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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.

SUBMITTER: Ma J

PROVIDER: S-EPMC2533685 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature

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The infinite sites model of genome evolution.

Ma Jian J Ratan Aakrosh A Raney Brian J BJ Suh Bernard B BB Miller Webb W Haussler David D

Proceedings of the National Academy of Sciences of the United States of America 20080911 38

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 ...[more]

PMID: 18787111

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