The processes of gene duplication, loss, and lineage sorting can result in incongruence between the phylogenies of genes and those of species. This incongruence complicates the task of inferring the latter from the former. We describe the use of reconciled trees to reconstruct the history of a gene tree with respect to a species tree. Reconciled trees allow the history of the gene tree to be visualized and also quantify the relationship between the two trees. The cost of a reconciled tree is the total number of duplications and gene losses required to reconcile a gene tree with its species tree. We describe the use of heuristic searches to find the species tree which yields the reconciled tree with the lowest cost. This method can be used to infer species trees from one or more gene trees.
History
Publication title
Molecular Phylogenetics and Evolution
Volume
7
Pagination
231-240
ISSN
1055-7903
Department/School
School of Natural Sciences
Publisher
Academic Press Inc Elsevier Science
Place of publication
525 B St, Ste 1900, San Diego, USA, Ca, 92101-4495