Approximating the true evolutionary distance between two genomes

Krister M. Swenson, Mark Marron, Joel V. Earnest-Deyoung, Bernard M.E. Moret

Research output: Contribution to journalArticlepeer-review

24 Scopus citations

Abstract

As more and more genomes are sequenced, evolutionary biologists are becoming increasingly interested in evolution at the level of whole genomes, in scenarios in which the genome evolves through insertions, duplications, deletions, and movements of genes along its chromosomes. In the mathematical model pioneered by Sankoff and others, a unichromosomal genome is represented by a signed permutation of a multiset of genes; Hannenhalli and Pevzner showed that the edit distance between two signed permutations of the same set can be computed in polynomial time when all operations are inversions. El-Mabrouk extended that result to allow deletions and a limited form of insertions (which forbids duplications); in turn we extended it to compute a nearly optimal edit sequence between an arbitrary genome and the identity permutation. In this paper we generalize our approach to compute distances between two arbitrary genomes, but focus on approximating the true evolutionary distance rather than the edit distance. We present experimental results showing that our algorithm produces excellent estimates of the true evolutionary distance up to a (high) threshold of saturation; indeed, the distances thus produced are good enough to enable the simple neighbor-joining procedure to reconstruct our test trees with high accuracy.

Original languageEnglish
Article number3.5
JournalJournal of Experimental Algorithmics
Volume12
DOIs
StatePublished - Jun 1 2008

Keywords

  • Duplications
  • Evolution
  • Inversions
  • Pairwise distances
  • Whole-genome data

ASJC Scopus subject areas

  • Theoretical Computer Science

Fingerprint

Dive into the research topics of 'Approximating the true evolutionary distance between two genomes'. Together they form a unique fingerprint.

Cite this