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Old herbarium specimens and historical floristic data give insight into regional floras for given time periods. They often cover historical time periods for which few other data are available. Herbaria thus allow the study of changes of the flora of a region across time. Using a 150-year-old regional herbarium together with a historical publication, we investigated to which extent the flora of the Swiss canton of Schaffhausen has changed, which habitats were particularly affected by local extinction, what the environmental requirements of extinct plants were and whether conclusions about the respective drivers such as land use change can be drawn. A total of 987 species were historically recorded in the study region of which 154 are currently no longer reported and are regionally extinct. This means that about one species disappeared from the region every year. Species that are currently in a high category of endangerment on the Swiss Red List have declined markedly in the canton of Schaffhausen, showing that Red Lists well portrait the endangerment of species. Looking at plant strategies, the more stress-tolerant and less competitive plants have disappeared. In addition, wetland, pioneer, ruderal and mountain species as well as agricultural weeds and light-demanding species showed highest extinction rates. In contrast, forest species had a low extinction rate, and species from fertilized meadows showed no decline. Our evaluation of a regional herbarium helps to inform nature conservation about particularly endangered habitats and possible drivers of species decline. [ABSTRACT FROM AUTHOR]

Environmental problems caused by human activities are increasing; biodiversity is disappearing at an unprecedented rate, soils are being irreversibly damaged, freshwater is increasingly in short supply, and the climate is changing. To reverse or even to reduce these trends will require a radical transformation in the relationship between humans and the natural environment. Just how this can be achieved within, at most, a few decades is unknown, but it is clear that academia must play a crucial role. Many believe, however, that academic institutions need to become more effective in helping societies move toward sustainability. We first synthesize current thinking about this crisis of research effectiveness. We argue that those involved in producing knowledge to solve societal problems face three particular challenges: the complexity of real-world sustainability problems, maintaining impartiality when expert knowledge is used in decision making, and ensuring the salience of the scientific knowledge for decision makers. We discuss three strategies to meet these challenges: conducting research in interdisciplinary teams, forming research partnerships with actors and experts from outside academia, and framing research questions with the aim of solving specific problems (problem orientation). However, we argue that implementing these strategies within academia will require both cultural and institutional change. We then use concepts from transition management to suggest how academic institutions can make the necessary changes. At the level of system optimization, we call for: quality criteria, career incentives, and funding schemes that reward not only disciplinary excellence but also achievements in inter-/transdisciplinary work; professional services and training through specialized centers that facilitate problem-oriented research and reciprocal knowledge exchange with society; and the integration of sustainability and inter-/transdisciplinary research practices into all teaching curricula. At the level of system innovation, we propose radical changes in institutional structures, research and career incentives, teaching programs, and research partnerships. We see much value in a view of change that emphasizes the complementarity of system innovation and system optimization. The goal must be a process of change that preserves the traditional strengths of academic research, with its emphasis on disciplinary excellence and scientific rigor, while ensuring that institutional environments and the skills, worldviews, and experiences of the involved actors adapt to the rapidly changing needs of society. [ABSTRACT FROM AUTHOR]

A general hypothesis on mating patterns in alpine plants states that self-fertilization should increase with increasing altitude as a result of pollinator limitation at higher altitudes. However, realized selfing rates under natural conditions, as based on genetic progeny analysis, have not yet been determined for any alpine species across altitude. We therefore assessed the realized selfing rates in about 100 open-pollinated families of the high-alpine cushion plant Eritrichium nanum, sampled along an altitudinal gradient in the Swiss Alps, by using progeny analysis based on six microsatellites. In marked contrast to the general hypothesis, realized selfing rates in E. nanum significantly decreased with increasing altitude, and only progenies from low altitudes were predominantly selfed. However, the higher selfing rates of individuals at lower altitudes could have been caused by unfavorable weather conditions during early growing season when low-elevation plants flowered. In summary, our results on selfing rates in an alpine plant across altitude as well as the results of other studies using experimental hand-pollinations and/or population genetic methods generally do not support the expectation of higher selfing rates at higher altitudes. We therefore ask for further critical examination of realized mating systems in alpine plants. [ABSTRACT FROM AUTHOR]

Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. However, genetic diversity has been largely neglected in biodiversity monitoring, and when addressed, it is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. We report an accounting of efforts to monitor population genetic diversity in Europe (genetic monitoring effort, GME), the evaluation of which can help guide future capacity building and collaboration towards areas most in need of expanded monitoring. Overlaying GME with areas where the ranges of selected species of conservation interest approach current and future climate niche limits helps identify whether GME coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area, financial resources and conservation policy influence GME, high values of which only partially match species' joint patterns of limits to suitable climatic conditions. Populations at trailing climatic niche margins probably hold genetic diversity that is important for adaptation to changing climate. Our results illuminate the need in Europe for expanded investment in genetic monitoring across climate gradients occupied by focal species, a need arguably greatest in southeastern European countries. This need could be met in part by expanding the European Union's Birds and Habitats Directives to fully address the conservation and monitoring of genetic diversity., (© 2024. The Author(s).)

