Phylogenetic models and model selection for noncoding DNA

Plant Systematics and Evolution

Volumn 282, Issue 3-4, 2009, Pages 109-126

  Kelchner, Scot A ^a  

^a Nucl Eng Idaho State University   (United States)

Author keywords

Intergenic spacers; Introns; Model adequacy; Model selection; Noncoding DNA; Sampling error

Indexed keywords

EID: 70350366917     PISSN: 03782697     EISSN: 16156110     Source Type: Journal    
DOI: 10.1007/s00606-008-0071-6     Document Type: Review

References (116)

1. Alvarez I, Wendel JF (2003) Ribosomal ITS sequences and plant phylogenetic inference. Molec Phylogenet Evol 29:417-434.
2. Baldwin BG, Sanderson MJ, Porter JM, Wojciechowski MF, Campbell CS, Donoghue MJ (1995) The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Ann Missouri Bot Gard 82:247-277.
3. Borsch T, Hilu KW, Quandt D, Wilde V, Neinhuis C, Barthlott W (2003) Noncoding plastid trnT-trnF sequences reveal a well-resolved phylogeny of basal angiosperms. J Evol Biol 16:558-576.
4. Borsch T, Hilu KW, Wiersema JH, Löhne C, Barthlott W, Wilde V (2007) Phylogeny of Nymphaea (Nymphaeaceae): evidence from substitutions and microstructural changes in the chloroplast trnT-trnF region. Int J Pl Sci 168:639-671.
5. Brinkmann H, van der Giezen M, Zhou Y, de Raucourt GP, Philippe H (2005) An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Syst Biol 54:743-757.
6. Brown JM, Lemmon AR (2007) The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Syst Biol 56:643-655.
7. Buckley TR (2002) Model misspecification and probabilistic tests of topology: evidence from empirical data sets. Syst Biol 51:509-523.
8. Buckley TR, Cunningham CW (2002) The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support. Molec Biol Evol 19:394-405.
9. Buckley TR, Simon C, Chambers GK (2001a) Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support. Syst Biol 50:67-86.
10. Buckley TR, Simon C, Shimodaira H, Chambers GK (2001b) Evaluating hypotheses on the origin and evolution of the New Zealand alpine cicadas (Maoricicada) using multiple-comparison tests of tree topology. Molec Biol Evol 18:223-234.
11. Bull JJ, Huelsenbeck JP, Cunningham CW, Swofford DL, Waddell PJ (1993) Partitioning and combining data in phylogenetic analysis. Syst Biol 42:384-397.
12. Burnham KP, Anderson DR (2002) Model selection and multimodel inference: a practical information-theoretic approach. Springer, New York.
13. Collins TM, Wimberger PH, Naylor GJP (1994) Compositional bias, character-state bias, and character-state reconstruction using parsimony. Syst Biol 43:482-496.
14. Cummings MP, Nugent JM, Olmstead RG, Palmer JD (2003) Phylogenetic analysis reveals five independent transfers of the chloroplast gene rbcL to the mitochondrial genome in angiosperms. Curr Genet 43:131-138.
15. Cunningham CW, Zhu H, Hillis DM (1998) Best-fit maximum-likelihood models for phylogenetic inference: empirical tests with known phylogenies. Evolution 52:978-987.
16. de Pamphilis CW, Palmer JD (1990) Loss of photosynthetic and chlororespiratory genes from the plastid genome of a parasitic flowering plant. Nature 348:337-339.
17. Dixon MT, Hillis DM (1993) Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis. Molec Biol Evol 10:256-267.
18. Drábkova L, Kirschner J, Vlcek C, Pacek V (2004) TrnL-trnF intergenic spacer and trnL intron define major clades within Luzula and Juncus (Juncaceae): importance of structural mutations. J Molec Evol 59:1-10.
19. Dumolin-Lapègue S, Pemonge M-H, Petit RJ (1998) Association between chloroplast and mitochondrial lineages in oaks. Molec Biol Evol 15:1321-1331.
20. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
21. Felsenstein J (2004) Inferring phylogenies. Sinauer, Sunderland.
22. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406-416.
23. Galtier N (2001) Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol Biol Evol 18:866-873.
24. Goldman N (1993) Statistical tests of models of DNA substitution. J Molec Evol 36:182-198.
25. Golenberg EM, Clegg MT, Durbin ML, Doebley J, Ma DP (1993) Evolution of a non-coding region of the chloroplast genome. Molec Phylogenet Evol 2:52-64.
26. Graham SW, Olmstead RG (2000) Evolutionary significance of an unusual chloroplast DNA inversion found in two basal angiosperm lineages. Curr Genet 37:183-188.
