Data from: Convergent regulatory evolution and loss of flight in palaeognathous birds

A core question in evolutionary biology is whether convergent phenotypic
evolution is driven by convergent molecular changes in proteins or
regulatory regions. We combined phylogenomic, developmental, and
epigenomic analysis of 11 new genomes of paleognathous birds, including an
extinct moa, to show that convergent evolution of regulatory regions, more
so than protein-coding genes, is prevalent among developmental pathways
associated with independent losses of flight. A Bayesian analysis of
284,001 conserved noncoding elements, 60,665 of which are corroborated as
enhancers by open chromatin states during development, identified 2355
independent accelerations along lineages of flightless paleognaths, with
functional consequences for driving gene expression in the developing
forelimb. Our results suggest that the genomic landscape associated with
morphological convergence in ratites has a substantial shared regulatory
component.