The Convention on Biological Diversity (CBD) aims at the conservation of all three levels of biodiversity, that is, ecosystems, species and genes. Genetic diversity represents evolutionary potential and is important for ecosystem functioning. Unfortunately, genetic diversity in natural populations is hardly considered in conservation strategies because it is difficult to measure and has been hypothesised to co-vary with species richness. This means that species richness is taken as a surrogate of genetic diversity in conservation planning, though their relationship has not been properly evaluated. We tested whether the genetic and species levels of biodiversity co-vary, using a large-scale and multi-species approach. We chose the high-mountain flora of the Alps and the Carpathians as study systems and demonstrate that species richness and genetic diversity are not correlated. Species richness thus cannot act as a surrogate for genetic diversity. Our results have important consequences for implementing the CBD when designing conservation strategies., (© 2012 Blackwell Publishing Ltd/CNRS.)

In lichen symbiosis, fungal and algal partners form close associations, often codispersed by vegetative propagules. Due to the particular interdependence, processes such as colonization, dispersal or genetic drift are expected to result in congruent patterns of genetic structure in the symbionts. To study the population structure of an obligate symbiotic system in Europe, we genotyped the fungal and algal symbionts of the epiphytic lichen Lobaria pulmonaria at eight and seven microsatellite loci, respectively, and analysed about 4300 L. pulmonaria thalli from 142 populations from the species' European distribution range. Based on a centroid approach, which localizes centres of genetic differentiation with a high frequency of geographically restricted alleles, we identified the South Italy-Balkan region as the primary glacial refugial area of the lichen symbiosis. Procrustean rotation analysis and a distance congruence test between the fungal and algal population graphs indicated general concordance between the phylogeographies of the symbionts. The incongruent patterns found in areas of postglacial recolonization may show the presence of an additional refugial area for the fungal symbiont, and the impact that horizontal photobiont transmission and different mutation rates of the symbionts have on their genotypic associations at a continental scale., (© 2012 Blackwell Publishing Ltd.)

Identifying landscape elements that influence gene flow and migration in wild species is the current main topic of landscape genetics. Most landscape genetic studies infer gene flow and migration from genetic distances among populations or individuals and statistically relate these measurements to landscape composition and configuration. This approach assumes symmetrical gene flow between pairs of populations. Such an assumption, however, will often be violated, especially in source–sink systems. Source populations provide more emigrants than they receive immigrants, and sink populations get many immigrants, but release few emigrants. Source–sink dynamics cannot be explored using common landscape genetic approaches relying on genetic distances. In this issue of Molecular Ecology, Andreasen et al. (2012) apply an alternative approach allowing them to infer asymmetrical migration. They use a Bayesian assignment test among objectively defined populations of mountain lions (Puma concolor) in western USA to estimate recent and directional migration rates. The study shows that an area with a high amount of wildlife refuges and low hunting pressure harbours a source population for mountain lion dispersal, while areas with high hunting pressures form sink populations; a result helpful in making informed decisions in conservation management.

Arctic-alpine biota occupy enormous areas in the Arctic and the northern hemisphere mountain ranges and have undergone major range shifts during their comparatively short history. The origins of individual arctic-alpine species remain largely unknown. In the case of the Purple saxifrage, Saxifraga oppositifolia, an important model for arctic-alpine plants, phylogeographic studies have remained inconclusive about early stages of the species' spatiotemporal diversification but have provided evidence for long-range colonization out of a presumed Beringian origin to cover today's circumpolar range. We re-evaluated the species' large-scale range dynamics based on a geographically extended sampling including crucial areas such as Central Asia and the (south-)eastern European mountain ranges and employing up-to-date phylogeographic analyses of a plastid sequence data set and a more restricted AFLP data set. In accordance with previous studies, we detected two major plastid DNA lineages also reflected in AFLP divergence, suggesting a long and independent vicariant history. Although we were unable to determine the species' area of origin, our results point to Europe (probably the Alps) and Central Asia, respectively, as the likely ancestral areas of the two main lineages. AFLP data suggested that contact areas between the two clades in the Carpathians, Northern Siberia and western Greenland were secondary. In marked contrast to high levels of diversity revealed in previous studies, populations from the major arctic refugium Beringia did not exhibit any plastid sequence polymorphism. Our study shows that adequate sampling of the southern, refugial populations is crucial for understanding the range dynamics of arctic-alpine species., (© 2012 Blackwell Publishing Ltd.)

