title: Genome-wide signature of local adaptation linked to variable CpG methylation in oak populations.
abstract: It has long been known that adaptive evolution can occur through genetic mutations in DNA sequence, but it is unclear whether adaptive evolution can occur through analogous epigenetic mechanisms, such as through DNA methylation. If epigenetic variation contributes directly to evolution, species under threat of disease, invasive competition, climate change or other stresses would have greater stores of variation from which to draw. We looked for evidence of natural selection acting on variably methylated DNA sites using population genomic analysis across three climatologically distinct populations of valley oaks. We found patterns of genetic and epigenetic differentiations that indicate local adaptation is operating on large portions of the oak genome. While CHG methyl polymorphisms are not playing a significant role and would make poor targets for natural selection, our findings suggest that CpG methyl polymorphisms as a whole are involved in local adaptation, either directly or through linkage to regions under selection.
authors.affiliation: Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Dr. E., Los Angeles, CA, 90095, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Platt
authors.affiliation: Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Dr. E., Los Angeles, CA, 90095, USA.
authors.forename: Paul F
authors.initials: PF
authors.lastname: Gugger
authors.affiliation: Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Dr. E., Los Angeles, CA, 90095, USA.
authors.forename: Matteo
authors.initials: M
authors.lastname: Pellegrini
authors.affiliation: Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Dr. E., Los Angeles, CA, 90095, USA.
authors.forename: Victoria L
authors.initials: VL
authors.lastname: Sork
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D002140:California; D018899:CpG Islands; D019175:DNA Methylation; D018744:DNA, Plant / Q000235:genetics; D044127:Epigenesis, Genetic; D005828:Genetics, Population; D011110:Polymorphism, Genetic; D029963:Quercus / Q000235:genetics*; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant
keywords: adaptation; angiosperms; bioinformatics/phyloinformatics; biotechnology; ecological genetics; natural selection and contemporary evolution