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Stethophyma grossum is a threatened Eurosiberian grasshopper species. Since it is bound to wetlands, S. grossum is often used as indicator for extensive wet meadows. To study its movement capability and dispersal habitat in landscape genetic analyses, we developed ten polymorphic microsatellite markers, making use of next generation sequencing. Markers were tested on 75 individuals collected in five populations from Switzerland. We found four to 18 alleles per locus. Observed and expected heterozygosities varied between 0.215-0.893 and 0.397-0.831, respectively. One marker seems to be sex-chromosome X-linked and one showed high null allele frequencies, a phenomenon generally detected in microsatellite studies on grasshoppers. [ABSTRACT FROM AUTHOR]

Premise of the study: Polymorphic microsatellite markers were developed for the inbred alpine perennial plant Arabis alpina to infer life-history parameters and measure patterns of contemporary gene flow 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 amplified di- and trinucleotide repeats with two to five alleles per locus. Conclusions: Previous attempts to isolate microsatellite loci in A. alpina using enrichment libraries and cross-amplification were difficult 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. [ABSTRACT FROM AUTHOR]

The article focuses on the promotion of landscape genetics which asses how landscape structure and composition affects movement, dispersal and gene flow of plants and animals. It combines the theory methods of population genetics with geographic information systems (GIS) applications, spatial analyses and modeling of landscape ecology. Landscape genetics uses three approaches in detecting the effects of landscape structure including genetic discontinuities, genetic distance and gene flow.

The European (Melolontha melolontha L.) and Forest (M. hippocastani F.) cockchafer are widespread pests throughout Central Europe. Both species exhibit a 3–5-year life cycle and occur in temporally shifted populations, which have been monitored and documented for more than 100 years. Visual identification of adults and larvae belonging to these morphologically similar species requires expertise and, particularly in the case of larvae, is challenging and equivocal. The goal of the study was the development of an efficient and fast molecular genetic tool for the identification and discrimination of M. melolontha and M. hippocastani. We established a collection of both species from Switzerland, Austria and Northern Italy in 2016, 2017 and 2018. An approximately 1550 bp long fragment of the cytochrome c oxidase subunit 1 (CO1) mitochondrial gene was amplified and sequenced in 13 M. melolontha and 13 M. hippocastani beetles. Alignment of the new sequences with reference sequences (NCBI GenBank and BOLDSYSTEMS databases) and subsequent phylogenetic analysis revealed consistent clustering of the two species. After the identification of M. melolontha and M. hippocastani species-specific single nucleotide polymorphisms (SNPs) in the CO1 alignment, we developed an effective SNP tool based on the ABI PRISM® SNaPshot™ Multiplex Kit for the rapid and accurate species discrimination of adults and larvae. [ABSTRACT FROM AUTHOR]

Biodiversity is currently experiencing an accelerated decline in terms of species and populations, mainly because of habitat loss. The designation of protected areas has therefore become essential for biodiversity conservation. However, compelling evidence for the long-term effectiveness of protected areas in maintaining species diversity is still scarce, especially for plant species, as analyses are often hampered by the limited availability of informative datasets from different time periods. Here we analysed the effectiveness of Swiss protected areas in maintaining vascular plant species typical for two habitat types, namely wetlands and dry grasslands. Furthermore, we tested whether the effect of protected areas on species persistence varies between low (<1000 m a.s.l.) and high elevations (≥1000 m a.s.l.). Data included several thousand historical occurrences, which were re-surveyed after 2002 at the scale of square kilometres. For each re-surveyed species, we identified the square kilometres where it had disappeared and those where it still occurred. We found that the amount of protected area within the square kilometres had a positive effect on the persistence of plant species in the studied habitat types. The effect, however, primarily occurred at low elevations, and even in square kilometres with the largest amount of protected area species declines were still observed. While protected areas at higher elevations are often embedded in a less intensively used matrix, which provides small habitat patches for threatened species, protected areas at lower elevations are often islands within an inhospitable, intensively managed matrix. This explains why protected areas at higher elevations are less important for the persistence of species within square kilometres studied here. Moreover, wetlands and dry grasslands have suffered from changes in land use or heavy exploitation during the past centuries, especially at lower elevations, with ongoing losses of species and populations occurring even within protected areas. Protected areas thus decelerate the landscape-scale loss of species but (apparently) do not fully stop it. [ABSTRACT FROM AUTHOR]

