Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical Study

Evolution operates on whole genomes through mutations that change the order and strandedness of genes within the genomes. Thus analyses of gene-order data present new opportunities for discoveries about deep evolutionary events, provided that sufficiently accurate methods can be developed to reconstruct evolutionary trees. In this paper we present two new methods of character coding for parsimony-based analysis of genomic rearrangements: one called MPBE-2, and a new parsimony-based method which we call MPME (based on an encoding of Bryant), both variants of the MPBE method. We then conduct computer simulations to compare this class of methods to distance-based methods (NJ under various distance measures). Our empirical results show that two of our new methods return highly accurate estimates of the true tree, outperforming the other methods significantly, especially when close to saturation.

[1]  M. Donoghue,et al.  The root of angiosperm phylogeny inferred from duplicate phytochrome genes. , 1999, Science.

[2]  Tandy J. Warnow,et al.  A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental Phylogenetic Analyses of Real and Synthetic Data , 2000, ISMB.

[3]  David A. Bader,et al.  A New Implmentation and Detailed Study of Breakpoint Analysis , 2000, Pacific Symposium on Biocomputing.

[4]  Linda A. Raubeson,et al.  Chloroplast DNA Evidence on the Ancient Evolutionary Split in Vascular Land Plants , 1992, Science.

[5]  David Bryant,et al.  A lower bound for the breakpoint phylogeny problem , 2000, J. Discrete Algorithms.

[6]  Tandy J. Warnow,et al.  New approaches for reconstructing phylogenies from gene order data , 2001, ISMB.

[7]  David Sankoff,et al.  Multiple Genome Rearrangement and Breakpoint Phylogeny , 1998, J. Comput. Biol..

[8]  Bernard M. E. Moret,et al.  New approaches for reconstructing phylogenies based on gene order , 2001 .

[9]  Ron Shamir,et al.  The median problems for breakpoints are NP-complete , 1998, Electron. Colloquium Comput. Complex..

[10]  Tandy J. Warnow,et al.  Estimating true evolutionary distances between genomes , 2001, STOC '01.

[11]  D. Sankoff,et al.  Gene Order Breakpoint Evidence in Animal Mitochondrial Phylogeny , 1999, Journal of Molecular Evolution.

[12]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[13]  Kevin Atteson,et al.  The Performance of Neighbor-Joining Methods of Phylogenetic Reconstruction , 1999, Algorithmica.

[14]  D. Sankoff,et al.  Comparative Genomics: "Empirical And Analytical Approaches To Gene Order Dynamics, Map Alignment And The Evolution Of Gene Families" , 2000 .

[15]  Daniel H. Huson,et al.  Hybrid tree reconstruction methods , 1999, JEAL.

[16]  J. Nadeau,et al.  Lengths of chromosomal segments conserved since divergence of man and mouse. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[17]  David A. Bader,et al.  A fast linear-time algorithm for inversion distance with an experimental comparison , 2001 .

[18]  P. Holland,et al.  Rare genomic changes as a tool for phylogenetics. , 2000, Trends in ecology & evolution.

[19]  B. Barrell,et al.  Prevalence of small inversions in yeast gene order evolution. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[20]  J. Palmer,et al.  Chloroplast DNA systematics: a review of methods and data analysis , 1994 .