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

Background Convergent evolution is the independent evolution of similar
traits in unrelated lineages across the Tree of Life. Various genomic
signatures can help identify cases of convergent evolution at the
molecular level, including changes in substitution rate in the same genes
or gene networks. In this study, utilizing tarsus measurements of ~5400
species of birds, we identify independent shifts in tarsus length and use
both comparative genomic and population genetic data to identify
convergent evolutionary changes among focal clades with shifts to shorter
optimal tarsus length. Results Using a newly generated, comprehensive and
broadly accessible set of 932,467 avian conserved non-exonic elements
(CNEEs) and a whole-genome alignment of 79 birds, we find strong evidence
for convergent acceleration in short-tarsus clades among 14,422 elements.
Analysis of 9854 protein-coding genes, however, yielded no evidence of
convergent patterns of positive selection. Accelerated elements in
short-tarsus clades are concentrated near genes with functions in
development, with the strongest enrichment associated with skeletal system
development. Analysis of gene networks support convergent changes in
regulation of broadly homologous limb developmental genes and pathways.
Conclusions Our results highlight the important role of regulatory
elements undergoing convergent acceleration in convergent skeletal traits
and are consistent with previous studies showing the roles of regulatory
elements and skeletal phenotypes.