<scp>flexsdm</scp>: An <scp>r</scp> package for supporting a comprehensive and flexible species distribution modelling workflow

Velazco, Santiago José Elías; Rose, M. Brooke; Andrade, André Felipe Alves de; Minoli, Ignacio; Franklin, Janet

doi:10.1111/2041-210x.13874

Cited by 48 publications

(35 citation statements)

References 36 publications

(40 reference statements)

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“…This distance threshold was defined as the maximum nearest neighbour distance among pairs of occurrences of the respective species (the ‘OBR’ approach in Mendes et al, 2020). Computations were performed in R 4.1.0 (R Core Team, 2021) using the package ENMTML (Andrade, Velazco, et al, 2020) for non‐rare species and the package flexsdm (Velazco et al, 2022) for rare species.…”

Section: Methodsmentioning

confidence: 99%

Pervasive impacts of climate change on the woodiness and ecological generalism of dry forest plant assemblages

et al. 2023

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1. Climate emergency is a significant threat to biodiversity in the 21st century, but species will not be equally affected. In summing up the responses of different species at the local scale, we can assess changes in the species quantity and composition of biotic assemblages. 2. We used more than 420K curated occurrence records of 3060 plant species to model current and future patterns of plant species distribution in one of the world's largest tropical dry forests-the Caatinga. While allowing different model extrapolation scenarios, we estimated potential changes in the species richness and composition of dryland plant assemblages in response to projected climate change, and assessed how the ecological generalism and woodiness of plant assemblages can be impacted by the climate crisis. 3. More than 99% of plant assemblages were projected to lose species by 2060, with biotic homogenisation-the decrease in spatial beta diversity-forecasted in 40% of the Caatinga. The replacement of narrow-range woody species by wide-range non-woody ones should impact at least 90% of Caatinga plant assemblages. The exacerbated species loss in the dryland plant assemblages was connected to the heterogenisation and homogenisation of biotic assemblages. Still, the magnitude of climate change impacts on ecological generalism and woodiness patterns of dryland plant assemblages differ according to the direction of the biotic change process. 4. Synthesis. The future increase in aridity will change the patterns of woodiness and ecological generalism of tropical dry forest plant assemblages by decreasing vegetation diversity and complexity. The projected biotic changes in dryland plant assemblages indicate the erosion of ecosystem services linked to biomass productivity and carbon storage. We highlight the importance of long-term conservation planning for maintaining tropical dry forests.

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Section: Methodsmentioning

confidence: 99%

Pervasive impacts of climate change on the woodiness and ecological generalism of dry forest plant assemblages

et al. 2023

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“…To reduce over fitting, we filtered the data in both geographic and environmental space. We retained one record per km 2 grid cell, then used the ‘occfilt_env’ function from the ‘flexsdm’ package version 1.3.2 (Velazco et al, 2022) with 12 bins to remove records with similar values across all environmental predictor variables. We also tested using 5 and 20 bins (more bins exclude less records), but settled on 12 as this appeared to achieve the best balance between the number of records returned and the evenness of environmental values.…”

Section: Methodsmentioning

confidence: 99%

Range reshuffling: Climate change, invasive species, and the case of Nothofagus forests in Aotearoa New Zealand

Mathias,

van Galen,

Jarvie

et al. 2023

Diversity and Distributions

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AimThe impact of climate change on forest biodiversity and ecosystem services will be partly determined by the relative fortunes of invasive and native forest trees under future conditions. Aotearoa New Zealand has high conservation value native forests and one of the world's worst invasive tree problems. We assess the relative effects of habitat redistribution on native Nothofagus and invasive conifer (Pinaceae) species in New Zealand as a case study on the compounding impacts of climate change and tree invasions.LocationAotearoa New Zealand.MethodsWe use species distribution models (SDMs) to predict the current and future distribution of habitat for five native Nothofagus species and 13 invasive conifer species under two 2070 climate scenarios. We calculate habitat loss/gain for all species and examine overlap between the invasive and native species now and in future.ResultsMost species will lose habitat overall. The native species saw large changes in the distribution of habitat with extensive losses in North Island and gains mostly in South Island. Concerningly, we found that most new habitat for Nothofagus was also suitable for at least one invasive species. However, there were refugia for the native species in the wetter parts of the climate space.Main ConclusionIf the predicted changes in habitat distribution translate to shifts in forest distribution, it would cause widespread ecological disruption. We discuss how acclimation, adaptation and biotic interactions may prevent/delay some changes. But we also highlight that the poor establishment capacity of Nothofagus, and the contrasting ability of the conifers to invade, will present persistent conservation challenges in areas of both new habitat and forest retreat. Pinaceae are problematic invaders globally, and our results highlight that control of invasions and active native forest restoration will likely be key to managing forest biodiversity under future climates.

