Journal of Molecular Evolution

, Volume 63, Issue 2, pp 240–250 | Cite as

Optimal Gene Trees from Sequences and Species Trees Using a Soft Interpretation of Parsimony

  • Ann-Charlotte Berglund-Sonnhammer
  • Pär Steffansson
  • Matthew J. Betts
  • David A. Liberles


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.


Parsimony Phylogeny Gene duplication/gene loss 



We are grateful to Jens Lagergren for helpful discussions and also to three anonymous reviewers for their comments. This work was funded by Vetenskapsrådet, the Swedish Foundation for Strategic Research, and FUGE, the Norwegian national functional genomics platform.


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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Ann-Charlotte Berglund-Sonnhammer
    • 1
    • 2
  • Pär Steffansson
    • 1
  • Matthew J. Betts
    • 3
    • 4
  • David A. Liberles
    • 1
    • 3
    • 5
  1. 1.Stockholm Bioinformatics CenterStockholm UniversitySweden
  2. 2.Linnaeus Centre for BioinformaticsUppsala UniversitySweden
  3. 3.Computational Biology Unit, BCCSUniversity of BergenNorway
  4. 4.EMBL HeidelbergGermany
  5. 5.Department of Molecular BiologyUniversity of WyomingLaramieUSA

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