SeqVis: A tool for detecting compositional heterogeneity among aligned nucleotide sequences

Methods in Molecular Biology

Volumn 537, Issue , 2009, Pages 65-91

  Jermiin, Lars Sommer ^a   Ho, Joshua Wing Kei ^b   Lau, Kwok Wai ^a   Jayaswal, Vivek ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

^b UNIVERSITY OF SYDNEY   (Australia)

Author keywords

cluster analysis; Compositional heterogeneity; matched pairs tests; nucleotide sequences; SeqVis; visualization

Indexed keywords

DNA; RNA;

ARTICLE; BIOLOGY; CHEMISTRY; COMPUTER INTERFACE; COMPUTER PROGRAM; DNA SEQUENCE; GENETICS; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DNA; MOLECULAR SEQUENCE DATA; RNA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 68049128028     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-251-9_4     Document Type: Article

References (110)

1. Jukes, T. H., and Bhushan, V. (1986) Silent nucleotide substitutions and GC content of some mitochondrial and bacterial genes. J Mol Evol 24, 39-44. (Pubitemid 17013871)
2. Jermiin, L. S., Graur, D., Lowe, R. M., and Crozier, R.H. (1994) Analysisofdirectional mutation pressure and nucleotide content in mitochondrial cytochrome b genes. J Mol Evol 39, 160-73. (Pubitemid 24226416)
3. Foster, P. G., Jermiin, L. S., and Hickey, D. A. (1997) Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J Mol Evol 44, 282-88. (Pubitemid 27098366)
4. IHGSC (2001) Initial sequencing and analysis of the human genome. Nature 409, 860-921.
5. Lee, K. Y., Wahl, R., and Barbu, E. (1956) Contenu en bases puriques et pyrimidiques des acides desoxyribonucleiques des bacteries. Annales de l'Institut Pasteur 91, 212-24.
6. Belozersky, A. N., and Spirin, A. S. (1958) A correlation between the compositions of deoxyribonucleic and ribonucleic acids. Nature 182, 111-12.
7. Rolfe, R., and Meselson, M. (1959) The relative homogeneity of microbial DNA. Proc Natl Acad Sci USA 45, 1039-42.
8. Sueoka, N. (1959) A statistical analysis of deoxyribonucleic acid distribution in density gradient centrifugation. Proc Natl Acad Sci USA 45, 1480-90.
9. Sueoka, N., Marmur, J., and Doty, P. (1959) Dependence of the density of deox-yribonucleic acids on guanine-cytosine content. Nature 183, 1429-31.
10. Crozier, R. H., and Crozier, Y. C. (1993) The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization. Genetics 133, 97-117. (Pubitemid 23011400)
11. Jermiin, L. S., Graur, D., and Crozier, R. H. (1995) Evidence from analysis of inter-genic regions for strand-specific directional mutation pressure in metazoan mitochondrial DNA. Mol Biol Evol 12, 558-63.
12. Bernardi, G., Olofsson, B., Filipski, J., Zerial, M., Salinas, J., Cuny, G., Meunier-Rotival, M., and Rodier, F. (1985) The mosaic genome of warm-blooded vertebrates. Science 228, 953-58. (Pubitemid 15028384)
13. Mouchiroud, D., D'Onofrio, G., Aissani, B., Macaya, G., Gautier, C., and Bernardi, G. (1991) The distribution of genes in the human genome. Gene 100, 181-87.
14. Bernardi, G. (2004) Structural and Evolutionary Genomics: Natural Selection in Genome Evolution, Elsevier, Amsterdam.
15. Sharp, P. M., and Lloyd, A. T. (1993) Regional base composition variation along yeast chomosome III: evolution of chromosome primary structure. Nucleic Acids Res 21, 179-83. (Pubitemid 23151884)
