The effect of incongruence on molecular dates

Taxon

Volumn 58, Issue 2, 2009, Pages 511-518

  Pfeil, Bernard E ^a  

^a CSIRO   (Australia)

Author keywords

Bias; Character simulation; Combined analysis; Concatenation; Divergence time estimation; Incongruence; Molecular dating; Separate analysis; Simultaneous analysis; Total evidence

Indexed keywords

DATA SET; DIVERGENCE; GENE EXPRESSION; LEGUME; MOLECULAR ANALYSIS; PHYLOGENETICS; TAXONOMY; TOPOLOGY;

FABACEAE; MEDICAGO;

EID: 67650000894     PISSN: 00400262     EISSN: None     Source Type: Journal    
DOI: 10.1002/tax.582015     Document Type: Article

References (42)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. 1990. Basic local alignment search tool. J. Molec. Biol. 215: 403-410.
2. Avise, J.C., Shapira, J.F., Daniel, S.W., Aquadro, C.F. & Lansman, R.A. 1983. Mitochondrial DNA differentiation during the speciation process Peromyscus. Molec. Biol. Evol. 1: 38-56.
3. Barrett, M., Donoghue, M.J. & Sober, E. 1991. Against consensus. Syst. Zool. 40: 486-493.
4. Bell, CD. 2007. Phylogenetic placement and biogeography of the North American species of Valerianella (Valeriana- ceae: Dipsacales) based on chloroplast and nuclear DNA. Molec. Phylog. Evol. 44: 929-941.
5. Bell, CD. & Donoghue, M.J. 2005. Phylogeny and biogeography of Valerianaceae (Dipsacales) with special reference to the South American valerians. Org. Div. Evol. 5:147-159.
6. Blanc, G. & Wolfe, K.H. 2004. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Pl. Cell 16: 1667-1678.
7. Blattner, F.R. 2006. Multiple intercontinental dispersals shaped the distribution area of Hordeum (Poaceae). New Phytol. 169: 603-614.
8. Bowers, J.E., Chapman, B.A., Rong, J. & Paterson, A.H. 2003. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422: 433-438.
9. Bull, J. J., Huelsenbeck, J.P., Cunningham, C.W., Swofford, D.L. & Waddell, P.J. 1993. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42: 384-397.
10. Crepet, W.L., Nixon, K.C. & Gandolfo, M.A. 2004. Fossil evidence and phytogeny: the age of major angiosperm clades based on mesofossil and macrofossil evidence from Cretaceous deposits. Amer. J. Bot. 91: 1666-1682.
11. Cronn, R.C., Small, R.L., Haselkorn, T. & Wendel, J.F. 2003. Cryptic repeated genomic recombination during speciation in Gossypium gossypioides. Evolution 57: 2475-2489.
12. Davalos, L.M. & Perkins, S.L. 2008. Saturation and base composition bias explain phylogenomic conflict in Plasmodium. Genomics 91: 433-442.
13. Doyle, J.J. 1992. Gene trees and species trees: molecular sys- tematics as one-character taxonomy. Syst. Bot. 17:144-163.
14. Fitch, W.M. 1970. Distinguishing homologous from analogous proteins. Syst. Zool. 19: 99-113.
15. Gatesy, J. & Baker, R.H. 2005. Hidden likelihood support in genomic data: can forty-five wrongs make a right? Syst. Biol. 54: 483-492.
16. Gaut, B.S., Muse, S.V., Clark, W.D. & Clegg, M.T. 1992. Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants. /. Molec. Evol. 35: 292-303.
17. Grant, T. & Kluge, A.G. 2003. Data exploration in phylogenetic inference: scientific, heuristic, or neither. Cladistics 19: 379-418.
18. Huelsenbeck, J.P., Bull, J.J. & Cunningham, C.W. 1996. Combining data in phylogenetic analysis. Trends Ecol. Evol. 11: 152-158.
19. Huelsenbeck, J.P. & Ronquist, F. 2001. Mr Bayes: Bayesian inference of phylogeny. Bioinformatics 17: 754-755.
