In today’s world, rapid environmental and economic developments and changes pose major threats to ecosystems and economic systems. In this context we explore if resilience can be increased by the spatial configuration of the rural landscape in an integrated ecological-genetic-economic way. We study the concept of landscape diversity from genetic, ecological and economic perspectives. We show that small-scale landscapes are potentially more resilient than large-scale landscapes, provided that ecosystem patch sizes are sufficiently large to support genetic diversity and ecosystem and economic functions. The basic premise underlying this finding is that more variation in a landscape generally leads to greater genetic and species diversity. This, in turn, stabilizes populations and strengthens the different ecosystem elements in the landscape. Greater variation in ecosystem elements provides for more varied ecosystem services, which may enhance the resilience of the local economy. We conclude that a resilient landscape is shaped within the context of economic and ecological possibilities and constraints, and is determined by landscape diversity and spatial organisation.

Black grouse (Tetrao tetrix) in Central Europe have undergone a severe contraction of their range in recent decades with only a few small isolated remaining populations. Here we compare genetic diversity of two contemporary isolated populations (Sallandse Heuvelrug, Netherlands and Lüneburger Heide, Germany) with historical samples from the same region collected within the last one hundred years. We use markers with both putatively neutral and functional variation to test whether the present small and highly fragmented populations hold lower genetic diversity compared to the former larger population. For this we applied three different types of genetic markers: nine microsatellites and 21 single nucleotide polymorphisms (SNPs), both sets which have been found to be neutral, and two functional major histocompatibility complex (MHC) genes for which there is evidence they are under selection. The contemporary small isolated populations displayed lower neutral genetic diversity compared to the corresponding historical samples. Furthermore, samples from Denmark showed that this now extinct population displayed lower genetic variation in the period immediately prior to the local extinction. Population structure was more pronounced among contemporary populations compared to historical populations for microsatellites and SNPs. This effect was not as distinct for MHC which is consistent with the possibility that MHC has been subjected to balancing selection in the past, a process which maintains genetic variation and may minimize population structure for such markers. Genetic differentiation among the present populations highlights the strong effects of population decline on the genetic structure of natural populations, which can be ultimately attributed to habitat loss following anthropogenic land use changes.

In crosses between evolutionarily diverged populations, genomic incompatibilities may result in sterile hybrids, indicating evolution of reproductive isolation. In several plant families, crosses within a population can also lead to male sterile progeny because of conflict between the maternally and biparentally inherited genomes. We examined hybrid fertility between subspecies of the perennial outcrossing self-incompatible Lyrate rockcress (Arabidopsis lyrata) in large reciprocal F2 progenies and three generations of backcrosses. In one of the reciprocal F2 progenies, almost one-fourth of the plants were male-sterile. Correspondingly, almost one-half of the plants in one of the four reciprocal backcross progenies expressed male sterility. In an additional four independent F2 and backcross families, three segregated male sterility. The observed asymmetrical hybrid incompatibility is attributable to male sterility factors in one cytoplasm, for which the other population lacks effective fertility restorers. Genotyping of 96 molecular markers and quantitative trait locus mapping revealed that only 60% of the plants having the male sterile cytoplasm and lacking the corresponding restorers were phenotypically male-sterile. Genotyping data showed that there is only one restorer locus, which mapped to a 600-kb interval at the top of chromosome 2 in a region containing a cluster of pentatricopeptide repeat genes. Male fertility showed no trade-off with seed production. We discuss the role of cytoplasm and genomic conflict in incipient speciation and conclude that cytoplasmic male sterility-lowering hybrid fitness is a transient effect with limited potential to form permanent reproductive barriers between diverged populations of hermaphrodite self-incompatible species.

Understanding the interactions of co‐occurring species within and across trophic levels provides key information needed for understanding the ecological and evolutionary processes that underlie biological diversity. As genetics has only recently been integrated into the study of community‐level interactions, the time is right for a critical evaluation of potential new, gene‐based approaches to studying communities. Next‐generation molecular techniques, used in parallel with field‐based observations and manipulative experiments across spatio‐temporal gradients, are key to expanding our understanding of community‐level processes. Here, we introduce a variety of ‘‐omics’ tools, with recent studies of plant–insect herbivores and of ectomycorrhizal systems providing detailed examples of how next‐generation approaches can revolutionize our understanding of interspecific interactions. We suggest ways that novel technologies may convert community genetics from a field that relies on correlative inference to one that reveals causal mechanisms of genetic co‐variation and adaptations within communities.

