Accounting for predator species identity reveals variable relationships between nest predation rate and habitat in a temperate forest songbird.

Nest predation is the primary cause of nest failure in most ground-nesting bird species. Investigations of relationships between nest predation rate and habitat usually pool different predator species. However, such relationships likely depend on the specific predator involved, partly because habitat requirements vary among predator species. Pooling may therefore impair our ability to identify conservation-relevant relationships between nest predation rate and habitat. We investigated predator-specific nest predation rates in the forest-dependent, ground-nesting wood warbler Phylloscopus sibilatrix in relation to forest area and forest edge complexity at two spatial scales and to the composition of the adjacent habitat matrix. We used camera traps at 559 nests to identify nest predators in five study regions across Europe. When analyzing predation data pooled across predator species, nest predation rate was positively related to forest area at the local scale (1000 m around nest), and higher where proportion of grassland in the adjacent habitat matrix was high but arable land low. Analyses by each predator species revealed variable relationships between nest predation rates and habitat. At the local scale, nest predation by most predators was higher where forest area was large. At the landscape scale (10,000 m around nest), nest predation by buzzards Buteo buteo was high where forest area was small. Predation by pine martens Martes martes was high where edge complexity at the landscape scale was high. Predation by badgers Meles meles was high where the matrix had much grassland but little arable land. Our results suggest that relationships between nest predation rates and habitat can depend on the predator species involved and may differ from analyses disregarding predator identity. Predator-specific nest predation rates, and their relationships to habitat at different spatial scales, should be considered when assessing the impact of habitat change on avian nesting success.

A predictive flight-altitude model for avoiding future conflicts between an emblematic raptor and wind energy development in the Swiss Alps.

Deployment of wind energy is proposed as a mechanism to reduce greenhouse gas emissions. Yet, wind energy and large birds, notably soaring raptors, both depend on suitable wind conditions. Conflicts in airspace use may thus arise due to the risks of collisions of birds with the blades of wind turbines. Using locations of GPS-tagged bearded vultures, a rare scavenging raptor reintroduced into the Alps, we built a spatially explicit model to predict potential areas of conflict with future wind turbine deployments in the Swiss Alps. We modelled the probability of bearded vultures flying within or below the rotor-swept zone of wind turbines as a function of wind and environmental conditions, including food supply. Seventy-four per cent of the GPS positions were collected below 200 m above ground level, i.e. where collisions could occur if wind turbines were present. Flight activity at potential risk of collision is concentrated on south-exposed mountainsides, especially in areas where ibex carcasses have a high occurrence probability, with critical areas covering vast expanses throughout the Swiss Alps. Our model provides a spatially explicit decision tool that will guide authorities and energy companies for planning the deployment of wind farms in a proactive manner to reduce risk to emblematic Alpine wildlife.

Mid- and long-term responses of land snail communities to the intensification of mountain hay meadows management.

BACKGROUND: Species-rich semi-natural grasslands are impacted by the severe land-use changes that are affecting mountain regions, compromising their high biodiversity value. In particular, sprinkler irrigation and increased fertilisation stimulate vegetation growth, modifying and homogenising habitat conditions for ground-dwelling invertebrates. Among them, land snails have been largely understudied despite their commonness and vulnerability to small-scale habitat alteration. This study investigated the mid- and long-term responses of land snail communities to management intensification of montane and subalpine hay meadows. Mid-term effects were studied using a randomised block design experiment, mimicking an intensification gradient with different levels of irrigation and fertilisation applied during 5 years. Long-term effects were examined relying on an observational approach that consisted in comparing snail communities in meadows managed intensively for > 20 years with those from the 5-year experimental module. RESULTS: We show that management intensification initially boosts snail densities, but erodes species richness by - 35% in intensively-managed meadows in the long term. Contrary to our expectations, drought-tolerant (xerophilous) snails benefitted from grassland intensification, whereas mesophilous species accounted for most species losses due to intensification in the long run, indicating that the latter may be especially sensitive to the hostile microclimate conditions abruptly prevailing in a meadow after mowing. Soil pH was also a principal determinant of land snail occurrence, with almost no specimen recorded in acidic meadows (pH < 5.5), while plant diversity favoured overall snail abundance. CONCLUSIONS: Despite the fact that xerophilous snails appear tolerant to management intensification, we found that several drought-sensitive species are lost in the long term. We conclude that the preservation of species-rich land snail communities in mountain hay meadows requires the conservation and restoration of low-input grasslands on basic soils for preventing further species losses of gastropod fauna.

