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Convergent regulatory evolution and loss of flight in paleognathous birds

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Science  05 Apr 2019:
Vol. 364, Issue 6435, pp. 74-78
DOI: 10.1126/science.aat7244

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All roads lead to regulation

Species from widely divergent taxa can experience similar changes in traits. What underlying genetic drivers cause these parallel changes remains an open question. Sackton et al. looked across groups of birds that have repeatedly lost flight, the ratites and tinamous, and found that there is convergence in the regulatory regions associated with genes related to flight, but not within the protein coding regions. Changes within these regulatory regions influenced limb development and may represent quick paths toward convergent change across taxa.

Science, this issue p. 74

Abstract

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.

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