Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics

BMC Bioinformatics

Volumn 15, Issue SUPPL.2, 2014, Pages

  Vera Ruiz, Victor A ^a   Lau, Kwok W ^a,b   Robinson, John ^a   Jermiin, Lars S ^a,b  

^a UNIVERSITY OF SYDNEY   (Australia)

^b CSIRO   (Australia)

Author keywords

homogeneity,reversibility; lumping; Markov model; nucleotides; Phylogeny; primates; recoding; stationarity

Indexed keywords

HOMOGENEITY,REVERSIBILITY; LUMPING; MARKOV MODEL; PHYLOGENY; PRIMATES; RECODING; STATIONARITY;

BIOLOGY; ESTIMATION; MAMMALS; NUCLEOTIDES; STATISTICAL TESTS; STATISTICS;

MARKOV PROCESSES;

MITOCHONDRIAL DNA; NUCLEOTIDE;

ANIMAL; ARTICLE; CHEMISTRY; DNA SEQUENCE; METHODOLOGY; PHYLOGENY; PRIMATE; PROBABILITY; SEQUENCE HOMOLOGY; STATISTICAL MODEL;

ANIMALS; DNA, MITOCHONDRIAL; LIKELIHOOD FUNCTIONS; MARKOV CHAINS; NUCLEOTIDES; PHYLOGENY; PRIMATES; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 84893564694     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-S2-S8     Document Type: Article

References (53)

