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    AN IMPROVED METRIC OF CODON ADAPTATION SHOWS SELECTION FOR DISORDER IN VERTEBRATE PROTEIN DOMAINS

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    Author
    WEIBEL, CATHERINE ANNE
    Issue Date
    2021
    Advisor
    Masel, Joanna
    
    Metadata
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    Publisher
    The University of Arizona.
    Rights
    Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
    Abstract
    The effectiveness of selection varies among species. It is often estimated by means of an “effective population size” based on neutral polymorphism, but this is confounded in complex ways with demography. The strength of codon bias more directly pertains to how well adaptation at many sites can be maintained in the face of deleterious mutations, but past metrics that compare codon bias across species are confounded by among-species variation in %GC content and/or amino acid composition. Here we propose a new Codon Adaptation Index of Species (CAIS) that corrects for both confounders. Unlike previous metrics, CAIS yields the expected relationship with adult vertebrate body mass. As an example of the use of CAIS, we ask whether protein domains evolve lower intrinsic structural disorder (ISD) when present in more exquisitely adapted species, as expected given that ISD is higher in eukaryotic proteomes than prokaryotic proteomes. Using phylogenetically corrected linear models, we find, contrary to expectations, that the ISD of a given protein domain evolves to be higher when in well- adapted species. This effect is stronger in young protein domains but is also present in ancient domains.
    Type
    Electronic thesis
    text
    Degree Name
    B.S.
    Degree Level
    bachelors
    Degree Program
    Mathematics
    Honors College
    Degree Grantor
    University of Arizona
    Collections
    Honors Theses

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