Efficiencies of genes and accuracy of tree-building methods in recovering a known Drosophila genealogy.
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.
Steinbachs
J E
JE
Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605-2496, USA.
Schizas
N V
NV
Ballard
J W
JW
D000818:Animals; D001499:Bayes Theorem; D004272:DNA, Mitochondrial / Q000235:genetics; D004330:Drosophila / Q000235:genetics*; D005260:Female; D017344:Genes, Insect; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny
D004272:DNA, Mitochondrial