A Likelihood Ratio Test to Detect Conflicting Phylogenetic Signal

Abstract

Molecular data are commonly used to reconstruct the evolutionary histories of organ- isms. However, evolutionary reconstructions from different molecular data sets sometimes conflict. It is generally unknown whether these different estimates of history result from random variation in the processes of nucleotide substitution or from fundamentally different evolutionary mecha- nisms underlying the histories of the genes analyzed. We describe a novel likelihood ratio test that compares different topologies (each estimated from a different data partition for the same taxa) to determine if they are significantly different. The results of this test indicate that different genes provide significantly different phylogenies for amniotes, supporting earlier suggestions based on less direct tests. These results suggest that some molecular data can give misleading information about evolutionary history. (Likelihood ratio test; maximum likelihood; phylogenetic methods; phylogenetic heterogeneity.) Debate about which kinds of data pro- vide the most accurate estimates of phy- logeny is fueled by observations that dif- ferent data sets for the same taxa sometimes yield discordant estimates. In some cases there is a good explanation for the different phylogenetic estimates. For example, horizontal gene transfer and re- combination in bacteria cause different portions of the genome to have different histories (Dykhuizen and Green, 1991; Maynard Smith et al., 1991; Medigue et al., 1991; Souza et al., 1992; Valdez and Pinero, 1992). Also, in many organisms, polymor- phisms that predate speciation may fail to reflect the phylogenetic history of the rest of the genome (the gene-tree vs. species- tree problem; Wilson et al., 1977; Pesole et al., 1991; Doyle, 1992). It is nonetheless generally accepted that most genes in higher taxa are free from these problems and that any differences in phylogenies produced with different data sets can be attributed to sampling. Statis- tical procedures such as bootstrapping re- veal that different estimates of phylogeny may arise purely as a consequence of sam- pling error. However, conflicting phyloge- nies may also arise when the underlying processes of molecular evolution differ among genes, even though the genes have