The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice, and we discuss how scaling-up to genome-wide inference can benefit traditional conservation genetic approaches and provide qualitatively novel insights. Yet, the generation of genomic data and subsequent analyses and interpretations are still challenging and largely confined to academic research in ecology and 20evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners. 3 Conservation biology and genomicsLike most of the life sciences, conservation biology is being confronted with the challenge of how to integrate the collection and analysis of large-scale genomic data into its toolbox. Conservation biologists pull from a wide array of disciplines in an effort to preserve biodiversity and ecosystem services [1]. Genetic data have helped in this regard by 30 detecting, for example, population substructure, measuring genetic connectivity, and identifying potential risks associated with demographic change and inbreeding [2]. Traditionally, conservation genetics (see Glossary) has relied on a handful of molecular markers ranging from a few allozymes to dozens of microsatellites [3]. But for close to a decade [4], genomics -broadly defined high-throughput sampling of nucleic acids [5] -has been touted as an important advancement to the field, a panacea of sorts for the unresolved conservation problems typically addressed 35 with genetic data [6,7]. This transition has led to much promise, but also hyperbole, where concrete empirical examples of genomic data having a conservation impact remain rare.Under the premise that assisting conservation of the world's biota is its ultimate purpose, the emerging field of conservation genomics must openly and pragmatically discuss its potential contribution towards this goal. While there 40are prominent examples where genetic approaches have made inroads influencing conservation efforts (e.g., Florida panther augmentation [8,9]) and wildlife enforcement (i.e., detecting illegal harvest [10]), it is not immediately clear that the conservation community and society more broadly have embraced genomics as a useful tool for conservation.Maintaining genetic diversity has largely been an afterthought when it comes to national biodiversity policies [11,12], and attempts to identify areas that might prove to be essential for conserving biological diversity rarely mention 45 genomics (e.g. [13,14]). An obvious reason for this disconnect is that many of the pressing conservation issues (e.g., [15,16]) simply do not need genomics, but instead need political will.The traditional use of gene...

Summary 1We studied the performance of 17 Dutch populations of the perennial Succisa pratensis , in relation to population size, genetic variation and habitat quality. We used a path-analytical model to analyse the possible relationships between these variables and performance. 2 Plants in smaller populations produced fewer seeds per flower head. Their seeds had lower germination rates and higher seedling mortality, and more seeds were dormant or non-viable. 3 Population size was also correlated with genetic measures. Small populations had higher inbreeding coefficients than large populations and observed heterozygosity was positively correlated with population size. The mean genetic diversity (expected heterozygosity) was relatively high (H exp = 0.42), but not correlated with population size. 4 Less eutrophic habitats appeared to support larger populations. High concentrations of NH 4 and NO 3 in the soil were significantly negatively correlated with population size. 5 Path-analysis showed that Succisa pratensis is vulnerable to habitat deterioration (eutrophication). Population size was strongly influenced by habitat quality. Reduced performance, however, was better explained by direct genetic effects and by habitat deterioration rather than by effects of population size per se . Both habitat quality and genetic effects are thus important for population persistence, even in the short term. The results suggest that there will be a continuing decline of the small populations, due to deteriorating habitat conditions, decreased genetic variation and a reduced reproductive capacity.

Summary Small and isolated populations of species are susceptible to loss of genetic diversity, owing to random genetic drift and inbreeding. This loss of diversity may reduce the evolutionary potential to adapt to changing environments, and may cause immediate loss of fitness (cf. inbreeding depression). Together with other population size‐dependent stochastic processes, this may lead to increased probabilities of population extinction. This set of processes and theories forms the core of conservation genetics and has developed into the conservation genetics paradigm. Many empirical studies have concentrated on the relationship between population size and genetic diversity, and in many cases evidence was found that small populations of plants do indeed have lower levels of genetic diversity and increased homozygosity. Although less empirical attention has been given to the relationship between low genetic diversity, fitness and, in particular, evolutionary potential, the paradigm is now widely accepted. Here we present five areas of the paradigm which could be refined, i.e. the ‘rough’ edges of the conservation genetics paradigm. Treating population size and isolation not as interchangeable parameters but as separate parameters affecting population genetics in different ways could allow more accurate predictions of the effects of landscape fragmentation on the genetic diversity and viability of populations. There is evidence that inbreeding depression may be a genotype‐specific phenomenon, rather than a population parameter. This sheds new light on the link between population inbreeding depression and the expected increased probability of extinction. Modern eco‐genomics offers the opportunity to study the population genetics of functional genes, to the extent that the role of selection can be distinguished from the effects of drift, and allowing improved insights into the effects of loss of genetic diversity on evolutionary potential. Incorporating multispecies considerations may result in the generally accepted notion that small populations are at peril being called into question. For instance, small populations may be less capable of sustaining parasites or herbivores. Comparative studies of endangered, common and invasive species may be a valuable approach to developing conservation biology from a phenomenological case study discipline into one investigating the general principles of what sustains biodiversity. The issues discussed set an agenda for further research within conservation genetics and may lead to a further refinement of our understanding and prediction of the genetic effects of habitat fragmentation. They also underline the need to integrate ecological and genetic approaches to the conservation of biodiversity, rather than regarding them as opposites.

