Whole Genome Analysis of Divergence.

(A) Genome-wide nucleotide-based divergence (CorrectedForAL) between the scarlet macaw (Ara macao; simple de novo assembly) and chicken genomes (Gallus gallus 2.1). (B) Genome-wide nucleotide-based divergence (CorrectedForAL) between the scarlet macaw (Ara macao; simple de novo assembly) and zebra finch genomes (Taeniopygia guttata 1.1, 3.2.4). Each histogram represents the full, ordered distribution of the composite variable defined as: . The observed ranges of the composite variable for pane (A) and pane (B) were 3.89591E-05–0.052631579, and 3.33792E-05–0.052631579, respectively. The left edges of the distributions represent extreme conservation, whereas the right edges indicate extreme putative divergence. Distributional outliers were predicted using a percentile-based approach (99.98th and 0.02th) to construct interval bounds capturing >99.9% of the total data points in each ordered distribution.