Landscape genetics aims to assess the effect of the landscape on intraspecific genetic structure. To quantify interdeme landscape structure, landscape genetics primarily uses landscape resistance surfaces (RSs) and least-cost paths or straight-line transects. However, both approaches have drawbacks. Parameterization of RSs is a subjective process, and least-cost paths represent a single migration route. A transect-based approach might oversimplify migration patterns by assuming rectilinear migration. To overcome these limitations, we combined these two methods in a new landscape genetic approach: least-cost transect analysis (LCTA). Habitat-matrix RSs were used to create least-cost paths, which were subsequently buffered to form transects in which the abundance of several landscape elements was quantified. To maintain objectivity, this analysis was repeated so that each landscape element was in turn regarded as migration habitat. The relationship between explanatory variables and genetic distances was then assessed following a mixed modelling approach to account for the nonindependence of values in distance matrices. Subsequently, the best fitting model was selected using the statistic. We applied LCTA and the mixed modelling approach to an empirical genetic dataset on the endangered damselfly, Coenagrion mercuriale. We compared the results to those obtained from traditional least-cost, effective and resistance distance analysis. We showed that LCTA is an objective approach that identifies both the most probable migration habitat and landscape elements that either inhibit or facilitate gene flow. Although we believe the statistical approach to be an improvement for the analysis of distance matrices in landscape genetics, more stringent testing is needed., (© 2012 Blackwell Publishing Ltd.)

Identifying adaptive genetic variation is a challenging task, in particular in non-model species for which genomic information is still limited or absent. Here, we studied distribution patterns of amplified fragment length polymorphisms (AFLPs) in response to environmental variation, in 13 alpine plant species consistently sampled across the entire European Alps. Multiple linear regressions were performed between AFLP allele frequencies per site as dependent variables and two categories of independent variables, namely Moran's eigenvector map MEM variables (to account for spatial and unaccounted environmental variation, and historical demographic processes) and environmental variables. These associations allowed the identification of 153 loci of ecological relevance. Univariate regressions between allele frequency and each environmental factor further showed that loci of ecological relevance were mainly correlated with MEM variables. We found that precipitation and temperature were the best environmental predictors, whereas topographic factors were rarely involved in environmental associations. Climatic factors, subject to rapid variation as a result of the current global warming, are known to strongly influence the fate of alpine plants. Our study shows, for the first time for a large number of species, that the same environmental variables are drivers of plant adaptation at the scale of a whole biome, here the European Alps., (© 2012 Blackwell Publishing Ltd.)

Species range shifts in response to climate and land use change are commonly forecasted with species distribution models based on species occurrence or abundance data. Although appealing, these models ignore the genetic structure of species, and the fact that different populations might respond in different ways because of adaptation to their environment. Here, we introduced ancestry distribution models, that is, statistical models of the spatial distribution of ancestry proportions, for forecasting intra-specific changes based on genetic admixture instead of species occurrence data. Using multi-locus genotypes and extensive geographic coverage of distribution data across the European Alps, we applied this approach to 20 alpine plant species considering a global increase in temperature from 0.25 to 4 °C. We forecasted the magnitudes of displacement of contact zones between plant populations potentially adapted to warmer environments and other populations. While a global trend of movement in a north-east direction was predicted, the magnitude of displacement was species-specific. For a temperature increase of 2 °C, contact zones were predicted to move by 92 km on average (minimum of 5 km, maximum of 212 km) and by 188 km for an increase of 4 °C (minimum of 11 km, maximum of 393 km). Intra-specific turnover-measuring the extent of change in global population genetic structure-was generally found to be moderate for 2 °C of temperature warming. For 4 °C of warming, however, the models indicated substantial intra-specific turnover for ten species. These results illustrate that, in spite of unavoidable simplifications, ancestry distribution models open new perspectives to forecast population genetic changes within species and complement more traditional distribution-based approaches., (© 2012 Blackwell Publishing Ltd.)

Amplified Fragment Length Polymorphisms (AFLPs) are a cheap and efficient protocol for generating large sets of genetic markers. This technique has become increasingly used during the last decade in various fields of biology, including population genomics, phylogeography, and genome mapping. Here, we present RawGeno, an R library dedicated to the automated scoring of AFLPs (i.e., the coding of electropherogram signals into ready-to-use datasets). Our program includes a complete suite of tools for binning, editing, visualizing, and exporting results obtained from AFLP experiments. RawGeno can either be used with command lines and program analysis routines or through a user-friendly graphical user interface. We describe the whole RawGeno pipeline along with recommendations for (a) setting the analysis of electropherograms in combination with PeakScanner, a program freely distributed by Applied Biosystems; (b) performing quality checks; (c) defining bins and proceeding to scoring; (d) filtering nonoptimal bins; and (e) exporting results in different formats.

Plants flowering together may influence each other's pollination and fecundity over a range of physical distances. Their effects on one another can be competitive, neutral, or facilitative. We manipulated the floral neighborhood of the high-alpine cushion plant Eritrichium nanum in the Swiss Alps and measured the effects of co-flowering neighbors on both the number of seeds produced and the degree of inbreeding and outbreeding in the offspring, as deduced from nuclear microsatellite markers. Seed set of E. nanum did not vary significantly with the presence or absence of two Saxifraga species growing as near neighbors, but it was higher in E. nanum cushions growing at low conspecific density than in those growing at high density. In addition, floral neighborhood had no detectable effect on the degree of selfing of E. nanum, but seeds from cushions growing at low conspecific density were more highly outbred than seeds from cushions at high density. Thus, there was no evidence of either competition or facilitation between E. nanum and Saxifraga spp. as mediated by pollinators at the spatial scale of our experimental manipulation. In contrast, the greater fecundity of E. nanum cushions at low density was consistent with reduced intraspecific competition for pollinators and might also represent a beneficial effect of highly outbred seeds as brought about by more long-distance pollinator flights under low-density conditions.