27. Graham SW, Reeves PA, Burns ACE, Olmstead RG (2000) Microstructural changes in noncoding chloroplast DNA: interpretation, evolution, and utility of indels and inversions in basal angiosperm phylogenetic inference. Int J Pl Sci 161:S83-S96.
28. Hamilton MB, Braverman JM, Soria-Hernanz DF (2003) Patterns and relative rates of nucleotide and insertion/deletion evolution at six chloroplast intergenic regions in the New World species of Lecythidaceae. Molec Biol Evol 20:1710-1721.
29. Holland BR, Penny D, Hendy MD (2003) Outgroup misplacement and phylogenetic inaccuracy under a molecular clock-a simulation study. Syst Biol 52:229-238.
30. Huelsenbeck JP, Neilsen R (1999) Effect of nonindependent substitution on phylogenetic accuracy. Syst Biol 48:317-328.
31. Huelsenbeck JP, Rannala B (1997) Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276:227-232.
32. Huelsenbeck JP, Rannala B (2004) Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst Biol 53:904-913.
33. Ingvarsson PK, Ribstein S, Taylor DR (2003) Molecular evolution of insertions and deletion in the chloroplast genome of Silene. Molec Biol Evol 20:1737-1740.
34. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21-123.
35. Kelchner SA (2000) The evolution of noncoding chloroplast DNA and its application in plant systematics. Ann Missouri Bot Gard 87:482-498.
36. Kelchner SA (2002) Group II introns as phylogenetic tools: structure, function, and evolutionary constraints. Amer J Bot 89:1651-1669.
37. Kelchner SA (2003) Phylogenetic structure, biogeography, and evolution of Myoporaceae. The Australian National University, Canberra.
38. Kelchner SA, Clark LG (1997) Molecular evolution and phylogenetic utility of the chloroplast rpl16 intron in Chusquea and the Bambusoideae (Poaceae). Molec Phylogenet Evol 8:385-397.
39. Kelchner SA, Thomas MA (2007) Model use in phylogenetics: nine key questions. Trends Ecol Evol 22:87-94.
40. Kelchner SA, Wendel JF (1996) Hairpins create minute inversions in non-coding regions of chloroplast DNA. Curr Genet 30:259-262.
41. Kim K-J, Lee H-L (2005) Widespread occurrence of small inversions in the chloroplast genomes of land plants. Mol Cells 19:104-113.
42. Knoop V (2004) The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective. Curr Genet 46:123-139.
43. Koch MA, Dobes C, Kiefer C, Schmickl R, Klimes L, Lysak MA (2006) Supernetwork identifies multiple events of plastid trnF(GAA) pseudogene evolution in the Brassicaceae. Molec Biol Evol 24:63-73.
44. Kudla J, Albertazzi FJ, Blazevic D, Hermann M, Bock R (2002) Loss of the mitochondrial cox2 intron 1 in a family of monocotyledonous plants and utilization of mitochondrial intron sequences for the construction of a nuclear intron. Molec Genet Genomics 267:223-230.
45. Laroche J, Bousquet J (1999) Evolution of the mitochondrial rps3 intron in perennial and annual angiosperms and homology to nad5 intron 1. Molec Biol Evol 16:441-452.
46. Lemmon AR, Moriarty EC (2004) The importance of proper model assumption in bayesian phylogenetics. Syst Biol 53:265-277.
47. Lewis PO (1998) Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data. In: Soltis DE, Soltis PS, Doyle JJ (eds) Molecular systematics of plants II: DNA sequencing. Kluwer Academic Publishers, Boston, pp 132-163.
48. Lewis PO (2001) A likelihood approach to estimating phylogeny from discrete morphological character data. Syst Biol 50:913-925.
49. Lockhart PJ, Steel MA, Hendy MD, Penny D (1994) Recovering evolutionary trees under a more realistic model of sequence evolution. Molec Biol Evol 11:605-612.
50. Lockhart P, Novis P, Milligan BG, Riden J, Rambaut A, Larkum T (2006) Heterotachy and tree building: a case study with plastids and eubacteria. Molec Biol Evol 23:40-45.
51. Löhne C, Borsch T (2005) Molecular evolution and phylogenetic utility of the petD group II intron: a case study in basal angiosperms. Molec Biol Evol 22:317-3332.
52. Lopez P, Casane D, Philippe H (2002) Heterotachy, and important process in protein evolution. Molec Biol Evol 19:1-7.
53. Lutzoni F, Wagner P, Reeb V, Zoller S (2000) Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Syst Biol 49:628-651.
54. Meimberg H, Thalhammer S, Brachmann A, Heubl G (2006) Comparative analysis of a translocated copy of the trnK intron in carnivorous family Nepenthaceae. Molec Phylogenet Evol 39:478-490.
55. Mes THM, Kuperus P, Kirschner J, Stepanek J, Oosterveld P, Storchova H, den Nijs JCM (2000) Hairpins involving both inverted and direct repeats are associated with homoplasious indels in non-coding chloroplast DNA of Taraxacum (Lactuceae: Asteraceae). Genome 43:634-641.
