ecospat: an R package to support spatial analyses and modeling of species niches and distributions

Cola, Valeria Di; Broennimann, Olivier; Petitpierre, Blaise; Breiner, Frank T.; D’Amen, Manuela; Randin, Christophe F.; Engler, Robin; Pottier, Julien; Pio, Dorothea; Dubuis, Anne; Pellissier, Loïc; Mateo, Rubén G.; Hordijk, Wim; Salamin, Nicolas; Guisan, Antoine

doi:10.1111/ecog.02671

Cited by 860 publications

(715 citation statements)

References 127 publications

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“…3.1.2, R Core Team) using the libraries 'ade4' (Dray et al 2007), 'adehabitatHR' (Calenge 2006), 'ecospat' (Di Cola et al 2017), 'maptools' (Bivand and Lewin-Koh 2014), 'raster' (Hijmans 2015), 'rgdal' (Bivand et al 2017), 'rgeos' (Bivand and Rundel 2015) and 'vegan' (Oksanen et al 2014). 3.1.2, R Core Team) using the libraries 'ade4' (Dray et al 2007), 'adehabitatHR' (Calenge 2006), 'ecospat' (Di Cola et al 2017), 'maptools' (Bivand and Lewin-Koh 2014), 'raster' (Hijmans 2015), 'rgdal' (Bivand et al 2017), 'rgeos' (Bivand and Rundel 2015) and 'vegan' (Oksanen et al 2014).…”

Section: Sdm Frameworkmentioning

confidence: 99%

Disentangling biotic interactions, environmental filters, and dispersal limitation as drivers of species co‐occurrence

et al. 2017

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A key focus in ecology is to search for community assembly rules. Here we compare two community modelling frameworks that integrate a combination of environmental and spatial data to identify positive and negative species associations from presenceabsence matrices, and incorporate an additional comparison using joint species distribution models (JSDM).The frameworks use a dichotomous logic tree that distinguishes dispersal limitation, environmental requirements, and interspecific interactions as causes of segregated or aggregated species pairs. The first framework is based on a classical null model analysis complemented by tests of spatial arrangement and environmental characteristics of the sites occupied by the members of each species pair (Classic framework). The second framework, (SDM framework) implemented here for the first time, builds on the application of environmentally-constrained null models (or JSDMs) to partial out the influence of the environment, and includes an analysis of the geographical configuration of species ranges to account for dispersal effects.We applied these approaches to examine plot-level species co-occurrence in plant communities sampled along a wide elevation gradient in the Swiss Alps. According to the frameworks, the majority of species pairs were randomly associated, and most of the non-random positive and negative species associations could be attributed to environmental filtering and/or dispersal limitation. These patterns were partly detected also with JSDM. Biotic interactions were detected more frequently in the SDM framework, and by JSDM, than in the Classic framework. All approaches detected species aggregation more often than segregation, perhaps reflecting the important role of facilitation in stressful high-elevation environments.Differences between the frameworks may reflect the explicit incorporation of elevational segregation in the SDM framework and the sensitivity of JSDM to the environmental data. Nevertheless, all methods have the potential to reveal general patterns of species co-occurrence for different taxa, spatial scales, and environmental conditions.

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Section: Sdm Frameworkmentioning

confidence: 99%

Disentangling biotic interactions, environmental filters, and dispersal limitation as drivers of species co‐occurrence

et al. 2017

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“…The process was repeated 1000 times for both ranges under comparison, and the observed D value was compared to the distribution of the randomized D values in a one-sided t-test (Broennimann et al 2012). All analyses were conducted using the 'ecospat' package in R (Di Cola et al 2017). 20, 50, and 100 km.…”

Section: Selection Of Climatic Variables Niche Breadth and Niche Simmentioning

confidence: 99%

Forecasting range shifts of a cold‐adapted species under climate change: are genomic and ecological diversity within species crucial for future resilience?

