Site likelihoods for the species simulated with x = 0.015 and y = 0.05. Site patterns are coded based on the different alleles observed at a site, with numbers representing the alleles from species A, B, C, D and E, in this order (0 corresponds to the nucleotide observed in the outgroup; every other number represents a different, derived nucleotide, regardless of identity). Top panel: the negative log-likelihood (smaller means more likely) of all possible site patterns under the maximum-likelihood branch lengths inferred from a concatenated alignment under the species tree topology (S) or anomalous gene tree topology (A). Middle panel: counts of all site patterns in the concatenated alignment (20,000 1-kb simulated loci; see Appendix B). Bottom panel: the product of the top and middle panels, expressed as the negative log-likelihood difference between the maximum-likelihood trees with the species tree and anomalous gene tree topologies (\delta -lnL = -lnLS - (-lnLA)). The species tree is more likely if the likelihood mass above zero summed across all site patterns is greater than that below zero. Data not shown for non-informative site patterns.