Beauveria brongniartii is a fungal pathogen that infects the beetle Melolontha melolontha, a significant agricultural pest in Europe. While research has primarily focused on the use of B. brongniartii for controlling M. melolontha, the genomic structure of the B. brongniartii population remains unknown. This includes whether its structure is influenced by its interaction with M. melolontha, the timing of beetle‐swarming flights, geographical factors, or reproductive mode. To address this, we analysed genome‐wide SNPs to infer the population genomics of Beauveria spp., which were isolated from infected M. melolontha adults in an Alpine region. Surprisingly, only one‐third of the isolates were identified as B. brongniartii, while two‐thirds were distributed among cryptic taxa within B. pseudobassiana, a fungal species not previously recognized as a pathogen of M. melolontha. Given the prevalence of B. pseudobassiana, we conducted analyses on both species. We found no spatial or temporal genomic patterns within either species and no correlation with the population structure of M. melolontha, suggesting that the dispersal of the fungi is independent of the beetle. Both species exhibited clonal population structures, with B. brongniartii fixed for one mating type and B. pseudobassiana displaying both mating types. This implies that factors other than mating compatibility limit sexual reproduction. We conclude that the population genomic structure of Beauveria spp. is primarily influenced by predominant asexual reproduction and dispersal. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Detecting the extrinsic selective pressures shaping genomic variation is critical for a better understanding of adaptation and for forecasting evolutionary responses of natural populations to changing environmental conditions. With increasing availability of geo-referenced environmental data, landscape genomics provides unprecedented insights into how genomic variation and underlying gene functions affect traits potentially under selection. Yet, the robustness of genotype–environment associations used in landscape genomics remains tempered due to various limitations, including the characteristics of environmental data used, sampling designs employed, and statistical frameworks applied. Here, we argue that using complementary or new environmental data sources and well-informed sampling designs may help improve the detection of selective pressures underlying patterns of local adaptation in various organisms and environments. The increasing availability of new, high-quality geo-referenced environmental data(bases) is stimulating landscape genomic studies of terrestrial and aquatic organisms. Environmental data (e.g., climate, soil, and topography) are now available at multiple spatial and temporal scales and, together with environmentally and genetically informed sampling designs, enable us to capture selection pressures at high resolution in various organisms. Statistical advances in genotype–environment association methods now allow testing the response of population genomic variation to complex environments, using nonredundant and informative environmental predictors. Our understanding of the environmental constraints underlying local adaptation of living organisms has provided insights into the potential responses of populations to environmental changes such as global warming. This understanding is a key component of well-informed biodiversity conservation programmes. [ABSTRACT FROM AUTHOR]

Success stories are rare in conservation science, hindered also by the research-implementation gap, where scientific insights rarely inform practice and practical implementation is rarely evaluated scientifically. Amphibian population declines, driven by multiple stressors, are emblematic of the freshwater biodiversity crisis. Habitat creation is a straightforward conservation action that has been shown to locally benefit amphibians, as well as other taxa, but does it benefit entire amphibian communities at large spatial scales? Here, we evaluate a landscape-scale pond-construction program by fitting dynamic occupancy models to 20 y of monitoring data for 12 pond-breeding amphibian species in the Swiss state Aargau, a densely populated area of the Swiss lowlands with intensive land use. After decades of population declines, the number of occupied ponds increased statewide for 10 out of 12 species, while one species remained stable and one species further declined between 1999 and 2019. Despite regional differences, in 77% of all 43 regional metapopulations, the colonization and subsequent occupation of new ponds stabilized (14%) or increased (63%) metapopulation size. Likely mechanisms include increased habitat availability, restoration of habitat dynamics, and increased connectivity between ponds. Colonization probabilities reflected species-specific preferences for characteristics of ponds and their surroundings, which provides evidence-based information for future pond construction targeting specific species. The relatively simple but landscape-scale and persistent conservation action of constructing hundreds of new ponds halted declines and stabilized or increased the state-wide population size of all but one species, despite ongoing pressures from other stressors in a human-dominated landscape. [ABSTRACT FROM AUTHOR]

