Analyzing the relationship between sequence divergence and nodal support using Bayesian phylogenetic analyses

Molecular Phylogenetics and Evolution

Volumn 57, Issue 2, 2010, Pages 485-494

  Makowsky, Robert ^a   Cox, Christian L ^a   Roelke, Corey ^a   Chippindale, Paul T ^a  

^a UNIVERSITY OF TEXAS AT ARLINGTON   (United States)

Author keywords

Bayesian; Divergence; Phylogenetics; Sequence

Indexed keywords

ANIMAL; ARTICLE; BAYES THEOREM; PHYLOGENY;

ANIMALS; BAYES THEOREM; PHYLOGENY;

VERTEBRATA;

EID: 78049386453     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.05.009     Document Type: Article

References (93)

1. Aguileta G., Marthey S., Chiapello H., Lebrun M.H., Rodolphe F., Fournier E., Gendrault-Jacquemard A., Giraud T. Assessing the performance of single-copy genes for recovering robust phylogenies. Syst. Biol. 2008, 57:613-627.
2. Avise J. Phylogeography 2000, Harvard University Press, Cambridge, Massachusetts.
3. Avise J.C., Saunders N.C. Hybridization and introgression among species of sunfish (Lepomis): analysis by mitochondrial DNA and allozyme analysis. Genetics 1984, 108:237-255.
4. Berendzen P., Simons A., Wood R. Phylogeography of the northern hogsucker, Hypentelium nigricans (Teleostei: Cypriniformes): genetic evidence for the evidence of the ancient Teays River. J. Biogeogr. 2003, 30:1139-1152.
5. Blouin M.S., Yowell C.A., Courtney C.H., Dame J.B. Substitution bias, rapid saturation, and the use of mtDNA for nematode systematics. Mol. Biol. Evol. 1998, 15:1719-1727.
6. Blouin C., Butt D., Roger A. Impact of taxon sampling on the estimation of rates of evolution at sites. Mol. Biol. Evol. 2004, 22:784-791.
7. Bruce R. Did Desmognathus salamanders reinvent the larval stage?. Herpetol. Rev. 2005, 36:107-112.
8. Bull J.J., Cunningham C.W., Molineux I.J., Badgett M.R., Hillis D.M. Experimental molecular evolution of bacteriophage T7. Evolution 1993, 47:993-1007.
9. Cao Y., Adachi J., Janke A., Pääbo S., Hasegawa M. Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene. J. Mol. Evol. 1994, 39:519-527.
10. Cao Y., Sorenson M.D., Kumazawa Y., Mindell D.P., Hasegawa M. Phylogenetic position of turtles among amniotes: evidence from mitochondrial and nuclear genes. Gene 2000, 259:139-148.
11. Castoe T.A., Doan T.M., Parkinson C.L. Data partitions and complex models in Bayesian analysis: the phylogeny of gymnophthalmid lizards. Syst. Biol. 2004, 53:448-469.
12. Castoe T.A., Jiang Z.J., Gu W., Wang Z.O., Pollock D.D. Adaptive evolution and functional redesign of core metabolic proteins in snakes. PLoS One 2008, 3:e2201.
13. Chippindale P., Bonett R., Baldwin A., Wiens J. Phylogenetic evidence for a major reversal of life-history evolution in plethodontid salamanders. Evolution 2004, 58:2809-2822.
14. Collins T.M., Fedrigo O., Naylor G.J.P. Choosing the best genes for the job: the case for stationary genes in genome-scale phylogenetics. Syst. Biol. 2005, 54:493-500.
15. Cotton J.A., Page R.D.M. Going nuclear: gene family evolution and vertebrate phylogeny reconciled. Proc. R. Soc. Lond., Ser. B: Biol. Sci. 2002, 269:1555-1561.
16. Creer S., Thorpe R.S., Malhotra A., Chou W.H., Stenson A.G. The utility of AFLPs for supporting mitochondrial DNA phylogeographical analyses in the Taiwanese bamboo viper, Trimeresurus stejnegeri. J. Evol. Biol. 2004, 17:100-107.
17. Cummings M.P., Handley S.A., Myers D.S., Reed D.L., Rokas A., Winka K. Comparing bootstrap and posterior probability values in the four-taxon case. Syst. Biol. 2003, 52:477-487.
18. Dawson M. Phylogeography in coastal marine animals: a solution from California. J. Biogeogr. 2001, 28:723-736.