56. Miyamoto MM, Fitch WM (1995) Testing species phylogenies and phylogenetic methods with congruence. Syst Biol 44:64-76.
57. Morrison DA (2006) Multiple sequence alignment for phylogenetic purposes. Austral Syst Bot 19:479-539.
58. Müller K (2006) Incorporating information from length-mutational events into phylogenetic analysis. Molec Phylogenet Evol 38:667-676.
59. Müller K, Borsch T (2005a) Phylogenetics of Utricularia (Lentibulariaceae) and molecular evolution of the trnK intron in a lineage with high substitutional rates. Pl Syst Evol 250:39-67.
60. Müller K, Borsch T (2005b) Phylogenetics of Amaranthaceae based on matK/trnK sequence data-evidence from parsimony, likelihood, and Bayesian analyses. Ann Missouri Bot Gard 92:66-102.
61. Müller K, Borsch T, Hilu KW (2006) Phylogenetic utility of rapidly evolving DNA at high taxonomical levels: contrasting matK, trnT-F, and rbcL in basal angiosperms. Molec Phylogenet Evol 41:99-117.
62. Muse SV (1995) Evolutionary analyses of DNA sequences subject to constraints on secondary structure. Genetics 139:1429-1439.
63. Naylor GJP, Brown WM (1998) Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. Syst Biol 47:61-76.
64. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, Oxford.
65. Neinhuis C, Wanke S, Hilu KW, Müller K, Borsch T (2005) Phylogeny of Aristolochiaceae based on parsimony, likelihood, and Bayesian analyses of trnL-trnF sequences. Pl Syst Evol 250:7-26.
66. Nylander JAA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL (2004) Bayesian phylogenetic analysis of combined data. Syst Biol 53:47-67.
67. Ogden TH, Rosenberg MS (2007) How should gaps be treated in parsimony? A comparison of approaches using simulation. Molec Phylogenet Evol 42:817-826.
68. Pagel M, Meade A (2004) A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Syst Biol 53:571-581.
69. Penny D, Hendy MD, Steel MA (1992) Progress with methods for constructing evolutionary trees. Trends Ecol Evol 7:73-79.
70. Penny D, McComish BJ, Charleston MA, Hendy MD (2001) Mathematical elegance with biochemical realism: the covarion model of molecular evolution. J Molec Evol 53:711-723.
71. Philippe H, Lopez P (2001) On the conservation of protein sequences in evolution. Trends Biochem Sci 26:414-416.
72. Phillips MJ, Delsuc F, Penny D (2004) Genome-scale phylogeny and the detection of systematic biases. Molec Biol Evol 21:1455-1458.
73. Pirie MD, Vargas MPB, Botermans M, Bakker FT, Chatrou LW (2007) Ancient paralogy in the cpDNA trnL-F region in Annonaceae: implications for plant molecular systematics. Amer J Bot 94:1003-1016.
74. Pol D (2004) Empirical problems of the hierarchical likelihood ratio test for model selection. Syst Biol 53:949-962.
75. Posada D, Buckley TR (2004) Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol 53:793-808.
76. Posada D, Crandall KA (1998) ModelTest: testing the model of DNA substitution. Bioinformatics 14:817-818.
77. Pupko T, Huchon D, Cao Y, Okada N, Hasegawa M (2002) Combining multiple data sets in a likelihood analysis: which models are the best? Molec Biol Evol 19:2294-2307.
78. Quandt D, Stech M (2004) Molecular evolution of the trnT(UGU)-trnF(GAA) region in bryophytes. Pl Biol 6:545-554.
79. Quandt D, Stech M (2005) Molecular evolution of the trnL-UAA intron in bryophytes. Molec Phylogenet Evol 36:429-443.
80. Quandt D, Müller K, Huttunen S (2003) Characterization of the chloroplast DNA psbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions. Pl Biol 5:400-410.
81. Quandt D, Müller K, Stech M, Frahm J-P, Frey W, Hilu KW, Borsch T (2004) Molecular evolution of the chloroplast trnL-F region in land plants. Monogr Syst Bot Missouri Bot Gard 98:13-37.
82. Rodríguez F, Oliver JL, Marín A, Medina JR (1990) The general stochastic model of nucleotide substitution. J Theor Biol 142:485-501.
83. Rodríguez-Ezpeleta N, Brinkmann H, Roure B, Lartillot N, Lang BF, Philippe H (2007) Detecting and overcoming systematic error in genome-scale phylogenies. Syst Biol 56:389-399.
84. Ronquist F, Huelsenbeck JP (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
85. Sanderson MJ (1995) Objections to bootstrapping phylogenies: a critique. Syst Biol 44:299-320.
86. Sanderson MJ, Kim J (2000) Parametric phylogenetics? Syst Biol 49:817-829.
87. Sang T, Crawford DJ, Stuessy TF (1997) Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). Amer J Bot 84:1120-1136.