Aims: Resurveys of vegetation plots are prone to several errors that can result in misleading conclusions. Minimizing such errors and finding alternative approaches for analyzing resurvey data are therefore important. We focused on inter‐observer error and excluded other sources of variation. Our main questions were: How large is the inter‐observer error (i.e. pseudoturnover) in vegetation surveys, and can it be reduced by simple data aggregation approaches? Which factors are affecting pseudoturnover and does it vary between morphological species groups or change over time? Is ecological inference robust against inter‐observer differences? Location: Switzerland. Methods: Over seven years, we double‐surveyed a total of 224 plots that were marked once in the field and then sampled by two observers independently on the same day. Both observers conducted full vegetation surveys, recording all vascular plant species, their cover, and additional plot information. We then calculated mean ecological indicator values and pseudoturnover. Results: Average pseudoturnover was 29% when raw species lists were compared. However, by applying simple aggregation steps to the species list, pseudoturnover was reduced to 17%. Pseudoturnover further varied among habitat types and declined over the years, indicating a training effect among observers. Most overlooked taxa, responsible for pseudoturnover, had low cover values. Mean ecological indicator values were robust against inter‐observer differences. Conclusions: To minimize pseudoturnover, we suggest continuous training of observers and species‐list aggregation prior to analysis. As mean ecological indicator values were robust against inter‐observer differences, we conclude that they can provide a reliable estimate of temporal vegetation and ecological changes. [ABSTRACT FROM AUTHOR]

Aim: Pleistocene erratic boulders are rocks that were relocated by glaciers during the Ice Ages. When their geology differs from the geology of the landscape that surrounds them, erratic boulders form habitat islands for regionally rare, edaphically specialised, rock‐dwelling cryptogams (bryophytes, ferns and lichens). Such boulders constitute terrestrial model systems for exploring island biogeographic predictions and the effect of environmental variables on species diversity and community composition, which we studied in order to provide basic knowledge of the ecology, with relevance for the conservation, of these unusual island systems. Location: Siliceous erratic boulders in the calcareous Swiss Plateau and Jura Mountains. Methods: For 160 erratic boulders we recorded all bryophyte species and a diverse set of environmental variables. For all species and for specialist species (acidophile rock‐dwellers) separately, we analysed species–area relationships and nestedness, and explored relationships between environmental variables, species diversity and community composition. Results: We found 138 bryophyte species, 19 of which were specialists of erratic boulders. A steeper species–area curve for boulder specialists than for total species richness underlined the island properties of boulders for specialist species. Large boulders were more likely to harbour numerous boulder specialists and communities on small boulders were nested within the communities present on large boulders. However, at the landscape level small boulders contributed more specialist species than a few large boulders of the same surface area. Erratic boulders near settlements were less likely to harbour boulder specialists. Boulders in open land harboured different and more specialist species than boulders in forests. Conclusions: Large undisturbed erratic boulders in open land harbour rare bryophyte communities with a large number of specialist species. Conservation should thus prioritise this type of boulders. Furthermore, conserving large boulders is logistically easier, and they may function as flagships for small boulders that also contribute to the biodiversity within landscapes. [ABSTRACT FROM AUTHOR]

