); TYLENCHIDA;

ARENARIA (PLANT); CAENORHABDITIS ELEGANS; GLOBODERA PALLIDA; HETERODERA GLYCINES; MELOIDOGYNE ARENARIA; MELOIDOGYNE JAVANICA; TYLENCHIDA;

EID: 21744452353     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2005.03.016     Document Type: Article

References (47)

1. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman Basic local alignment search tool J. Mol. Biol. 215 1990 403 410
2. D.McK. Bird, S.W. Clifton, T. Kepler, J.J. Kieber, J. Thorne, and C.H. Opperman Genomic dissection of a nematode-plant interaction: a tool to study plant biology Plant Physiol. 129 2002 394 395
3. D.McK. Bird, and I. Kaloshian Are roots special? Nematodes have their say Physiol. Mol. Plant P. 62 2003 115 123
4. M.L. Blaxter, P. DeLey, J. Garey, L.X. Liu, P. Scheldeman, A. Vierstraete, J. Vanfletern, L.Y. Mackey, M. Dorris, L.M. Frisse, J.T. Vida, and W.K. Thomas A molecular evolutionary framework for the phylum Nematoda Nature 392 1998 71 75
5. J.R. Brown, C.J. Douady, M.J. Italia, W.E. Marshall, and M.J. Stanhope Universal trees based on large combined protein sequence data sets Nat. Genet. 28 2001 281 285
6. P. Castagnone-Sereno, C. Piotte, J. Uijthof, P. Abad, E. Wajnberg, F. Vanlerberghe-Masutti, M. Bongiovanni, and A. Dalmasso Phylogenetic relationships between amphimictic and parthenogenetic nematodes of the genus Meloidogyne as inferred from repetitive DNA analysis Heredity 70 1993 195 204
7. The C. elegans Sequencing Consortium, 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012-2018.
8. A. Dalmasso, and J.G. Bergé Molecular polymorphism and phylogenetic relationship in some Meloidogyne spp.: application to the taxonomy of Meloidogyne J. Nematol. 10 1978 323 332
9. K.G. Davies, M. Fargette, G. Balla, A.I. Daud, R. Duponnois, S.R. Gowen, T. Mateille, M.S. Phillips, A. Sawadogo, C. Trivino, E. Vouyoukalou, and D.L. Trudgill Cuticle heterogeneity as exhibited by Pasteuria spore attachment is not linked to the phylogeny of parthenogenetic root-knot nematodes (Meloidogyne spp.) Parasitology 122 2001 111 120
10. I.T. DeLey, P. DeLey, A. Vierstraete, G. Karssen, M. Moens, and J. Vanfleteren Phylogenetic analyses of Meloidogyne small subunit rDNA J. Nematol. 34 2002 319 327
11. D.W. Dickson, D. Huisingh, and J.N. Sasser Dehydrogenases, acid and alkaline phosphatases, and esterases for chemotaxonomy of selected Meloidogyne, Ditylenchus, Heterodera, and Aphelenchus spp J. Nematol. 3 1971 1 16
12. M. Dorris, P. DeLey, and M.L. Blaxter Molecular analysis of nematode diversity and the evolution of parasitism Parasitol. Today 15 1999 188 193
13. J.J. Doyle Gene trees and species tree: molecular systematics as one-character taxonomy Syst. Bot. 17 1992 144 163
14. J.D. Eisenbeck, and H.H. Triantaphyllou Root-knot nematodes: Meloidogyne species and races W.R. Nickle Manual of Agricultural Nematology 1991 Marcel Dekker New York 191 274
15. P.R. Esbenshade, and A.C. Triantaphyllou Enzymatic relationships and evolution in the genus Meloidogyne (Nematoda: Tylenchida) J. Nematol. 19 1987 8 18
16. Felsenstein, J., 1993. PHYLIP (Phylogeny Inference Package) version 3.6a2. Department of Genetics, University of Washington, Seattle, WA.
17. T.W. Harris, R. Lee, E. Schwarz, K. Bradnam, D. Lawson, W. Chen, D. Blasier, E. Kenny, F. Cunningham, R. Kishore, J. Chan, H.-M. Muller, A. Petcherski, G. Thorisson, A. Day, T. Bieri, A. Rogers, C.-K. Chen, J. Spieth, P. Sternberg, R. Durbin, and L.D. Stein WormBase: a cross-species database for comparative genomics Nucleic Acids Res. 31 2003 133 137
18. D.M. Hillis, and M.T. Dixon Ribosomal DNA: molecular evolution and phylogenetic inference Q. Rev. Biol. 66 1991 411 453
19. J.P. Huelsenbeck, and F. Ronquist MRBAYES: Bayesian inference of phylogeny Bioinformatics 17 2001 754 755
20. A. Hugall, J. Stanton, and C. Mortiz Reticulate evolution and the origins of ribosomal internal transcribed spacer diversity in apomictic Meloidogyne Mol. Biol. Evol. 16 1999 157 164
