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Among-site rate variation (α) and transition bias (κ) have been shown, most often as independent parameters, to be important dynamics in DNA evolution. Accounting for these dynamics should result in better estimates of phylogenetic relationships. To test this idea, we simultaneously estimated overall (averaged over all codon positions) and codon-specific values of α and κ, using maximum likelihood analyses of cytochrome b data from all genera of pipits and wagtails (Aves: Motacillidae), and six outgroup species, using initial trees generated with default values. Estimates of α and κ were robust to initial tree topology and suggested substantial among-site rate variation even within codon classes; α was lowest (large among-site rate variation) at second-codon and highest (low among-site rate variation) at third-codon positions. When overall values were applied, there were shifts in tree topology and dramatic …