1. Irwin DM, Kocher TD, Wilson AC. Evolution of the cytochrome b gene in mammals. Journal of Molecular Evolution 1991, 32:128-144. 10.1007/BF02515385, 1901092.
2. Adkins RM, Honeycutt RL. Molecular phylogeny of the superorder Arconta. Proceedings of the National Academy of Science of the United States of America 1991, 88:10317-10321.
3. Adkins RM, Honeycutt RL. Evolution of the primate cytochrome c oxidase subunit II gene. Journal of Molecular Evolution 1994, 38:215-231.
4. Woese CR, Achenbach L, Rouviere P, Mandelco L. Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts. Systematic and Applied Microbiology 1991, 14:364-371. 10.1016/S0723-2020(11)80311-5, 11540072.
5. Phillips MJ, Penny D. The root of the mammalian tree inferred from whole mithocondrial genomes. Molecular Phylogenetics and Evolution 2003, 28:171-185. 10.1016/S1055-7903(03)00057-5, 12878457.
6. Cavender JA, Felsenstein J. Invariants of phylogenies in a simple case with discrete states. Journal of Classification 1987, 4:57-71.
7. Gibson A, Gowri-Shankar V, Higgs PG, Rattray M. A comprehensive analysis of mammalian mithochondrial genome base composition and improved phylogenetic methods. Molecular Biology and Evolution 2005, 22:251-264.
8. Millen RS, Olmstead RG, Adams KL, Palmer JD, Lao NT, Heggie L, Kavanagh TA, Hibberd JM, Gray JC, Morden CW, Calie PJ, Jermiin LS, Wolfe KH. Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. The Plant Cell 2001, 13:645-658. 135507, 11251102.
9. Phillips MJ, Lin YH, Harrison GL, Penny D. Mitochondrial genomes of a bandicoot and a brushtail possum confirm the monophyly of australidelphian marsupials. Proceedings of the Royal Society London Series B 2001, 268:1533-1538.
10. Kosiol C, Goldman N, Buttimore NH. A new criterion and method for amino acid classification. Journal of Theoretical Biology 2004, 228:97-106. 10.1016/j.jtbi.2003.12.010, 15064085.
11. Kosiol C. Markov models for protein sequence evolution. PhD thesis 2006, University of Cambridge.
12. Phillips MJ, Delsuc F, Penny D. Genome-scale phylogeny and the detection of systematic biases. Molecular Biology and Evolution 2004, 21:1455-1458. 10.1093/molbev/msh137, 15084674.
13. Ho JWK, Adams CE, Lew JB, Matthews TJ, Ng CC, Shahabi-Sirjani A, Tan LH, Zhao Y, Easteal S, Wilson SR, Jermiin LS. SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides. Bioinformatics 2006, 221:2162-2163.
14. Susko E, Roger AJ. On reduced amino acid alphabets for phylogenetic inference. Molecular Biology and Evolution 2007, 24:2139-2150. 10.1093/molbev/msm144, 17652333.
15. Anisimova M, Kosiol C. Investigating protein-coding sequence evolution with probabilistic codon substitution models. Molecular Biology and Evolution 2004, 26:255-271.
16. Masta SE, Longhorn SJ, Boore JL. Arachnid relationships based on mitochondrial genomes: asymmetric nucleotide and amino acid bias affects phylogenetic analyses. Molecular Phylogenetics and Evolution 2009, 50:117-128. 10.1016/j.ympev.2008.10.010, 18992830.
17. Phillips MJ, Gibb GC, Crimp EA, Penny D. Tinamous and moa flock together: mitochondrial genome sequence analysis reveals independent losses of flight among ratites. Systematic Biology 2010, 59:90-107. 10.1093/sysbio/syp079, 20525622.
18. Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, Wetzer R, Martin JW, Cunningham CW. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 2010, 463:1079-1083. 10.1038/nature08742, 20147900.
19. Criscuolo A, Gribaldo S. Large-scale phylogenomic analyses indicate a deep origin of primary plastids within Cyanobacteria. Molecular Biology and Evolution 2011, 28:3019-3032. 10.1093/molbev/msr108, 21652613.
20. Regier JC, Zwick A. Sources of signal in 62 protein-coding nuclear genes for higher-level phylogenetics of arthropods. PLoS ONE 2011, 6:e23408. 10.1371/journal.pone.0023408, 3150433, 21829732.
21. Cho S, Zwick A, Regier JC, Mitter C, Cummings MP, Yao J, Du Z, Zhao H, Kawahara AY, Weller S, Davis DR, Baixeras J, Brown JW, Parr C. Can deliberately incomplete gene sample augmentation improve a phylogeny estimate for the advanced moths and butterflies (Hexapoda: Lepidoptera)?. Systematic Biology 2011, 60:782-796. 10.1093/sysbio/syr079, 3193767, 21840842.
22. White NE, Phillips MJ, Gilbert MTP, Alfaro-Nunez A, Willerslev E, Mawson PR, Spencer PBS, Bunce M. The evolutionary history of cockatoos (Aves: Psittaciformes: Cacatuidae). Molecular Phylogenetics and Evolution 2011, 59:615-622. 10.1016/j.ympev.2011.03.011, 21419232.
23. Zwick A, Regier JC, Cummings MP, Mitter C. Increased gene sampling yields robust support for higher-level clades within Bombycoidea (Lepidoptera). Systematic Entomology 2011, 36:31-43.
24. Niehuis O, Hartig G, Grath S, Pohl H, Lehmann J, Tafer H, Donath A, Krauss V, Eisenhardt C, Hertel J, Petersen M, Mayer C, Meusemann K, Peters RS, Stadler PF, Beutel RG, Bornberg-Bauer E, McKenna DD, Misof B. Genomic and morphological evidence converge to resolve the enigma of Strepsiptera. Current Biology 2012, 22:1309-1313. 10.1016/j.cub.2012.05.018, 22704986.
25. Regier JC, Brown JW, Mitter C, Baixeras J, Cho S, Cummings MP, Zwick A. A molecular phylogeny for the leaf-roller moths (Lepidoptera: Tortricidae) and its implications for classification and life history evolution. PLoS ONE 2012, 7:e35574. 10.1371/journal.pone.0035574, 3334928, 22536410.
