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1. ENMeval 2.0: Redesigned for customizable and reproducible modeling of species’ niches and distributions

   https://doi.org/10.1111/2041-210X.13628  

   Kass, Jamie M. ; Muscarella, Robert ; Galante, Peter J. ; Bohl, Corentin L. ; Pinilla‐Buitrago, Gonzalo E. ; Boria, Robert A. ; Soley‐Guardia, Mariano ; Anderson, Robert P. ( June 2021 , Methods in Ecology and Evolution)

   Quantitative evaluations to optimize complexity have become standard for avoiding overfitting of ecological niche models (ENMs) that estimate species’ potential geographic distributions.ENMevalwas the first R package to make such evaluations (often termed model tuning) widely accessible for the Maxent algorithm. It also provided multiple methods for partitioning occurrence data and reported various performance metrics.

   Requests by users, recent developments in the field, and needs for software compatibility led to a major redesign and expansion. We additionally conducted a literature review to investigate trends inENMevaluse (2015–2019).

   ENMeval2.0 has a new object‐oriented structure for adding other algorithms, enables customizing algorithmic settings and performance metrics, generates extensive metadata, implements a null‐model approach to quantify significance and effect sizes, and includes features to increase the breadth of analyses and visualizations. In our literature review, we found insufficient reporting of model performance and parameterization, heavy reliance on model selection with AICc and low utilization of spatial cross‐validation; we explain howENMeval2.0 can help address these issues.

   This redesigned and expanded version can promote progress in the field and improve the information available for decision‐making.

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2. Species residency status affects model selection and hypothesis testing in freshwater community ecology

   https://doi.org/10.1111/fwb.12800  

   Bried, Jason T. ; Siepielski, Adam M. ; Dvorett, Daniel ; Jog, Suneeti K. ; Patten, Michael A. ; Feng, Xiao ; Davis, Craig A. ( July 2016 , Freshwater Biology)

   Species occurrences have multiple ecological states that may strongly influence community analysis and inference. This may be especially true in freshwater systems where many animals have complex life cycles with adult dispersal and juvenile resident stages.

   The effects of ecological state variation on standard empirical approaches are largely unknown. Here, we analysed the effects of natal resident versus non‐natal immigrant species occurrence on community‐level environmental gradient modelling and spatial–environmental hypothesis testing using adult dragonflies and damselflies as model taxa.

   Resident and total (resident + immigrant) occurrences of these taxa responded to different sets of environmental variables and resident occurrences reduced model selection uncertainty in 75% of test cases.

   Effects of environmental gradients, spatial gradients or both were observed in residents but not immigrants, and supported predictions of dispersal limitation and niche‐based species sorting often implicated for structuring freshwater communities.

   These results indicate that resident‐only analysis of the dispersal stage should improve multi‐model inference and detection of spatial–environmental effects in freshwater community ecology. The species resident–immigrant dichotomy neglects population dynamics and individual variation yet apparently marks an ecologically significant boundary that scales up to influence community‐level occurrence patterns.

    

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3. Nemo‐age : Spatially explicit simulations of eco‐evolutionary dynamics in stage‐structured populations under changing environments

   https://doi.org/10.1111/2041-210X.13460  

   Cotto, Olivier ; Schmid, Max ; Guillaume, Frédéric ; Münkemüller, ed., Tamara ( August 2020 , Methods in Ecology and Evolution)

   Anticipating and preparing for the effect of environmental changes on biodiversity requires to understand and predict both the ecological and evolutionary responses of populations. Tools and methods to efficiently integrate these complex processes are lacking.

   We present the genetically and spatially explicit individual‐based simulation softwareNemo‐agecombining ecological and evolutionary processes.Nemo‐agehas a strong emphasis on modelling complex life histories. We here provide a methodology to predict changes in species distribution for given climate projections usingNemo‐age.