Premise of the Study: Polymorphic microsatellite markers were developed for the inbred alpine perennial plant Arabis alpine to infer life-history parameters and measure patterns of contemporary gene fl ow within populations., Methods and Results: Using the 454 pyrosequencing technique, 19 microsatellite primer sets were developed for A. alpina . The primer sets were tested on 60 individuals sampled from three sub-populations in the Swiss Alps. The primers amplifi ed di- and trinucleotide repeats with two to fi ve alleles per locus., Conclusions: Previous attempts to isolate microsatellite loci in A. alpina using enrichment libraries and cross-amplifi cation were diffi cult and produced an insufficient number of polymorphic microsatellite loci. In contrast, next-generation sequencing technology was successful in identifying microsatellite repeats in A. alpina. These newly developed microsatellite primers will be useful to further develop A. alpina into a model species for eco-genomic studies.

Landscape genetics is the amalgamation of landscape ecology and population genetics to help with understanding microevolutionary processes such as gene flow and adaptation. In this review, we examine why landscape genetics of plants lags behind that of animals, both in number of studies and consideration of landscape elements. The classical landscape distance/resistance approach to study gene flow is challenging in plants, whereas boundary detection and the assessment of contemporary gene flow are more feasible. By contrast, the new field of landscape genetics of adaptive genetic variation, establishing the relationship between adaptive genomic regions and environmental factors in natural populations, is prominent in plant studies. Landscape genetics is ideally suited to study processes such as migration and adaptation under global change., (Copyright © 2010 Elsevier Ltd. All rights reserved.)

The dwarf bulrush (Typha minima Funck ex Hoppe) is an endangered pioneer plant species of riparian flood plains. In Switzerland, only 3 natural populations remain, but reintroductions are planned. To identify suitable source populations for reintroductions, we developed 17 polymorphic microsatellite markers with perfect repeats using the 454 pyrosequencing technique and tested them on 20 individuals with low-cost M13 labeling. We detected 2 to 7 alleles per locus and found expected and observed heterozygosities of 0.05-0.76 and 0.07-1, respectively. The whole process was finished in less than 6 weeks and cost approximately USD 5000. Due to low costs and reduced expenditure of time, the use of next-generation sequencing techniques for microsatellite development represent a powerful tool for population genetic studies in nonmodel species, as we show in this first application of the approach to a plant species of conservation importance.

Landscape genetics has seen rapid growth in number of publications since the term was coined in 2003. An extensive literature search from 1998 to 2008 using keywords associated with landscape genetics yielded 655 articles encompassing a vast array of study organisms, study designs and methodology. These publications were screened to identify 174 studies that explicitly incorporated at least one landscape variable with genetic data. We systematically reviewed this set of papers to assess taxonomic and temporal trends in: (i) geographic regions studied; (ii) types of questions addressed; (iii) molecular markers used; (iv) statistical analyses used; and (v) types and nature of spatial data used. Overall, studies have occurred in geographic regions proximal to developed countries and more commonly in terrestrial vs. aquatic habitats. Questions most often focused on effects of barriers and/or landscape variables on gene flow. The most commonly used molecular markers were microsatellites and amplified fragment length polymorphism (AFLPs), with AFLPs used more frequently in plants than animals. Analysis methods were dominated by Mantel and assignment tests. We also assessed differences among journals to evaluate the uniformity of reporting and publication standards. Few studies presented an explicit study design or explicit descriptions of spatial extent. While some landscape variables such as topographic relief affected most species studied, effects were not universal, and some species appeared unaffected by the landscape. Effects of habitat fragmentation were mixed, with some species altering movement paths and others unaffected. Taken together, although some generalities emerged regarding effects of specific landscape variables, results varied, thereby reinforcing the need for species-specific work. We conclude by: highlighting gaps in knowledge and methodology, providing guidelines to authors and reviewers of landscape genetics studies, and suggesting promising future directions of inquiry.

Landscape features exist at multiple spatial and temporal scales, and these naturally affect spatial genetic structure and our ability to make inferences about gene flow. This article discusses how decisions about sampling of genotypes (including choices about analytical methods and genetic markers) should be driven by the scale of spatial genetic structure, the time frame that landscape features have existed in their current state, and all aspects of a species' life history. Researchers should use caution when making inferences about gene flow, especially when the spatial extent of the study area is limited. The scale of sampling of the landscape introduces different features that may affect gene flow. Sampling grain should be smaller than the average home-range size or dispersal distance of the study organism and, for raster data, existing research suggests that simplifying the thematic resolution into discrete classes may result in low power to detect effects on gene flow. Therefore, the methods used to characterize the landscape between sampling sites may be a primary determinant for the spatial scale at which analytical results are applicable, and the use of only one sampling scale for a particular statistical method may lead researchers to overlook important factors affecting gene flow. The particular analytical technique used to correlate landscape data and genetic data may also influence results; common landscape-genetic methods may not be suitable for all study systems, particularly when the rate of landscape change is faster than can be resolved by common molecular markers.