20. Jobson, R.W. & Albert, V.A. 2002. Molecular rates parallel diversification contrasts between carnivorous plant sister lineages. Cladistics 18:127-136.
21. Kluge, A.G. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38: 7-25.
22. Kluge, A.G. & Wolf, A.J. 1993. Cladistics: what's in a word? Cladistics 9: 183-199.
23. Maddison, W.P. 1997. Gene trees in species trees. Syst. Biol. 46: 523-536.
24. Maddison, W.P. & Maddison, D.R. 2006. Mesquite: a modular system for evolutionary analysis, version 1.12. http://mesquiteproject.org.
25. Maureira Butler, I.J., Pfeil, B.E., Muangprom, A., Osborn, T.C. & Doyle, J.J. 2008. The reticulate history of Medi- cago (Fabaceae). Syst. Biol. 57: 466-482.
26. Miyamoto, M.M. & Fitch, W.M. 1995. Testing species phylogenies and phylogenetic methods with congruence. Syst. Biol. 44: 64-76.
27. Mudge, J., Cannon, S.B., Kalo, P., Oldroyd, G.E.D., Roe, B.A., Town, CD. & Young, N.D. 2005. Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana. BMC Pl. Biol. 5: doi:10.1186/1471-2229-5-15.
28. Nixon, K.C. & Carpenter, J.M. 1996. On simultaneous analysis. Cladistics 12: 221-241.
29. Pfell, B.E., Schlueter, J.A., Shoemaker, R.C. & Doyle, J.J. 2005. Placing paleopolyploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families. Syst. Biol. 54: 441-454.
30. Rieseberg, L.H., Raymond, O., Rosenthal, D.M., Lai, Z., Livingstone, K., Nakazato, T., Durphy, J.L., Schwarz- bach, A.E., Donovan, L.A. & Lexer, C. 2003. Major ecological transitions in wild sunflowers facilitated by hybridization. Science 301: 1211-1216.
31. Rosenberg, N.A. & Nordborg, M. 2002. Genealogical tree, co- alescent theory and the analysis of genetic polymorphisms. Nat. Rev. Genet. 3: 380-390.
32. Sanderson, M.J. 2003. r8s; inferring absolute rates of evolution and divergence times in the absence of a molecular clock. Bioinformatics 19: 301-302.
33. Sanderson, M.J. & Doyle, J.J. 1992. Reconstruction of or- ganismal and gene phylogenies from data on multigene families: concerted evolution, homoplasy, and confidence. Syst. Biol. 41:4-17.
34. Schlueter, J.A., Dixon, P., Granger, C, Grant, D., Clark, L., Doyle, J.J. & Shoemaker, R.C. 2004. Mining the EST databases to determine evolutionary events in the legumes and grasses. Genome 47: 868-876.
35. Stefanovic, S., Pfeil, B.E., Doyle, J.J. & Palmer, J.D. 2009. Chloroplast phylogenetic relationships among phaseoloid legumes. Syst. Bot. 34: 115-128.
36. Straub, S.C.K., Pfeil, B.E. & Doyle, J.J. 2006. Testing the polyploid past of soybean using a low-copy nuclear gene-is Glycine (Fabaceae: Papilionoideae) an auto- or allopolyploid? Molec. Phylog. Evol. 39: 580-584.
37. Sullivan, J. & Swofford, D.L. 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylo- genetics. J. Mamm. Evol. 4: 77-86.
38. Trueman, J.W.H. 1998. Reverse successive weighting. Syst. Biol. 47: 733-737.
39. Vawter, L. & Brown, W.M. 1993. Rates and patterns of base change in the small subunit ribosomal RNA gene. Genetics 134: 597-608.
40. Wendel, J.F. & Doyle, J.J. 1998. Phylogenetic incongruence: window into genome history and molecular evolution. Pp. 265-296 in: Soltis, D.E., Soltis, P.S. & Doyle, J.J. (eds.), Molecular Systematics of Plants II: DNA Sequencing. Klu- wer Academic Publishers, Norwell.
41. Wilson, A.C., Carlson, S.S. & White, T.J. 1977. Biochemical evolution. Annual Rev. Biochem. 46: 573-639.
42. Yang, Z. & Yoder, A.D. 2003. Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species. Syst. Biol. 52: 705-716.