Spatio-temporal variation in the wintering associations of an alpine bird.

Many animals make behavioural changes to cope with winter conditions, being gregariousness a common strategy. Several factors have been invoked to explain why gregariousness may evolve during winter, with individuals coming together and separating as they trade off the different costs and benefits of living in groups. These trade-offs may, however, change over space and time as a response to varying environmental conditions. Despite its importance, little is known about the factors triggering gregarious behaviour during winter and its change in response to variation in weather conditions is poorly documented. Here, we aimed at quantifying large-scale patterns in wintering associations over 23 years of the white-winged snowfinch Montifringilla nivalis nivalis. We found that individuals gather in larger groups at sites with harsh wintering conditions. Individuals at colder sites reunite later and separate earlier in the season than at warmer sites. However, the magnitude and phenology of wintering associations are ruled by changes in weather conditions. When the temperature increased or the levels of precipitation decreased, group size substantially decreased, and individuals stayed united in groups for a shorter time. These results shed light on factors driving gregariousness and points to shifting winter climate as an important factor influencing this behaviour.

Transfer of invertebrates with hay during restoration operations of extensively managed grasslands in Switzerland.

INTRODUCTION: Hay transfer from a speciose donor meadow to a species-poor receiver grassland is an established method to restore species-rich grassland plant communities. However, it has rarely been investigated to which extent invertebrates can be transferred with hay during such operations, which was the aim of this study. METHODS: Sampling was conducted in eight sites of the Swiss lowlands with one donor meadow and two receiver sites each. On the receiver sites, three to four white bed sheets of one square meter each were deployed on the ground to receive a standard quantity of fresh hay just transferred from the donor meadow. All living invertebrates were collected from these sheets with an aspirator and subsequently identified to order level. RESULTS: On average (± SD), 9.2 ± 11.3 living invertebrates per square meter were transferred with the hay. Beetles were the most abundant species group, representing 46.9% of all transferred invertebrates, followed by true bugs (8.9%) and spiders (7.0%). More individuals were transferred when the donor meadow was mown with a hand motor bar mower than with a rotary disc mower. Similarly, more invertebrates were transferred when the hay was transported loosely with a forage wagon than compacted as bales. DISCUSSION: While this study demonstrates that living invertebrates can be transferred with the hay, their subsequent survival and establishment remains to be explored. IMPLICATIONS FOR INSECT CONSERVATION: We recommend using a hand motor bar mower and a forage wagon for increasing the survival probability of invertebrates in hay transfer.

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. We experimentally tested the effects of fertilization and irrigation on vascular plant species richness and the functional composition of mountain grasslands in the Swiss Alps. After five years, fertilization increased yield but the relationship was quadratic with maximum yield reached at intermediate fertilizer levels (58 kg N ha-1year-1). The species richness of all vascular plants and forbs decreased, on average, by 6 and 5 species respectively, per 50 kg N of extra fertilizer (ha-1 year-1) applied. Fertilization also favored fast-growing plants (increased mean specific leaf area) and plants typically found in productive environments (increased mean indicator values for soil productivity and moisture). In contrast, we found no effects of irrigation on plant community composition, which suggests that irrigation does not affect vascular plant diversity to the same extent as fertilization in these mesic mountain hay meadows, at least in the mid-term. Our finding that maximum yield can be achieved at intermediate fertilizer levels is very important from an applied, agronomical and conservation point of view. It suggests that without loss of yield, farming costs and at the same time environmental pollution and negative effects on biodiversity can be reduced by applying less fertilizer. We therefore recommend maintaining non-intensive land use and keeping fertilizer inputs as low as possible to maintain the high plant diversity of mountain grasslands.

