We describe epiGBS, a reduced representation bisulfite sequencing method for cost-effective exploration and comparative analysis of DNA methylation and genetic variation in hundreds of samples de novo. This method uses genotyping by sequencing of bisulfite-converted DNA followed by reliable de novo reference construction, mapping, variant calling, and distinction of single-nucleotide polymorphisms (SNPs) versus methylation variation (software is available at https://github.com/thomasvangurp/epiGBS). The output can be loaded directly into a genome browser for visualization and into RnBeads for analysis of differential methylation.

Conservation genetics is expanding its research horizon with a genomic approach, by incorporating the modern techniques of next-generation sequencing (NGS). Application of NGS overcomes many limitations of conservation genetics. First, NGS allows for genome-wide screening of markers, which may lead to a more representative estimation of genetic variation within and between populations. Second, NGS allows for distinction between neutral and non-neutral markers. By screening populations on thousands of single nucleotide polymorphism markers, signals of selection can be found for some markers. Variation in these markers will give insight into functional rather than neutral genetic variation. Third, NGS facilitates the study of gene expression. Conservation genomics will increase our insight in how the environment and genes interact to affect phenotype and fitness. In addition, the NGS approach opens a way to study processes such as inbreeding depression and local adaptation mechanistically. Conservation genetics programs are directed to a fundamental understanding of the processes involved in conservation genetics and should preferably be started in species for which large databases on ecology, demography and genetics are available. Here, we describe and illustrate the connection between the application of NGS technologies and the research questions in conservation. The perspectives of conservation genomics programs are also discussed.

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In this study we investigated the possibilities for host race formation in Galerucella nymphaeae. This is a chrysomelid beetle feeding on four different hosts, belonging to two different plant families, the Nymphaeaceae and Polygonaceae. Previous results showed that beetles living on the two different host families differ in morphology, i.e., body length, mandibular width, and color of the elytra. In the current study, the preference of G. nymphaeae for four hosts was investigated, together with larval performance on these hosts. In a multichoice experiment, both parents and offspring showed a strong feeding preference for their natal host plant family: between 88-98% of the total consumption consisted of the natal host plant family. Females preferred to lay eggs on their natal host family: 81-100% of the egg clutches were laid on the natal host family. Host preference was accompanied by differences in offspring performance. Offspring survival was 1.2-25 times as high on the host family from which their parents originated than on the hosts of the other plant family. Furthermore, larval development tended to progress faster on the natal than on the other host family. Since the beetles use their host plant as a mating place, positive assortative mating is a likely consequence of the beetles' host preference. Together, these results suggest that there are two host races of G. nymphaeae: one living on Nymphaeaceae and the other on Polygonaceae.

The frequency of annuals, monocarpic perennials and polycarpic perennials among the dicotyledonous, herbaceous representatives of the European plant families are compared and related to various characteristics of plant architecture. It is suggested that the evolution of life-history may be governed by plant architecture. A comparison between annual and biennial Centaurium species suggests that the selective advantage of bienniality could relate to the production of a large stem within a short period. The typical architecture of a monocarpic perennial does not automatically imply an allometric relation between seed production and plant size. Size-dependent seed allocation, when present, is due to disproportionality between the plant's size and the amount of resources available for reproductive allocation, and not to the size constraints imposed by the plant's architecture. The evolution of monocar pic perenniality is therefore not a simple allometric step. Interpopulation differences in seed allocation may arise from differences in the nature or the availability of that particular resource that limits the reproductive allocation of biomass, and do not necessarily reflect differences in partitioning strategies.