A robust sequencing assay of a thousand amplicons for the high-throughput population monitoring of Alpine ibex immunogenetics.

Polymorphism for immune functions can explain significant variation in health and reproductive success within species. Drastic loss in genetic diversity at such loci constitutes an extinction risk and should be monitored in species of conservation concern. However, effective implementations of genome-wide immune polymorphism sets into high-throughput genotyping assays are scarce.

Disentangling adaptation from drift in bottlenecked and reintroduced populations of Alpine ibex.

Identifying local adaptation in bottlenecked species is essential for conservation management. Selection detection methods have an important role in species management plans, assessments of adaptive capacity, and looking for responses to climate change. Yet, the allele frequency changes exploited in selection detection methods are similar to those caused by the strong neutral genetic drift expected during a bottleneck.

Declines in occurrence of plants characteristic for a nutrient-poor meadow habitat are partly explained by their responses to nutrient addition and competition.

Species losses and local extinctions are alarmingly common, frequently as a consequence of habitat destruction. Nevertheless, many intact habitats also face species losses, most likely due to environmental changes. However, the exact drivers, and why they affect some species more than others in apparently intact habitats, are still poorly understood.

Macrogenetic studies must not ignore limitations of genetic markers and scale.

Millette et al. (Ecology Letters, 2020, 23:55-67) reported no consistent worldwide anthropogenic effects on animal genetic diversity using repurposed mitochondrial DNA sequences. We reexamine data from this study, describe genetic marker and scale limitations which might lead to misinterpretations with conservation implications, and provide advice to improve future macrogenetic studies.

Effects of fertilization and irrigation on vascular plant species richness, functional composition and yield in mountain grasslands.

Land-use intensification is a major threat to biodiversity in agricultural grasslands and fertilization is one of the main drivers. The effects of fertilization on biodiversity and plant functional composition (community-weighted mean traits and mean ecological indicator values) are well studied in lowland regions, but have received less attention in mountain grasslands. Moreover, in inner-alpine dry valleys, fertilizer is often applied in combination with irrigation, and irrigation effects are less well known.

The distribution of climbing chalk on climbed boulders and its impact on rock-dwelling fern and moss species.

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.

The results of biodiversity-ecosystem functioning experiments are realistic.

A large body of research shows that biodiversity loss can reduce ecosystem functioning. However, much of the evidence for this relationship is drawn from biodiversity-ecosystem functioning experiments in which biodiversity loss is simulated by randomly assembling communities of varying species diversity, and ecosystem functions are measured. This random assembly has led some ecologists to question the relevance of biodiversity experiments to real-world ecosystems, where community assembly or disassembly may be non-random and influenced by external drivers, such as climate, soil conditions or land use.

Plant species richness increases with light availability, but not variability, in temperate forests understorey.

Background: Temperate forest understorey vegetation poses an excellent study system to investigate whether increases in resource availability lead to an increase in plant species richness. Most sunlight is absorbed by the species-poor tree canopy, making the much more species-rich understorey species inhabit a severely resource-limited habitat. Additionally, the heterogeneity of light availability, resulting from management-moderated tree composition and age structure, may contribute to species coexistence.

Determining the Suitability of MinION's Direct RNA and DNA Amplicon Sequencing for Viral Subtype Identification.

The MinION sequencer is increasingly being used for the detection and outbreak surveillance of pathogens due to its rapid throughput. For RNA viruses, MinION's new direct RNA sequencing is the next significant development. Direct RNA sequencing studies are currently limited and comparisons of its diagnostic performance relative to different DNA sequencing approaches are lacking as a result.

Multiscale Determinants Drive Parasitization of Drosophilidae by Hymenopteran Parasitoids in Agricultural Landscapes.

(1) The management of agricultural landscapes for pest suppression requires a thorough understanding of multiple determinants controlling their presence. We investigated the ecological preferences of indigenous parasitoids and their drosophilid hosts to understand the role of native parasitoids as biological control agents of the invasive frugivorous . (2) Using data from an extensive field survey across different habitat types we analyzed the influence of abiotic and biotic factors on parasitoid and drosophilid communities at multiscale levels.

Evidence for a possible extinction debt in Swiss wetland specialist plants.

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.

The -Resistant Olive Cultivar "Leccino" Has Stable Endophytic Microbiota during the Olive Quick Decline Syndrome (OQDS).

is a highly virulent pathogen that causes Olive Quick Decline Syndrome (OQDS), which is currently devastating olive plantations in the Salento region (Apulia, Southern Italy). We explored the microbiome associated with -infected (-infected) and -uninfected (-uninfected) olive trees in Salento, to assess the level of dysbiosis and to get first insights into the potential role of microbial endophytes in protecting the host from the disease. The resistant cultivar "Leccino" was compared to the susceptible cultivar "Cellina di Nardò", in order to identify microbial taxa and parameters potentially involved in resistance mechanisms.

