Convergent regulatory evolution and loss of flight in paleognathous birds

A major question in evolutionary biology is whether convergent phenotypes are driven by convergence at the level of the genome. We have approached this question by comparing genomes among paleognathous birds, which include the volant tinamous of the New World and the flightless ratites, which are thought to have lost flight multiple times convergently.  We produced 11 new high-quality paleognath genomes, including a genome of an extinct moa, and aligned these to 32 additional genomes from birds and non-avian reptiles. Novel statistical tools to detect convergent changes in evolutionary rate for both protein-coding genes and noncoding regulatory regions suggests a prominent role for regulatory regions in the evolution of flightlessness, a result confirmed by transcriptome and epigenetic comparisons of developing fore- and hindlimbs. Overall our results suggest that loss of flight involves repeated evolution of shared regulatory networks that are otherwise conserved across 100 million years of bird evolution.