16. Bradnam, K. R., Seoighe, C., Sharp, P. M., and Wolfe, K. H. (1999) G+C content variation along and among Saccharomyces cerevisiae chromosomes. Mol Biol Evol 16, 666-75. (Pubitemid 29215379)
17. Hori, H., and Osawa, S. (1987) Origin and evolution of organisms as deduced from 5S ribosomal RNA sequences. Mol Biol Evol 4, 445-72.
18. Weisburg, W. G., Giovannoni, S. J., and Woese, C. R. (1989) The Deinococcus -Thermus phylum and the effect of ribosomal RNA composition on phylogenetic tree construction. Syst Appl Microbiol 11, 128-34.
19. Lockhart, P. J., Howe, C. J., Bryant, D. A., Beanland, T. J., and Larkum, A. W. D. (1992) Substitutional bias confounds infer ence of cyanelle origins from sequence data. J Mol Evol 34, 153-62.
20. Lockhart, P. J., Penny, D., Hendy, M. D., Howe, C. J., Beanland, T. J., and Larkum, A. W. D. (1992) Controversy on chloroplast origins. FEBS Lett 301, 127-31.
21. Hasegawa, M., and Hashimoto, T. (1993) Ribosomal RNA trees misleading? Nature 361, 23.
22. Olsen, G. J., and Woese, C. R. (1993) Ribosomal RNA: a key to phylogeny. FASEB J 7, 113-23. (Pubitemid 23034021)
23. Sogin, M. L., Hinkle, G., and Leipe, D. D. (1993) Universal tree of life. Nature 362, 795.
24. Forterre, P., Benachenhou-Lafha, N., and Lebadan, B. (1993) Universal tree of life. Nature 362, 795.
25. Klenk, H. P., Palm, P., and Zillig, W. (1994) DNA-dependent RNA polymerases as phylogenetic marker molecules. Syst Appl Microbiol 16, 638-47. (Pubitemid 24075066)
26. Pettigrew, J. D. (1994) Genomic evolution: flying DNA. Curr Biol 4, 277-80. (Pubitemid 2054866)
27. Schultes, E., Hraber, P. T., and LaBean, T. H. (1997) Global similarities in nucleotide base composition among disparate func tional classes of single-stranded RNA imply adaptive evolutionary convergence. RNA 3, 792-806. (Pubitemid 27291122)
28. van den Bussche, R. A., Baker, R. J., Huelsenbeck, J. P., and Hillis, D. M. (1998) Base compositional bias and phylogenetic analyses: a test of the ''flying DNA'' hypothesis. Mol Phylogenet Evol 10, 408-16. (Pubitemid 128349347)
29. Foster, P. G., and Hickey, D. A. (1999) Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J Mol Evol 48, 284-90. (Pubitemid 29116073)
30. Chang, B. S. W., and Campbell, D. L. (2000) Bias in phylogenetic reconstruction of vertebrate rhodopsin sequences. Mol Biol Evol 17, 1220-31. (Pubitemid 30617148)
31. Tarŕio, R., Rodriguez-Trelles, F., and Ayala, F. J. (2001) Shared nucleotide composition biases among species and their impact on phylogenetic reconstructions of the Drosophilidae. Mol Biol Evol 18, 1464-73. (Pubitemid 32735094)
32. Ho, S. Y. W., and Jermiin, L. S. (2004) Tracing the decay of the historical signal in biological sequence data. Syst Biol 53, 623-37. (Pubitemid 39301078)
33. Goremykin, V. V., and Hellwig, F. H. (2005) Evidence for the most basal split in land plants dividing bryophyte and tracheo-phyte lineages. Plant Systemat Evol 254, 93-103. (Pubitemid 41187196)
34. Murray, S., Flø Jørgensen, M., Ho, S. Y. W., Patterson, D. J., and Jermiin, L. S. (2005) Improving the analysis of dinoflagelate phy-logeny based on rDNA. Protist 156, 269-86. (Pubitemid 41543169)
35. Jayaswal, V., Jermiin, L. S., and Robinson, J. (2005) Estimation of phylogeny using a general Markov model. Evol Bioinf Online 1, 62-80.
