Antoine Guisan

University of Lausanne | UNIL

The increasing online availability of biodiversity data and advances in ecological modeling have led to a proliferation of open‐source modeling tools. In particular, R packages for species distribution modeling continue to multiply without guidance on how they can be employed together, resulting in high fidelity of researchers to one or several pac...

Climate projections for continental Europe indicate drier summers, increased annual precipitation, and less snowy winters, which are expected to cause shifts in species' distributions. Yet, most regions/countries currently lack comprehensive climate‐driven biodiversity projections across taxonomic groups, challenging effective conservation efforts....

Numerous plant species are expanding their native ranges due to anthropogenic environmental change. Because cytotypes of polyploid complexes often show similar morphologies, there may be unnoticed range expansions (i.e. cryptic invasions) of one cytotype into regions where only the other cytotype is native. We critically revised herbarium specimens...

Global environmental change will cause shifts in species communities, with non‐native species likely replacing native ones at an unprecedented rate. This will have consequences for biodiversity and ecosystem services, in addition to the ecological and economic damage caused by those non‐native species that are invasive. Understanding general patter...

Biotic interactions shape the ecology of species and communities, yet their integration into ecological niche modeling methods remains challenging. Despite being a central topic of research for the past decade, the impact of biotic interactions on species distributions and community composition is often overlooked. Mutualistic systems offer ideal c...

Species distribution models (SDMs) are algorithms designed to infer the distribution of species using environmental and biotic variables and have become an important tool for ecologists and conservation biologists seeking to understand the implications of environmental change. Global datasets of environmental variables at resolutions of a few metre...

Over the last half-century, nature conservation has shifted through several steps from 'nature for itself' to 'nature and people', corresponding to a new perspective that all species count to ensure ecosystem functioning, and with them that nature's contributions to people (NCPs) are effective and maintained. Yet, despite these conceptual shifts in...

Within scenario-based research of social-ecological systems, there has been a growing recognition of the importance of normative scenarios that define positive outcomes for both nature and society. While several frameworks exist to guide the co-creation of normative scenario narratives, examples of operationalizing these narratives in quantitative...

Macroclimatic data are widely used to estimate the realized environmental niche of species and predict the current or the future spatial distribution of species. Because the realized niche is a subset of the fundamental niche—constrained by biotic interactions and dispersal limitations—proxies of the fundamental niche (e.g., thermal limits obtained...

The rapid loss of biodiversity in freshwater systems asks for a robust and spatially explicit understanding of species' occurrences. As two complementing approaches, habitat suitability models provide information about species' potential occurrence, while environmental DNA (eDNA) based assessments provide indication of species' actual occurrence. I...

The ability of climatic niche models to predict species extinction risks can be hampered if niches are incompletely quantified. This can occur when niches are estimated considering only currently available climatic conditions, disregarding the fact that climate change can open up portions of the fundamental niche that are currently inaccessible to...

Spatial truncation in species distribution models (SDMs) might cause niche truncation and model transferability issues, particularly when extrapolating models to non‐analog environmental conditions. While broad calibration extents reduce truncation issues, they usually overlook local ecological factors driving species distributions at finer resolut...

Soil microbes play a key role in shaping terrestrial ecosystems. It is therefore essential to understand what drives their distribution. While multivariate analyses have been used to characterise microbial communities and drivers of their spatial patterns, few studies have focused on predicting the distribution of amplicon sequence variants (ASVs)....

Numerous plant species are expanding their native ranges due to anthropogenic environmental change. Because cytotypes of polyploid complexes show often similar morphologies, there may be unnoticed range expansions (i.e., cryptic invasions) of one cytotype into regions where only the other cytotype is native. We critically revised 13,078 herbarium s...

Changes in climate and land use represent significant risks of biodiversity loss globally, affect ecological stability, impact nature’s contributions to people (NCP, i.e. ecosystem services) and compromise human livelihood. As framings of conservation evolve to consider the interdependence between species and human needs, there is a growing recogni...

