Dr. Koen Verhoeven

• Ecological epigenetics: causes and consequences of natural epigenetic variation in asexual plants (VIDI project 2011-2016; with Carla Oplaat and Julie Ferreira de Carvalho): In recent years it has become clear that epigenetic mechanisms such as DNA methylation can be responsible for stable and heritable variation in plant traits, also in absence of sequence variation. The question now is if, or to what extent, epigenetic inheritance contributes to heritable variation and adaptation in nature. We address this question in apomictic dandelions – apomicts are nice models for exploring causes and consequences of epigenetic variation that is not confounded with genetic variation. We study transgenerational consequences of stress at the level of DNA methylation, metabolomes, transcriptomes and traits, and we address consequences of stress-induced variation for selection and under natural conditions. We also explore natural, heritable epigenetic variation that has built up between clone members within widespread apomictic dandelion lineages - does such variation contribute to within-lineage adpative differentiation?

Stress exposure triggers DNA methylation changes at msAFLP loci that are transmitted to offspring

• Epigenetic variation in natural populations: effects of range expansion and climate change (PhD project Veronica Preite, in collaboration with Wim van der Putten): Apomicts have limited potential for genetic adaptation, yet individual apomictic dandelion lineages are very successful range expanders and biological invaders. Epigenetic variation may play a relevant role in adaptation of such lineages. We study the epigenetic consequences of exposure to novel natural environments in apomictic dandelions, both experimentally (in reciprocal field transplants and in greenhouse experiments) and in natural populations along a south-north transect of postglacial range expansion. We test if this historic and climate change-induced range expansion has left an epigenetic footprint in the plants’ genomes.

PhD students Thomas van Gurp and Veronica Preite visiting with Taraxacum experts Jan Kirschner and Jan Stepanek, Czech Botanical Institute, Pruhonice

• Transgenerational effects of stress: ecological genomics approaches (PhD project Thomas van Gurp, in collaboration with Arjen Biere): We use next generation sequencing to characterize the heritable consequences of stress exposure for gene expression in subsequent generations (RNA-seq), and we explore its use for high-density methylation genotyping in the dandelion system. These methods are applied to gain more insight in the underlying mechanisms of stress-induced transgenerational effects and epigenetic inheritance. For instance, can we detect effects on gene expression that persist for multiple unexposed generations? And which loci undergo DNA methylation changes upon stress exposure? We also test if we can artificially select on induced epigenetic variation, in populations that lack genetic (sequence) variation.

• Plant-pathogen interactions and sex-asex variation in dandelions: The common dandelion has both sexually reproducing and apomictic genotypes. This natural sex-asex variation can be used to empirically test ecological predictions of the Red Queen hypothesis that coevolution with specialized pests and pathogens selects for host sexual reproduction. I explored this during a 2005-2009 VENI postdoc project. Continued work is establishing a long term time series in a single apomictic dandelion population in which we track clonal host frequencies and infection patterns by a specialized rust fungus. This can reveal negative frequency dependent selection and its temporal dynamics, a hallmark prediction of the Red Queen.

      
Dandelion sex-asex variation shows a classical pattern of geographic parthenogenesis (left); rust-infected capitulum (right)

• Effects of population admixture in native and invasive Lythrum populations (PhD student Jun Shi, co-supervised with Mirka Macel and based at Tübingen University): Post-introduction evolution is an important factor in the invasive success of introduced species. We study the interplay between local adaptation, inbreeding depression and population admixture in Lythrum salicaria populations, and we compare this between native and invasive ranges in order to gain insight in how local adaptation affects strategies to maintain high population fitness. Special emphasis is on the effects of invasion and admixture on plant chemical defenses, and we aim to measure selection on chemical defenses in native and invasive populations.