Gaps: An Elusive Source of Phylogenetic Information

Systematic Biology

Volumn 61, Issue 6, 2012, Pages 1075-1082

  Saurabh, Kumar ^a,b   Holland, Barbara R ^a,c   Gibb, Gillian C ^a   Penny, David ^a  

^a MASSEY UNIVERSITY   (New Zealand)

^b INDIAN INSTITUTE OF TECHNOLOGY GUWAHATI   (India)

^c UNIVERSITY OF TASMANIA   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; BIRD; CLASSIFICATION; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; NOTE; PHYLOGENY; SEQUENCE ALIGNMENT;

ANIMALS; BIRDS; EVOLUTION, MOLECULAR; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 84868035220     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/sys043     Document Type: Note

References (50)

1. Anisimova M., Cannarozzi G.M., Liberles D.A. 2010. Finding the bal-ance between mathematical and biological optima in multiple se-quence alignment. Trends Evol. Biol. 2:e7.
2. Baker A.J., Pereira S.L., Paton T.A. 2007. Phylogenetic relationships and divergence times of Charadriformes genera: multigene evi-dence for the Cretaceous origin of at least 14 clades of shorebirds. Biol. Lett. 3:205-209.
3. Bonilla A.J., Braun E.L., Kimball R.T. 2010. Comparative molecular evolution and phylogenetic utility of 30-UTRs and introns in Galli-formes. Mol. Phylogenet. Evol. 56:536-542.
4. Carroll H., Ridge P, Clement M., Snell Q. 2006. Effects of gap open and gap extension penalties. Biotechnology and Bioinformatics Sympo-sium (BIOT). Provo (UT): Brigham Young University p. 19.
5. Edgar R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl. Acids Res. 32:1792-1797.
6. Fain M.G., Houde P. 2004. Parallel radiations in the primary clades of birds. Evolution. 58:2558-2573.
7. Gillespie JJ., Yoder MJ., Wharton R.A. 2005. Predicted secondary structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): impact on sequence alignment and phylogeny estimation. J. Mol. Evol. 61:114-137.
8. Golenberg E.M., Clegg M.T., Durbin M.L., Doebley J., Ma D. P. 1993. Evolution of a noncoding region of the chloroplast genome. Mol. Phylogenet. Evol. 2:52-64.
9. Golubchik T., Wise M.J., Easteal S., Jermiin L.S. 2007. Mind the gaps: evidence of bias in estimates of multiple sequence alignments. Mol. Biol. Evol. 24:2433-2442.
10. Hackett S.J., Kimball R.T., Reddy S., Bowie R.C.K., Braun E.L., Braun MJ., Chojnowski J.L., Cox W.A., Han K.-L., Harshman J., Huddleston CJ., Marks B.D., Miglia K.J., Moore W.S., Sheldon F.H., Steadman D.W., Witt C.C., Yuri, T. 2008. A phylogenomic study of birds reveals their evolutionary history Science. 320:1763-1768.
11. Han K.-L., Braun E.L., Kimball R.T., Reddy S., Bowie R.C.K., Braun M.J., Chojnowski J.L., Hackett S.J., Harshman J., Huddleston C.J., Marks B.D., Miglia K.J., Moore W.S., Sheldon F.H., Steadman D.W., Witt C.C., Yuri T. 2011. Are transposable element insertions homoplasy free? An examination using the avian tree of life. Syst. Biol. 60:375-386.
12. Hazkani-Covo E. 2009. Mitochondrial insertions into primate nuclear genomes suggests the use of numts as a tool for phylogeny Mol. Biol. Evol. 26:2175-2179.
13. Hein J. 1990. Unifed approach to alignment and phylogenies. Methods Enzymol. 183:626-645.
14. Holland B., Delsuc F., Moulton V. 2005a. Visualizing conficting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentals and hexapods. Syst. Biol. 54:66-76.
15. Holland B.R., Huber K., Penny D., Moulton V. 2005b. The MinMax Squeeze: guaranteeing a minimal tree for population data. Mol. Biol. Evol. 22:235-242.
16. Johnson K.P 2004. Deletion bias in avian introns over evolutionary timescales. Mol. Biol. Evol. 21:599-602.
17. Katoh K., Misawa K., Kuma K., Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on Fast Fourier Transform. Nucl. Acids Res. 30:3059-3066.
18. Kjer K.M., Gillespie J.J., Ober K.A. 2007. Opinions on multiple sequence alignment, and an empirical comparison of repeatability and accuracy between POY and structural alignment. Syst. Biol. 56:133-146.
19. Kjer K.M. 1995. Use of rRNA secondary structure in phylogenetc studies to identify homologous positions: an example of alignment and data presentation from the frogs. Mol. Phylogenet. Evol. 4:314-340.
20. Liu K., Linder C.R., Warnow T. 2010. Multiple sequence alignment: a major challenge to large-scale phylogenetics. PLoS Curr. Tree Life. 2:RRN1198.
21. Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564.
22. Lockhart PJ., Penny D., Hendy M.D., Howe C.J., Beanland T.J., Larkum A.W.D. 1992. Controversy on chloroplast origins. FEBS Lett. 301:127-131.
23. Löhne C., Borsch T. 2005. Molecular evolution and phylogenetic utility of the petD Group II intron: a case study in basal angiosperms. Mol. Biol. Evol. 22:317-332.
24. Martin W., Roettger M., Lockhart PJ. 2007. A reality check for alignments and trees. Trends Genet. 23:478-480.
25. Morgan-Richards M., Trewick S., Bartosch-Härlid A., Kardailsky O., Phillips M.J., McLenachan PA., Penny D. 2008. Bird evolution: testing the Metaves clade with six new mitochondrial genomes. BMC Evol. Biol. 8:20.
26. Morrison D.A. 2009. Why would phylogeneticists ignore computerized sequence alignment? Syst. Biol. 58:150-158.
27. Mossel E., Steel M. 2004. A phase transition for a random cluster model onphylogenetic trees. Math. BioSci. 187:189-203.
28. Nilsson M.A., Churakov G., Sommer M., Van Tran N., Zemann A., Brosius J., Schmitz J. 2010. Tracking marsupial evolution using archaic genomic retroposon insertions. PLoS Biol. 8:e1000436.
29. Notredame C., Higgins D.G., Heringa J. 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302:205-217.
30. Paton T.A., Baker A.J. 2006. Sequences from 14 mitochondrial genes provide a well-supported phylogeny of the Charadriiform birds congruent with the nuclear RAG-1 tree. Mol. Phylogenet. Evol. 39:657-667.
31. Paton T.A., Baker A.J., Groth J.G., Barrowclough G.F. 2003. RAG-1 sequences resolve phylogenetic relationships within Charadriiform birds. Mol. Phylogenet. Evol. 29:268-278.
32. Penny D., Hendy M.D., Steel M.A. 1991. Testing the theory of descent. In: Miyamoto M.M., Cracraft J., editors. Phylogenetic analysis of DNA sequences. New York: Oxford University Press. pp 155-183.
33. Penny D., Phillips MJ. 2004. The rise of birds and mammals: are microevolutionary processes suffcient for macroevolution. Trends Ecol. Evol. 19:516-522.
34. Phillips M.J., Gibb G.C., Crimp E.A., Penny D. 2010. Tinamous and moa fock together: mitochondrial genome sequence analysis reveals independent losses of fight among ratites. Syst. Biol. 59: 90-107.
35. Pratt R.C., Gibb G.C., Morgan-Richards M., Phillips M.J., Hendy M.D., Penny D. 2009. Toward resolving deep Neoaves phylogeny: data, signal enhancement, and priors. Mol. Biol. Evol. 26:313-326.
36. Rokas A., Holland P.W.H. 2000. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15:454-459.
37. Simmons M.P, Muller K.F., Webb C.T. 2010. The deterministic effects of alignment bias in phylogenetic inference. Cladistics. 26:1-16.
38. Steel M. 2011. Can we avoid "SIN" in the house of "No Common Mechanism"? Syst. Biol. 60:96-109.
39. Steel M.A., Hendy M.D., Penny D. 1992. Signifcance of the length of the shortest tree. J Classif. 9:71-90.
40. Steel M.A., Penny D. 2000. Parsimony likelihood and the role of models in molecular phylogenetics. Mol. Biol. Evol. 17:839-850.
41. Steel M.A., Penny D. 2005. Maximum parsimony and the phylogenetic information in multistate characters. In: Albert V., editor. Parsimony phylogeny and genomics. New York: Oxford University Press. p. 163-178.
42. Suchard M.A., Redelings B.D. 2006. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny Bioinformatics. 22: 2047-2048.
43. Swofford D.M. 2002. PAUP 4.0b10 phylogenetic analysis using parsimony (and other methods). Sunderland (MA): Sinaur Associates.
44. Thatte B.D. 2006. Invertibility of the TKF model of sequence evolution. Math. Biosci. 200:58-75.
45. Thomas G.H., Wills M.A., Székely T. 2004. A supertree approach to shorebird phylogeny BMC Evol. Biol. 4:28.
46. Thompson J.D., Higgins D.G., Gibson T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specifc gap penalties and weight matrix choice. Nucl. Acids Res. 22:4673-4680.
47. Thorne J.L., Kishino H., Felsenstein J. 1991. An evolutionary model for maximum likelihood alignment of DNA sequences. J. Mol. Evol. 33:114-124.
48. Thorne J.L., Kishino H., Felsenstein J. 1992. Inching toward reality: an improved likelihood model of sequence evolution. J. Mol. Evol. 34:3-16.
49. Wheeler W.C. 2003. Iterative pass optimization of sequence data. Cladistics 19:254-260.
50. Wong K.M., Suchard M.A., Huelsenbeck J.P 2008. Alignment uncertainty and genomic analysis. Science. 319:473-476.