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“…We therefore cleaned the pooled occurrence records by removing duplicates, masking to terrestrial landmasses, and removing occurrences intersecting within a 2 km radius of zoo, herbaria and country capital centroids with the CoordinateCleaner R package (Zizka et al, 2019). Lastly, to further correct for sampling biases in our presence records we applied spatial thinning to include one presence per 1 km 2 grid cell to match the spatial resolution of our environmental variables with the FLEXSDM v1.3.2 R package (Velazco et al, 2022). For distribution modelling, we produced an equal sample of pseudo-absences to cleaned presences and randomly distributed them outside of a 1 km buffer of each presence point for each model (Velazco et al, 2022).…”

Section: Methodsmentioning

confidence: 99%

The grass that built the Central Highland of Madagascar: environmental niches and morphological diversity ofLoudetia simplex

Almary,

White,

Rasaminirina

et al. 2023

Preprint

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SUMMARY1) Research Aims —Loudetia simplexis a common and dominant species throughout grassland ecosystems in mainland Africa and Madagascar. It is highly polymorphic, often classified as two taxa endemic to Madagascar:L. simplexsubsp.stipoidesandL. madagascariensis. A better understanding of the inter- and intra-specific variation between these taxa and its contributing environmental factors could improve our understanding of the history of Madagascar’s grasslands.2) Methods — The taxonomic status ofL. simplexsubsp.stipoidesandL. madagascariensiswas evaluated by morphometric analyses of 119 herbarium specimens. Species distribution modelling was used to determine the most important environmental factors underlyingthe L. simplexdistribution in Madagascar versus other African grasslands. We investigated ifL. simplexin Madagascar could be predicted by distributions across mainland Africa with niche overlap analyses.3) Key Result — African and Malagasy species exhibited variation potentially associated with environment. Specimens from northern and western Madagascar were taller with smaller spikelets than those from Southern Africa and central Madagascar.Loudetia simplextypically occurred in cooler temperatures with high precipitation and pronounced seasonality, but taller populations were found in warmer conditions. Projecting ecological niches of Southern Africa and East Tropical Africa onto Madagascar demonstrates much of the present distribution in the Central Highlands is expected from other natural African grasslands.4) Key Point — Malagasy and African individuals represent a single species, and the Malagasy species can be considered as a synonym of L. simplex. Distribution models are congruent with pre-human presence of grasslands in Madagascar.SOCIETAL IMPACT STATEMENTUnderstanding dominant species likeLoudetia simplexis necessary to understand the fire-driven grassy ecosystems they create. In Madagascar, grasslands are considered a low-value ecosystem despite their unique biodiversity and crucial importance as zebu rangeland. Only 1.8% of Madagascar’s grasslands are protected despite facing similar threats to forests and biodiversity loss. This study of common grasses will support the management of protected areas by providing information on resource management of vulnerable open ecosystems in Madagascar. Distribution models of common grass species and clear taxonomic classification can help land management stakeholders identify natural grasslands versus degraded forests.

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flexsdm: An r package for supporting a comprehensive and flexible species distribution modelling workflow

Cited by 48 publications

References 36 publications

Pervasive impacts of climate change on the woodiness and ecological generalism of dry forest plant assemblages

Pervasive impacts of climate change on the woodiness and ecological generalism of dry forest plant assemblages

Range reshuffling: Climate change, invasive species, and the case of Nothofagus forests in Aotearoa New Zealand

The grass that built the Central Highland of Madagascar: environmental niches and morphological diversity ofLoudetia simplex

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