A likelihood ratio test to detect conflicting phylogenetic signal

Molecular data are commonly used to reconstruct the evolutionary histories of organisms. 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 mehanisms 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.