Research Article

A genetic signature of the evolution of loss of flight in the Galapagos cormorant

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Science  02 Jun 2017:
Vol. 356, Issue 6341, eaal3345
DOI: 10.1126/science.aal3345

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  • Gene regulatory adaptations in the evolution of loss of flight in the Galapagos cormorant
    • Mark J. Berger, Graduate Student, Stanford Unversity
    • Other Contributors:
      • Gill Bejerano, Professor, Stanford Unversity

    In article “A genetic signature of the evolution of loss of flight in the Galapagos cormorant”, Burga et al. found striking coding mutations in key cilia development, hedgehog signaling, and planar cell polarity (PCP) pathway genes which likely contribute to flightlessness in the Galapagos cormorant (P.harrisi). Surprisingly, the authors could not identify non-coding regions which may contribute to the species’ loss of flight (1), kindling the debate about the relative contribution of coding and non-coding mutation to species evolution (2).

    Burga et al. searched elements conserved in a human anchored pan-vertebrate 100-way alignment, losing many elements highly conserved among birds. They searched each element against whole genomes, ignoring any synteny information. They demanded a reciprocal best hit in all four cormorant species. Sequencing quality, assembly gaps, or partial non-syntenic matches in any species would disqualify many elements. We thus endeavored to: build a bird-specific whole genome multiple alignment, and define bird-specific conserved elements (3).

    Burga et al. found 40,812 conserved elements, only 11 were accelerated in P.harrisi at 5% false discovery rate (FDR), and none overlapped limb enhancer marks. In comparison, we found 430,015 bird conserved elements, 577 P.harrisi accelerated even at 1% FDR, with 48 overlapping limb enhancer marks (3). Many of these 48 limb enhancers lie next to genes that control the very same processes highli...

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    Competing Interests: None declared.