Changes in gene representation across the phylogeny.

A) The number of gains and losses of gene representation at each stage are shown for all clades with at least three species. A threshold of FPKM = 1 was used throughout. There are more stage 5 changes (499 transcripts) than stage 2 changes (245), when gradual transitions are included. Only transitions between adjacent nodes are shown. Gains in representation are as common as losses, if not more abundant, across both stages. B) Examples of genes with changes in transcript representation at different stages, in the obscura group (first two panels), the melanogaster subgroup (third panel), and with highly variable patterns across stages and species (fourth panel).