title: The infinite sites model of genome evolution.
abstract: 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.
authors.affiliation: Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.
authors.forename: Jian
authors.initials: J
authors.lastname: Ma
authors.forename: Aakrosh
authors.initials: A
authors.lastname: Ratan
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Raney
authors.forename: Bernard B
authors.initials: BB
authors.lastname: Suh
authors.forename: Webb
authors.initials: W
authors.lastname: Miller
authors.forename: David
authors.initials: D
authors.lastname: Haussler
mesh_terms: D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D019143:Evolution, Molecular; D016678:Genome; D006801:Humans; D051379:Mice; D008957:Models, Genetic; D009154:Mutation / Q000235:genetics; D014960:X Chromosome
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