Papers by Olivier Broennimann
Conservation Science and Practice
ContextHuman-induced changes in landscape structure are among the main causes of biodiversity los... more ContextHuman-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 landscape is rarely assessed.ObjectivesWe assessed the effect of landscape structure on soil protist alpha and beta diversity in meadows in the western Swiss Alps.MethodsWe sampled 178 plots along an elevation gradient representing a broad range of environmental conditions and land-use. We measured landscape structure around each plot at 5 successive spatial scales (i.e. neighbourhood windows of increasing radius, ranging from 100 to 2000 m around a plot). We investigated the changes of protist alpha and beta diversity as a function of landscape structure, local environmental conditions and geographic distance.ResultsLandscape structures ...
Biodiversity and Climate Change, 2019
Ecological Applications, 2021
Many species distribution models (SDMs) are built with precise but geographically restricted pres... more Many species distribution models (SDMs) are built with precise but geographically restricted presence-absence datasets (e.g. a country) where only a subset of the environmental conditions experienced by a species across its range is considered (i.e. spatial niche truncation). This type of truncation is worrisome because it can lead to incorrect predictions e.g. when projecting to future climatic conditions belonging to the species niche but unavailable in the calibration area. Data from citizen-science programs, species range maps or atlases covering the full species range can be used to capture those parts of the species' niche that are missing regionally. However, these data usually are too coarse or too biased to support regional management. Here, we aim to (1) demonstrate how varying degrees of spatial niche truncation affect SDMs projections when calibrated with climatically-truncated regional datasets and (2) test the performance of different methods to harness information from larger-scale datasets presenting different spatial resolutions to solve the spatial niche truncation problem. We used simulations to compare the performance of the different methods, and applied them to a real dataset to predict the future distribution of a plant species (Potentilla aurea) in Switzerland. SDMs calibrated with geographically restricted datasets expectedly provided biased predictions when projected outside the calibration area or time period. Approaches integrating information from larger-scale datasets using hierarchical data integration methods usually reduced this bias. However, their performance varied depending on the level of spatial niche truncation and how data were combined. Interestingly, while some methods (e.g. data pooling, downscaling) performed well on both simulated and real data, others (e.g. those based on a Poisson point process) performed better on real data, indicating a dependency of model performance on the simulation process (e.g. shape of simulated response curves). Based on our results, we recommend to use different data integration methods and, whenever possible, to make a choice depending on model performance. In any case, an ensemble modelling approach can be used to account for uncertainty in how niche truncation is accounted for and identify areas where similarities/dissimilarities exist across methods.
Nature Climate Change, 2015
Wisz et al. reply-Ingvaldsen et al. 1 comment on our study assessing global fish interchanges bet... more Wisz et al. reply-Ingvaldsen et al. 1 comment on our study assessing global fish interchanges between the North Atlantic and Pacific oceans for more than 500 species during the entire twenty-first century 2. They propose that discrepancies between our model projections and observed data for cod in the Barents Sea are the result of the choice of atmosphere-ocean general circulation models (AOGCMs). We address this assertion here, re-running the cod model with additional observation data from the Barents Sea 1,3 , and show that the lack of open-access archived data for the Barents Sea was the primary cause of local prediction mismatch. This finding highlights the importance of systematic deposit of biodiversity data in global databases.
Alpine Entomology
Coprophagous beetles are essential for fecal matter removal and are thus considered key ecosystem... more 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 distribution of coprophagous beetles in the Western Swiss Alps. We used our own sampled data and existing national data from the Swiss faunal database to calibrate, for each species, a regional and a national SDM respectively. In both models, the best predictors were temperature and rock cover proportion, while a soil characteristic (∂13C) indicating its organic content and texture was important in the regional models and precipitations in the Swiss models. The model performed better for species specialized on low or high altitudes than for generalist species occurring in a large altitudinal range. The model performances were neither influe...
