Accumulation of deleterious mutations
Relaxation of selection can result in an accumulation of deleterious
mutations in the genome. To evaluate whether the genome of the
black-faced spoonbill accumulated a significant number of deleterious
mutations, we counted the number of nonsynonymous substitutions in both
spoonbill species. First, we used ANNOVAR (Wang, Li, &
Hakonarson, 2010) to annotate substitutions in the coding region of both
spoonbill species to two categories, synonymous and non-synonymous
substitutions. Due to the lack of a suitable outgroup, we defined the
dominant allele in a species as the ancestral allele, and the minor
allele as the derived allele. Assuming that non-synonymous substitutions
are deleterious, we counted the number of non-synonymous substitutions
in each individual as accumulated deleterious mutations also known as
genetic load. To further quantify the deleterious effect of
non-synonymous substitutions, we used the Grantham score(Grantham, 1974)
to measure their potential phenotypic effect. The Grantham score
quantifies the differences in physiochemical similarity and evolutionary
exchangeability between two amino acids, where a higher score indicates
more physiochemical difference and lower evolutionary exchangeability
(i.e. higher deleterious phenotypic effect of nonsynonymous
substitution). Grantham scores can be classified into three
categories(Chun & Fay, 2009), conservative changes (0-50), moderate
changes (51-100) and radical changes (>100). Assuming
conservative changes in amino acids to be neutral and different
deleterious non-synonymous substitutions to have an independent and
additive effect, we counted the accumulated deleterious effect of
non-synonymous substitutions by summing up the Grantham scores
categorized as moderate or radical changes for each individual.