Gene tree parsimony vs uninode coding for phylogenetic reconstruction


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 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 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.

In Molecular Phylogenetics and Evolution 29:298–308
James Cotton
James Cotton
Senior Staff Scientist

My research interests are in the genomics, and particularly population genomics of parasites, particularly those that cause neglected tropical diseases