Modeling the effects of grassland management intensity on biodiversity.

A growing food demand and advanced agricultural techniques increasingly affect farmland ecosystems, threatening invertebrate populations with cascading effects along the food chain upon insectivorous vertebrates. Supporting farmland biodiversity thus optimally requires the delineation of species hotspots at multiple trophic levels to prioritize conservation management. The goal of this study was to investigate the links between grassland management intensity and orthopteran density at the field scale and to upscale this information to the landscape in order to guide management action at landscape scale. More specifically, we investigated the relationships between grassland management intensity, floral indicator species, and orthopteran abundance in grasslands with different land use in the SW Swiss Alps. Field vegetation surveys of indicator plant species were used to generate a management intensity proxy, to which field assessments of orthopterans were related. Orthopteran abundance showed a hump-shaped response to management intensity, with low values in intensified, nutrient-rich grasslands and in nutrient-poor, xeric grasslands, while it peaked in middle-intensity grasslands. Combined with remote-sensed data about grassland gross primary productivity, the above proxy was used to build landscape-wide, spatially explicit projections of the potential distribution of orthopteran-rich grasslands as possible foraging grounds for insectivorous vertebrates. This spatially explicit multitrophic approach enables the delineation of focal farmland areas in order to prioritize conservation action.

SDMtune: An R package to tune and evaluate species distribution models.

Balancing model complexity is a key challenge of modern computational ecology, particularly so since the spread of machine learning algorithms. Species distribution models are often implemented using a wide variety of machine learning algorithms that can be fine-tuned to achieve the best model prediction while avoiding overfitting. We have released SDMtune, a new R package that aims to facilitate training, tuning, and evaluation of species distribution models in a unified framework. The main innovations of this package are its functions to perform data-driven variable selection, and a novel genetic algorithm to tune model hyperparameters. Real-time and interactive charts are displayed during the execution of several functions to help users understand the effect of removing a variable or varying model hyperparameters on model performance. SDMtune supports three different metrics to evaluate model performance: the area under the receiver operating characteristic curve, the true skill statistic, and Akaike's information criterion corrected for small sample sizes. It implements four statistical methods: artificial neural networks, boosted regression trees, maximum entropy modeling, and random forest. Moreover, it includes functions to display the outputs and create a final report. SDMtune therefore represents a new, unified and user-friendly framework for the still-growing field of species distribution modeling.

Disentangling the spatial and temporal causes of decline in a bird population.

The difficulties in understanding the underlying reasons of a population decline lie in the typical short duration of field studies, the often too small size already reached by a declining population or the multitude of environmental factors that may influence population trend. In this difficult context, useful demographic tools such as integrated population models (IPM) may help disentangling the main reasons for a population decline. To understand why a hoopoe Upupa epops population has declined, we followed a three step model analysis. We built an IPM structured with respect to habitat quality (approximated by the expected availability of mole crickets, the main prey in our population) and estimated the contributions of habitat-specific demographic rates to population variation and decline. We quantified how much each demographic rate has decreased and investigated whether habitat quality influenced this decline. We tested how much weather conditions and research activities contributed to the decrease in the different demographic rates. The decline of the hoopoe population was mainly explained by a decrease in first-year apparent survival and a reduced number of fledglings produced, particularly in habitats of high quality. Since a majority of pairs bred in habitats of the highest quality, the decrease in the production of locally recruited yearlings in high-quality habitat was the main driver of the population decline despite a homogeneous drop of recruitment across habitats. Overall, the explanatory variables we tested only accounted for 19% of the decrease in the population growth rate. Among these variables, the effects of spring temperature (49% of the explained variance) contributed more to population decline than spring precipitation (36%) and research activities (maternal capture delay, 15%). This study shows the power of IPMs for identifying the vital rates involved in population declines and thus paves the way for targeted conservation and management actions.

