Epigenetics and the evolution of darwin's finches

Abstract

Theprevailing theory for themolecular basisof evolution involves geneticmutations that ultimately generate theheritable phenotypic variation onwhich natural selection acts.However, epigenetic transgenerational inheritance of phenotypic variationmay also play an important role in evolutionary change. A growing number of studies have demonstrated the presence of epigenetic inheritance in a variety of different organisms that can persist for hundreds of generations. The possibility that epigenetic changes can accumulate over longer periods of evolutionary time has seldombeen testedempirically. This study was designed to compare epigenetic changes among several closely related species of Darwin's finches, a well-known example of adaptive radiation. Erythrocyte DNA was obtained from five species of sympatric Darwin's finches that vary in phylogenetic relatedness. Genome-wide alterations in genetic mutations using copy number variation (CNV) were compared with epigenetic alterations associated with differential DNA methylation regions (epimutations). Epimutationsweremore common than genetic CNVmutations among the five species; furthermore, the number of epimutations increased monotonically with phylogenetic distance. Interestingly, the number of genetic CNV mutations did not consistently increase with phylogenetic distance. The number, chromosomal locations, regional clustering, and lack of overlap of epimutations and genetic mutations suggest that epigenetic changes are distinct and that they correlate with the evolutionary history of Darwin's finches. The potential functional significance of the epimutations was explored by comparing their locations on the genome to the location of evolutionarily important genes and cellular pathways in birds. Specific epimutationswere associated with genes related to the bone morphogenic protein, toll receptor, and melanogenesis signaling pathways. Speciesspecific epimutationswere significantly overrepresented in these pathways.As environmental factors are known to result in heritable changes intheepigenome, it ispossible that epigenetic changes contribute tothemolecularbasis of the evolutionof Darwin'sfinches. © The Author(s) 2014.