Soil Biology and Biochemistry
Although widely used in ecology, comparative analyses of diversity and niche properties are still... more Although widely used in ecology, comparative analyses of diversity and niche properties are still lacking for microorganisms, especially concerning niche variations. In this study, we identi ed important topoclimatic, edaphic, spatial and biotic drivers of the alpha and beta diversity of bacterial, archaeal, fungal and protist communities. Then, we calculated the niche breadth and position of each taxon along environmental gradients within all taxonomic groups, to determine how these vary within and between groups. Quantifying the niches of microbial taxa is necessary to then forecast how taxa and the communities they compose might respond to environmental changes. We found that edaphic properties were the most important drivers of both community diversity and composition for all microbial groups. Protists presented the largest niche breadths, followed by bacteria and archaea, with fungi displaying the smallest. Niche breadth generally decreased towards environmental extremes, especially along edaphic gradients, suggesting increased specialisation of microbial taxa in highly selective environments. Overall, we showed that microorganisms have well de ned niches, as do macro-organisms, likely driving part of the observed spatial patterns of community variations. Assessing niche variation more widely in microbial ecology should open new perspectives, especially to tackle global change effects on microbes.
Environmental variables used in the analyses.
Ecography, 2020
A comprehensive understanding of the relationship between land cover, climate change and disturba... more A comprehensive understanding of the relationship between land cover, climate change and disturbance dynamics is needed to inform scenarios of vegetation change on the African continent. Although significant advances have been made, large uncertainties exist in projections of future biodiversity and ecosystem change for the world's largest tropical landmass. To better illustrate the effects of climate-disturbance-ecosystem interactions on continental-scale vegetation change, we apply a novel statistical multivariate envelope approach to subfossil pollen data and climate model outputs (TraCE-21ka). We target paleoenvironmental records across continental Africa, from the African Humid Period (AHP: ca 14 700-5500 yr BP)-an interval of spatially and temporally variable hydroclimatic conditions-until recent times, to improve our understanding of overarching vegetation trends and to compare changes between forest and grassy biomes (savanna and grassland). Our results suggest that although climate variability was the dominant driver of change, forest and grassy biomes responded asymmetrically: 1) the climatic envelope of grassy biomes expanded, or persisted in increasingly diverse climatic conditions, during the second half of the AHP whilst that of forest did not; 2) forest retreat occurred much more slowly during the mid to late Holocene compared to the early AHP forest expansion; and 3) as forest and grassy biomes diverged during the second half of the AHP, their ecological relationship (envelope overlap) fundamentally changed. Based on these asymmetries and associated changes in human land use, we propose and discuss three hypotheses about the influence of anthropogenic disturbance on continental-scale vegetation change.
Global Change Biology, 2020
Assessing the degree to which climate explains the spatial distributions of different taxonomic a... more Assessing the degree to which climate explains the spatial distributions of different taxonomic and functional groups is essential for anticipating the effects of climate change on ecosystems. Most effort so far has focused on above-ground organisms, which offer only a partial view on the response of biodiversity to environmental gradients. Here including both above-and below-ground organisms, we quantified the degree of topoclimatic control on the occurrence patterns of >1,500 taxa and phylotypes along a This is an open access article under the terms of the Creat ive Commo ns Attri butio n-NonCo mmerc ial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
BackgroundThe niche concept describes the range of conditions supporting the establishment and pe... more BackgroundThe niche concept describes the range of conditions supporting the establishment and persistence of species in the environment. Although widely used in ecology, it has not been often applied to microbes, for which comparative niche analyses are still lacking. Yet, quantifying the niche of microbial taxa is necessary to forecast how taxa and the communities they compose might respond to environmental changes. In this study, we identified important topoclimatic, edaphic, spatial and biotic drivers of the alpha and beta diversity of bacterial, archaeal, fungal and protist communities. Then, we established a method to calculate the niche breadth and position of each taxon along environmental gradients to determine whether microorganisms have distinct environmental niches. ResultsFor all microbial groups, edaphic properties were identified as the most important drivers of both community diversity and composition. Protists presented the largest niche breadths, followed by bacter...