19. Douady C.J., Douzery E.J.P. Molecular estimation of eulipotyphlan divergence times and the evolution of " Insectivora" Mol. Phylogenet. Evol. 2003, 28:285-296.
20. Downie D. Phylogeography in a galling insect, grape phylloxera, Daktulosphaira vitifoliae (Phylloxeridae) in the fragmented habitat of the Southwest USA. J. Biogeogr. 2004, 31:1759-1768.
21. Erixon P., Svennblad B., Britton T., Oxelman B. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst. Biol. 2003, 52:665-673.
22. Felsenstein J. Parsimony in systematics: biological and statistical issues. Ann. Rev. Ecol. Syst. 1983, 14:313-333.
23. Felsenstein J. Inferring Phylogenies 2004, Sinauer Associates, Sunderland, Massachusetts.
24. Frost D., Grant T., Faivovich J., Bain R., Haas A., Haddad C., de Sa R., Channing A., Wilkinson M., Donnellan S., Raxworthy C., Campbell J., Blotto B., Moler P., Drewes R., Nussbaum R., Lynch J., Green D., Wheeler W. The amphibian tree of life. Bull. Am. Museum Nat. Hist. 2006, 297:1-370.
25. Graur D., Li W.-H. Fundamentals of Molecular Evolution 2000, Sinauer Associates, Sunderland, Massachusetts.
26. Graybeal A. The phylogenetic utility of cytochrome b: lessons from bufonid frogs. Mol. Phylogenet. Evol. 1993, 2:256-269.
27. Hare M.P. Prospects for nuclear gene phylogeography. Trends Ecol. Evol. 2001, 16:700-706.
28. Harrison L.B., Larsson H.C.E. Estimating evolution of temporal sequence changes: a practical approach to inferring ancestral developmental sequences and sequence heterochrony. Syst. Biol. 2008, 57:378-387.
29. Heath T.A., Hedtke S.M., Hillis D.M. Taxon sampling and the accuracy of phylogenetic analysis. J. Syst. Evol. 2008, 46:239-257.
30. Hedges S.B., Poling L.L. A molecular phylogeny of reptiles. Science 1999, 283:998-1001.
31. Hillis D.M. SINEs of the perfect character. Proc. Natl. Acad. Sci. USA 1999, 96:9979-9981.
32. Hillis D.M., Huelsenbeck J.P. To tree the truth: biological and numerical simulations of phylogeny. Molecular Evolution of Physiological Processes 1994, 55-67. Rockefeller University Press. D.M. Fambrough (Ed.).
33. Molecular Systematics 1996, Sinauer Associates, Sunderland, Massachusetts. D.M. Hillis, C. Moritz, B.K. Mable (Eds.).
34. Hudelot C., Gowri-Shankar V., Jow H., Rattray M., Higgs P.G. RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences. Mol. Phylogenet. Evol. 2003, 28:241-252.
35. Huelsenbeck J., Ronquist F. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 2001, 17:754-755.
36. Hugall A.F., Foster R., Lee M.S.Y. Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1. Syst. Biol. 2007, 56:543-563.
37. Jermiin L.S., Poladian L., Charleston M.A. Is the " Big Bang" in animal evolution real?. Science 2005, 310:1910-1911.
38. Jiang Z., Castoe T., Austin C., Burbrink F., Herron M., McGuire J., Parkinson C., Pollock D. Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region. BMC Evol. Biol. 2007, 7:123.
39. Ketmaier V., Giusti F., Caccone A. Molecular phylogeny and historical biogeography of the land snail genus Solatopupa (Pulmonata) in the peri-Tyrrhenian area. Mol. Phylogenet. Evol. 2006, 39:439-451.
40. Koopman W.I.M. Phylogenetic signal in AFLP data sets. Syst. Biol. 2005, 54:197-217.
41. Kumazawa Y., Azuma Y., Nishida M. Tempo of mitochondrial gene evolution: Can mitochondrial DNA be used to date old divergences?. Endocytobiosis Cell Res. 2004, 15:136-142.
42. Lemmon A., Moriarty E. The importance of proper model assumption in Bayesian phylogenetics. Syst. Biol. 2004, 53:265-277.
43. Lin Y.-H., McLenachan P.A., Gore A.R., Phillips M.J., Ota R., Hendy M.D., Penny D. Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. Mol. Biol. Evol. 2002, 19:2060-2070.