36. Ababneh, F., Jermiin, L. S., Ma, C., and Robinson, J. (2006) Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences. Bioinformatics 22, 1225-31. (Pubitemid 43779015)
37. Ho, J. W. K., Adams, C. E., Lew, J. B., Matthews, T. J., Ng, C. C., Shahabi-Sirjani, A., Tan, L. H., Zhao, Y., Easteal, S., Wilson, S. R., and Jermiin, L. S. (2006) SeqVis: Visualization of compositional heterogeneity in large alignments of nucleo-tides. Bioinformatics 22, 2162-63. (Pubitemid 44390910)
38. Jayaswal, V., Robinson, J., and Jermiin, L. S. (2007) Estimation of phylogeny and invariant sites under the General Markov model of nucleotide sequence evolution. Syst Biol 56, 155-62. (Pubitemid 46474673)
39. Hyman, I. T., Ho, S. Y. W., and Jermiin, L. S. (2007) Molecular phylogeny of Australian Helicarionidae, Microcystidae and related groups (Gastropoda: Pulmo-nata: Stylommatophora) based on mito-chondrial DNA. Mol Phylogenet Evol 45, 792-812. (Pubitemid 350102823)
40. Jermiin, L. S., Jayaswal, V., Ababneh, F., and Robinson, J. (2008) Bioinformatics: Data, Sequence Analysis, and Evolution (Keith, J., Ed.), Vol. I, pp. 331-64, Humana Press, Totowa, NJ.
41. Bryant, D., Galtier, N., and Poursat, M.-A. (2005) Mathematics in Evolution and Phylogeny (Gascuel, O., Ed.), pp. 33-62, Oxford University Press, Oxford.
42. Ababneh, F., Jermiin, L. S., and Robinson, J. (2006) Generation of the exact distribution and simulation of matched nucleotide sequences on a phylogenetic tree. J Math Model Algorithm 5, 291-308. (Pubitemid 43848159)
43. Kolmogoroff, A. (1936) Zur theorie der Markoffschen ketten. Math Ann 112, 155-60.
44. Lockhart, P. J., Steel, M. A., Hendy, M. D., and Penny, D. (1994) Recovering evolutionary trees under a more realistic model of sequence evolution. Mol Biol Evol 11, 605-12. (Pubitemid 24198536)
45. Conant, G. C., and Lewis, P. O. (2001) Effects of nucleotide composition bias on the success of the parsimony criterion on phylogenetic inference. Mol Biol Evol 18, 1024-33. (Pubitemid 32520475)
46. Jermiin, L. S., Ho, S. Y. W., Ababneh, F., Robinson, J., and Larkum, A. D. W. (2004) The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated. Syst Biol 53, 638-43. (Pubitemid 39290203)
47. Gowri-Shankar, V., and Rattray, M. (2006) Compositional heterogeneity across sites: effects on phylogenetic inference and modelling the correlations between base frequencies and substitution rate. Mol Biol Evol 23, 352-64.
48. Jukes, T. H., and Cantor, C. R. (1969) Mammalian Protein Metabolism (Munro, H. N., Ed.), pp. 21-132, Academic Press, New York.
49. Lanave, C., Preparata, G., Saccone, C., and Serio, G. (1984) A new method for calculating evolutionary substitution rates. J Mol Evol 20, 86-93. (Pubitemid 14116237)
50. Barry, D., and Hartigan, J. A. (1987) Statistical analysis of hominoid molecular evolution. Stat Sci 2, 191-210.
51. Reeves, J. (1992) Heterogeneity in the substitution process of amino acid sites of proteins coded for by the mitochondrial DNA. J Mol Evol 35, 17-31.
52. Steel, M. A., Lockhart, P. J., and Penny, D. (1993) Confidence in evolutionary trees from biological sequence data. Nature 364, 440-42. (Pubitemid 23263213)
53. Lake, J. A. (1994) Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proc Natl Acad Sci USA 91, 1455-59.
54. Steel, M. A. (1994) Recovering a tree from the leaf colourations it generates under a Markov model. Appl Math Lett 7, 19-23.