CHclim25 is a climatic dataset with a 25 m resolution for Switzerland that includes daily, monthly and yearly layers for temperature, precipitation, relative sunshine duration, growing degree-days, potential evapotranspiration, bioclimatic variables and aridity. The dataset is downscaled from a daily 1 km resolution dataset from the Swiss federal a...

Mounting evidence points to the need for high-resolution climatic data in biodiversity analyses under globalchange. As we move to finer resolution, other factors than climate, including other abiotic variables and biotic interactions play, however, an increasing role, raising the question of our ability to predict community composition at fine scal...

We present forecasts of land-use/land-cover (LULC) change for Switzerland for three time-steps in the 21st century under the representative concentration pathways 4.5 and 8.5, and at 100-m spatial and 14-class thematic resolution. We modelled the spatial suitability for each LULC class with a neural network (NN) using > 200 predictors and accountin...

Standard and easily accessible cross-thematic spatial databases are key resources in ecological research. In Switzerland, as in many other countries, available data are scattered across computer servers of research institutions and are rarely provided in standard formats (e.g., different extents or projections systems, inconsistent naming conventio...

Despite the importance of healthy soils for human livelihood, wellbeing, and safety, current gaps in our knowledge and understanding of biodiversity in soil are numerous, undermining conservation efforts. These gaps are particularly wide in mountain regions where healthy soils are especially important for human safety and yet evidence is accumulati...

Predicting the presence or absence (occurrence-state) of species in a certain area is highly important for conservation. Occurrence-state can be assessed by network models that take suitable habitat patches as nodes, connected by potential dispersal of species. To determine connections, a connectivity threshold is set at the species’ maximum disper...

Aim The diversity and distribution of soil microorganisms and their potential for long‐distance dispersal (LDD) are poorly documented, making the threats posed by climate change difficult to assess. If microorganisms do not disperse globally, regional endemism may develop and extinction may occur due to environmental changes. Here, we addressed thi...

Aim Eurasian grapevine (Vitis vinifera), one of the most important fruit crops worldwide, diverged from its wild and currently endangered relative (V. vinifera ssp. sylvestris) about 11,000 years ago. In the 19th century, detrimental phylloxera and disease outbreaks in Europe forced grapevine cultivation to use American Vitis species as rootstocks,...

Soil microbes play a key role in shaping terrestrial ecosystems. It is therefore essential to understand what drives their distributions. While multivariate analyses have been used to characterise microbial communities and drivers of their spatial patterns, few studies focused on modelling the distribution of Operational Taxonomic Units (OTUs). Her...

Epiphytes offer an appealing framework to disentangle the contributions of chance, biotic and abiotic drivers of species distributions. In the context of the stress‐gradient theory, we test the hypotheses that (i) deterministic ( i.e. , non‐random) factors play an increasing role in communities from young to old trees, (ii) negative biotic interact...

Monitoring of terrestrial and aquatic species assemblages at large spatial scales based on environmental DNA (eDNA) has the potential to enable evidence-based environmental policymaking. The spatial coverage of eDNA-based studies varies substantially, and the ability of eDNA metabarcoding to capture regional biodiversity remains to be assessed; thu...

Evidence for the need of shifting scales in biodiversity analyses under global change is mounting, raising the question of the variables operating at fine scales. We evaluated the extent to which community composition of one guild of land plants (bryophytes vs tracheophytes) can be predicted from abiotic variables, species composition and architect...

Aim Snow cover persistence (SCP) has significant effects on plants in high‐elevation ecosystems. It determines the length of the growing season, provides insulation against low temperatures and influences water availability, thereby shaping the vegetation mosaic. Despite its importance, SCP is rarely used in plant species distribution modelling. In...

The predictive power of species distribution models (SDMs) varies substantially among species depending on their ecological and life‐history traits, but which of these traits are the most relevant and how they influence species ‘predictability' remains an area of debate. Here, we address these questions in bryophytes. SDMs employing macroclimatic,...

