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.