44. Linder P., Hardy C., Rutschmann F. Taxon sampling effects in molecular clock dating: an example from the African Restionaceae. Mol. Phylogenet. Evol. 2005, 35:569-582.
45. Liu F.-G.R., Miyamoto M.M., Freire N.P., Ong P.Q., Tennant M.R., Young T.S., Gugel K.F. Molecular and morphological supertrees for eutherian (placental) mammals. Science 2001, 291:1786-1789.
46. Lopez P., Forterre P., Philippe H. The root of the tree of life in the light of the covarion model. J. Mol. Evol. 1999, 49:496-508.
47. Maddison W.P. Gene trees in species trees. Syst. Biol. 1997, 46:523-536.
48. Maddison W.P., Knowles L.L. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 2006, 55:21-30.
49. Maddison, W.P., Maddison, D.R., 2009. Mesquite: a modular system for evolutionary analyses. Version 2.6. Available from: http://mesquiteproject.org.
50. Mank J.E., Promislow D.E.L., Avise J.C. Phylogenetic perspectives in the evolution of parental care in ray-finned fishes. Evolution 2005, 59:1570-1578.
51. Meyer A. Shortcomings of the cytochrome b gene as a molecular marker. Trends Ecol. Evol. 1994, 9:278-280.
52. Min M., Yang S., Bonett R., Vieites D., Brandon R., Wake D. Discovery of the first Asian plethodontid salamander. Nature 2005, 435:87-90.
53. Miya M., Takeshima H., Endo H., Ishiguro N.B., Inoue J.G., Mukai T., Satoh T.P., Yamaguchi M., Kawaguchi A., Mabuchi K., Shirai S.M., Nishida M. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol. Phylogenet. Evol. 2003, 26:121-138.
54. Morgan J.A.T., Blair D. Relative merits of nuclear ribosomal internal transcribed spacers and mitochondrial CO1 and ND1 genes for distinguishing among Echinostoma species (Trematoda). Parasitology 1998, 116:289-297.
55. Mueller R.L. Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic analysis. Syst. Biol. 2006, 55:289-300.
56. Mueller R., Macey J., Jaekel M., Wake D., Boore J. Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes. Proc. Natl. Acad. Sci. USA 2004, 101:13820-13825.
57. Murata S., Takasaki N., Saitoh M., Okada N. Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution. Proc. Natl. Acad. Sci. USA 1993, 90:6995-6999.
58. Murphy W.J., Eizirik E., O'Brien S.J., Madsen O., Scally M., Douady C.J., Teeling E., Ryder O.A., Stanhope M.J., de Jong W.W., Springer M.S. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 2001, 294:2348-2351.
59. Nylander J. MrModeltest (Program distributed by the author) 2004, Evolutionary Biology Centre, Uppsala University.
60. Nylander J.A., Ronquist F., Huelsenbeck J.P., Nieves-Aldrey J.L. Bayesian phylogenetic analysis of combined data. Syst. Biol. 2004, 53:47-67.
61. Nylander J.A., Wilgenbusch J.C., Warren D.L., Swofford D.L. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 2008, 24:581-583.
62. Palumbi S.R., Cipriano F., Hare M.P. Predicting nuclear gene coalescence from mitochondrial data: the three-times rule. Evolution 2001, 55:5.
63. Phillips M.J., Penny D. The root of the mammalian tree inferred from whole mitochondrial genomes. Mol. Phylogenet. Evol. 2003, 28:171-185.
64. Pollock D.D., Zwickl D.J., McGuire J.A., Hillis D.M. Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 2002, 51:664-671.
65. Prasad A.B., Allard M.W., Program N.C.S., Green E.D. Confirming the phylogeny of mammals by use of large comparative sequence datasets. Mol. Biol. Evol. 2008, 25:1795-1808.
66. Pratt R.C., Gibb G.C., Morgan-Richards M., Phillips M.J., Hendy M.D., Penny D. Toward resolving deep neoaves phylogeny: data, signal enhancement, and priors. Mol. Biol. Evol. 2009, 26:313-326.
67. Rannala B., Huelsenbeck J., Yang Z., Nielsen R. Taxon sampling and the accuracy of large phylogenies. Syst. Biol. 1998, 47:702-710.
