Gene tree parsimony vs. uninode coding for phylogenetic reconstruction

Cotton, J.A. and Page, R.D.M. (2003) Gene tree parsimony vs. uninode coding for phylogenetic reconstruction. Molecular Phylogenetics and Evolution, 29(2), pp. 298-308. (doi: 10.1016/S1055-7903(03)00109-X) (PMID:13678685)

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Simmons and Freudenstein (2002) have suggested that there are important weaknesses of gene tree parsimony in reconstructing phylogeny in the face of gene duplication, weaknesses that are addressed by Simmons et al.'s (2000) method of uninode coding. Here, we discuss Simmons and Freudenstein's criticisms and suggest a number of reasons why gene tree parsimony is preferable to uninode coding. During this discussion we introduce a number of recent developments of gene tree parsimony methods overlooked by Simmons and Freudenstein. Finally, we present a re-analysis of data from Page (2000) that produces a more reasonable phylogeny than that found by Simmons and Freudenstein, suggesting that gene tree parsimony outperforms uninode coding, at least on these data.

Item Type:Articles
Glasgow Author(s) Enlighten ID:Page, Professor Roderic and Cotton, Professor James
Authors: Cotton, J.A., and Page, R.D.M.
Subjects:Q Science > QH Natural history > QH426 Genetics
College/School:College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
Journal Name:Molecular Phylogenetics and Evolution
ISSN (Online):1095-9513

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