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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.

Background Microsatellite markers are widely used for estimating genetic diversity within and differentiation among populations. However, it has rarely been tested whether such estimates are useful proxies for genome-wide patterns of variation and differentiation. Here, we compared microsatellite variation with genome-wide single nucleotide polymorphisms (SNPs) to assess and quantify potential marker-specific biases and derive recommendations for future studies. Overall, we genotyped 180 Arabidopsis halleri individuals from nine populations using 20 microsatellite markers. Twelve of these markers were originally developed for Arabidopsis thaliana (cross-species markers) and eight for A. halleri (species-specific markers). We further characterized 2 million SNPs across the genome with a pooled whole-genome re-sequencing approach (Pool-Seq). Results Our analyses revealed that estimates of genetic diversity and differentiation derived from cross-species and species-specific microsatellites differed substantially and that expected microsatellite heterozygosity (SSR- H e ) was not significantly correlated with genome-wide SNP diversity estimates (SNP- H e and θ Watterson ) in A. halleri . Instead, microsatellite allelic richness ( A r ) was a better proxy for genome-wide SNP diversity. Estimates of genetic differentiation among populations ( F ST ) based on both marker types were correlated, but microsatellite-based estimates were significantly larger than those from SNPs. Possible causes include the limited number of microsatellite markers used, marker ascertainment bias, as well as the high variance in microsatellite-derived estimates. In contrast, genome-wide SNP data provided unbiased estimates of genetic diversity independent of whether genome- or only exome-wide SNPs were used. Further, we inferred that a few thousand random SNPs are sufficient to reliably estimate genome-wide diversity and to distinguish among populations differing in genetic variation. Conclusions We recommend that future analyses of genetic diversity within and differentiation among populations use randomly selected high-throughput sequencing-based SNP data to draw conclusions on genome-wide diversity patterns. In species comparable to A. halleri , a few thousand SNPs are sufficient to achieve this goal.

Europe is currently being re-colonized by large carnivore species such as brown bear Ursus arctos, Eurasian lynx Lynx lynx and grey wolf Canis lupus. Approximately one-third of Europe currently hosts at least one of these large carnivore species: they show permanent occurrence in some regions and sporadic occurrence without reproduction in others. We investigated potential future range expansions of these three large carnivores using three different analyses. First, we compared niche overlap between the historical, current permanent and current sporadic occurrences using n-dimensional hypervolumes. Second, we identified the environmental variables that best explain differences between current sporadic and permanent occurrences through multi-model inference. Third, we projected permanent occurrences into the future across a range of land-use change scenarios. We also determined future refuges (i.e. sub-optimal habitat in the environmental model, good habitat in the human disturbance model) and ecological traps (i.e. good habitat in the environmental model, sub-optimal habitat in the human disturbance model). In the three large carnivore species, ecological niche overlap was higher between historical and current permanent occurrences than between historical and current sporadic occurrences, and we also found low ecological niche overlap between current permanent and sporadic occurrences. Between 20 and 24% (corresponding to 86 800 to 173 200 km2) of the current sporadic occurrences could result in permanent settlement of large carnivores in the year 2040, while 17–24% (corresponding to 122 200 to 104 100 km2) and 2.7–4.6% (corresponding to 11 800 to 28 400 km2) of the current sporadic occurrences are likely to become refuges and ecological traps, respectively. Factors affecting range expansion are human activities, which were negatively related to permanent occurrences of all three species. In light of our results, human-dominated European landscapes provide ample space for the future recolonization of large carnivores.

Genetic diversity is important for the maintenance of the viability and the evolutionary or adaptive potential of populations and species. However, there are two principal types of genetic diversity: adaptive and neutral – a fact widely neglected by non-specialists. We introduce these two types of genetic diversity and critically point to their potential uses and misuses in population or landscape genetic studies. First, most molecular-genetic laboratory techniques analyse neutral genetic variation. This means that the gene variants detected do not have any direct effect on fitness. This type of genetic variation is thus selectively neutral and tells us nothing about the adaptive or evolutionary potential of a population or a species. Nevertheless, neutral genetic markers have great potential for investigating processes such as gene flow, migration or dispersal. Hence, they allow us to empirically test the functional relevance of spatial indices such as connectivity used in landscape ecology. Second, adaptive genetic variation, i.e. genetic variation under natural selection, is analysed in quantitative genetic experiments under controlled and uniform environmental conditions. Unfortunately, the genetic variation (i.e. heritability) and population differentiation at quantitative, adaptive traits is not directly linked with neutral genetic diversity or differentiation. Thus, neutral genetic data cannot serve as a surrogate of adaptive genetic data. In summary, neutral genetic diversity is well suited for the study of processes within landscapes such as gene flow, while the evolutionary or adaptive potential of populations or species has to be assessed in quantitative genetic experiments. Landscape ecologists have to mind these differences between neutral and adaptive genetic variation when interpreting the results of landscape genetic studies.