55. Galtier, N., and Gouy, M. (1995) Inferring phylogenies from DNA sequences of unequal base compositions. Proc Natl Acad Sci USA 92, 11317-21.
56. Steel, M. A., Lockhart, P. J., and Penny, D. (1995) A frequency-dependent significance test for parsimony. Mol Phylogenet Evol 4, 64-71.
57. Yang, Z., and Roberts, D. (1995) On the use of nucleic acid sequences to infer early branches in the tree of life. Mol Biol Evol 12, 451-58.
58. Gu, X., and Li, W.-H. (1996) Bias-corrected paralinear and logdet distances and tests of molecular clocks and phylogenies under nonstationary nucleotide frequencies. Mol Biol Evol 13, 1375-83. (Pubitemid 26408943)
59. Gu, X., and Li, W.-H. (1998) Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution. Proc Natl Acad Sci USA 95, 5899-905. (Pubitemid 28248937)
60. Galtier, N., and Gouy, M. (1998) Inferring pattern and process: maximum-likelihood implementation of a nonhomogenous model of DNA sequence evolution for phylogenetic analysis. Mol Biol Evol 15, 871-79. (Pubitemid 28321885)
61. Galtier, N., Tourasse, N., and Gouy, M. (1999) A nonhyperthermophilic common ancestor to extant life forms. Science 283, 220-21.
62. Tamura, K., and Kumar, S. (2002) Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Mol Biol Evol 19, 1727-36.
63. Foster, P. G. (2004) Modelling compositional heterogeneity. Syst Biol 53, 485-95.
64. Thollesson, M. (2004) LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences. Bioinformatics 20, 416-18. (Pubitemid 38262774)
65. Lanave, C., Tommasi, S., Preparata, G., and Saccone, C. (1986) Transition and transversion rate in the evolution of animal mitochondrial DNA. Bio Systems 19, 273-83. (Pubitemid 17207153)
66. Hashimoto, T., Nakamura, Y., Nakamura, F., Shirakura, T., Adachi, J., Goto, N., Okamoto, K.-I., and Hasegawa, M. (1994) Protein phylogeny gives a robust estimation for early divergences of eukaryoptes: phylogenetic place of a mitochondria-lacking protozoan, Giardia lamblia. Mol Biol Evol 11, 65-71. (Pubitemid 24034124)
67. Hashimoto, T., Nakamura, Y., Kamaishi, T., Nakamura, F., Adachi, J., Okamoto, K.-I., and Hasegawa, M. (1995) Phylogenetic place of mitochondrial-lacking protozoan, Giardia lamblia, inferred from amino acid sequences of elongation factor 2. Mol Biol Evol 12, 782-93.
68. von Haeseler, A., Janke, A., and Pääbo, S. (1993) Molecular phylogenetics. Verhandlung der Deutschen Zoologischen Gesellschaft 86, 119-29.
69. Preparata, G., and Saccone, C. (1987) A simple quantitative model of the molecular clock. J Mol Evol 26, 7-15.
70. Dowton, M., and Austin, A. D. (1997) The evolution of strand-specific compositional bias. A case study in the hymenopteran mitochondrial 16S rRNA gene. Mol Biol Evol14, 109-12.
71. Swofford, D. L. (2002), PAUP*: Phyloge-netic analysis using parsimony (* and other methods), Version 4 Sinauer Associates, Sunderland, Massachusetts.
72. Strimmer, K., and von Haeseler, A. (1996) Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol Biol Evol 13, 964-69. (Pubitemid 26284912)
73. Schmidt, H. A., Strimmer, K., Vingron, M., and von Haeseler, A. (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18, 502-04. (Pubitemid 34284960)
74. Bowker,A. H. (1948) A test for symmetry in contingency tables. J Am Stat Assoc 43, 572-74.