68. Ranwez V., Delsuc F., Ranwez S., Belkhir K., Tilak M.-K., Douzery E. OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics. BMC Evol. Biol. 2007, 7:241.
69. Richard M., Thorpe R.S. Can microsatellites be used to infer phylogenies? Evidence from population affinities of the Western Canary Island Lizard (Gallotia galloti). Mol. Phylogenet. Evol. 2001, 20:351-360.
70. Ripplinger J., Sullivan J. Does choice in model selection affect maximum likelihood analysis?. Syst. Biol. 2008, 57:76-85.
71. Rodiguez-Ezpeleta N., Brinkmann H., Roure B., Lartillot N., Lang B.F., Philippe H. Detecting and overcoming systematic errors in genome-scale phylogenies. Syst. Biol. 2007, 56:389-399.
72. Rokas A., Carroll S. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol. Biol. Evol. 2005, 22:1337-1344.
73. Rokas A., Carroll S.B. Bushes in the tree of life. PLoS Biol. 2006, 4:e352.
74. Rokas A., Williams B.L., King N., Carroll S.B. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003, 425:798-804.
75. Ronquist F., Huelsenbeck J. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
76. Ros V.I.D., Breeuwer J.A.J. Spider mite (Acari: Tetranychidae) mitochondrial COI phylogeny reviewed: host plant relationships, phylogeography, reproductive parasites and barcoding. Exp. Appl. Acarol. 2007, 42:239-262.
77. Rosenberg M.S., Kumar S. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl. Acad. Sci. USA 2001, 98:10751-10756.
78. Russo C.A., Takezaki N., Nei M. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol. 1996, 13:525-536.
79. Rzhetsky A., Sitnikova T. When is it safe to use an oversimplified substitution model in tree-making?. Mol. Biol. Evol. 1996, 13:1255-1265.
80. Seo T.-K., Kishino H. Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins. Syst. Biol. 2008, 57:367-377.
81. Sullivan J., Lavoue S., Arnegard M., Hopkins C. AFLPs resolve phylogeny and reveal mitochondrial introgression within a species flock of African Electric fish (Mormyroidea: Teleostei). Evolution 2004, 58:825-841.
82. Takahashi K., Terai Y., Nishida M., Okada N. Phylogenetic relationships and ancient incomplete lineage sorting among cichlid fishes in Lake Tanganyika as revealed by analysis of the insertion of retroposons. Mol. Biol. Evol. 2001, 18:2057-2066.
83. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
84. Townsend J.P. Profiling phylogenetic informativeness. Syst. Biol. 2007, 56:222-231.
85. Vekemans X., Beauwens T., Lemaire M., Roldan-Ruiz I. Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Mol. Ecol. 2002, 11:139-151.
86. Vos P., Hogers R., Bleeker M., Reijans M., Lee T.v.d., Hornes M., Frijters A., Pot J., Peleman J., Kuiper M. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995, 23:4407-4414.
87. Waddell P.J., Shelley S. Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, [gamma]-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models. Mol. Phylogenet. Evol. 2003, 28:197-224.
88. Weisrock D., Harmon L., Larson A. Resolving deep phylogenetic relationships in salamanders: analyses of mitochondrial and nuclear genomic data. Syst. Biol. 2005, 54:758-777.
89. Wiens J.J., Bonett R.M., Chippindale P.T. Ontogeny discombobulates phylogeny: paedomorphosis and higher-level salamander relationships. Syst. Biol. 2005, 54:91-110.
90. Wiens J.J., Kuczynski C.A., Smith S.A., Mulcahy D.G., Sites J.W., Townsend T.M., Reeder T.W. Branch lengths, support, and congruence: testing the phylogenomic approach with 20 nuclear loci in snakes. Syst. Biol. 2008, 57:420-431.
91. 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.
92. Yang Z. On the best evolutionary rate for phylogenetic analysis. Syst. Biol. 1998, 47:125-133.
93. Zwickl D.J., Hillis D.M. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 2002, 51:588-598.