et al. 2018

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Cold-adapted taxa are experiencing severe range shifts due to climate change and are expected to suffer a significant reduction of their climatically suitable habitats in the next few decades. However, it has been proposed that taxa with sufficient standing genetic and ecologic diversity will better withstand climate change. These taxa are typically more broadly distributed in geographic and ecological niche space, therefore they are likely to endure higher levels of populations loss than more restricted, less diverse taxa before the effects of those losses impact their overall diversity and resilience. Here, we explore the potential relationship between intraspecific genetic and ecological diversity and future resilience, using the cold-adapted plant Primula farinosa. We employ high-throughput sequencing to assess the genomic diversity of phylogeographic lineages in P. farinosa. Additionally, we use current climatic variables to define niche breadth and niche differentiation across lineages. Finally, we calibrate species distribution models (SDMs) and project the climatic preferences of each lineage on future climate to predict lineagespecific shifts in climatically suitable habitats. Our study predicts relative persistence of future suitable habitats for the most genetically and ecologically diverse lineages of the cold-adapted P. farinosa, but significant reduction of them for two out of its four lineages. While we do not provide specific experiments aimed at identifying the causal links between genetic diversity and resilience to climate change, our results indicate that greater genetic diversity and wider ecological breadth may buffer species responses to rapid climatic changes. This study further highlights the importance of integrating knowledge of intraspecific diversity for predicting species fate in response to climate change.

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“…We report all results based on the additional variable sets in the supplementary material (i.e. Thus, in order to test for robustness of our hypervolume analyses, we additionally calculated all niche quantifications based on the approach developed by Broennimann et al (2012), implemented in the 'ecospat' R package (Di Cola et al 2017). Because all results from these robustness analyses of variable sets were highly congruent with the results based on our original variable choice (Supplementary material), we here present results based on the above mentioned set of 12 bioclim variables that facilitate the interpretation of climatic dimensions in our study area.…”

Section: Niche Hypervolumes and Species Distribution Modelingmentioning

confidence: 99%

Quantifying the climatic niche of symbiont partners in a lichen symbiosis indicates mutualist‐mediated niche expansions

et al. 2017

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The large distributional areas and ecological niches of many lichenized fungi may in part be due to the plasticity in interactions between the fungus (mycobiont) and its algal or cyanobacterial partners (photobionts). On the one hand, broad-scale phylogenetic analyses show that partner compatibility in lichens is rather constrained and shaped by reciprocal selection pressures and codiversification independent of ecological drivers. On the other hand, sub-species-level associations among lichen symbionts appear to be environmentally structured rather than phylogenetically constrained. In particular, switching between photobiont ecotypes with distinct environmental preferences has been hypothesized as an adaptive strategy for lichen-forming fungi to broaden their ecological niche. The extent and direction of photobiont-mediated range expansions in lichens, however, have not been examined comprehensively at a broad geographic scale. Here we investigate the population genetic structure of Lasallia pustulata symbionts at sub-species-level resolution across the mycobiont's Europe-wide range, using fungal MCM7 and algal ITS rDNA sequence markers. We show that variance in occurrence probabilities in the geographic distribution of genetic diversity in mycobiontphotobiont interactions is closely related to changes in climatic niches. Quantification of niche extent and overlap based on species distribution modeling and construction of Hutchinsonian climatic hypervolumes revealed that combinations of fungal-algal interactions change at the sub-species level along latitudinal temperature gradients and in Mediterranean climate zones. Our study provides evidence for symbiontmediated niche expansion in lichens. We discuss our results in the light of symbiont polymorphism and partner switching as potential mechanisms of environmental adaptation and niche evolution in mutualisms.

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ecospat: an R package to support spatial analyses and modeling of species niches and distributions

Cited by 860 publications

References 127 publications

Disentangling biotic interactions, environmental filters, and dispersal limitation as drivers of species co‐occurrence

Disentangling biotic interactions, environmental filters, and dispersal limitation as drivers of species co‐occurrence

Forecasting range shifts of a cold‐adapted species under climate change: are genomic and ecological diversity within species crucial for future resilience?

Quantifying the climatic niche of symbiont partners in a lichen symbiosis indicates mutualist‐mediated niche expansions

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