Near intron pairs and the metazoan tree

Molecular Phylogenetics and Evolution

Volumn 66, Issue 3, 2013, Pages 811-823

  Lehmann, Jörg ^a   Stadler, Peter F ^a,b,c,d,e,f   Krauss, Veiko ^a  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b MAX PLANCK INSTITUTE FOR MATHEMATICS IN THE SCIENCES   (Germany)

^c FRAUNHOFER INSTITUTE FOR CELL THERAPY AND IMMUNOLOGY   (Germany)

^d UNIVERSITY OF VIENNA   (Austria)

^e UNIVERSITY OF COPENHAGEN   (Denmark)

^f SANTA FE INSTITUTE   (United States)

Author keywords

Ecdysozoa; Intron evolution; Maximum parsimony; Metazoan phylogeny; Molecular phylogenetics; Rare genomic changes

Indexed keywords

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CHORDATA; CLASSIFICATION; DNA SEQUENCE; GENETICS; INTRON; INVERTEBRATE; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CHORDATA; EVOLUTION, MOLECULAR; INTRONS; INVERTEBRATES; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

ACARI; ANIMALIA; ARTHROPODA; BILATERIA; CHORDATA; CNIDARIA; CTENOPHORA (COELENTERATES); DEUTEROSTOMIA; ECDYSOZOA; EUMETAZOA; METAZOA; MNEMIOPSIS; NEMATODA; PLACOZOA; PLATYHELMINTHES; PORIFERA; PROTOSTOMIA; SPIRALIA; TROCHOZOA; VERTEBRATA;

EID: 84873140185     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.11.012     Document Type: Article

References (69)