Habitat amount mediates the effect of fragmentation on a pollinator's reproductive performance, but not on its foraging behaviour.

Agricultural intensification, with its associated habitat loss and fragmentation, is among the most important drivers of the ongoing pollination crisis. In this quasi-experimental study, conducted in intensively managed vineyards in southwestern Switzerland, we tested the separate and interdependent effects of habitat amount and fragmentation on the foraging activity and reproductive performance of bumblebee Bombus t. terrestris colonies. Based on a factorial design, we selected a series of spatially replicated study sites across a dual gradient of habitat amount (area of ground-vegetated vineyards) and fragmentation (density of ground-vegetated vineyard fields) in a landscape predominantly consisting of vineyards with bare grounds. The foraging activity of individual bumblebees was measured using the radio frequency identification (RFID) technology, and we assessed final colony size to measure reproductive performance. We found an interactive effect of habitat amount and fragmentation on colony size. More specifically, the degree of fragmentation had a negative effect on bumblebee colony size when the amount of habitat was low, while it had a weak positive effect on colony size in landscapes with high amounts of habitat. At the level of individual vineyard fields, ground vegetation cover exerted a positive effect on bumblebee colony size. Fragmentation, but not habitat amount, significantly influenced foraging activity, with more foraging trips in sites with lower degrees of fragmentation. Our results emphasise the importance of studying the separate and interdependent effects of habitat amount and fragmentation to understand their influence on pollinators, providing guidance for optimising the spatial configuration of agricultural landscapes from a biodiversity viewpoint.

Author Correction: A global database for metacommunity ecology, integrating species, traits, environment and space.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A global database for metacommunity ecology, integrating species, traits, environment and space.

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; "CESTES". Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology.

Species interactions and climate change: How the disruption of species co-occurrence will impact on an avian forest guild.

Interspecific interactions are crucial in determining species occurrence and community assembly. Understanding these interactions is thus essential for correctly predicting species' responses to climate change. We focussed on an avian forest guild of four hole-nesting species with differing sensitivities to climate that show a range of well-understood reciprocal interactions, including facilitation, competition and predation. We modelled the potential distributions of black woodpecker and boreal, tawny and Ural owl, and tested whether the spatial patterns of the more widespread species (excluding Ural owl) were shaped by interspecific interactions. We then modelled the potential future distributions of all four species, evaluating how the predicted changes will alter the overlap between the species' ranges, and hence the spatial outcomes of interactions. Forest cover/type and climate were important determinants of habitat suitability for all species. Field data analysed with N-mixture models revealed effects of interspecific interactions on current species abundance, especially in boreal owl (positive effects of black woodpecker, negative effects of tawny owl). Climate change will impact the assemblage both at species and guild levels, as the potential area of range overlap, relevant for species interactions, will change in both proportion and extent in the future. Boreal owl, the most climate-sensitive species in the guild, will retreat, and the range overlap with its main predator, tawny owl, will increase in the remaining suitable area: climate change will thus impact on boreal owl both directly and indirectly. Climate change will cause the geographical alteration or disruption of species interaction networks, with different consequences for the species belonging to the guild and a likely spatial increase of competition and/or intraguild predation. Our work shows significant interactions and important potential changes in the overlap of areas suitable for the interacting species, which reinforce the importance of including relevant biotic interactions in predictive climate change models for increasing forecast accuracy.

Unravelling migration connectivity reveals unsustainable hunting of the declining ortolan bunting.

In France, illegal hunting of the endangered ortolan bunting Emberiza hortulana has been defended for the sake of tradition and gastronomy. Hunters argued that ortolan buntings trapped in southwest France originate from large and stable populations across the whole of Europe. Yet, the European Commission referred France to the Court of Justice of the European Union (EU) in December 2016 for infringements to legislation (IP/16/4213). To better assess the impact of hunting in France, we combined Pan-European data from archival light loggers, stable isotopes, and genetics to determine the migration strategy of the species across continents. Ortolan buntings migrating through France come from northern and western populations, which are small, fragmented and declining. Population viability modeling further revealed that harvesting in southwest France is far from sustainable and increases extinction risk. These results provide the sufficient scientific evidence for justifying the ban on ortolan harvesting in France.

