Genetic and epigenetic divergence between disturbed and undisturbed subpopulations of a Mediterranean shrub:a 20-year field experiment

Little is known on the potential of ecological disturbance to cause genetic andepigenetic changes in plant populations. We take advantage of a long-term fieldexperiment initiated in 1986 to study the demography of the shrub Lavandulalatifolia, and compare genetic and epigenetic characteristics of plants in twoadjacent subplots, one experimentally disturbed and one left undisturbed,20 years after disturbance. Experimental setup was comparable to an unrepli-cated ‘Before-After-Control-Impact’ (BACI) design where a single pair of per-turbed and control areas were compared. When sampled in 2005, plants in thetwo subplots had roughly similar ages, but they had established in contrastingenvironments: dense conspecific population (‘Undisturbed’ subpopulation) ver-sus open area with all conspecifics removed (‘Disturbed’ subpopulation). Plantswere characterized genetically and epigenetically using amplified fragmentlength polymorphism (AFLP) and two classes of methylation-sensitive AFLP(MSAP) markers. Subpopulations were similar in genetic diversity but differedin epigenetic diversity and multilocus genetic and epigenetic characteristics.Epigenetic divergence between subpopulations was statistically unrelated togenetic divergence. Bayesian clustering revealed an abrupt linear boundarybetween subpopulations closely coincident with the arbitrary demarcation linebetween subplots drawn 20 years back, which supports that genetic and epige-netic divergence between subpopulations was caused by artificial disturbance.There was significant fine-scale spatial structuring of MSAP markers in bothsubpopulations, which in the Undisturbed one was indistinguishable from thatof AFLP markers. Genetic differences between subpopulations could beexplained by divergent selection alone, while the concerted action of divergentselection and disturbance-driven appearance of new methylation variants in theDisturbed subpopulation is proposed to explain epigenetic differences. Thisstudy provides the first empir