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    1. Biochemistry and Chemical Biology
    2. Evolutionary Biology

    Functional trade-offs and environmental variation shaped ancient trajectories in the evolution of dim-light vision

    Gianni M Castiglione, Belinda SW Chang
    The evolution of the light-sensitive visual pigment rhodopsin involved functional tradeoffs that may have sacrificed rod photosensitivity for active-state protein stability to mitigate phototoxicity in tetrapods, but not in fishes.
    1. Evolutionary Biology

    Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment

    Erik M Quandt et al.
    A long-term evolution experiment with Escherichia coli shows that the appearance and optimization of a new trait can require both co-opting existing cellular pathways for new roles and reversing a history of previous adaptation.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    A map of directional genetic interactions in a metazoan cell

    Bernd Fischer et al.
    A systematic analysis of gene–gene dependencies using high-throughput imaging of cells detects causal and temporal relationships between genes.
    1. Computational and Systems Biology

    The genetic landscape of a physical interaction

    Guillaume Diss, Ben Lehner
    First comprehensive analysis of how many different mutations combine within and between two genes to alter a molecular phenotype.
    1. Evolutionary Biology
    2. Microbiology and Infectious Disease

    Mapping mutational effects along the evolutionary landscape of HIV envelope

    Hugh K Haddox et al.
    Deep mutational scanning of Env proteins from two transmitted-founder strains of HIV shows how the accessible evolutionary space changes as the virus evolves.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Fitness benefits in fluoroquinolone-resistant Salmonella Typhi in the absence of antimicrobial pressure

    Stephen Baker et al.
    The major evolutionary routes to drug resistance in Salmonella Typhi are associated with fitness benefits, not fitness costs, implying that prudent antimicrobial use will have no effect as a public health intervention in controlling typhoid fever.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Two locus inheritance of non-syndromic midline craniosynostosis via rare SMAD6 and common BMP2 alleles

    Andrew T Timberlake et al.
    Epistatic interactions of rare loss of function mutations in SMAD6 and a common variant modifier near BMP2 are the most common cause of midline craniosynostosis in humans.
    1. Evolutionary Biology

    Metabolism: Evolution retraces its steps to advance

    Daniel J Kliebenstein
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    1. Biochemistry and Chemical Biology
    2. Computational and Systems Biology

    Coevolution-based inference of amino acid interactions underlying protein function

    Victor H Salinas, Rama Ranganathan
    A deep mutational coupling study demonstrates the ability of sequence coevolution methods to reveal the pattern of amino acid interactions underlying protein function.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Science Forum: Viral factors in influenza pandemic risk assessment

    Marc Lipsitch et al.
    We identify key strengths and limitations in use of viral genotyping and phenotyping to estimate pandemic risk from influenza A viruses, focusing on 3 traits, hemagglutinin binding specificity, hemagglutinin pH of activation, and polymerase complex efficiency.