21. D.T. Jones, W.R. Taylor, and J.M. Thornton The rapid generation of mutation data matrices from protein sequences Comp. Appl. Biosci. 8 1992 275 282
22. K. Kiontke, N.P. Gavin, Y. Raynes, C. Roehrig, F. Piano, and D.H.A. Fitch Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss PNAS 101 2004 9003 9008
23. Y. Kumazawa, and M. Nishida Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics J. Mol. Evol. 37 1993 380 398
24. J. McCarter, P. Abad, J.T. Jones, and D.McK. Bird Rapid gene discovery in plant parasitic nematodes via expressed sequence tags Nematology 2 2000 719 731
25. J.P. McCarter, M.D. Mitreva, J. Martin, M. Dante, T. Wylie, U. Rao, D. Pape, Y. Bowers, B. Theising, C. Murphy, A.P. Kloek, B. Chiapelli, S.W. Clifton, D.McK. Bird, and R. Waterston Analysis and functional classification of transcripts from the root-knot nematode Meloidogyne incognita Genome Biol. 4 2003 R26.1 R26.19
26. W. Messier, and C.-B. Stewart Episodic adaptive evolution of primate lysozymes Nature 385 1997 151 154
27. D.P. Mindell, and R.L. Honeycutt Ribosomal RNA in vertebrates: evolution and phylogenetic applications Annu. Rev. Ecol. Syst. 21 1990 541 566
28. P. Pamilo, and M. Nei Relationships between gene trees and species trees Mol. Biol. Evol. 5 1988 568 583
29. J.D. Parsons Improved tools for DNA comparison and clustering Bioinformatics 11 1995 603 613
30. D. Posada, and K. Crandall MODELTEST: testing the model of DNA substitution Bioinformatics 14 1998 817 818
31. T.O. Powers, E.G. Platzer, and B.C. Hyman Species-specific restriction site polymorphism in root-knot nematode mitochondrial DNA J. Nematol. 18 1986 288 293
32. T.O. Powers, and L.J. Sandall Estimation of genetic divergence in Meloidogyne mitochondrial DNA J. Nematol. 20 1988 505 511
33. A. Rokas, B.L. Williams, N. King, and S.B. Carroll Genome-scale approaches to resolving incongruence in molecular phylogenies Nature 425 2003 798 804
34. J.N. Sasser Root-knot nematodes: a global menace to crop production Plant Dis. 64 1980 36 41
35. E.H. Scholl, J.L. Thorne, J.P. McCarter, and D.McK. Bird Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach Genome Biol. 4 2003 R39
36. J.B. Slowinski, and R.D.M. Page How should species phylogenies be inferred from sequence data? Syst. Biol. 48 1999 814 825
37. A.B. Smith RNA sequence data in phylogenetic reconstruction: testing the limits of its resolution Cladistics 5 1989 321 344
38. N. Takahata Gene genealogy in three related populations: consistency probability between gene and population trees Genetics 122 1989 957 966
39. R.L. Tatusov, D.A. Natale, I.V. Garkavtsev, T.A. Tatusova, U.T. Shankavaram, B.S. Rao, B. Kiryutin, M.Y. Galperin, N.D. Fedorova, and E.V. Koonin The COG database: new developments in phylogenetic classification of proteins from complete genomes Nucleic Acids Res. 29 1997 22 28
40. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1994 4673 4680
41. A.C. Triantaphyllou Polyploidy and reproductive patterns in the root-knot nematode Meloidogyne hapla J. Morphol. 118 1966 403 414
42. A.C. Triantaphyllou Cytogenetics, cytotaxonomy, and phylogeny of root-knot nematodes J.N. Sasser C.C. Carter An advanced treatise on Meloidogyne, vol. I. Biology and control 1985 North Carolina State University Graphics Raleigh, NC 113 126
43. D.L. Wheeler, D.M. Church, A.E. Lash, D.D. Leipe, T.L. Madden, J.U. Pontius, G.D. Schuler, L.M. Schriml, T.A. Tatusova, L. Wagner, and B.A. Rapp Database resources of the National Center for Biotechnology Information: 2002 update Nucleic Acids Res. 30 2002 13 16
44. C. Wu Inferences of species phylogeny in relation to segregation of ancient polymorphisms Genetics 127 1991 429 435
45. B. Xue, D. Baillie, K. Beckenbach, and J. Webster DNA hybridization probes for studying the affinities of three Meloidogyne populations Fundam. Appl. Nematol. 15 1992 35 41
46. Z. Yang PAML: a program package for phylogenetic analysis by maximum likelihood Comp. Appl. Biosci. 13 1997 555 556
47. Z. Yang Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution Mol. Biol. Evol. 15 1998 568 573