Convergent evolution of noncoding elements associated with short tarsus length in birds

Convergent evolution is the independent evolution of similar traits in unrelated lineages across the Tree of Life. Various factors underlie convergent evolution including convergent rate changes through consistent shifts in substitution rate in the same genes or gene networks. In this study, we use comprehensive phenotypic data to identify seven bird clades with independent shortening in tarsus length and use both comparative genomic and population genetic data to identify convergent evolutionary changes among four target clades with shifts to shorter optimal tarsus length. Using a newly generated, comprehensive set of avian conserved non-exonic elements (CNEEs), we find strong evidence for convergent acceleration in short-tarsi clades among CNEEs, but not protein-coding genes. Accelerated CNEEs in short-tarsi clades are preferentially located near genes with functions in development, with the strongest enrichment associated with skeletal system development. Further analysis of gene networks highlighted this larger role of changes in regulation of broadly homologous developmental genes and pathways as being an integral aspect of limb size variability in birds.