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.

Summary• The effects of increasing ammonium concentrations in combination with different pH levels were studied on five heathland plant species to determine whether their occurrence and decline could be attributed to ammonium toxicity and/or pH levels.• Plants were grown in growth media amended with four different ammonium concentrations (10, 100, 500 and 1000 µmol l − 1 ) and two pH levels resembling acidified (pH 3.5 or 4) and weakly buffered (pH 5 or 5.5) situations.• Survival of Antennaria dioica and Succisa pratensis was reduced by low pH in combination with high ammonium concentrations. Biomass decreased with increased ammonium concentrations and decreasing pH levels. Internal pH of the plants decreased with increasing ammonium concentrations. Survival of Calluna vulgaris , Deschampsia flexuosa and Gentiana pneumonanthe was not affected by ammonium. Moreover, biomass increased with increasing ammonium concentrations. Biomass production of G. pneumonanthe reduced at low pH levels.• A decline of acid-sensitive species in heathlands was attributed to ammonium toxicity effects in combination with a low pH.

Inbreeding depression (i.e. negative fitness effects of inbreeding) is central in evolutionary biology, affecting numerous aspects of population dynamics and demography, such as the evolution of mating systems, dispersal behaviour and the genetics of quantitative traits. Inbreeding depression is commonly observed in animals and plants. Here, we demonstrate that, in addition to genetic processes, epigenetic processes may play an important role in causing inbreeding effects. We compared epigenetic markers of outbred and inbred offspring of the perennial plant Scabiosa columbaria and found that inbreeding increases DNA methylation. Moreover, we found that inbreeding depression disappears when epigenetic variation is modified by treatment with a demethylation agent, linking inbreeding depression firmly to epigenetic variation. Our results suggest an as yet unknown mechanism for inbreeding effects and demonstrate the importance of evaluating the role of epigenetic processes in inbreeding depression.

While it is well established that ecosystems display strong responses to elevated nitrogen deposition, the importance of the ratio between the dominant forms of deposited nitrogen (NH(x) and NO(y)) in determining ecosystem response is poorly understood. As large changes in the ratio of oxidised and reduced nitrogen inputs are occurring, this oversight requires attention. One reason for this knowledge gap is that plants experience a different NH(x):NO(y) ratio in soil to that seen in atmospheric deposits because atmospheric inputs are modified by soil transformations, mediated by soil pH. Consequently species of neutral and alkaline habitats are less likely to encounter high NH(4)(+) concentrations than species from acid soils. We suggest that the response of vascular plant species to changing ratios of NH(x):NO(y) deposits will be driven primarily by a combination of soil pH and nitrification rates. Testing this hypothesis requires a combination of experimental and survey work in a range of systems.

Habitat fragmentation and climate change are recognized as major threats to biodiversity. The major challenge for present day plant populations is how to adapt and cope with altered abiotic and biotic environments caused by climate change, when at the same time adaptive and evolutionary potential is decreased as habitat fragmentation reduces genetic variation and increases inbreeding. Although the ecological and evolutionary effects of fragmentation and climate change have been investigated separately, their combined effects remained largely unexplored. In this review, we will discuss the individual and joint effects of habitat fragmentation and climate change on plants and how the abilities and ways in which plants can respond and cope with climate change may be compromised due to habitat fragmentation.