Erratic boulders provide habitat for rock-dwelling species and contribute to the biodiversity of landscapes. In the calcareous Swiss lowlands, siliceous erratic boulders are exclusive habitat islands for the regionally critically endangered fern Asplenium septentrionale, about 20 bryophyte species and numerous lichens. Focusing on island biogeographical processes, we analysed the conservation genomics of A. septentrionale and the moss Hedwigia ciliata on insular erratic boulders in the Swiss lowlands and the adjacent “mainland” in siliceous mountains. We genotyped both species using double digest restriction associated DNA sequencing (ddRAD). For the tetraploid A. septentrionale, abundant identical multilocus genotypes within populations suggested prevalent intragametophytic selfing, and six out of eight boulder populations consisting of a single multilocus genotype each indicated single spore founder events. The genetic structure of A. septentrionale mainland populations coincided with Pleistocene glacial refugia. Four genetic lineages of H. ciliata were identified, and populations consisting of a single multilocus genotype were less common than in A. septentrionale. For both taxa, multilocus genotype diversity on boulders was lower than in mainland populations. The absence of common genetic groups among boulder populations, and the absence of isolation by distance patterns, suggested colonisation of boulders through independent long-distance dispersal events. Successful boulder colonisation of A. septentrionale seems to be rare, while colonisation by H. ciliata appears to be more frequent. We conclude that pivotal principles of conservation biology, such as connectivity and genetic diversity, are of less importance for the studied cryptogams on insular erratic boulders because of long-distance dispersal, intragametophytic selfing and polyploidy.

Revisitation studies use historical information from literature or museum collections to assess rates of local extinction. However, revisitation studies suffer from the bias that they can only detect decline or stasis relative to the number of historical sites, as newly colonized sites are not detected. This drawback can be avoided with complete resurveys of study areas. We used 100‐year‐old historical information on 99 mountain plants from a 174 km2 area in Switzerland and performed a revisitation study and a complete resurvey. The resurvey was used to determine the magnitude of the bias of revisitation. In the revisitation study, we found an average loss of historical sites of plant species of 51.1% (SE = 3.4%). When sites newly observed in the resurvey were also considered and assumed to represent new colonizations, the average loss in sites declined to 26.8% (SE = 5.7%). However, if newly observed sites were treated as historically overlooked sites the loss of sites was only 45.7% (SE = 3.4%). Our results thus show that revisitation studies can overestimate local extinction, but that the corresponding bias depends on whether newly observed sites are considered as historically overlooked sites or as new colonizations. Revisitation studies using historical information from literature or museums to assess the rate of local extinction of species suffer from the bias that they can only find decline or stasis in the number of historical sites, while newly colonized sites are not detected. In a study also considering newly colonized sites we show that the bias of revisitation studies can be substantial.

Genetic diversity is a fundamental component of biological diversity, and its conservation is considered key to ensure the long-term survival of natural populations and species. National and international legislation increasingly mandates a monitoring of genetic diversity. Examples are the United Nation’s Convention on Biological Diversity (CBD) Aichi target 13 and the current post-2020 negotiations to specify a new target for maintaining genetic diversity. To date, only a few pilot projects have been launched that systematically monitor genetic diversity over time in natural populations of a broad variety of wild species. The Swiss Federal Office for the Environment mandated a feasibility study in 2019 for implementing a national monitoring of genetic diversity in natural populations. To obtain information on whether stakeholders are interested in such a systematic monitoring, what they would expect from such a monitoring and where they see respective caveats, we conducted an online survey, which 138 (42% of those surveyed) Swiss stakeholders answered. We find that Swiss stakeholders are generally aware of the lacking evidence regarding the status of genetic diversity in wild populations and species. Accordingly, most stakeholders are interested in a monitoring of genetic diversity and see opportunities for the application of its results in their work. Nevertheless, stakeholders also expressed concerns regarding financial resources and that the results of a genetic diversity monitoring program would not benefit conservation practice. Our findings highlight the importance of stakeholder engagement and demonstrate the value of a detailed stakeholder analysis prior to developing and implementing a genetic diversity monitoring program. A powerful tool for examining the constellation and interactions of the different stakeholders are social network analyses (SNAs). Finally, it is particularly important to communicate transparently about the possibilities and limitations of a genetic diversity monitoring program as well as to closely involve stakeholders from the beginning to increase the acceptance of genetic diversity monitoring and facilitate its implementation.

