DOI: 10.5061/dryad.157d7
title: Data from: Conserved genes, sampling error, and phylogenomic inference

description: 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
 conflict inherent in the data supporting specific internodes of the
 phylogeny. Based on this measure, S&R claim that slowly-evolving
 genes are a main source of conflict, suggesting that they should be
 avoided in favor of genes with strong phylogenetic signals. Their
 conclusion that strong signal reduces incongruence is drawn from the
 comparative phylogenetic analysis of protein alignments of the yeast
 genomes as well as from a reanalysis of published vertebrate and metazoan
 data. The notion that slowly-evolving genes are a bad choice to resolve
 basal nodes at deep phylogenetic levels is contrary to widespread practice
 in recent studies (e.g., Li, C., Orti, G., et al. 2007, Jian, S., Soltis,
 P.S., et al. 2008, Li, C., Lu, G., et al. 2008, Regier, J.C., Shultz,
 J.W., et al. 2008, Zhang, N., Zeng, L., et al. 2012, Lang, J.M., Darling,
 A.E., et al. 2013). We challenge S&R’s interpretations herein with
 new analyses of their yeast data. We first demonstrate that the high
 phylogenetic incongruence among conserved genes observed by S&R is
 likely an artifact due to sampling error. Secondly, we challenge their
 premise that bootstrap support is a reliable measure of historical signal
 of genes as it excludes systematic error as an alternative explanation of
 observed pattern, which has previously been shown to have consequences for
 phylogenetic analyses of yeast genomes (Collins, T.M., Fedrigo, O., et al.
 2005). Finally, we note that S&R’s recommendations make the task
 of choosing genes upon which to base phylogenetic inferences impossible,
 as measures of phylogenetic signal can only be determined after data have
 been collected. Recommendations to focus on selective data partitions
 assessed by phylogenetic analysis may become relevant in the future,
 however, once complete genomes are available for all species of interest.
description: Datasets from Salichos
 & Rokas (2013)The files include
 individual gene (protein) alignments for the 1070 genes as well as RAxML
 gene treesRokasDatasets.zipBinned_DataBinned data: alignment and tree filesList_Genes_260C_131SList of genes in the 260C and 131S setsSupplementary Figure 1Molecular properties for the 260 most conserved (260C) genes and the 131 genes with strongest phylogenetic signal (131S). ***U test P &lt; 0.00001.Supplementary_Fig1_GeneProperties.pdf