Background Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species. Results We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n = 2x = 24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa , the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis , grape, poplar, Medicago , and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype. Conclusions This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the Fagaceae.

This article is a summary report of the international conference "Forest ecosystem genomics and adaptation" organized by the EVOLTREE Network of Excellence in San Lorenzo de El Escorial (Madrid), Spain, from 9 to 11 June 2010. Main achievements and results of the network are presented for the eight thematic sessions and a stakeholder session. The conference has shown that adaptive responses of trees to biotic or abiotic selection pressures can now be investigated at the gene level for traits of adaptive significance. Candidate genes have been catalogued for phenological and drought-related traits in important tree families (Salicaceae, Fagaceaea and Pinaceae), and their variation in natural populations is being explored. Genomics can now be integrated in ecological research to investigate evolutionary response to climate changes in a wide range of species. New avenues of research were also highlighted as the exploration of gene networks involved in adaptive responses and the combination of experimental and modelling approaches to disentangle components of evolutionary changes triggered by climate change. The main focus of the conference was the adaptation of trees to environmental changes. The conference was organized in eight thematic sessions ranging from genomic approaches aiming at identifying genes of adaptive significance to practical issues regarding mitigation options for combating climate change. A dialogue between scientists and end users took place in the form of an ad hoc stakeholder session. A panel of end users from various forest and policy-making institutions expressed their expectations, and the discussions with the scientists addressed the potential applications of research findings to the management of genetic resources in the context of climate changes. The conference was introduced by two keynote speakers Dr. Pierre Mathy from the European Commission, Directorate General of Research, and Dr. Allen Solomon, former National Program Leader for Global Change, US Forest Service. All the thematic sessions were introduced by high-level invited speakers from the respective fields.

Assessing the viability of reintroduced animal populations is a complicated task. Reintroductions are usually carried out with a small number of individuals, thereby, limiting the possibilities for monitoring because of the possible negative effects of intensive monitoring on survival and reproduction. Moreover, reintroduction studies are part of a socioeconomic interplay of forces, thereby, also limiting monitoring possibilities. Also, knowledge of population demography and abundance can be incomplete or unattainable. Here, we illustrate how we combined traditional telemetry and novel non-invasive genetic methodology to construct a detailed life table of a small reintroduced otter population in The Netherlands. Combining an appropriate capture-mark-recapture framework with a matrix modelling approach provides, in general, useful insights for such populations. The data indicated that (i) male survival is lower than female survival, (ii) the reintroduced population is currently growing (estimated λ=1.26: range [1.06, 1.42]) and seems viable, (iii) increasing adult survival is currently the critical stage at which efforts of field managers should concentrate, and (iv) the modelling framework allowed us to determine the boundary conditions for the vital rates under which the population would go extinct. The applied approach directs at measurements that help field managers to implement the right conservation strategy after reintroductions.

Background: Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut).Results: A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.Conclusion: We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.

We have studied a small isolated population of black grouse (Tetrao tetrix) in the Netherlands to examine the impact of isolation and reduction in numbers on genetic diversity. We compared the genetic diversity in the last extant Dutch population with Dutch museum samples and three other black grouse populations (from England, Austria and Norway, respectively) representing isolated and continuous populations. We found significantly lower allelic richness, observed and expected heterozygosities in the present Dutch population compared to the continuous populations (Austria and Norway) and also to the historical Dutch population. However, using a bottleneck test on each population, signs of heterozygosity excess were only found in the likewise isolated English population despite that strong genetic drift was evident in the present Dutch population in comparison to the reference populations, as assessed both in pairwise FST and structure analyses. Simulating the effect of a population reduction on the Dutch population from 1948 onwards, using census data and with the Dutch museum samples as a model for the genetic diversity in the initial population, revealed that the loss in number of alleles and observed heterozygosity was according to genetic drift expectations and within the standard error range of the present Dutch population. Thus, the effect of the strong decline in the number of grouse on genetic diversity was only detectable when using a reference from the past. The lack of evidence for a population reduction in the present Dutch population by using the program bottleneck was attributed to a rapidly found new equilibrium as a consequence of a very small effective population size.

