Reconstructing chromosomal evolution

Li San Wang, Tandy Warnow

Research output: Contribution to journalArticle

Abstract

Chromosomes evolve through genome rearrangement events, including inversions, transpositions, and inverted transpositions, that change the order and strandedness of genes within chromosomes. In this paper we present a method for estimating evolutionary histories for chromosomes based upon such events. The fundamental mathematical challenge of our approach is to estimate the true evolutionary distance between every pair of chromosomes, where the true evolutionary distance is the number of rearrangement events that took place in the evolutionary history between the chromosomes. We present two techniques, Exact- and Approx-IEEP, for estimating true evolutionary distances and prove guarantees about the accuracy of these techniques under a very general stochastic model of chromosomal evolution. We then show how we can use these estimated distances to obtain highly accurate estimates of chromosomal evolutionary history, significantly improving upon the previous best techniques.

Original languageEnglish (US)
Pages (from-to)99-131
Number of pages33
JournalSIAM Journal on Computing
Volume36
Issue number1
DOIs
StatePublished - Dec 1 2006
Externally publishedYes

Fingerprint

Chromosomes
Chromosome
Transposition
Genes
Genome Rearrangement
Stochastic models
Rearrangement
Estimate
Stochastic Model
Inversion
Gene
History

Keywords

  • Distance correction
  • Genome rearrangements
  • Inversions
  • Markov chain
  • Nadeau-Taylor model
  • Neighbor joining
  • Phylogeny reconstruction
  • Transpositions

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computational Theory and Mathematics
  • Applied Mathematics

Cite this

Reconstructing chromosomal evolution. / Wang, Li San; Warnow, Tandy.

In: SIAM Journal on Computing, Vol. 36, No. 1, 01.12.2006, p. 99-131.

Research output: Contribution to journalArticle

Wang, Li San ; Warnow, Tandy. / Reconstructing chromosomal evolution. In: SIAM Journal on Computing. 2006 ; Vol. 36, No. 1. pp. 99-131.
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