Predicting species occurrences with habitat network models.

Biodiversity conservation requires modeling tools capable of predicting the presence or absence (i.e., occurrence-state) of species in habitat patches.

Estimated six per cent loss of genetic variation in wild populations since the industrial revolution.

Genetic variation is fundamental to population fitness and adaptation to environmental change. Human activities are driving declines in many wild populations and could have similar effects on genetic variation. Despite the importance of estimating such declines, no global estimate of the magnitude of ongoing genetic variation loss has been conducted across species.

Conservation genetics: Linking science with practice.

Conservation genetics is a well-established scientific field. However, limited information transfer between science and practice continues to hamper successful implementation of scientific knowledge in conservation practice and management. To mitigate this challenge, we have established a conservation genetics community, which entails an international exchange-and-skills platform related to genetic methods and approaches in conservation management.

Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae).

Advances in high-throughput sequencing have promoted the collection of reference genomes and genome-wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single-nucleotide polymorphisms (SNPs) and largely ignored the often major fraction of genomes represented by transposable elements (TEs). Despite accumulating evidence supporting the evolutionary significance of TEs, comprehensive surveys remain scarce.

Impact of polymorphic transposable elements on linkage disequilibrium along chromosomes.

Recombination and selection drive the extent of linkage disequilibrium (LD) among loci and therefore affect the reshuffling of adaptive genetic variation. However, it is poorly known to what extent the enrichment of transposable elements (TEs) in recombinationally-inert regions reflects their inefficient removal by purifying selection and whether the presence of polymorphic TEs can modify the local recombination rate. In this study, we investigate how TEs and recombination interact at fine scale along chromosomes and possibly support linked selection in natural populations.

Using transcriptome sequencing and pooled exome capture to study local adaptation in the giga-genome of Pinus cembra.

Despite decreasing sequencing costs, whole-genome sequencing for population-based genome scans for selection is still prohibitively expensive for organisms with large genomes. Moreover, the repetitive nature of large genomes often represents a challenge in bioinformatic and downstream analyses. Here, we use in-depth transcriptome sequencing to design probes for exome capture in Swiss stone pine (Pinus cembra), a conifer with an estimated genome size of 29.

Genetic and Phenotypic Characterization of Cryphonectria hypovirus 1 from Eurasian Georgia.

(CHV-1) infects the chestnut blight fungus and acts as a biological control agent against this harmful tree disease. In this study, we screened the recently characterized population in Eurasian Georgia for the presence of CHV-1. We found 62 CHV-1 infected isolates (9.

Transmembrane transport and stress response genes play an important role in adaptation of Arabidopsis halleri to metalliferous soils.

When plants adapt to local environments, strong signatures of selection are expected in the genome, particularly in high-stress environments such as trace metal element enriched (metalliferous) soils. Using Arabidopsis halleri, a model species for metal homeostasis and adaptation to extreme environments, we identifid genes, gene variants, and pathways that are associated with soil properties and may thus contribute to adaptation to high concentrations of trace metal elements. We analysed whole-genome Pool-seq data from two metallicolous (from metalliferous soils) and two non-metallicolous populations (in total 119 individuals) and associated allele frequencies of the identified single-nucleotide polymorphisms (SNPs) with soil variables measured on site.

Evaluating Dryocosmus Kuriphilus-induced Damage on Castanea Sativa.

Dryocosmus kuriphilus Yasumatsu has become a major pest for Castaneasativa since its arrival in Europe. Its galling activity results in the formation of different gall types and prevents the development of normal shoots. Repeated and uncontrolled attacks cause, besides the production of galls and the attendant gall-related reduction in leaf area, progressive corruption of the branch architecture, including the death of branch parts, and an increase in dormant bud activation.

Modeled Tracheidograms Disclose Drought Influence on Tree-Rings Structure From Siberian Forest-Steppe.

Wood formation allows trees to adjust in a changing climate. Understanding what determine its adjustment is crucial to evaluate impacts of climatic changes on trees and forests growth. Despite efforts to characterize wood formation, little is known on its impact on the xylem cellular structure.

Specific Fluorescence Hybridization (FISH) Test to Highlight Colonization of Xylem Vessels by in Naturally Infected Olive Trees ( L.).

The colonization behavior of the strain CoDiRO, the causal agent of olive quick decline syndrome (OQDS), within the xylem of L. is still quite controversial. As previous literature suggests, even if xylem vessel occlusions in naturally infected olive plants were observed, cell aggregation in the formation of occlusions had a minimal role.