Understanding the genetic basis of species adaptation in the context of global change poses one of the greatest challenges of this century. Although we have begun to understand the molecular basis of adaptation in those species for which whole genome sequences are available, the molecular basis of adaptation is still poorly understood for most non-model species. In this paper, we outline major challenges and future research directions for correlating environmental factors with molecular markers to identify adaptive genetic variation, and point to research gaps in the application of landscape genetics to real-world problems arising from global change, such as the ability of organisms to adapt over rapid time scales. High throughput sequencing generates vast quantities of molecular data to address the challenge of studying adaptive genetic variation in non-model species. Here, we suggest that improvements in the sampling design should consider spatial dependence among sampled individuals. Then, we describe available statistical approaches for integrating spatial dependence into landscape analyses of adaptive genetic variation.

Understanding the genetic basis of adaptation in response to environmental variation is fundamental as adaptation plays a key role in the extension of ecological niches to marginal habitats and in ecological speciation. Based on the assumption that some genomic markers are correlated to environmental variables, we aimed to detect loci of ecological relevance in the alpine plant Arabis alpina L. sampled in two regions, the French (99 locations) and the Swiss (109 locations) Alps. We used an unusually large genome scan [825 amplified fragment length polymorphism loci (AFLPs)] and four environmental variables related to temperature, precipitation and topography. We detected linkage disequilibrium among only 3.5% of the considered AFLP loci. A population structure analysis identified no admixture in the study regions, and the French and Swiss Alps were differentiated and therefore could be considered as two independent regions. We applied generalized estimating equations (GEE) to detect ecologically relevant loci separately in the French and Swiss Alps. We identified 78 loci of ecological relevance (9%), which were mainly related to mean annual minimum temperature. Only four of these loci were common across the French and Swiss Alps. Finally, we discuss that the genomic characterization of these ecologically relevant loci, as identified in this study, opens up new perspectives for studying functional ecology in A. alpina, its relatives and other alpine plant species.

Background and Aims: A previous study detected no allozyme diversity in Iberian populations of the buckler-fern Dryopteris aemula. The use of a more sensitive marker, such as microsatellites, was thus needed to reveal the genetic diversity, breeding system and spatial genetic structure of this species in natural populations., Methods: Eight microsatellite loci for D. aemula were developed and their cross-amplification with other ferns was tested. Five polymorphic loci were used to characterize the amount and distribution of genetic diversity of D. aemula in three populations from the Iberian Peninsula and one population from the Azores., Key Results: Most microsatellite markers developed were transferable to taxa close to D. aemula. Overall genetic variation was low (H(T) = 0.447), but was higher in the Azorean population than in the Iberian populations of this species. Among-population genetic differentiation was high (F(ST) = 0.520). All loci strongly departed from Hardy-Weinberg equilibrium. In the population where genetic structure was studied, no spatial autocorrelation was found in any distance class., Conclusions: The higher genetic diversity observed in the Azorean population studied suggested a possible refugium in this region from which mainland Europe has been recolonized after the Pleistocene glaciations. High among-population genetic differentiation indicated restricted gene flow (i.e. lack of spore exchange) across the highly fragmented area occupied by D. aemula. The deviations from Hardy-Weinberg equilibrium reflected strong inbreeding in D. aemula, a trait rarely observed in homosporous ferns. The absence of spatial genetic structure indicated effective spore dispersal over short distances. Additionally, the cross-amplification of some D. aemula microsatellites makes them suitable for use in other Dryopteris taxa.

A general hypothesis on mating patterns in alpine plants states that self-fertilization should increase with increasing altitude as a result of pollinator limitation at higher altitudes. However, realized selfing rates under natural conditions, as based on genetic progeny analysis, have not yet been determined for any alpine species across altitude. We therefore assessed the realized selfing rates in about 100 open-pollinated families of the high-alpine cushion plant Eritrichium nanum, sampled along an altitudinal gradient in the Swiss Alps, by using progeny analysis based on six microsatellites. In marked contrast to the general hypothesis, realized selfing rates in E. nanum significantly decreased with increasing altitude, and only progenies from low altitudes were predominantly selfed. However, the higher selfing rates of individuals at lower altitudes could have been caused by unfavorable weather conditions during early growing season when low-elevation plants flowered. In summary, our results on selfing rates in an alpine plant across altitude as well as the results of other studies using experimental hand-pollinations and/or population genetic methods generally do not support the expectation of higher selfing rates at higher altitudes. We therefore ask for further critical examination of realized mating systems in alpine plants.