1. Aguinaldo A.M., Turbeville J.M., Linford L.S., Rivera M.C., Garey J.R., Raff R.A., Lake J.A. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 1997, 387:489-493.
2. Belinky F., Cohen O., Huchon D. Large-scale parsimony analysis of metazoan indels in protein-coding genes. Mol. Biol. Evol. 2010, 27(2):441-451.
3. Bininda-Emonds O.R. transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences. BMC Bioinformatics 2005, 6:156.
4. Bourlat S.J., Nielsen C., Economou A.D., Telford M.J. Testing the new animal phylogeny: a phylum level molecular analysis of the animal kingdom. Mol. Phylogenet. Evol. 2008, 49:23-31.
5. Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., Madden T.L. BLAST+: architecture and applications. BMC Bioinformatics 2009, 10:421.
6. Carmel L., Wolf Y.I., Rogozin I.B., Koonin E.V. Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res. 2007, 17:1034-1044.
7. Cho S., Jin S.W., Cohen A., Ellis R.E. A phylogeny of Caenorhabditis reveals frequent loss of introns during nematode evolution. Genome Res. 2004, 14(7):1207-1220.
8. Churakov G., Sadasivuni M.K., Rosenbloom K.R., Huchon D., Brosius J., Schmitz J. Rodent evolution: back to the root. Mol. Biol. Evol. 2010, 27:1315-1326.
9. Coghlan A., Wolfe K.H. Origins of recently gained introns in Caenorhabditis. Proc. Natl. Acad. Sci. USA 2004, 101(31):11362-11367.
10. Conant G.C., Stadler P.F. Solvent exposure imparts similar selective pressures across a range of yeast proteins. Mol. Biol. Evol. 2009, 26:1155-1161.
11. Csurös M., Holey J.A., Rogozin I.B. In search of lost introns. Bioinformatics 2007, 23(13):i87-i96.
12. Delsuc F., Brinkmann H., Chourrout D., Philippe H. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 2006, 439:965-968.
13. 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., Schmidt-Rhaesa A., Okusu A., Kristensen R.M., Wheeler W.C., Martindale M.Q., Giribet G. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 2008, 452(7188):745-749.
14. Ebersberger I., Strauss S., von Haeseler A. HaMStR: profile hidden markov model based search for orthologs in ESTs. BMC Evol. Biol. 2009, 9:157.
15. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32(5):1792-1797.
16. Edgecombe G., Giribet G., Dunn C., Hejnol A., Kristensen R., Neves R., Rouse G., Worsaae K., Srensen M. Higher-level metazoan relationships: recent progress and remaining questions. Organ. Divers. Evol. 2011, 11:151-172.
17. Farris J.S. The retention index and the rescaled consistency index. Cladistics 1989, 5:417-419.
18. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 1978, 27:401-410.
19. Flicek P., Amode M.R., Barrell D., Beal K., Brent S., Chen Y., Clapham P., Coates G., Fairley S., Fitzgerald S., Gordon L., Hendrix M., Hourlier T., Johnson N., Kähäri A., Keefe D., Keenan S., Kinsella R., Kokocinski F., Kulesha E., Larsson P., Longden I., McLaren W., Overduin B., Pritchard B., Riat H.S., Rios D., Ritchie G.R., Ruffier M., Schuster M., Sobral D., Spudich G., Tang Y.A., Trevanion S., Vandrovcova J., Vilella A.J., White S., Wilder S.P., Zadissa A., Zamora J., Aken B.L., Birney E., Cunningham F., Dunham I., Durbin R., Fernández-Suarez X.M., Herrero J., Hubbard T.J., Parker A., Proctor G., Vogel J., Searle S.M. Ensembl 2011. Nucleic Acids Res. 2011, 39(Database issue):D800-D806.
20. Halanych K.M., Bacheller J.D., Aguinaldo A.M., Liva S.M., Hillis D.M., Lake J.A. Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. Science 1995, 267:1641-1643.
21. Hejnol A. A twist in time-the evolution of spiral cleavage in the light of animal phylogeny. Integr. Comp. Biol. 2010, 50(5):695-706.
22. Hejnol A., Obst M., Stamatakis A., Ott M., Rouse G.W., Edgecombe G.D., Martinez P., Baguna J., Bailly X., Jondelius U., Wiens M., Müller W.E., Seaver E., Wheeler W.C., Martindale M.Q., Giribet G., Dunn C.W. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc. Biol. Sci. 2009, 276(1677):4261-4270.
23. Irimia M., Roy S.W. Spliceosomal introns as tools for genomic and evolutionary analysis. Nucleic Acids Res. 2008, 36(5):1703-1712.
24. Jow H., Hudelot C., Rattray M., Higgs P.G. Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution. Mol. Biol. Evol. 2002, 19:1591-1601.
25. Krauss V., Pecyna M., Kurz K., Sass H. Phylogenetic mapping of intron positions: a case study of translation initiation factor eIF2gamma. Mol. Biol. Evol. 2005, 22:74-84.
26. Krauss V., Thümmler C., Georgi F., Lehmann J., Stadler P.F., Eisenhardt C. Near intron positions are reliable phylogenetic markers: an application to holometabolous insects. Mol. Biol. Evol. 2008, 25(5):821-830.
27. Kriegs J.O., Churakov G., Kiefmann M., Jordan U., Brosius J., Schmitz J. Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biol. 2006, 4(4):e91.
28. Kriegs J.O., Zemann A., Churakov G., Matzke A., Ohme M., Zischler H., Brosius J., Kryger U., Schmitz J. Retroposon insertions provide insights into deep lagomorph evolution. Mol. Biol. Evol. 2010, 27(12):2678-2681.
29. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., Higgins D.G. Clustal W and clustal X version 2.0. Bioinformatics 2007, 23(21):2947-2948.
30. Lartillot N., Lepage T., Blanquart S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 2009, 25:2286-2288.
31. Lartillot N., Philippe H. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Philos. Trans. R Soc. Lond. B Biol. Sci. 2008, 363(1496):1463-1472.
32. Lehmann J., Eisenhardt C., Stadler P.F., Krauss V. Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication. BMC Evol. Biol. 2010, 10(1):156.
33. Long M., Deutsch M. Association of intron phases with conservation at splice site sequences and evolution of spliceosomal introns. Mol. Biol. Evol. 1999, 16(11):1528-1534.
