Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution.

The discovery of the genetic mechanisms underlying the emergence of phenotypic novelties is a cornerstone of evolutionary biology. To identify sequences in vertebrate genomes leading to the emergence of clade defining traits, we uncover genomic regions conserved across vertebrates that accumulated substitutions in a faster than neutral rate in the Avian or in the Mammalian basal lineages. We identify 2888 and 3476 noncoding avian and mammals accelerated regions, respectively, accumulating in key developmental genes in each lineage. Interestingly, we find that the neuronal transcription factor NPAS3, that carries the largest number of human accelerated regions, also accumulates the largest amount of noncoding mammals accelerated regions. We also detect that four NPAS3 noncoding mammals accelerated regions overlap previously identified human accelerated regions. Thus, we show that noncoding regions of particular large-effect genes are repeatedly targets of accelerated evolution, suggesting the existence of evolutionary hotspots underlying phenotypic innovation in different lineages.