Autopolyploidy is more common in plants than traditionally assumed, but has received little attention compared with allopolyploidy. Hence, the advantages and disadvantages of genome doubling per se compared with genome doubling coupled with hybridizations in allopolyploids remain unclear. Autopolyploids are characterized by genomic redundancy and polysomic inheritance, increasing effective population size. To shed light on the evolutionary consequences of autopolyploidy, we review a broad range of studies focusing on both synthetic and natural autopolyploids encompassing levels of biological organization from genes to evolutionary lineages. The limited evidence currently available suggests that autopolyploids neither experience strong genome restructuring nor wide reorganization of gene expression during the first generations following genome doubling, but that these processes may become more important in the longer term. Biogeographic and ecological surveys point to an association between the formation of autopolyploid lineages and environmental change. We thus hypothesize that polysomic inheritance may provide a short-term evolutionary advantage for autopolyploids compared to diploid relatives when environmental change enforces range shifts. In addition, autopolyploids should possess increased genome flexibility, allowing them to adapt and persist across heterogeneous landscapes in the long run.

Natural genetic breaks may indicate limitations to gene flow or the presence of contact zones of previously isolated populations. Molecular evidence suggests that genetic breaks have aggregated in distinct geographical areas. We propose a new application of well-established statistical methods for analysing multilocus genetic data to identify intraspecific genetic breaks. The methodological approach combines Bayesian clustering with a spatially explicit maximum-difference algorithm to visualize and quantify breaks between clusters. We used amplified fragment length polymorphism data of two co-distributed, silicicolous alpine plant species, Geum montanum and Geum reptans, exhaustively sampled on a consistent, regular grid over their entire range of the European Alps and the Carpathians. We found a distinct and highly similar allocation of genetic breaks in both species. The pattern of breaks did not conform to scenarios of glacial refugial survival, alternatively in peripheral refugia or on nunataks, as expected because of the species' ecologies (late-successional low alpine vs. early-successional high alpine). Our findings rather substantiated the postulate of a general pattern of genetic breaks in alpine plants and corresponded well with biogeographical regions formerly described. Our approach could serve as a tool not only for landscape genetics and comparative phylogeography, but also for floristics or faunistics to compare biogeographic with phylogeographic breaks.

Landscape fragmentation has often been seen as an only ecological problem. However, fragmentation also has a societal perspective, namely, in how humans perceive landscape fragmentation and in how landscape fragmentation potentially influences human well-being. These latter aspects have rarely been addressed so far. The inter-relationship of ecological and human dimensions of landscape fragmentation becomes especially evident when looking at the landscape where most people in industrial countries live, namely in suburban and urban areas. In these areas, landscape planners and environmental managers are confronted with the problem that landscapes should fulfill various functions, often with conflicting goals, e.g. nature reserves to enhance species richness vs. recreational areas for city-dwellers. We reviewed the ecological and sociological literature relevant for fragmentation in suburban and urban landscapes. In an interdisciplinary approach, we evaluated whether there are similarities and dissimilarities between the ecological and the human aspects of landscape fragmentation. We found important similarities. An example is that for both, humans and biodiversity, the loss of semi-natural areas has more drastic effects than the fragmentation of these areas per se. However, there are also relevant differences. We concluded that in densely populated landscapes a shift from responsive planning to an intentional design of environments is therefore needed.

Climatic history and ecology are considered the most important factors moulding the spatial pattern of genetic diversity. With the advent of molecular markers, species' historical fates have been widely explored. However, it has remained speculative what role ecological factors have played in shaping spatial genetic structures within species. With an unprecedented, dense large-scale sampling and genome-screening, we tested how ecological factors have influenced the spatial genetic structures in Alpine plants. Here, we show that species growing on similar substrate types, largely determined by the nature of bedrock, displayed highly congruent spatial genetic structures. As the heterogeneous and disjunctive distribution of bedrock types in the Alps, decisive for refugial survival during the ice ages, is temporally stable, concerted post-glacial migration routes emerged. Our multispecies study demonstrates the relevance of particular ecological factors in shaping genetic patterns, which should be considered when modelling species projective distributions under climate change scenarios.

Background and Aims: European white oaks (Quercus petraea, Q. pubescens, Q. robur) have long puzzled plant biologists owing to disputed species differentiation. Extensive hybridization or shared ancestry have been proposed as alternative hypotheses to explain why genetic differentiation between these oak species is low. Species delimitation is usually weak and often shows gradual transitions in leaf morphology. Hence, individual identification may be difficult, but remains a critical step for both scientific work and practical management., Methods: Multilocus genotype data (five nuclear microsatellites) were used from ten Swiss oak stands for taxon identification without a priori grouping of individuals or populations, using model-based Bayesian assignment tests., Key Results: Three groups best structured the data, indicating that the taxonomical signal was stronger than the spatial signal. Most individuals showed high posterior probabilities for either of three genetic groups that were best circumscribed as taxonomical units. The assignment of a subset of trees, whose taxonomic status had been previously characterized in detail, supported this classification scheme., Conclusions: Molecular-genetic assignment tests are useful in the identification of species status in critical taxon complexes such as the European white oaks. Such an approach is of practical importance for forest management, e.g. for stand certification or in seed trade to trace the origin of forest products.