75. Stuart, A. (1955) A test for homogeneity of the marginal distributions in a two-way classification. Biometrika 42, 412-16.
76. Tavaré, S. (1986) Some probabilistic and statistical problems on the analysis of DNA sequences. Lect Math Life Sci 17, 57-86.
77. Lanave, C, and Pesole, G. (1993) Stationary MARKOV processes in the evolution of biological macromolecules. Binary 5,191-95.
78. Waddell, P. J., and Steel, M. A. (1997) General time reversible distances with unequal rates across sites: mixing T and inverse Gaussian distributions with invariant sites. Mol PhylogenetEvol 8, 398-414. (Pubitemid 127347898)
79. Waddell, P. J., Cao, Y., Hauf, J., and Hasegawa, M. (1999) Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant. SystBiol48, 31-53. (Pubitemid 129481122)
80. Zhang, Y., Chen, M., Zhou, B. B., Jermiin, L. S., and Larkum, A. W. D. (2007) Evolution of the inner light-harvesting antennae protein family of cyanobacteria, algae and plants. J Mol Evol 64, 321-31. (Pubitemid 46364876)
81. Beiko, R. G.,andCharlebois,R. L. (2007) A simulation test bed for hypotheses of genome evolution. Bioinformatics 23, 825-31. (Pubitemid 47049916)
82. Rodŕiguez-Ezpeleta, N., Brinkmann, H., Roure, B., Lartillot, N., Lang, B. F., and Philippe, H. (2007) Overcoming systematic errors in genome-scale phylogenies. Syst Biol 56, 389-99. (Pubitemid 46826902)
83. Rzhetsky, A., and Nei, M. (1995) Tests of applicability of several substitution models for DNA sequence data. Mol Biol Evol 12, 131-51.
84. Kumar, S., and Gadagkar, S. R. (2001) Disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences. Genetics 158, 1321-27. (Pubitemid 32667114)
85. Kumar, S., and Gadagkar, S. R. (2001) Corrigendum-disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences. Genetics 159, 913-14. (Pubitemid 33035130)
86. Phillips, M. J., and Penny, D. (2003) The root of the mammalian tree inferred from whole mitochondrial genomes. Mol Phylogenet Evol 28, 171-85. (Pubitemid 37446823)
87. Susko, E., and Roger, A. J. (2007) On reduced amino acid alphabets for phylo-genetic inference. Mol Biol Evol 24, 2139-50.
88. Marquez, R., Smit, S., and Knight, R. (2005) Do universal codon-usage patterns minimize the effects of mutation and translation error? Genome Biol 6, R91.
89. Smit, S., Yarus, M., and Knight, R. (2006) Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categories. RNA 12, 1-14. (Pubitemid 43037448)
90. Bourlat, S. J., Juliusdottir, T., Lowe, C. J., Freeman, R., Aronowicz, J., Kirschner, M., Lander, E. S., Thorndyke, M., Nakano, H., Kohn, A. B., Heyland, A., Moroz, L. L., Copley, R. R., and Telford, M. J. (2006) Deuterostome phylogeny reveals monophy-letic chordates and the new phylum Xeno-turbellida. Nature 444, 85-88. (Pubitemid 44684760)
91. Woese, C. R., Achenbach, L., Rouviere, P., and Mandelco, L. (1991) Archaeal phylo-geny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts. Syst Appl Microbiol 14, 364-71.
92. Millen, R. S., Olmstead, R. G., Adams, K. L., Palmer, J. D., Lao, N. T., Heggie, L., Kavanagh, T. A., Hibberd, J. M., Gray, J. C., Morden, C. W., Calie, P. J., Jermiin, L. S., and Wolfe, K. H. (2001) Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell 13, 645-58. (Pubitemid 32265381)