Addressing sustainability challenges in mountains requires multi-actorcollaboration and interdisciplinarity. Yet, such processes of knowledge co-creation need to account for the existence of diverse representations of mountain socio-ecological systems amongst actors. We build on literature and picture-based interviews with local actors to first exp...

Since the late 1990s, Nature’s Contributions to People (NCPs; i.e. ecosystem services) were used as a putative leverage for fostering nature preservation. NCPs have largely been defined and mapped at the landscape level using land use and cover classifications. However, NCP mapping attempts based directly on individual species are still uncommon. G...

Ecological processes are often spatially and temporally structured, potentially leading to autocorrelation either in environmental variables or species distribution data. Because of that, spatially-biased in-situ samples or predictors might affect the outcomes of ecological models used to infer the geographic distribution of species and diversity....

The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodologica...

The processes governing soil bacteria biogeography are still not fully understood. It remains unknown how the importance of environmental filtering and dispersal differs between bacterial taxonomic and functional biogeography, and whether their importance is scale-dependent. We sampled soils across the Tibet plateau, with distances among plots rang...

Predicting contemporary and future species distributions is relevant for science and decision making, yet the development of high‐resolution spatial predictions for numerous taxonomic groups and regions is limited by the scalability of available modelling tools. Uniting species distribution modelling (SDM) techniques into one high‐performance compu...

Sample size is a key issue in species distribution modelling. While many studies focused on the relevance of sample size for model calibration, the importance of the size of the dataset used for model evaluation has received much less attention. Here, we highlight two previously published approaches to address the problem, and which are relatively...

1. Selecting the best subset of covariates out of a panel of many candidates is a key and highly influential stage of the species distribution modelling process. Yet, there is currently no commonly accepted and widely adopted standard approach by which to perform this selection. 2. We introduce a two-step “embedded” covariate selection procedure a...

The predictive power of species distribution models (SDMs) substantially varies among species depending on their ecological and life-history traits, but which of these traits are the most relevant and how they influence species ‘predictability’ remains an area of debate. Here, we address these questions in bryophytes. SDMs were calibrated for 411 s...

Different host species associate with distinct gut microbes in mammals, a pattern sometimes referred to as phylosymbiosis. However, the processes shaping this host specificity are not well understood. One model proposes that barriers to microbial transmission promote specificity by limiting microbial dispersal between hosts. This model predicts tha...

Context Human-induced changes in landscape structure are among the main causes of biodiversity loss. Despite their important contribution to biodiversity and ecosystem functioning, microbes—and particularly protists—remain spatially understudied. Soil microbiota are most often driven by local soil properties, but the influence of the surrounding la...

Dans un contexte d’accroissement de la vulnérabilité des êtres humains et des sociétés humaines face au dérèglement climatique et à l’effondrement de la biodiversité, il devient indispensable de mener une réflexion approfondie sur les liens complexes qu’entretiennent l’environnement et notre santé. Appréhender un sujet aussi multidimensionnel néces...

Comparing the impacts of future scenarios is essential for developing and guiding the political sustainability agenda. This review-based analysis compares six IPBES scenarios for their impacts on 17 Sustainable Development Goals (SDGs) and 20 biodiversity targets (Aichi targets) for the Europe and Central Asia regions. The comparison is based on a...

Epiphytes typically exhibit clustered distribution patterns, but predicting the spatial variation of their distribution at fine scales has long been a challenge. Taking advantage of a canopy crane giving access to 1.1 ha of lowland seasonal rainforest in Yunnan (China), we assess here which factors promote the probability that a given tree hosts ep...

The introduction of alien plant species can lead to biological invasions, which have major impacts on people and the environment. Trachycarpus fortunei (Hook.) H. Wendl. (Arecaceae) is an alien plant (palm tree) that has been introduced as an ornamental into urban areas across the world, but in many regions, it has started invading forests and othe...

