A LIKELIHOOD RATIO TEST TO DETECT CONFLICTING PHYLOGENETIC SIGNAL

Molecular data are commonly used to reconstruct the evolutionary histo ries of organisms. However, evolutionary reconstructions from differen t molecular data sets sometimes conflict. It is generally unknown whet her these different estimates of history result from random variation in the processes of nucleotide substitution or from fundamentally diff erent evolutionary mehanisms underlying the histories of the genes ana lyzed. We describe a novel likelihood ratio test that compares differe nt topologies (each estimated from a different data partition for the same taxa) to determine if they are significantly different. The resul ts of this test indicate that different genes provide significantly di fferent 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.