EFFICIENCIES OF GENES AND ACCURACY OF TREE-BUILDING METHODS IN RECOVERING A KNOWN DROSOPHILA GENEALOGY

1 December 2000

proceedings article
Published by World Scientific Pub Co Pte Ltd in Pacific Symposium on Biocomputing

p. 606-17
https://doi.org/10.1142/9789814447362_0058

Abstract

Phylogenetic hypotheses generated from seven Drosophila mitochondrial genomes support a well-corroborated genealogy with a single evolutionary history. These mitochondrial data form a model system for investigating the efficiency of genes and accuracy of different tree-building methods in recovering a well-supported genealogy. We consider 15 genes (13 protein-coding and 2 rRNAs) and 83 tree-building methods (27 distance, 4 parsimony, 50 maximum likelihood, and 2 Bayesian). Among the 15 genes examined, ND4 recovered the true genealogy most efficiently (82 out of 83 methods). Generally, maximum likelihood models enforcing a clock most accurately reclaim the true genealogy. Surprisingly, however, this method fails to recover the well-supported topology for more than half of the genes. Additional studies are required to test the generality of the results presented here.

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