Larval and phenological traits predict insect community response to mowing regime manipulations.

For the restoration of biodiversity in agricultural grasslands, it is essential to understand how management acts as an ecological filter on the resident species. Mowing constitutes such a filter: only species that possess functional traits enabling them to withstand its consequences can persist in the community. We investigated how the timing of mowing modulates this filtering effect for insects. We predicted that two traits drive species responses. Species with larval development within the meadow vegetation will suffer more from mowing than species whose larvae develop in or on the ground, or outside the meadows, while species with a later phenology should benefit from later mowing. We conducted a five-year experiment, replicated at 12 sites across the Swiss lowlands, applying three different mowing regimes to low-intensity hay meadows: (1) first cut of the year not earlier than 15 June (control regime); (2) the first cut delayed until 15 July; and (3) leaving an uncut grass refuge on 10-20% of the meadow area (after earliest first cut on 15 June). Before the first cut in years 4 or 5, we sampled larvae of Lepidoptera and sawflies, and adults of moths, parasitoid wasps, wild bees, hoverflies, ground beetles, and rove beetles. Overall, before the first cut of the year, abundances of species with vegetation-dwelling larvae were higher in meadows with delayed mowing or an uncut grass refuge, with some taxon-specific variation. In contrast, species whose larval development is independent of the meadow vegetation showed no differences in abundance between mowing regimes. Species richness did not differ among regimes. For species with vegetation-dwelling larvae, a fourth-corner analysis showed an association between early phenology and the control regime. No associations were found for the other functional groups. Our results show that slight modifications of mowing regimes, easily implementable in agri-environmental policy schemes, can boost invertebrate abundance, potentially benefitting insectivorous vertebrates.

Effects of forest wildfire on inner-Alpine bird community dynamics.

As major disturbance agents, natural catastrophes impact habitats, thereby maintaining the dynamics of ecological communities. Such discrete events are expected to positively affect biodiversity because they generate high habitat heterogeneity and thus numerous ecological niche opportunities. Species typical of open and semi-open habitats, which are often of high conservation concern in modern anthropized landscapes, may benefit most from recurrent natural catastrophes that regularly reset ecosystems. We investigated bird community changes and species-specific responses to wildfire at two recently burnt temperate, montane-subalpine forest stands in an inner-Alpine Swiss valley, with a special focus on red-listed and conservation priority species. We compared bird community changes in burnt forests (spanning 13 years) with bird assemblages occurring in adjacent non-burned forest stands that served as quasi-experimental controls. Strong species-specific responses to wildfire were evidenced, resulting in a dramatic post-fire decrease in overall bird abundance and species richness. Yet, red-listed bird species and conservation priority species in Switzerland were substantially more common in burnt than in control forest stands. Many red-listed species showed a bell-shaped numeric response to wildfire over time, suggesting low habitat suitability just after fire, high habitat suitability at pioneer and early stages of vegetation succession, followed by a long-term decrease in suitability while vegetation becomes denser, especially at ground level. As established for Mediterranean regions where wildfires are especially frequent, this study shows that forest fires can also boost the populations of red-listed and priority bird species typical of open and semi-open habitats in temperate biomes. Prescribed forest fire might represent a management option for preserving threatened elements of biodiversity despite the intense public debate it will trigger.

Direct and indirect effects of land use on bryophytes in grasslands.

