Abstract
Evolution operates on whole genomes by operations that change the order and strandedness of genes within the genomes. This type of data presents new opportunities for discoveries about deep evolutionary rearrangement events. Several distance-based phylogenetic reconstruction methods have been proposed [12],[21],[19] that use neighbor joining (NJ) [16] with the expected breakpoint or inversion distances after k rearrangement events. In this paper we study the variance of the breakpoint and inversion distances. The result is combined with Weighbor [5], an improved version of NJ using the variance of true evolutionary distance estimators, to yield two new methods, Weighbor-IEBP and Weighbor-EDE. Experiments show the new methods have better accuracy than all previous distance-based methods, and are robust against model parameter misspecifications.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
K. Atteson. The performance of the neighbor-joining methods of phylogenetic reconstruction. Algorithmica, 25(2/3):251–278, 1999.
D. A. Bader, B. M. E. Moret, and M. Yan. A linear-time algorithm for computing inversion distances between signed permutations with an experimental study. J. Comput. Biol., 8(5):483–491, 2001.
V. Bafna and P. Pevzner. Sorting permutations by transpositions. In Proc. 6th Annual ACM-SIAM Symp. on Disc. Alg. SODA95, pages 614–623. ACM Press, 1995.
M. Blanchette, M. Kunisawa, and D. Sankoff. Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol., 49:193–203, 1999.
W. J. Bruno, N. D. Socci, and A. L. Halpern. Weighted neighbor joining: A likelihood-based approach to distance-based phylogeny reconstruction. Mol. Biol. Evol., 17:189–197, 2000. http://www.t10.lanl.gov/billb/weighbor/.
S. R. Downie and J. D. Palmer. Use of chloroplast DNA rearrangements in reconstructing plant phylogeny. In P. Soltis, D. Soltis, and J.J. Doyle, editors, Molecular Systematics of Plants, volume 49, pages 14–35. Chapman & Hall, 1992.
O. Gascuel. BIONJ: an improved version of the nj algorithm based on a smple model of sequence data. Mol. Biol. Evol., 14:685–695, 1997. http://www.crt.umontreal.ca/~olivierg/bionj.html.
O. Gascuel. Personal communication, April 2001.
R. L. Graham, D. E. Knuth, and O. Patashnik. Concrete Mathematics. Addison-Wesley, 1994. 2nd ed.
S. Hannenhalli and P. Pevzner. Transforming cabbage into turnip (polynomial algorithm for genomic distance problems). In Proc. 27th Annual ACM Symp. on Theory of Comp. STOC95, pages 178–189. ACM Press, NY, 1995.
S. Kumar. Minimum evolution trees. Mol. Biol. Evol., 15:584–593, 1996.
B. M. E. Moret, L.-S. Wang, T. Warnow, and S. Wyman. New approaches for reconstructing phylogenies based on gene order. In Proc. 9th Intl. Conf. on Intel. Sys. for Mol. Bio. (ISMB 2001), pages 165–173. AAAI Press, 2001.
G. W. Oehlert. A note on the delta method. Amer. Statist., 46:27–29, 1992.
R. G. Olmstead and J. D. Palmer. Chloroplast DNA systematics: a review of methods and data analysis. Amer. J. Bot., 81:1205–1224, 1994.
L. A. Raubeson and R. K. Jansen. Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science, 255:1697–1699, 1992.
N. Saitou and M. Nei. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. & Evol., 4:406–425, 1987.
D. Sankoff and M. Blanchette. Probability models for genome rearrangements and linear invariants for phylogenetic inference. Proc. 3rd Int’l Conf. on Comput. Mol. Bio. (RECOMB99), pages 302–309, 1999.
D. Swoffrd. PAUP* 4.0. Sinauer Associates Inc, 2001.
L.-S. Wang. Improving the accuracy of evolutionary distances between genomes. In Lec. Notes in Comp. Sci. No. 2149: Proc. 1st Workshop for Alg. & Bio. Inform. WABI 2001, pages 175–188. Springer Verlag, 2001.
L.-S. Wang, R. K. Jansen, B. M. E. Moret, L. A. Raubeson, and T. Warnow. Fast phylogenetic methods for the analysis of genome rearrangement data: An empirical study. In Proc. 7th Pacific Symp. Biocomputing (PSB 2002), pages 524–535, 2002.
L.-S. Wang and T. Warnow. Estimating true evolutionary distances between genomes. In Proc. 33th Annual ACM Symp. on Theory of Comp. (STOC 2001), pages 637–646. ACM Press, 2001.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2002 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Li-San, W. (2002). Genome Rearrangement Phylogeny Using Weighbor. In: Guigó, R., Gusfield, D. (eds) Algorithms in Bioinformatics. WABI 2002. Lecture Notes in Computer Science, vol 2452. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45784-4_9
Download citation
DOI: https://doi.org/10.1007/3-540-45784-4_9
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-44211-0
Online ISBN: 978-3-540-45784-8
eBook Packages: Springer Book Archive