It has long been discussed to what extent related species develop similar genetic mechanisms to adapt to similar environments. Most studies documenting such convergence have either used different lineages within species or surveyed only a limited portion of the genome. Here, we investigated whether similar or different sets of orthologous genes were involved in genetic adaptation of natural populations of three related plant species to similar environmental gradients in the Alps. We used whole‐genome pooled population sequencing to study genome‐wide SNP variation in 18 natural populations of three Brassicaceae (Arabis alpina, Arabidopsis halleri, and Cardamine resedifolia) from the Swiss Alps. We first de novo assembled draft reference genomes for all three species. We then ran population and landscape genomic analyses with ~3 million SNPs per species to look for shared genomic signatures of selection and adaptation in response to similar environmental gradients acting on these species. Genes with a signature of convergent adaptation were found at significantly higher numbers than expected by chance. The most closely related species pair showed the highest relative over‐representation of shared adaptation signatures. Moreover, the identified genes of convergent adaptation were enriched for nonsynonymous mutations, suggesting functional relevance of these genes, even though many of the identified candidate genes have hitherto unknown or poorly described functions based on comparison with Arabidopsis thaliana. We conclude that adaptation to heterogeneous Alpine environments in related species is partly driven by convergent evolution, but that most of the genomic signatures of adaptation remain species‐specific. [ABSTRACT FROM AUTHOR]

It is generally accepted that the spatial distribution of neutral genetic diversity within a species' native range mostly depends on effective population size, demographic history, and geographic position. However, it is unclear how genetic diversity at adaptive loci correlates with geographic peripherality or with habitat suitability within the ecological niche. Using exome‐wide genomic data and distribution maps of the Alpine range, we first tested whether geographic peripherality correlates with four measures of population genetic diversity at > 17,000 SNP loci in 24 Alpine populations (480 individuals) of Swiss stone pine (Pinus cembra) from Switzerland. To distinguish between neutral and adaptive SNP sets, we used four approaches (two gene diversity estimates, FST outlier test, and environmental association analysis) that search for signatures of selection. Second, we established ecological niche models for P. cembra in the study range and investigated how habitat suitability correlates with genetic diversity at neutral and adaptive loci. All estimates of neutral genetic diversity decreased with geographic peripherality, but were uncorrelated with habitat suitability. However, heterozygosity (He) at adaptive loci based on Tajima's D declined significantly with increasingly suitable conditions. No other diversity estimates at adaptive loci were correlated with habitat suitability. Our findings suggest that populations at the edge of a species' geographic distribution harbour limited neutral genetic diversity due to demographic properties. Moreover, we argue that populations from suitable habitats went through strong selection processes, are thus well adapted to local conditions, and therefore exhibit reduced genetic diversity at adaptive loci compared to populations at niche margins. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The changes in agricultural practice during the last century resulted in high-input farming in lowlands and the abandonment of crop fields in marginally profitable mountain regions. In Switzerland abandoned fields were converted into grassland. These fields had a rich historical flora and the few still existing fields still belong to the most species rich. As many arable weeds produce persistent seeds, abandoned fields should have a high potential to promote rare and threatened arable plants if tilled again. To test this hypothesis we collected 21 soil samples down to 20 cm depth in each the centre and the border of 38 abandoned fields. The centre and border samples of each field were each pooled, and afterwards the present seeds washed out. These seeds were then sown in pots and germination monitored in a greenhouse during six months. A total of 119 plant species were identified. Of these, 48 species were typical arable weeds and only one was red listed in Switzerland. The number of arable weeds per former field was lower at higher altitudes. Hence, the surveyed meadows have a small potential to promote threatened arable weeds if tilled again. Likely, some seeds were no longer viable because the fields were not tilled for a too long. If on newly established conservation fields no threatened species grow spontaneously after a few years, the reintroduction of desired plant species should be considered. The source of the seeds should preferably be a nearby species pool. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]