Small populations of self-incompatible plants are assumed to be threatened by a limitation of compatible mating partners due to low genetic diversity at the self-incompatibility (S) locus. In contrast, we show by using a PCR-RFLP approach for S-genotype identification that 15 small populations (N = 8-88) of the rare wild pear (Pyrus pyraster) displayed no mate limitation. S-allele diversity within populations was high (N = 9-21) as was mate availability (92.9-100%). Although population size and S-allele diversity were strongly related, no relationship was found between population size and mate availability, gene diversity (He), or fixation index (F(IS)), based on five neutral microsatellite loci. As we determined the principal mate availability within populations based on the S-genotypes observed, the realized mate availability under natural conditions may differ from our estimates, for example, due to spatially limited pollen dispersal. We therefore urge studies on self-incompatible plants to proceed from the simple assessment of principal mate availability to the determination of realized mate availability in natural populations.

Epiphytes are strongly affected by the population dynamics of their host trees. Owing to the spatio-temporal dynamics of host tree populations, substantial dispersal rates--corresponding to high levels of gene flow--are needed for populations to persist in a landscape. However, several epiphytic lichens have been suggested to be dispersal-limited, which leads to the expectation of low gene flow at the landscape scale. Here, we study landscape-level genetic structure and gene flow of a putatively dispersal-limited epiphytic lichen, Lobaria pulmonaria. The genetic structure of L. pulmonaria was quantified at three hierarchical levels, based on 923 thalli collected from 41 plots situated within a pasture-woodland landscape and genotyped at six fungal microsatellite loci. We found significant isolation by distance, and significant genetic differentiation both among sampling plots and among trees. Landscape configuration, i.e. the effect of a large open area separating two forested regions, did not leave a traceable pattern in genetic structure, as assessed with partial Mantel tests and analysis of molecular variance. Gene pools were spatially intermingled in the pasture-woodland landscape, as determined by Bayesian analysis of population structure. Evidence for local gene flow was found in a disturbed area that was mainly colonized from nearby sources. Our analyses indicated high rates of gene flow of L. pulmonaria among forest patches, which may reflect the historical connectedness of the landscape through gene movement. These results support the conclusion that dispersal in L. pulmonaria is rather effective, but not spatially unrestricted.

Polyploidy plays a pivotal role in plant evolution. However, polyploids with polysomic inheritance have hitherto been severely underrepresented in plant population genetic studies, mainly due to a lack of appropriate molecular genetic markers. Here we report the establishment and experimental validation of six fully informative microsatellite markers in tetraploid gynodioecious Thymus praecox agg. Sequence data of 150 microsatellite alleles and their flanking regions revealed high variation, which may be characteristic for polyploids with a reticulate evolutionary history. Understanding the patterns of mutation (indels and substitutions) in microsatellite flanking-sequences was a prerequisite for the development of co-dominant markers for fragment analyses. Allelic segregation patterns among progeny arrays from ten test crosses revealed tetrasomic inheritance in T. praecox agg. No evidence of frequent double reduction was detected. Polymerase chain reaction (PCR) based dosage effects allowed for precise assignment of allelic configuration at all six microsatellite loci. The quantification of allele copy numbers in PCR was verified by comparisons of observed and expected gametic allele frequencies and heterozygosities in test crosses. Our study illustrates how PCR based markers can provide reliable estimates of heterozygosity and, thus, powerful tools for breeding system and population genetic analyses in polyploid organisms.

Dispersal is a process critical for the dynamics and persistence of metapopulations, but it is difficult to quantify. It has been suggested that the old-forest lichen Lobaria pulmonaria is limited by insufficient dispersal ability. We analyzed 240 DNA extracts derived from snow samples by a L. pulmonaria-specific real-time PCR (polymerase chain reaction) assay of the ITS (internal transcribed spacer) region allowing for the discrimination among propagules originating from a single, isolated source tree or propagules originating from other locations. Samples that were detected as positives by real-time PCR were additionally genotyped for five L. pulmonaria microsatellite loci. Both molecular approaches demonstrated substantial dispersal from other than local sources. In a landscape approach, we additionally analyzed 240 snow samples with real-time PCR of ITS and detected propagules not only in forests where L. pulmonaria was present, but also in large unforested pasture areas and in forest patches where L. pulmonaria was not found. Monitoring of soredia of L. pulmonaria transplanted to maple bark after two vegetation periods showed high variance in growth among forest stands, but no significant differences among different transplantation treatments. Hence, it is probably not dispersal limitation that hinders colonization in the old-forest lichen L. pulmonaria, but ecological constraints at the stand level that can result in establishment limitation. Our study exemplifies that care has to be taken to adequately separate the effects of dispersal limitation from a limitation of establishment.

