N. Joop Ouborg

Conservation genetics in transition to conservation genomics.

Over the past twenty years conservation genetics has progressed from being mainly a theory-based field of population biology to a full-grown empirical discipline. Technological developments in molecular genetics have led to extensive use of neutral molecular markers such as microsatellites in conservation biology. This has allowed assessment of the impact of genetic drift on genetic variation, of the level of inbreeding within populations, and of the amount of gene flow between or within populations. Recent developments in genomic techniques, including next generation sequencing, whole genome scans and gene-expression pattern analysis, have made it possible to step up from a limited number of neutral markers to genome-wide estimates of functional genetic variation. Here, we focus on how the transition of conservation genetics to conservation genomics leads to insights into the dynamics of selectively important variation and its interaction with environmental conditions, and into the mechanisms behind this interaction.

Genomics and the challenging translation into conservation practice

The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. 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.

Habitat fragmentation, climate change, and inbreeding in plants

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.

Early Root Overproduction Not Triggered by Nutrients Decisive for Competitive Success Belowground

Background Theory predicts that plant species win competition for a shared resource by more quickly preempting the resource in hotspots and by depleting resource levels to lower concentrations than its competitors. Competition in natural grasslands largely occurs belowground, but information regarding root interactions is limited, as molecular methods quantifying species abundance belowground have only recently become available. Principal Findings In monoculture, the grass Festuca rubra had higher root densities and a faster rate of soil nitrate depletion than Plantago lanceolata, projecting the first as a better competitor for nutrients. However, Festuca lost in competition with Plantago. Plantago not only replaced the lower root mass of its competitor, but strongly overproduced roots: with only half of the plants in mixture than in monoculture, Plantago root densities in mixture were similar or higher than those in its monocultures. These responses occurred equally in a nutrient-rich and nutrient-poor soil layer, and commenced immediately at the start of the experiment when root densities were still low and soil nutrient concentrations high. Conclusions/Significance Our results suggest that species may achieve competitive superiority for nutrients by root growth stimulation prior to nutrient depletion, induced by the presence of a competitor species, rather than by a better ability to compete for nutrients per se. The root overproduction by which interspecific neighbors are suppressed independent of nutrient acquisition is consistent with predictions from game theory. Our results emphasize that root competition may be driven by other mechanisms than is currently assumed. The long-term consequences of these mechanisms for community dynamics are discussed.

Evaluation of the extent of among-family variation in inbreeding depression in the perennial herb Scabiosa columbaria (Dipsacaceae).

Significantly different maternal line responses to inbreeding provide a mechanism for the invasion of a selfing variant into a population. The goal of this study was to examine the extent of family-level variation in inbreeding depression in the mixed-mating, perennial herb Scabiosa columbaria. Plants from one population were raised, and hand-pollinated to produce selfed and outcrossed progeny, and the effects of inbreeding depression on life-cycle traits were analyzed. Inbreeding depression significantly affected early life cycle traits. The pollination treatment by family interaction was significant for almost all traits, indicating a high family-level variation in inbreeding depression. The correlations between inbreeding depression values (e.g., percentage germination and flowering date, and flowering date and aboveground biomass) exhibited alternate signs, illustrating the type of association between inbreeding depression loci for different traits across the life cycle. Overall, it is concluded that the extent of among-family variation in inbreeding depression might allow a selfing variant of S. columbaria to invade an outcrossing population, though the pattern of correlations between inbreeding depression values might prevent effective purging of the deleterious genetic load.

An essay on the necessity and feasibility of conservation genomics

The basic premise of conservation genetics is that small populations may be genetically threatened. The two steps leading to this premise are: (1) due to prominent influence of random genetic drift and inbreeding allelic and genotypic diversity in small populations is expected to be low, and (2) low allelic diversity and high homozygosity are expected to lead to immediate fitness decreases (inbreeding depression) and a compromised potential for evolutionary adaptation. Conservation genetic research has been strongly stimulated by the application of neutral molecular markers like microsatellites and AFLPs. In general these marker studies have provided evidence for step 1. It is less evident how these markers may provide evidence for step 2. In this essay we argue that, in order to get detailed insight in step 2, adopting a conservation genomic approach, in which conservation genetics will use approaches from ecological and evolutionary functional genomics (ecogenomics), is both necessary and feasible. Conservation genomics is necessary for studying functional genomic variation as function of drift and inbreeding, for studying the mechanisms that relate low genetic variation to low fitness, for integrating environmental and genetic approaches to conservation biology, and for developing modern, fast monitoring tools. The rapid technical and financial developments in genomics currently make conservation genomics feasible, and will improve feasibility in the very near future even further. We therefore argue that conservation genomics personifies part of the near future of conservation genetics.