Rock climbing is popular, and the number of climbers rises worldwide. Numerous studies on the impact of climbing on rock‐dwelling plants have reported negative effects, which were mainly attributed to mechanical disturbances such as trampling and removal of soil and vegetation. However, climbers also use climbing chalk (magnesium carbonate hydroxide) whose potential chemical effects on rock‐dwelling species have not been assessed so far. Climbing chalk is expected to alter the pH and nutrient conditions on rocks, which may affect rock‐dwelling organisms. We elucidated two fundamental aspects of climbing chalk. (a) Its distribution along nonoverhanging climbing routes was measured on regularly spaced raster points on gneiss boulders used for bouldering (ropeless climbing at low height). These measurements revealed elevated climbing chalk levels even on 65% of sampling points without any visual traces of climbing chalk. (b) The impact of climbing chalk on rock‐dwelling plants was assessed with four fern and four moss species in an experimental setup in a climate chamber. The experiment showed significant negative, though varied effects of elevated climbing chalk concentrations on the germination and survival of both ferns and mosses. The study thus suggests that along climbing routes, elevated climbing chalk concentration can occur even were no chalk traces are visible and that climbing chalk can have negative impacts on rock‐dwelling organisms. Rock climbing is popular all around the globe and so is the use of climbing chalk (magnesium carbonate hydroxide powder that is applied to enhance grip friction). However, the impact of climbing chalk on rock‐dwelling organisms has not been properly studied so far. The article presents a first assessment of the effects of climbing chalk. We found distinctively elevated climbing chalk concentrations along climbing routes and pronounced effects of climbing chalk on the germination and survival of ferns and mosses in an experiment.

Habitat loss leading to smaller patch sizes and decreasing connectivity is a major threat to global biodiversity. While some species vanish immediately after a change in habitat conditions, others show delayed extinction, that is, an extinction debt. In case of an extinction debt, the current species richness is higher than expected under present habitat conditions. We investigated wetlands of the canton of Zürich in the lowlands of Eastern Switzerland where a wetland loss of 90% over the last 150 years occurred. We related current species richness to current and past patch area and connectivity (in 1850, 1900, 1950, and 2000). We compared current with predicted species richness in wetlands with a substantial loss in patch area based on the species‐area relationship of wetlands without substantial loss in patch area and studied relationships between the richness of different species groups and current and historical area and connectivity of wetland patches. We found evidence of a possible extinction debt for long‐lived wetland specialist vascular plants: in wetlands, which substantially lost patch area, current species richness of long‐lived specialist vascular plants was higher than would have been expected based on current patch area. Additionally and besides current wetland area, historical area also explained current species richness of these species in a substantial and significant way. No evidence for an extinction debt in bryophytes was found. The possible unpaid extinction debt in the wetlands of the canton of Zürich is an appeal to nature conservation, which has the possibility to prevent likely future extinctions of species through specific conservation measures. In particular, a further reduction in wetlands must be prevented and restoration measures must be taken to increase the number of wetlands. We found several lines of evidence for a possible unpaid extinction debt for vascular plants in the wetlands of the canton of Zurich, that is, historic wetland area is still reflected in today's wetland specialist species richness but not in the species richness of generalist species or bryophytes. Specialist species which are in the focus of nature conservation management may thus vanish from wetlands in the future. Increasing the area of wetlands should be a main focus of the nature conservation agencies to prevent future extinctions.

The European cockchafer Melolontha melolontha is an agricultural pest in many European countries. Populations have a synchronized 3 or 4 years life cycle, leading to temporally isolated populations. Despite the economic importance and availability of comprehensive historical as well as current records on cockchafer occurrence, population genomic analyses of M. melolontha are missing. For example, the effects of geographic separation caused by the mountainous terrain of the Alps and of temporal isolation on the genomic structure of M. melolontha still remain unknown. To address this gap, we genotyped 475 M. melolontha adults collected during 3 years from 35 sites in a central Alpine region. Subsequent population structure analyses discriminated two main genetic clusters, i.e., the South Tyrol cluster including collections located southeast of the Alpine mountain range, and a northwestern alpine cluster with all the other collections, reflecting distinct evolutionary history and geographic barriers. The “passo di Resia” linking South and North Tyrol represented a regional contact zone of the two genetic clusters, highlighting genomic differentiation between the collections from the northern and southern regions. Although the collections from northwestern Italy were assigned to the northwestern alpine genetic cluster, they displayed evidence of admixture with the South Tyrolean genetic cluster, suggesting shared ancestry. A linear mixed model confirmed that both geographic distance and, to a lower extent, also temporal isolation had a significant effect on the genetic distance among M. melolontha populations. These effects may be attributed to limited dispersal capacity and reproductive isolation resulting from synchronized and non‐synchronized swarming flights, respectively. This study contributes to the understanding of the phylogeography of an organism that is recognized as an agricultural problem and provides significant information on the population genomics of insect species with prolonged temporally shifted and locally synchronized life cycles.