Lichens associated with old forest are commonly assumed to be negatively affected by tree logging or natural disturbances. However, in this study performed in a spruce-dominated sylvopastoral landscape in the Swiss Jura Mountains, we found that genetic diversity of the epiphytic old-forest lichen Lobaria pulmonaria depends on the type of disturbance. We collected 923 thalli from 41 sampling plots of 1 ha corresponding to the categories stand-replacing disturbance (burnt), intensive logging (logged) and uneven-aged forestry (uneven-aged), and analysed the thalli at six mycobiont-specific microsatellite loci. We found evidence for multiple independent immigrations into demes located in burnt and logged areas. Using spatial autocorrelation methods, the spatial scale of the genetic structure caused by the clonal and recombinant component of genetic variation was determined. Spatial autocorrelation of genotype diversity was strong at short distances up to 50 m in logged demes, up to 100 m in uneven-aged demes, with the strongest autocorrelation up to 150 m for burnt demes. The spatial autocorrelation was predominantly attributed to clonal dispersal of vegetative propagules. After accounting for the clonal component, we did not find significant spatial autocorrelation in gene diversity. This pattern may indicate low dispersal ranges of clonal propagules, but random dispersal of sexual ascospores. Genetic diversity was highest in logged demes, and lowest in burnt demes. Our results suggest that genetic diversity of epiphytic lichen demes may not necessarily be impacted by stand-level disturbances for extended time periods.

A geostatistical perspective on spatial genetic structure may explain methodological issues of quantifying spatial genetic structure and suggest new approaches to addressing them. We use a variogram approach to (i) derive a spatial partitioning of molecular variance, gene diversity, and genotypic diversity for microsatellite data under the infinite allele model (IAM) and the stepwise mutation model (SMM), (ii) develop a weighting of sampling units to reflect ploidy levels or multiple sampling of genets, and (iii) show how variograms summarize the spatial genetic structure within a population under isolation-by-distance. The methods are illustrated with data from a population of the epiphytic lichen Lobaria pulmonaria, using six microsatellite markers. Variogram-based analysis not only avoids bias due to the underestimation of population variance in the presence of spatial autocorrelation, but also provides estimates of population genetic diversity and the degree and extent of spatial genetic structure accounting for autocorrelation.

Many lichen species produce both sexual and asexual propagules, but, aside from being minute, these diaspores lack special adaptations for long-distance dispersal. So far, molecular studies have not directly addressed isolation and genetic differentiation of lichen populations, both being affected by gene flow, at a regional scale. We used six mycobiont-specific microsatellite loci to investigate the population genetic structure of the epiphytic lichen Lobaria pulmonaria in two regions that strongly differed with respect to anthropogenic impact. In British Columbia, L. pulmonaria grows in continuous old-growth forests, while its populations in the old cultural landscape of Switzerland are comparably small and fragmented. Populations from both British Columbia and Switzerland were genetically diverse at the loci. Geographically restricted alleles, low historical gene flow, and analyses of genetic distance (upgma tree) and of differentiation (amova) indicated that populations from Vancouver Island and from the Canadian mainland were separated from each other, except for one, geographically intermediate population. This differentiation was attributed to different glacial and postglacial histories of coastal and inland populations in British Columbia. In contrast to expectations, the three investigated Swiss populations were genetically neither isolated nor differentiated from each other despite the long-lasting negative human impact on the lichen's range size in Central Europe. We propose that detailed studies integrating local landscape and regional scales are now needed to understand the processes of dispersal and gene flow in lichens.

Saxifraga oppositifolia (Saxifragaceae) is an important model system for the evolution of Arctic-Alpine plant species. Sequences of the psbA-trnH intergenic spacer of chloroplast DNA and of the internal transcribed spacer region, ITS1-5.8S-ITS2, of the nuclear ribosomal DNA were used to investigate the intraspecific evolution and phylogeography of this species. Samples from nearly the species' entire circumpolar distribution were included in the analysis as well as samples from the closely related taxa S. smalliana from Alaska and S. blepharophylla and S. biflora from the Alps (S. aizoides served as outgroup). These latter taxa showed a low number of parsimony informative characters, in both cpDNA and ITS sequences, which separated them from S. oppositifolia. Two main cpDNA haplotypes were detected within S. oppositifolia, one with a Eurasian distribution and one with an East Asian-North American distribution. This confirmed the existence of two cpDNA lineages with different geographical distributions in this species, which had previously been reported based on a RFLP analysis. The ITS phylogeny was not useful with respect to the intraspecific evolution and phylogeography of S. oppositifolia, because it showed a largely unresolved topology with low statistical support. The cpDNA sequence analysis, however, also suggested a putative long-distance dispersal event. All investigated taxa had cpDNA haplotypes that were congruent with their geographical origin rather than their phylogeny. This could point to putative lineage sorting in S. oppositifolia and related taxa.

Anemone nemorosa is a perennial rhizomatous plant of European woodlands. The "probability of clonal identity" method estimated the relative proportion of sexual to vegetative reproduction in this species to be 4.4% from allozyme genotype distributions. This result is congruent with investigations on the germination, short-term demography, population genetics, and breeding system of this species, and supports the hypothesis that even low levels of seedling recruitment can maintain considerable intrapopulational genetic diversity.