Duplication and loss of developmental gene-family members in our dataset. Duplications (bold, black background) and losses (italics, white background) were mapped onto a consensus species tree [79, 104, 109]. Multiple duplications or losses in a phylogenetic interval are indicated in parentheses. Gene names are color coded by their function in Drosophila eye development. Reconciliation of gene trees onto the species tree was performed with Notung using Maximum Likelihood gene family trees (see Methods).