A hybrid micro-macroevolutionary approach to gene tree reconstruction

Journal of Computational Biology

Volumn 13, Issue 2, 2006, Pages 320-335

  Durand, Dannie ^a   Halldórsson, Bjarni V ^b   Vernot, Benjamin ^a  

^a CARNEGIE MELLON UNIVERSITY   (United States)

^b DECODE GENETICS   (Iceland)

Author keywords

Duplication loss Parsimony; Gene duplication; Gene family; Phylogeny; Reconciliation

Indexed keywords

ALGORITHM; COMPUTER INTERFACE; COMPUTER PROGRAM; CONFERENCE PAPER; GENE DUPLICATION; GENE LOSS; GENE SEQUENCE; GENE TREE RECONSTRUCTION; GENETIC CODE; GENETIC LINE; HIGH THROUGHPUT SCREENING; HUMAN; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; PARSIMONY ANALYSIS; PHYLOGENETIC TREE CONSTRUCTION METHOD; PHYLOGENY; POINT MUTATION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; SEQUENCE ANALYSIS; TAXONOMY;

ALGORITHMS; ATP-BINDING CASSETTE TRANSPORTERS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE DELETION; GENE DUPLICATION; GLUTATHIONE TRANSFERASE; MODELS, GENETIC; MULTIGENE FAMILY; MUTATION; SOFTWARE;

EID: 33645981936     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2006.13.320     Document Type: Conference Paper

References (41)

