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Optimal gene trees from sequences and species trees using a soft interpretation of parsimony
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
2006 (English)In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 63, no 2, 240-250 p.Article in journal (Refereed) Published
Abstract [en]

Gene duplication and gene loss as well as other biological events can result in multiple copies of genes in a given species. Because of these gene duplication and loss dynamics, in addition to variation in sequence evolution and other sources of uncertainty, different gene trees ultimately present different evolutionary histories. All of this together results in gene trees that give different topologies from each other, making consensus species trees ambiguous in places. Other sources of data to generate species trees are also unable to provide completely resolved binary species trees. However, in addition to gene duplication events, speciation events have provided some underlying phylogenetic signal, enabling development of algorithms to characterize these processes. Therefore, a soft parsimony algorithm has been developed that enables the mapping of gene trees onto species trees and modification of uncertain or weakly supported branches based on minimizing the number of gene duplication and loss events implied by the tree. The algorithm also allows for rooting of unrooted trees and for removal of in-paralogues (lineage-specific duplicates and redundant sequences masquerading as such). The algorithm has also been made available for download as a software package, Softparsmap.

Place, publisher, year, edition, pages
2006. Vol. 63, no 2, 240-250 p.
Keyword [en]
parsimony, phylogeny, gene duplication/gene loss
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-155799DOI: 10.1007/s00239-005-0096-1ISI: 000239297700009PubMedID: 16830091OAI: oai:DiVA.org:uu-155799DiVA: diva2:428295
Available from: 2011-06-30 Created: 2011-06-30 Last updated: 2011-06-30Bibliographically approved

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