The Giant Hogweed (Heracleum mantegazzianum), an invasive giant herb native from Caucasus, was fi... more The Giant Hogweed (Heracleum mantegazzianum), an invasive giant herb native from Caucasus, was first introduced in Switzerland (Geneva) in 1895 and cultivated in alpine botanical gardens because of its spectacular inflorescence. Since then, it escaped repeatedly from gardens, becoming invasive and leading to ecological, economical and health problems. In this study, we evaluated the invasion status of this alien invasive species in the Western Swiss Alps, by modelling its potential distribution and estimating current and future density and cost estimations. These assessment measures provide useful tools for an action plan in conservation biology. In the continuity of a previous study in 2004, we used a model-based sampling design to improve occurrences data and ultimately improve predictive models of the species distribution. Since we did not found as much occurrences as expected, different models were carrying out with different available data sets. The first predictive maps were based on naturalized occurrences versus all available presences and the second, on a set of absence sites stratified according to the strata of a previous available model. We tested two different estimations of the giant hogweed's population size: a design-based estimation and a model-based estimation. We first proceed to the Thompson design-based estimation through a randomstratified adaptive sampling. This estimation provided current population size of the focal species. The future potential population size of the focal species was achieved with the models resulting from the field sampling. For management cost, communes included in the study area were set as management units and assessed individually. A binary model using threshold value optimising ratio of omission to commission errors provided future potential costs. Finally, this filtered binomial model permits us to underline which communes should receive special attention for eradication.
Climate Change Management, 2019
Alien plant species have been essential for farming and agro-forestry systems and for their suppl... more Alien plant species have been essential for farming and agro-forestry systems and for their supply of food, fiber, tannins, resins or wood from antiquity to the present. They also contributed to supporting functions and regulating services (water, soil, biodiversity) and to the design of landscapes with high cultural and scenic value. Some of those species were intentionally introduced, others arrived accidentally, and a small proportion escaped, naturalized and became invasive in natural ecosystems-these are known as invasive alien species (IAS). Here, invasive means that these species have some significant negative impact, either by spreading from human-controlled environments (e.g. fields, gardens) to natural ecosystems, where they can cause problems to native species, or to other production systems or urban areas, impacting on agricultural, forestry activities or human
Global Ecology and Biogeography, 2021
This is an open access article under the terms of the Creat ive Commo ns Attri bution License, wh... more This is an open access article under the terms of the Creat ive Commo ns Attri bution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Biodiversity and Climate Change
Nature Communications, 2021
One key hypothesis explaining the fate of exotic species introductions posits that the establishm... more One key hypothesis explaining the fate of exotic species introductions posits that the establishment of a self-sustaining population in the invaded range can only succeed within conditions matching the native climatic niche. Yet, this hypothesis remains untested for individual release events. Using a dataset of 979 introductions of 173 mammal species worldwide, we show that climate-matching to the realized native climatic niche, measured by a new Niche Margin Index (NMI), is a stronger predictor of establishment success than most previously tested life-history attributes and historical factors. Contrary to traditional climatic suitability metrics derived from species distribution models, NMI is based on niche margins and provides a measure of how distant a site is inside or, importantly, outside the niche. Besides many applications in research in ecology and evolution, NMI as a measure of native climatic niche-matching in risk assessments could improve efforts to prevent invasions a...
Diversity and Distributions, 2020
Aim: Niche-based species distribution models (SDMs) have become a ubiquitous tool in ecology and ... more Aim: Niche-based species distribution models (SDMs) have become a ubiquitous tool in ecology and biogeography. These models relate species occurrences with the environmental conditions found at these sites. Climatic variables are the most commonly used environmental data and are usually included in SDMs as averages of a reference period (30-50 years). In this study, we analyse the impact of including inter-annual climatic variability on the estimation of species niches and predicted distributions when assessing plant demographic response to extreme climatic episodes. Location: Mediterranean basin, SE Iberian Peninsula. Methods: We first characterized species niches with inter-annual and average climate in the same environmental space. We then compare the respective capacities of climatic suitability obtained from averaged climate-based and from inter-annual variability-based niches to explain population demographic responses to extreme drought. Furthermore, we assessed the relative increase in niche size when including climatic variability for a set of Mediterranean species exhibiting a wide range of distribution areas. Results: We found that climatic suitability obtained from inter-annual variabilitybased niches showed higher explanatory capacity than average climate-based suitability, especially for populations living in climatically marginal conditions, although both niches quantifications significantly explained species demographic responses. In addition, species with restricted distribution ranges increased relatively more their niche space when considering climatic variability, probably because in widely distributed species spatial variability compensates for temporal variability. Main conclusions: The common use of climatic averages when characterizing species niches could lead to underestimations of species distribution and misunderstanding of demographic behaviour, with implications for conservation plans derived from SDMs, for example, overestimations of species extinction risk under climate change, or underestimations of alien species invasion' risk. We highlight that including climatic variability in niche modelling can be particularly important when dealing with species with restricted distribution and populations at the margin of their species niche. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Uploads
Papers by Olivier Broennimann