88. Schöniger M, von Haeseler A (1994) A stochastic model for the evolution of autocorrelated DNA sequences. Molec Phylogenet Evol 3:240-247.
89. Shahmuradov IA, Akbarova YY, Solovyev VV, Aliyev JA (2003) Abundance of plastid DNA insertions in nuclear genomes of rice and Arabidopsis. Pl Molec Biol 52:923-934.
90. Shimodaira H (2002) An approximately unbiased test of phylogenetic tree selection. Syst Biol 51:492-508.
91. Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molec Biol Evol 16:1114-1116.
92. Simmons MP, Ochoterena H (2000) Gaps as characters in sequence-based phylogenetic analyses. Syst Biol 49:369-381.
93. Steel M, Huson D, Lockhart PJ (2000) Invariable sites models and their use in phylogeny reconstruction. Syst Biol 49:225-232.
94. Stefanovic S, Rice D, Palmer JD (2004) Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots? BMC Evol Biol 4:35-54.
95. Sullivan J, Joyce P (2005) Model selection in phylogenetics. Annual Rev Ecol Evol Syst 36:445-466.
96. Sullivan J, Swofford DL (2001) Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution patterns are violated? Syst Biol 50:723-729.
97. Sullivan J, Holsinger KE, Simon C (1995) Among-site rate variation and phylogenetic analysis of 12S rRNA in Sigmodontine rodents. Molec Biol Evol 12:988-1001.
98. Sullivan J, Arellano E, Rogers DS (2000) Comparative phylogeography of Mesoamerican highland rodents: concerted versus independent response to climatic fluctuations. Amer Naturalist 155:755-768.
99. Swofford DL (1998) PAUP*. Phylogenetic analysis using parsimony (* and other methods). Sinauer, Sunderland.
100. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM (1996) Phylogenetic inference. In: Hillis DM, Moritz C, Mable B (eds) Molecular systematics. Sinauer, Sunderland, pp 407-514.
101. Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Rogers JS (2001) Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst Biol 50:525-539.
102. Tillier ERM, Collins RA (1995) Neighbor joining and maximum likelihood with RNA sequences: addressing the interdependence of sites. Molec Biol Evol 12:7-15.
103. van Ham RCHJ, t'Hart H, Mes THM, Sandbrink JM (1994) Molecular evolution of non-coding regions of the chloroplast genome in the Crassulaceae and related species. Curr Genet 25:558-566.
104. Vijverberg K, Bachmann K (1999) Molecular evolution of a tandemly repeated trnF (GAA) gene in the chloroplast genome of Microseris (Asteraceae) and the use of structural mutations in phylogenetic analysis. Molec Biol Evol 16:1329-1340.
105. Waddell PJ (1995) Statistical methods of phylogenetic analysis, including Hadamard conjugations, LogDet transforms, and maximum likelihood. Massey University, Palmerston North, New Zealand.
106. Wakeley J (1994) Substitution-rate variation among sites and the estimation of transition bias. Molec Biol Evol 11:436-442.
107. Wakeley J (1996) The excess of transitions among nucleotide substitutions: new methods of estimating transition bias underscore its significance. Trends Ecol Evol 11:158-163.
108. Wanke S, Jaramillo MA, Borsch T, Samain M-S, Quandt D, Neinhuis C (2007) Evolution of Piperales-matK gene and trnK intron sequence data reveal lineage specific resolution contrast. Molec Phylogenet Evol 42:477-497.
109. Whelan S, Lio P, Goldman N (2001) Molecular phylogenetics: state of the art methods for looking into the past. Trends Genet 17:262-272.
110. Wilgenbusch J, de Queiroz K (2000) Phylogenetic relationships among the Phrynosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes. Syst Biol 49:592-612.
111. Wolfe AD, Randle CP (2004) Recombination, heteroplasmy, haplotype polymorphism, and paralogy in plastid genes: implications for plant molecular systematics. Syst Bot 29:1011-1020.
112. Won H, Renner SS (2003) Horizontal gene transfer from flowering plants to Gnetum. Proc Natl Acad Sci USA 100:10824-10829.
113. Won H, Renner SS (2005) The chloroplast trnT-trnF region in the seed plant lineage Gnetales. J Molec Evol 61:425-436.
114. Worberg A, Quandt D, Barniske A-M, Löhne C, Hilu KW, Borsch T (2007) Phylogeny of basal eudicots: insights from non-coding and rapidly evolving DNA. Organisms Diver Evol 7:55-77.
115. Yang Z (1995) A space-time process model for the evolution of DNA sequences. Genetics 139:993-1005.
116. Yang Z (1996) Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol Evol 11:367-372.