34. Mallatt J., Craig C.W., Yoder M.J. Nearly complete rRNA genes assembled from across the metazoan animals: effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction. Mol. Phylogenet. Evol. 2010, 55(1):1-17.
35. Meusemann K., von Reumont B.M., Simon S., Roeding F., Strauss S., Kück P., Ebersberger I., Walzl M., Pass G., Breuers S., Achter V., von Haeseler A., Burmester T., Hadrys H., Wägele J.W., Misof B. A phylogenomic approach to resolve the arthropod tree of life. Mol. Biol. Evol. 2010, 27(1):2451-2464.
36. Mortazavi A., Schwarz E.M., Williams B., Schaeffer L., Antoshechkin I., Wold B.J., Sternberg P.W. Scaffolding a Caenorhabditis nematode genome with RNA-seq. Genome Res. 2010, 20:1740-1747.
37. Nesnidal M.P., Helmkampf M., Bruchhaus I., Hausdorf B. Compositional heterogeneity and phylogenomic inference of metazoan relationships. Mol. Biol. Evol. 2010, 27:2095-2104.
38. Nguyen H.D., Yoshihama M., Kenmochi N. Phase distribution of spliceosomal introns: implications for intron origin. BMC Evol. Biol. 2006, 6:69.
39. 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 R.S., Stadler P.F., Beutel R.G., Bornberg-Bauer E., McKenna D.D., Misof B. Genomic and morphological evidence converge to resolve the enigma of strepsiptera. Curr. Biol. 2012, 22(14):1309-1313.
40. Penny D., McComish B.J., Charleston M.A., Hendy M.D. Mathematical elegance with biochemical realism: the covarion model of molecular evolution. J. Mol. Evol. 2001, 53:711-723.
41. Philippe H., Brinkmann H., Lavrov D.V., Littlewood D.T., Manuel M., Wörheide G., Baurain D. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol. 2011, 9:e1000602.
42. Philippe H., Snell E.A., Bapteste E., Lopez P., Holland P.W., Casane D. Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol. Biol. Evol. 2004, 21(9):1740-1752.
43. Philippe H., Zhou Y., Brinkmann H., Rodrigue N., Delsuc F. Heterotachy and long-branch attraction in phylogenetics. BMC Evol. Biol. 2005, 5:50.
44. Pick K.S., Philippe H., Schreiber F., Erpenbeck D., Jackson D.J., Wrede P., Wiens M., Alié A., Morgenstern B., Manuel M., Wörheide G. Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol. Biol. Evol. 2010, 27:1983-1987.
45. Prager E.M., Wilson A.C. Ancient origin of lactalbumin from lysozyme: analysis of DNA and amino acid sequences. J. Mol. Evol. 1988, 27(4):326-335.
46. Qiu W.G., Schisler N., Stoltzfus A. The evolutionary gain of spliceosomal introns: sequence and phase preferences. Mol. Biol. Evol. 2004, 21(7):1252-1263.
47. Rogozin I.B., Lyons-Weiler J., Koonin E.V. Intron sliding in conserved gene families. Trends. Genet. 2000, 16(10):430-432.
48. Rogozin I.B., Sverdlov A.V., Babenko V.N., Koonin E.V. Analysis of evolution of exon-intron structure of eukaryotic genes. Brief Bioinform. 2005, 6:118-134.
49. Roy S.W., Gilbert W. Resolution of a deep animal divergence by the pattern of intron conservation. Proc. Natl. Acad. Sci. USA 2005, 102(12):4403-4408.
50. Roy S.W., Irimia M. Rare genomic characters do not support Coelomata: intron loss/gain. Mol. Biol. Evol. 2008, 25(4):620-623.
51. Saeys Y., Rouzé P., Van de Peer Y. In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists. Bioinformatics 2007, 23(4):414-420.
52. Sankoff D. Minimal mutation trees of sequences. SIAM J. Appl. Math. 1974, 28(1):35-42.
53. Sankoff D., Rousseau P. Locating the vertices of a steiner tree in an arbitrary metric space. Math Programming 1975, 9(1):240-246.
54. Savard J., Tautz D., Richards S., Weinstock G.M., Gibbs R.A., Werren J.H., Tettelin H., Lercher M.J. Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of holometabolous insects. Genome Res. 2006, 16:1334-1338.
55. Savill N.J., Hoyle D.C., Higgs P.G. RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods. Genetics 2001, 157:399-411.
56. Schierwater B., Eitel M., Jakob W., Osigus H.J., Hadrys H., Dellaporta S.L., Kolokotronis S.O., Desalle R. Concatenated analysis sheds light on early metazoan evolution and fuels a modern urmetazoon hypothesis. PLoS Biol. 2009, 7(1):e20.
57. Slater G.S., Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 2005, 6:31.
58. Srivastava M., Simakov O., Chapman J., Fahey B., Gauthier M.E., Mitros T., Richards G.S., Conaco C., Dacre M., Hellsten U., Larroux C., Putnam N.H., Stanke M., Adamska M., Darling A., Degnan S.M., Oakley T.H., Plachetzki D.C., Zhai Y., Adamski M., Calcino A., Cummins S.F., Goodstein D.M., Harris C., Jackson D.J., Leys S.P., Shu S., Woodcroft B.J., Vervoort M., Kosik K.S., Manning G., Degnan B.M., Rokhsar D.S. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 2010, 466(7307):720-726.
59. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22(21):2688-2690.
60. Swofford, D.L., 2003. PAUP* Portable.
61. Talavera G., Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 2007, 56(4):564-577.
62. Templeton A.R. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 1983, 37(2):221.
63. Trautwein M.D., Wiegmann B.M., Beutel R., Kjer K.M., Yeates D.K. Advances in insect phylogeny at the dawn of the postgenomic era. Annu. Rev. Entomol. 2012, 57:449-468.
64. Weir M., Eaton M., Rice M. Challenging the spliceosome machine. Genome Biol. 2006, 7(1):R3.
65. Wiegmann B.M., Trautwein M.D., Kim J.W., Cassel B.K., Bertone M.A., Winterton S.L., Yeates D.K. Single-copy nuclear genes resolve the phylogeny of the holometabolous insects. BMC Biol. 2009, 7:34.
66. Wilkerson M.D., Ru Y., Brendel V.P. Common introns within orthologous genes: software and application to plants. Brief Bioinform. 2009, 10(6):631-644.
67. Wolf Y.I., Rogozin I.B., Koonin E.V. Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res. 2004, 14:29-36.
68. Zdobnov E.M., Bork P. Quantification of insect genome divergence. Trends. Genet. 2007, 23:16-20.
69. Zheng J., Rogozin I.B., Koonin E.V., Przytycka T.M. Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation. Mol. Biol. Evol. 2007, 24(11):2583-2592.