   Modelling complex life histories, spatial distribution and evolutionary processes unravel possible eco‐evolutionary mechanisms that have been previously overlooked when populations endure rapid environmental changes.

   The interface ofNemo‐ageis designed to integrate species' data from different fields, from demography to genetic architecture and spatial distributions, thus representing a versatile tool to model a variety of applied and theoretical scenarios.

    

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4. NetworkExtinction : An R package to simulate extinction propagation and rewiring potential in ecological networks

   https://doi.org/10.1111/2041-210X.14126  

   Ávila‐Thieme, M. Isidora ; Kusch, Erik ; Corcoran, Derek ; Castillo, Simón P. ; Valdovinos, Fernanda S. ; Navarrete, Sergio A. ; Marquet, Pablo A. ( June 2023 , Methods in Ecology and Evolution)

   Earth's biosphere is undergoing drastic reorganization due to the sixth mass extinction brought on by the Anthropocene. Impacts of local and regional extirpation of species have been demonstrated to propagate through the complex interaction networks they are part of, leading to secondary extinctions and exacerbating biodiversity loss. Contemporary ecological theory has developed several measures to analyse the structure and robustness of ecological networks under biodiversity loss. However, a toolbox for directly simulating and quantifying extinction cascades and creating novel interactions (i.e. rewiring) remains absent.

   Here, we presentNetworkExtinction—a novel R package which we have developed to explore the propagation of species extinction sequences through ecological networks and quantify the effects of rewiring potential in response to primary species extinctions. WithNetworkExtinction, we integrate ecological theory and computational simulations to develop functionality with which users may analyse and visualize the structure and robustness of ecological networks. The core functions introduced withNetworkExtinctionfocus on simulations of sequential primary extinctions and associated secondary extinctions, allowing user‐specified secondary extinction thresholds and realization of rewiring potential.

   With the packageNetworkExtinction, users can estimate the robustness of ecological networks after performing species extinction routines based on several algorithms. Moreover, users can compare the number of simulated secondary extinctions against a null model of random extinctions. In‐built visualizations enable graphing topological indices calculated by the deletion sequence functions after each simulation step. Finally, the user can estimate the network's degree distribution by fitting different common distributions. Here, we illustrate the use of the package and its outputs by analysing a Chilean coastal marine food web.

   NetworkExtinctionis a compact and easy‐to‐use R package with which users can quantify changes in ecological network structure in response to different patterns of species loss, thresholds and rewiring potential. Therefore, this package is particularly useful for evaluating ecosystem responses to anthropogenic and environmental perturbations that produce nonrandom and sometimes targeted, species extinctions.

    

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5. Topographic path analysis for modelling dispersal and functional connectivity: Calculating topographic distances using the topoDistance r package

   https://doi.org/10.1111/2041-210X.13317  

   Wang, Ian J. ; Goslee, ed., Sarah ( November 2019 , Methods in Ecology and Evolution)

   Estimating biologically meaningful geographic distances is essential for research in disciplines ranging from landscape genetics to community ecology. Topographically correcting distances to account for the total overland distance between locations imposed by topographic relief provides one method for calculating geographic distances that account for landscape structure.

   Here, I presenttopoDistance, anrpackage for calculating shortest topographic distances, weighted topographic paths and topographic least cost paths (LCPs). Topographic distances are calculated by weighting the edges of a graph by the hypotenuse of the horizontal and vertical distances between raster cells and then finding the shortest total path between cells of interest. The package also includes tools for mapping topographic paths and plotting elevation profiles.

   Examples from a species with moderate dispersal abilities, the western fence lizard, inhabiting a topographically complex landscape, Yosemite National Park (USA), demonstrate that topographic distances can vary significantly from straight‐line distances, and topographic LCPs can trace very different routes from LCPs and shortest topographic paths.

   Topographic paths and distances are broadly useful for modelling geographic isolation resulting from dispersal limitation for organisms that interact with the topographic structure of a landscape during movement and dispersal.

    

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