Conserved genes, sampling error, and phylogenomic inference

Disagreement or conflict among phylogenetic hypotheses obtained by analysis of large, genome-wide databases has incited debate over potential benefits, pitfalls, and best practices associated with phylogenomic approaches (Jeffroy, O., Brinkmann, H., et al. 2006, Philippe, H., Derelle, R., et al. 2009, Philippe, H., Brinkmann, H., et al. 2011). In a recent article, Salichos, L. and Rokas, A. (2013; S&R) assert that accuracy of phylogenetic inference from genomic data can be improved by focusing on the subset of genes that have “strong” phylogenetic signals as measured by bootstrap support of their inferred trees. In that study, S&R compared 23 yeast genomes and observed that genealogies obtained for 1070 orthologous genes were all different from each other and also differed from the topology obtained either by concatenating all genes or by an extended consensus phylogeny of all gene trees. They developed a new measure of incongruence (“internode certainty”) to gauge the level of ...