The infinite sites model of genome evolution

Jian Ma, Aakrosh Ratan, Brian J. Raney, Bernard B. Suh, Webb Miller, David Haussler

Research output: Contribution to journalArticlepeer-review


We formalize the problem of recovering the evolutionary history of a set of genomes that are related to an unseen common ancestor genome by operations of speciation, deletion, insertion, duplication, and rearrangement of segments of bases. The problem is examined in the limit as the number of bases in each genome goes to infinity. In this limit, the chromosomes are represented by continuous circles or line segments. For such an infinite-sites model, we present a polynomial-time algorithm to find the most parsimonious evolutionary history of any set of related present-day genomes.

Original languageEnglish (US)
Pages (from-to)14254-14261
Number of pages8
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number38
StatePublished - Sep 23 2008
Externally publishedYes


  • Ancestral reconstruction
  • Gene duplication
  • Genome rearrangements

ASJC Scopus subject areas

  • General


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