Complementary genomic and epigenomic adaptation to environmental heterogeneity

While adaptation is commonly thought to result from selection on DNA
sequence-based variation, recent studies have highlighted an analogous
epigenetic component as well. However, the relative roles of these
mechanisms in facilitating population persistence under environmental
heterogeneity remain unclear. To address the underlying genetic and
epigenetic mechanisms and their relationship during environmental
adaptation, we screened the genomes and epigenomes of nine global
populations of a predominately sessile marine invasive tunicate, Botryllus
schlosseri. We detected clear population differentiation at the genetic
and epigenetic levels. Patterns of genetic and epigenetic structure were
significantly influenced by local environmental variables. Among these
variables, minimum annual sea surface temperature was simultaneously
identified as the top explanatory variable for both genetic and epigenetic
variation. However, patterns of population structure driven by genetic and
epigenetic variation were somewhat distinct, suggesting possible autonomy
of epigenetic variation. We found both shared and specific genes and
biological pathways among genetic and epigenetic loci associated with
environmental factors, consistent with complementary and independent
contributions of genetic and epigenetic variation to environmental
adaptation in this system. Collectively, these mechanisms may facilitate
population persistence under environmental change and sustain successful
invasions across novel environments.