Evolution, Tout de Suite | The Scientist

Evolution, Tout de Suite | The Scientist: Frank Johannes at the University of Groningen in The Netherlands has been trying to understand the intricacies of epigenetic inheritance—specifically, how methylation of DNA bases can contribute to the inheritance of particular characteristics in Arabidopsis. “People are beginning to speculate,” he says. “ ‘ Wait a minute. What’s going on in nature? Does this contribute significantly to adaptation?’ ”

But it’s hard to tell in most natural populations whether inheritance is due to DNA sequence variation or epigenetic changes. “We cannot delineate these two causes very well,” Johannes says. So with his collaborator, Fabrice Roux at the University of Science and Technology in Lille, France, he has been studying a large population of Arabidopsis plants with disrupted methylation patterns. The plants were derived from two Arabidopsis parents with essentially identical genomes, but with one having a mutated DDM1 DNA methylation gene. DDM1 is required for normal methylation—the conversion of cytosine, in cytosine-guanine pairs in the DNA, into 5-methylcytosine—and its mutation reduces genomic methylation by 70 percent.

The reduction of mutation allows more random evolution to predominate such as random matings, more normal offspring from this tend to the center of the normal curve and deviants to this are often less fit and survive less often. Methylation however can be chaotic, it creates a change here in one plant that affects how and where it grows in the next generation, which in turn can affect how often it seeds and where it gets pollen from. Increasing the mutation rate through epigenetics can allow V-Bi plants that evolve randomly to innovate more as Iv-B plants. For example this methylation switch might be turned on and off randomly, if conditions are stable then this might switch it off partially. If conditions change then the suppression of this methylation switch might be lost and the plant innovates with mutations until it reaches a stable environment again when this methylation is switched off again. This behavior would be an evolutionary advantage so a methylation switch like this is more likely to evolve than one for example that only switched on in stable environments or was random.

A team headed by Vincent Colot, now at the École Normale Supérieure in Paris, backcrossed the first generation offspring and selected progeny that were homozygous for the wild type DDM1 gene; in other words, with fully functional methylation machinery. They propagated the plants through a further six rounds of inbreeding, creating “epigenetic recombinant inbred lines” (epiRILs), which carried a mosaic of the parental epigenome. When Roux grew them in a common garden in northern France to subject the almost 6,000 plants to “realistic” ecological selection, they found that the epiRILs yielded plants with distinctly different phenotypes despite being effectively genetically identical.
The segregation and heritability of these traits—which included flowering time and plant height—mirrored those found in naturally divergent Arabidopsis populations, in which phenotypic variation represents adaptations to different environmental conditions. But natural populations have had thousands of years to generate these variations: the epiRILs managed to do it in just eight generations. Andrew Hudson at the University of Edinburgh says there is a clear implication that “DNA methylation and epigenetic changes are important in evolution.”