Habitat suitability calculated from species distribution models (SDMs) has been used to assess population performance, but empirical studies have provided weak or inconclusive support to this approach. Novel approaches measuring population distances to niche centroid and margin in environmental space have been recently proposed to explain populatio...

Unsuitable livestock farming is considered as a main driver of biodiversity loss. In the high elevation areas across the world, many subalpine and alpine natural herbaceous communities are highly sensitive to sheep overgrazing. Such habitats of high biogeographic and conservation value are refugia for slow-growing, locally rare, and cold-adapted sp...

We used Arapaima as a model species to model its climate suitability and the level of protection of Amazon floodplains. We used open-source high-resolutoin climate and habitat predictors and recent modelling techniques. We identified severe protection gaps (70% of suitable areas for Arapaima are unprotected). This gap is predicted to worsen with cl...

To withstand the surge of species loss worldwide, (re)introduction of endangered plant species has become an increasingly common technique in conservation biology. Successful (re)introduction plans, however, require identifying sites that provide the optimal ecological conditions for the target species to thrive. In this study, we propose a two‐ste...

While conservation ecology was highlighted by the creation of the IUCN redlist in the 1960s, it was in the 1990s that conservationists and economists decided to integrate the services provided by nature to humans to increase motivations to conserve our environment, later renamed Nature ‘s contributions to people (NCP). Yet, conservation planning ha...

Species Distribution Models (SDMs) are essential tools for predicting climate change impact on species’ distributions and are commonly employed as an informative tool on which to base management and conservation actions. Focusing only on a part of the entire distribution of a species for fitting SDMs is a common approach. Yet, geographically restri...

The Amazon floodplains represent important surfaces of highly valuable ecosystems, yet they remain neglected from protected areas. Although the efficiency of the protected area network of the Amazon basin may be jeopardized by climate change, floodplains are exposed to important consequences of climate change but are omitted from species distributi...

Regos A, Gonçalves J, Arenas-Castro S, Alcaraz-Segura D, Guisan A & Honrado JP (2022). Incorporating remotely sensed ecosystem functioning into species distribution models: limitations, advantages and future avenues. IALE 2022 European Landscape Ecology Congress Jul 11 – 15, 2022. Warsaw, Poland (Online).

Coprophagous beetles are essential for fecal matter removal and are thus considered key ecosystem services providers. Yet, our knowledge of these beetles' distribution and ecology remains very limited. Here, we used Species Distribution Models (SDM) to investigate the species-environment relationships (i.e. their niche) and predict the geographic d...

Mountains are hotspots of biodiversity and ecosystem services, but they are warming about twice as fast as the global average. Climate change may reduce alpine snow cover and increase vegetation productivity, as in the Arctic. Here, we demonstrate that 77% of the European Alps above the tree line experienced greening (productivity gain) and <1% bro...

Understanding the drivers of infection risk helps us to detect the most at-risk species in a community and identify species whose intrinsic characteristics could act as potential reservoirs of pathogens. This knowledge is crucial if we are to predict the emergence and evolution of infectious diseases. To date, most studies have only focused on infe...

Context Human-induced changes in landscape structure are among the main causes of biodiversity loss. However, despite their important contribution to biodiversity and ecosystem functioning, microbes – and particularly protists – remain spatially understudied. Furthermore, soil microbiota are most often related to the local soil properties, whereas...

Although widely used in ecology, comparative analyses of diversity and niche properties are still lacking for microorganisms, especially focusing on niche variations. Quantifying the niches of microbial taxa is necessary to then forecast how taxa and the communities they compose might respond to environmental changes. In this study, we first identi...

Different mammalian species host distinct gut microbes but the processes shaping this specificity are not well understood. One model proposes that barriers to microbial transmission promote specificity by limiting dispersal between hosts and predicts that specificity levels measured across individual hosts and microbes is correlated to individual d...