  Cryptic genetic sequences have attenuated effects on phenotypes. In the
classic view, relaxed selection allows cryptic genetic diversity to build up
across individuals in a population, providing alleles that may later contribute
to adaptation when co-opted - e.g. following a mutation increasing expression
from a low, attenuated baseline. This view is described, for example, by the
metaphor of the spread of a population across a neutral network in genotype
space. As an alternative view, consider the fact that most phenotypic traits
are affected by multiple sequences, including cryptic ones. Even in a strictly
clonal population, the co-option of cryptic sequences at different loci may
have different phenotypic effects and offer the population multiple adaptive
possibilities. Here, we model the evolution of quantitative phenotypic
characters encoded by cryptic sequences, and compare the relative contributions
of genetic diversity and of variation across sites to the phenotypic potential
of a population. We show that most of the phenotypic variation accessible
through co-option would exist even in populations with no polymorphism. This is
made possible by a history of compensatory evolution, whereby the phenotypic
effect of a cryptic mutation at one site was balanced by mutations elsewhere in
the genome, leading to a diversity of cryptic effect sizes across sites rather
than across individuals. Cryptic sequences might accelerate adaptation and
facilitate large phenotypic changes even in the absence of genetic diversity,
as traditionally defined in terms of alternative alleles.