1. Arvestad, L., Berglund, A.-C., Lagergren, J., and Sennblad, B. 2003. Bayesian gene/species tree reconciliation and orthology analysis using MCMC. Bioinformatics 19(Suppl. 1), i7-15.
2. Arvestad, L., Berglund, A.-C., Lagergren, J., and Sennblad, B. 2004. Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. Proc. 8th Ann. Int. Conf. on Computational Molecular Biology, 326-335.
3. Bailey, T., and Elkan, C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28-36.
4. Chen, K., Durand, D., and Farach-Colton, M. 2000. Notung: A program for dating gene duplications and optimizing gene family trees. J. Comp. Biol. 7, 429-447.
5. Chor, B., and Tuller, T. 2005. Maximum likelihood of evolutionary trees is hard. Proc. 9th Ann. Int. Conf. on Computational Molecular Biology (RECOMB 2005), Lecture Notes in Bioinformatics. Springer Verlag.
6. Cintron, R., Nicholas Jr., H.B., Ferrer, I., Gonzalez, R., Vernot, B., Durand, D., and Serrano, A.E. 2004. The ABC superfamily: Evolutionary implications for drug resistance in Plasmodia, in Functional Genomics and Bioinformatics Approaches to Infectious Disease Research, American Society for Microbiology. Abstract book.
7. Day, W.H. 1987. Computational complexity of inferring phylogenies from dissimilarity matrices. Bull. Math. Biol. 49, 461-467.
8. Day, W.H.E., Johnson, D.S., and Sankoff, D. 1986. The computational complexity of inferring rooted phylogenies by parsimony. Math. Biosci. 81, 33-42.
9. Dufayard, J.-F., Duret, L., Penel, S., Gouy, M., Rechenmann, F., and Perrire, G. 2005. Tree pattern matching in phylogenetic trees: Automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics 21, 2596-2603. http://dx.doi.org/10.1093/bioinformatics/bti325.
10. Efron, B., and Gong, G. 1983. A leisurely look at the bootstrap, jackknife, and cross-validation. The American Statistician 37, 36-48.
11. Eulenstein, O., Mirkin, B., and Vingron, M. 1996. Comparison of annotating duplication, tree mapping, and copying as methods to compare gene trees with species trees. Mathematical Hierarchies and Biology, DIMACS Series in Discrete Mathematics and Theoretical Computer Science 37, 71-93.
12. Eulenstein, O., Mirkin, B., and Vingron, M. 1998. Duplication-based measures of difference between gene and species trees. J. Comp. Biol. 5, 135-148.
13. Felsenstein, J. 2003. Inferring Phylogenies, Sinauer, Sunderland, MA.
14. Goodman, M., Czelusniak, J., Moore, G.W., Romero-Herrera, A.E., and Matsuda, G. 1979. Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28, 132-163.
15. Gorecki, P. 2004. Reconciliation problems for duplication, loss and horizontal gene transfer. Proc. 8th Ann. Int. Conf. on Computational Molecular Biology, 316-325.
16. Guigo, R., Muchnik, I., and Smith, T. 1996. Reconstruction of ancient phylogenies. Molecular Phylogenetics and Evolution 6, 189-213.
17. Hallett, M., Lagergren, J., and Tofigh, A. 2004. Simultaneous identification of duplications and lateral transfers. Proc. 8th Ann. Int. Conf. on Computational Molecular Biology, 347-356.
18. Hallett, M.T., and Lagergren, J. 2000. New algorithms for the duplication-loss model. RECOMB 2000.
19. Hallett, M.T., and Lagergren, J. 2001. Efficient algorithms for lateral gene transfer problems. Proc. 5th Ann. Int. Conf. on Computational Biology, 149-156. http://doi.acm.org/10.1145/369133.369188.
20. Hughes, A.L. 1998. Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1. Mol. Biol. Evol. 15, 854-870.
21. Ma, B., Li, M., and Zhang, L. 2000. From gene trees to species trees. SIAM J. on Comput.
22. Mirkin, B., Muchnik, I., and Smith, T. 1995. A biologically consistent model for comparing molecular phylogenies. J. Comp. Biol. 2, 493-507.
23. Newick Taxonomy. 1986. The Newick tree format. Extithttp://evolution. genetics.washington.edu/phylip/newicktree.html.
24. Nicholas, H.N., and Deerfield, D. 1997. Genedoc: Analysis and visualization of genetic variation. EMBNEW.NEWS 4, 14. www.psc.edu/biomed/ genedoc/.
25. Notredame, C., Higgins, D., and Heringa, J. 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205-217. http://dx.doi.org/10.1006/jmbi.2000.4042.
26. Page, R. 1994. Maps between trees and cladistic analysis of historical associations among genes, organisms and areas. Syst. Zool. 43, 58-77.
27. Page, R. 1998. GeneTree: Comparing gene and species phylogenies using reconciled trees. Bioinformatics 14, 819-820.
28. Page, R., and Charleston, M. 1996. Reconciled trees and incongruent gene and species trees. Mathematical Hierarchies and Biology, DIMACS Series in Discrete Mathematics and Theoretical Computer Science 37, 57-70.
29. Page, R., and Charleston, M. 1997. From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem. Molecular Phylogenetics and Evolution 7, 231-240.
30. Page, R., and Charleston, M. 1998. Trees within trees: Phylogeny and historical associations. Trends in Ecology and Evolution 13, 356-359.
31. Pebusque, M.-J., Coulier, F., Birnbaum, D., and Pontarotti, P. 1998. Ancient large-scale genome duplications: Phylogenetic and linkage analyses shed light on chordate genome evolution. Mol. Biol. Evol. 15, 1145-1159.
32. Ronquist, E, and Huelsenbeck, J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574.
33. Ropelewski, A.J., Nicholas, H.B., and Deerfield, D. 2000. Selective and sensitive comparison of genetic sequence data on high performance computers, in Koniges, A., ed., Parallel Applications Technology Program, 453-479, Morgan Kaufmann, San Matea, CA.
34. Ruvinsky, I., and Silver, L.M. 1997. Newly indentified paralogous groups on mouse chromosomes 5 and 11 reveal the age of a T-box cluster duplication. Genomics 40, 262-266.
35. Saitou, N., and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4, 406-425.
36. Sheehan, D., Meade, G., Foley, V., and Dowd, C. 2001. Structure, function and evolution of glutathione transferases: Implications for classification of non-mammalian members of an ancient enzyme superfamily. Biochem. J. 360, 1-16.
37. Stege, U. 1999. Gene trees and species trees: The gene-duplication problem is fixed-parameter tractable. Proc. 6th Int. Workshop on Algorithms and Data Structures (WADS '99).
38. Thompson, J., Higgins, D., and Gibson, T. 1994. Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput. Appl. Biosci. 10, 19-29.
39. Zhang, L. 1997. On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies. J. Comp. Biol. 4, 177-188.
40. Zmasek, C.M., and Eddy, S.R. 2001a. ATV: Display and manipulation of annotated phylogenetic trees. Bioinformatics 17, 383-384. http://bioinformatics. oupjournals.org/cgi/reprint/17/4/383.
41. Zmasek, C.M., and Eddy, S.R. 2001b. A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 17, 821-828. http://bioinformatics.oupjournals.org/cgi/reprint/17/9/821.