Antoine Kremerl, Manuela Casasoli2, Teresa ~ar reneche~, Catherine Bod6n2s1, Paul Sisco4, Thomas ~ub i s i ak~ , Marta Scalfi6, Stefano Leonardi6, Erica ~ a k k e r ~ , Joukje ~uiteveld', Jeanne ~omero-Seversong, Kathiravetpillai Arumuganathanlo, Jeremy ~ e r o r ~ ' , Caroline scotti-~aintagne", Guy Roussell, Maria Evangelista Bertocchil, Christian kxerl2, Ilga porth13, Fred ~ e b a r d ' ~ , Catherine clark15, John carlson16, Christophe Plomionl, Hans-Peter Koelewijn8, and Fiorella villani17

Summary1. Leptodora is a key species in many temperate freshwater systems, but so far its role in the food web could not be properly evaluated because detailed information about its secondary production was lacking. As we wanted to estimate the secondary production of Leptodora, we measured its development and growth rates in the laboratory.2. Employing improved methods to estimate growth and instar durations, we cultured Leptodora kindtii in the laboratory at four constant temperatures (15, 17.5, 20 and 25 °C). Growth in length and development times of eggs and instar stages were assessed.3. Growth rates at 15, 17.5 and 20 °C were similar, but at 25 °C growth was distinctly faster. At 17.5 °C we observed seven juvenile instar stages before the first adult instar stage was reached.

Many plants display limited seed dispersal, thereby creating an opportunity for sibling competition, i.e. fitness-determined interactions between related individuals. Here I investigated the consequences of intra-specific competition, by varying density and genetic composition of neighbors, on the performance of seedlings derived by selfing or outcrossing of the partially self-fertilizing plant Plantago coronopus (L.). Seedlings from eight plants, randomly selected from an area of about 50 m2 in a natural population, were used in (i) a density series with either one, four or eight siblings of each cross type per pot and (ii) a replacement series with eight plants per pot where selfed and outcrossed siblings were grown intermixed in varying frequencies. Density had a pronounced effect on plant performance. But, except for singly grown individuals, no differences were detected between selfed and outcrossed progenies in vegetative and reproductive biomass. When grown intermixed, selfed offspring were always inferior to their outcrossed relatives. The magnitude of reduction in performance was dependent on the number of outcrossed relatives a selfed seedling had to compete with, giving rise to a frequency-dependent fitness advantage to outcrossed seedlings. The major result of this study is (i) that the relative fitness of inbred progeny is strongly affected by the type of competitors (inbred or outbred) and (ii) that inbreeding depression varies according to the density and frequency of outbred plants and could be considered as a density- and frequency-dependent phenomenon. It is argued that sibling competition, due to the small genetic neighborhood of P. coronopus, might be an important selective force in natural populations of this species.

Inbreeding depression is a major selective force favoring outcrossing in flowering plants. However, some self-fertilization should weaken the harmful effects of inbreeding by exposing deleterious alleles to selection. This study examines the maintenance of inbreeding depression in the predominantly outcrossing species Pinus sylvestris L. (Scots pine). Open-pollinated and self-fertilized progeny of 23 maternal trees, originating from a natural stand in southern Finland, were grown at two sites. We observed significant inbreeding depression in two of the four life stages measured. Inbreeding depression was largest for seed maturation (δ = 0.74), where seedset in open-pollinated strobili (70.9%) was about four times higher than in selfed strobili (18.3%). Inbreeding depression in postgermination survival (upto an age of 23 years) was also high (δ = 0.62-0.75). No significant differences in height (δ = 0.05) or flowering (δ = 0.14) of the trees after 23 years were observed. Cumulative inbreeding depression was high (δ = 0.90-0.94) and differed significantly among maternal families (range 0.45-1.00). The magnitude of inbreeding depression among the 23 maternal parents was not significantly correlated between early (seed maturation) and later (postgermination survival) life stages, suggesting that its genetic basis varies across the life cycle. Size differences among the progeny types diminished in time due to nonrandom size-specific mortality, causing a decrease in the inbreeding depression estimates for height over time. Our results indicate that Scots pine exhibits high levels of inbreeding depression during both early and later stages of the life cycle. It is argued that self-fertilization in Scots pine is inefficient in purging the genetic load caused by highly deleterious mutations because of the nearly complete loss of selfed individuals over time. This results in an effectively random mating outcrossing population.