Ancestral State Reconstruction and Rates of Evolution
To understand the evolutionary history of prealternate molt and seasonal dichromatism, among separate species and feather regions, we constructed ancestral state estimates of molts and dichromatism as discrete variables by feather region (Figure 4). We conducted ancestral state reconstruction of presence of molts and dichromatism on the whole body, and by feather region. To convert continuous characters to presence, we converted any nonzero integer to a 1, to indicate that the molt or dichromatism is present in the region of interest. We then evaluated the probability of presence and absence of molts and dichromatism for the entire body and by feather region at each node using a likelihood framework in the package APE (Paradis et al. 2004) in R. We conducted model testing by reconstructing ancestral states under both equal rates (ER) are all-rates-different (ARD) models and used likelihood ratio tests to choose the best model with which to reconstruct ancestral states to help us understand whether we were correctly evaluating the rates of gains and losses over time. We also evaluated molts and dichromatism as continuous characters, scored as the number of feather regions involved, and reconstructed their ancestral states to evaluate their ancestral states and rates of evolution as continuous characters across the bodies of these birds.