Given an observed parallel substitution between a pair of branches, we classified it as a radical amino acid substitution if the ancestral and the derived amino acid belong to a different physicochemical group, using an amino acid classification that is based on charge, polarity, and aromaticity: aliphatic and nonpolar (A,I,L,M,V,G), polar and uncharged (S,T,C,P,N,Q), positive charge (R,K,H), negative charge (E,D), and nonpolar and aromatic (F,W,Y). A parallel substitution in a conserved position satisfies the following two criteria. First, all species that descend from both branches share the derived amino acid. Second, at least 90% of the species outside of the two convergent lineages share the ancestral amino acid (fig. S1, B to E). By filtering for radical substitutions in conserved positions, we enrich for parallel substitutions that are more likely to affect protein function, regardless of whether these amino acid substitutions involve a single or more than one nucleotide mutation.

Note: The content above has been extracted from a research article, so it may not display correctly.

Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.

We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.