26. Regier JC, Mitter C, Solis MA, Hayden JE, Landry B, Nuss M, Simonsen TJ, Yen S-H, Zwick A, Cummings MP. A molecular phylogeny for the pyraloid moths (Lepidoptera: Pyraloidea) and its implications for higher-level classification. Systematic Entomology 2012, 37:635-656.
27. Zwick A, Regier JC, Zwickl DJ. Resolving discrepancy between nucleotides and amino acids in deeplevel arthropod phylogenomics: differentiating serine codons in 21-amino-acid models. PLoS ONE 2012, textbf7:e47450.
28. Gibb GC, Kennedy M, Penny D. Beyond phylogenetics and evolution: pelecaniform and Ciconiiform birds, and long-term niche stability. Molecular Phylogenetics and Evolution 2013, 68:229-238. 10.1016/j.ympev.2013.03.021, 23562800.
29. Regier JC, Mitter C, Zwick A, Bazinet AL, Cummings MP, Kawahara AY, Sohn J-C, Zwickl DJ, Cho S, Davis DR, Baixeras J, Brown J, Parr C, Weller S, Lees DC, Mitter KT. A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (Moths and Butterflies). PLoS ONE 2013, 8:e58568. 10.1371/journal.pone.0058568, 3595289, 23554903.
30. Rota-Stabelli O, Lartillot N, Philippe H, Pisani D. Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study. Systematic Biology 2013, 62:121-133. 10.1093/sysbio/sys077, 22962005.
31. Sohn J-C, Regier JC, Mitter C, Davis D, Landry J-F, Zwick A, Cummings MP. A molecular phylogeny for Yponomeutoidea (Insecta, Lepidoptera, Ditrysia) and its implications for classification, biogeography and the evolution of host plant use. PLoS ONE 2013, textbf8:e55066.
32. Lau KW. Studies of methods used to infer molecular phylogeny: Dealing with the effect of compositional heterogeneity. PhD thesis 2009, University of Sydney, School of Biological Sciences;.
33. Guédon Y, d'Aubenton-Carafa Y, Thermes C. Analysing grouping of nucleotides in DNA sequences using lumped processes constructed from Markov chains. Journal of Mathematical Biology 2006, 52:343-372. 10.1007/s00285-005-0358-y, 16463190.
34. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM. Phylogenetic inference. Molecular Systematics 1996, 407-514. Sunderland: Sinauer Associates, Hillis DM, Moritz C, Mable BK.
35. Nomenclature Committee of the International Union of Biochemistry, (NC-IUB) Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences: Recommendations 1984. Proceedings of the National Academy of Sciences of the United States of America 1986, 83:4-8. 322779, 2417239, Nomenclature Committee of the International Union of Biochemistry, (NC-IUB).
36. Bryant D, Galtier N, Poursat MA. Likelihood calculation in molecular phylogenetics. Mathematics evolution and phylogeny 2005, 33-92. New York: Oxford University Press, Gascuel O.
37. Jayaswal V, Jermiin LS, Robinson J. Estimation of phylogeny using a general Markov model. Evolutionary Bioinformatics 2005, 1:62-80.
38. Ababneh F, Jermiin LS, Ma C, Robinson J. Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences. Bioinformatics 2006, 22:1225-1231. 10.1093/bioinformatics/btl064, 16492684.
39. Jermiin LS, Jayaswal V, Ababneh F, Robinson J. Phylogenetic model evaluation. Bioinformatics: Data, sequence analysis, and evolution - Volume 1 2008, 331-363. Humana Press. Totawa, Keith J.
40. Ababneh F, Jermiin LS, Robinson J. Generation of the exact distribution and simulation of matched nucleotide sequences on a phylogenetic tree. Journal of Mathematical Modelling and Algorithms 2006, 5:291-303.
41. Iosifescu M. Finite Markov processes and their applications 1980, Chichester: John Wiley and Sons, Ltd.
42. Kemeny JG, Snell JL. Finite Markov chains 1983, New York: Springer-Verlag.
43. Jukes TH, Cantor CR. Evolution of protein molecules. Mammalian Protein Metabolism 1969, 21-132. Academic Press. New York, Munro HN.
44. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 1981, 17:368-376. 10.1007/BF01734359, 7288891.
45. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 1980, 16:111-120. 10.1007/BF01731581, 7463489.
46. Kishino H, Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 1985, 22:160-174. 10.1007/BF02101694, 3934395.
47. Jernigan RW, Baran RH. Testing lumpability in Markov chains. Statistics and Probability Letters 2003, 64:17-23.
48. Schweder T, Spjotvoll E. Plots of P-values to evaluate many tests simultaneously. Biometrika 1982, 69:493-502.
49. Lanave C, Preparata G, Saccone C, Serio G. A new method for calculating evolutionary substitution rates. Journal of Molecular Evolution 1984, 20:86-93. 10.1007/BF02101990, 6429346.
50. Tosi AJ, Detwiler KM, Disotell TR. X-chromosomal window into the evolutionary history of the guenons (Primates: Cercopithecini). Molecular Phylogenetics and Evolution 2005, 36:58-66. 10.1016/j.ympev.2005.01.009, 15904856.
51. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. Genbank. Nucleic Acids Research 2013, 41:D36-D42. 10.1093/nar/gks1195, 3531190, 23193287.
52. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution 2013, 30:772-780. 10.1093/molbev/mst010, 3603318, 23329690.
53. Gouy M, Guindon S, Gascuel O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 2010, 27:221-224. 10.1093/molbev/msp259, 19854763.