Conserved Genes, Sampling Error, and Phylogenomic Inference

Abstract

Disagreement or conflict among phylogenetic hypotheses obtained by analysis of large, genomewide data sets has incited debate over potential benefits, pitfalls, and best practices associated with phylogenomic approaches (Jeffroy et al. 2006; Philippe et al. 2009; Philippe et al. 2011). Phylogenetic analyses of genomic data typically reveal high levels of topological incongruence among gene trees. Incongruence can be real, where different genes have different genealogies due to the complex dynamics of the evolutionary processes (e.g., paralogy, horizontal transfer, or incomplete lineage sorting; Maddison 1997; Edwards et al. 2007; Rosenberg and Tao 2008; Degnan and Rosenberg 2009; Edwards 2009; Kubatko et al. 2009; Liu et al. 2009; Huang et al. 2010), or it can be the consequence of methodological artifacts. Methodological artifacts include spurious results due to sampling error (low signal-to-noise ratio), or a failure of evolutionary models to accommodate convoluted patterns in the data (e.g., Lopez et al. 2002; Pagel and Meade 2004; Collins et al. 2005; Lockhart et al. 2006; Phillips et al. 2006; Rasmussen and Kellis 2007; Galtier and Daubin 2008; Sheffield et al. 2009; Roure and Philippe 2011; Betancur-R. et al. 2013; Romiguier et al. 2013). The ultimate effect of gene-tree discordances on inferences of organismal phylogeny will thus depend on character sampling, biological processes, and the methods and models used to attempt to correct for errors caused by one or more of these factors. In a recent article, Salichos and Rokas (2013; SR Jian et al. 2008; Li et al. 2008; Regier et al. 2008; Zhang et al. 2012; Lang et al. 2013). We challenge SR Lemmon et al. 2012; Li et al. 2013).