Land-use intensification is the major threat for biodiversity in agricultural grasslands, and fertilization has been suggested as the most important driver. A common explanation for the decline of bryophyte diversity with higher land-use intensity is an indirect negative effect via the increase in vascular plant productivity, which reduces light levels for bryophytes. However, direct negative effects of land-use intensification may also be important. Here, we disentangle direct and vascular plant biomass mediated indirect effects of land use on bryophytes. We analyzed two complementary datasets from agricultural grasslands, an observational study across 144 differently managed grasslands in Germany and an experimental fertilization and irrigation study of eleven grasslands in the Swiss Alps. We found that bryophyte richness and cover strongly declined with land-use intensity and in particular with fertilization. However, structural equation modelling revealed that although both direct and indirect effects were important, the direct negative effect of fertilization was even stronger than the indirect effect mediated by increased plant biomass. Thus, our results challenge the widespread view that the negative effects of fertilization are mostly indirect and mediated via increased light competition with vascular plants. Our study shows that land use intensification reduces bryophyte diversity through several different mechanisms. Therefore, only low-intensity management with limited fertilizer inputs will allow the maintenance of bryophyte-rich grasslands.

Mitigating the negative impacts of tall wind turbines on bats: Vertical activity profiles and relationships to wind speed.

Wind turbines represent a source of hazard for bats, especially through collision with rotor blades. With increasing technical development, tall turbines (rotor-swept zone 50-150 m above ground level) are becoming widespread, yet we lack quantitative information about species active at these heights, which impedes proposing targeted mitigation recommendations for bat-friendly turbine operation. We investigated vertical activity profiles of a bat assemblage, and their relationships to wind speed, within a major valley of the European Alps where tall wind turbines are being deployed. To monitor bat activity we installed automatic recorders at sequentially increasing heights from ground level up to 65 m, with the goal to determine species-specific vertical activity profiles and to link them to wind speed. Bat call sequences were analysed with an automatic algorithm, paying particular attention to mouse-eared bats (Myotis myotis and Myotis blythii) and the European free-tailed bat (Tadarida teniotis), three locally rare species. The most often recorded bats were the Common pipistrelle (Pipistrellus pipistrellus) and Savi's pipistrelle (Hypsugo savii). Mouse-eared bats were rarely recorded, and mostly just above ground, appearing out of risk of collision. T. teniotis had a more evenly distributed vertical activity profile, often being active at rotor level, but its activity at that height ceased above 5 ms-1 wind speed. Overall bat activity in the rotor-swept zone declined with increasing wind speed, dropping below 5% above 5.4 ms-1. Collision risk could be drastically reduced if nocturnal operation of tall wind turbines would be restricted to wind speeds above 5 ms-1. Such measure should be implemented year-round because T. teniotis remains active in winter. This operational restriction is likely to cause only small energy production losses at these tall wind turbines, although further analyses are needed to assess these losses precisely.

Spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus revealed by museum genomics.

Analyzing genetic variation through time and space is important to identify key evolutionary and ecological processes in populations. However, using contemporary genetic data to infer the dynamics of genetic diversity may be at risk of a bias, as inferences are performed from a set of extant populations, setting aside unavailable, rare, or now extinct lineages. Here, we took advantage of new developments in next-generation sequencing to analyze the spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus, a steppic Southwestern-Palearctic species. We applied a recently developed hybridization capture (hyRAD) protocol that allows retrieving orthologous sequences even from degraded DNA characteristic of museum specimens. We identified single nucleotide polymorphisms in 68 historical and 51 modern samples in order to (i) unravel the spatial genetic structure across part of the species distribution and (ii) assess the loss of genetic diversity over the past century in Swiss populations. Our results revealed (i) the presence of three potential glacial refugia spread across the European continent and converging spatially in the Alpine area. In addition, and despite a limited population sample size, our results indicate (ii) a loss of allelic richness in contemporary Swiss populations compared to historical populations, whereas levels of expected heterozygosities were not significantly different. This observation is compatible with an increase in the bottleneck magnitude experienced by central European populations of O. decorus following human-mediated land-use change impacting steppic habitats. Our results confirm that application of hyRAD to museum samples produces valuable information to study genetic processes across time and space.