GENETICALLY BASED POLYMORPHISMS IN MORPHOLOGY AND LIFE HISTORY ASSOCIATED WITH PUTATIVE HOST RACES OF THE WATER LILY LEAF BEETLE, GALERUCELLA NYMPHAEAE

Abstract A host race is a population that is partially reproductively isolated from other conspecific populations as a direct consequence of adaptation to a specific host. The initial step in host race formation is the establishment of genetically based polymorphisms in, for example, morphology, preference, or performance. In this study we investigated whether polymorphisms observed in Galerucella nymphaeae have a genetic component. Galerucella nymphaeae, the water lily leaf beetle, is a herbivore which feeds and oviposits on the plant hosts Nuphar lutea and Nymphaea alba (both Nymphaeaceae) and Rumex hydrolapathum and Polygonum amphibium (both Polygonaceae).

Effects of Multi-Generational Stress Exposure and Offspring Environment on the Expression and Persistence of Transgenerational Effects in Arabidopsis thaliana

Plant phenotypes can be affected by environments experienced by their parents. Parental environmental effects are reported for the first offspring generation and some studies showed persisting environmental effects in second and further offspring generations. However, the expression of these transgenerational effects proved context-dependent and their reproducibility can be low. Here we study the context-dependency of transgenerational effects by evaluating parental and transgenerational effects under a range of parental induction and offspring evaluation conditions. We systematically evaluated two factors that can influence the expression of transgenerational effects: single- versus multiple-generation exposure and offspring environment. For this purpose, we exposed a single homozygous Arabidopsis thaliana Col-0 line to salt stress for up to three generations and evaluated offspring performance under control and salt conditions in a climate chamber and in a natural environment. Parental as well as transgenerational effects were observed in almost all traits and all environments and traced back as far as great-grandparental environments. The length of exposure exerted strong effects; multiple-generation exposure often reduced the expression of the parental effect compared to single-generation exposure. Furthermore, the expression of transgenerational effects strongly depended on offspring environment for rosette diameter and flowering time, with opposite effects observed in field and greenhouse evaluation environments. Our results provide important new insights into the occurrence of transgenerational effects and contribute to a better understanding of the context-dependency of these effects.

Belowground DNA-based techniques: untangling the network of plant root interactions

Plant roots are a central driver of ecosystem productivity, as plant investments belowground often comprise more than half of total plant biomass (Jackson et al. 1996). Despite this general observation, almost nothing is known about the distribution of roots in ecosystems; generally because roots of different species are morphologically indistinguishable, restricting species identification. This is in strict contrast to plant identification aboveground, which is straightforward after initial taxonomic training. Although in species poor systems containing roots of two species morphological identification has been possible in a few cases (Genney et al. 2002; Janecek et al. 2004; Mommer et al. 2011), disentangling and identifying roots from species-rich systems is impossible. To overcome problems of species identification, pioneering DNA-based techniques have been applied to plant roots (Jackson et al. 1999; Linder et al. 2000) and are now being used in experimental and observational studies of species-rich plant communities (e.g. Mommer et al. 2010; Kesanakurti et al. 2011; Dumbrell et al. 2011). In this paper, we discuss the current state of molecular techniques for plant species identification and quantification from mixed root samples. We focus on crucial aspects in the methodology regarding primer choice, DNA extraction and PCR inhibition, showing the potential caveats and their solutions. Finally we briefly discuss a few questions in the field of root ecology that will be advanced significantly by the appropriate use of these molecular tools.

Differences in morphology and reproductive traits of Galerucella nymphaeae from four host plant species

The water lily beetle Galerucella nymphaeae L. (Coleoptera: Chrysomelidae) exploits different hosts, including Nuphar lutea Sm. and Nymphaea alba L. (both Nymphaeaceae), as well as Polygonum amphibium L. and Rumex hydrolapathum Hudson (both Polygonaceae). The present study investigates whether within‐species differences in morphological and reproductive traits are associated with differences in host species exploitation. A total of 1103 adult beetles were collected from 11 localities in The Netherlands, one of which contained all four hosts and three other localities contained hosts from both families (sympatric localities). Adults originating from Nuphar and Nymphaea were on average darker in colour and larger in size and had disproportionally bigger mandibles than beetles originating from Polygonum and Rumex across the 11 localities. Head capsules of first instar larvae from Nymphaeaceae hosts were between 17% and 28% larger than those of larvae from Polygonaceae hosts. Furthermore, beetles from Nuphar and Nymphaea laid larger sized eggs, but fewer eggs per clutch than beetles originating from Polygonum and Rumex. Although host related variation was less pronounced at the sympatric localities than in the allopatric localities, differences in larval and adult size were still highly significant at the sympatric localities. It is not clear whether the observed differences are genetically based, as opposed to host induced. However, leaf toughness varied among species in a way suggesting that leaf toughness may be partly responsible for host related differences in G. nymphaeae.