93. Phillips, M. J., Lin, Y. H., Harrison, G. L., and Penny, D. (2001) Mitochondrial genomes of a bandicoot and a brushtail possum confirm the monophyly of australidelphian marsupials. Proc R Soc Lond B Biol Sci 268, 1533-38. (Pubitemid 32675442)
94. Phillips, M., Delsuc, F., and Penny, D. (2004) Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol 21, 1455-58. (Pubitemid 38823748)
95. Gibson, A., Gowri-Shankar, V., Higgs, P.G., and Rattray, M. (2005) A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylo-genetic methods. Mol Biol Evol 22, 251-64. (Pubitemid 40130193)
96. Cannings, C., and Edwards, A. W. F. (1968) Natural selection and the de Finetti diagram. Ann Hum Genet 31, 421-28.
97. Adkins, R. M., and Honeycutt, R. L. (1994) Evolution of the primate cytochrome c oxi-dase subunit II gene. JMol Evol 38, 215-31. (Pubitemid 24076861)
98. Amano, K., Nakamura, H., and Ichikawa, H. (2003) Self-organizing clustering: a novel non-hierarchical method for clustering large amount of DNA sequences. Genome Informatics 14, 575-76.
99. Halanych, K. M., Bacheller, J. D., Aguinaldo, A. M. A., Liva, S. M., Hillis, D. M., and Lake, J. A. (1995) Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. Science 267, 1641-43.
100. Aguinaldo, A. M. A., Turbeville, J. M., Linford, L. S., Rivera, M. C., Garey, J. R., Raff, R. A., and Lake, J. A. (1997) Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 387, 489-93. (Pubitemid 27235464)
101. Giribet, G. (2002) Current advances in the phylogenetic reconstruction of metazoan evolution. A new paradigm for the Cambrian explosion? Mol Phylogenet Evol 24, 345-57.
102. Halanych, K. M. (2004) The new view of animal phylogeny. Annu Rev Ecol Evol Systemat 35, 229-56. (Pubitemid 40059720)
103. Philippe, H., Snell, E. A., Bapteste, E., Lopez, P., Holland, P. W. H., and Casane, D. (2004) Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol Biol Evol 21, 1740-52. (Pubitemid 39096890)
104. Philip, G. K., Creevey, C. J., and McInerney, J. O. (2005) The Opisthokonta and the Ecdysozoa may not be clades: Stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Exdysozoa. Mol Biol Evol 22, 1175-84. (Pubitemid 40577755)
105. Rokas, A., Krüger, D., and Carroll, S. B. (2005) Animal evolution and the molecular signature of radiations compressed in time. Science 310, 1933-38. (Pubitemid 43005982)
106. Philippe, H., Lartillot, N., and Brinkmann, H. (2005) Multigene analysis of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa and Protosto-mia. Mol Biol Evol 22, 1246-53. (Pubitemid 40577762)
107. Delsuc, F., Brinkmann, H., Chourrout, D., and Philippe, H. (2006) Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439, 965-68. (Pubitemid 43292413)
108. Philippe, H., Brinkmann, H., Martinez, P., Riutort, M., and Baguñà, J. (2007) Acoel flatworms are not platyhelminthes: evidence from phylogenomics. PLoS One 2, e717.
109. Baurain, D., Brinkmann, H., and Philippe, H. (2007) Lack of resolution in the animal phylogeny: closely spaced cladogenesis or undetected systematic errors? Mol Biol Evol 24, 6-9. (Pubitemid 46026274)
110. Dunn, C. W., Hejnol, A., Matus, D. Q., Pang, K., Browne, W. E., Smith, S. A., Seaver, E., Rouse, G. W., Obst, M., Edgecombe, G. D., Sørensen, M. V., Haddock, S. H. D., Schmidt-Rhaesa, A., Okusu, A., Kristensen, R. M., Wheeler, W. C., Martindale, M. Q., and Giribet, G. (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452, 745-50.