Habitats as predictors in species distribution models: Shall we use continuous or binary data?

The representation of a land cover type (i.e. habitat) within an area is often used as an explanatory variable in species distribution models. However, it is possible that a simple binary presence/absence of the suitable habitat might be the most important determinant of the presence/absence of some species and, thus, be a better predictor of species occurrence than the continuous parameter (area). We hypothesize that the binary predictor is more suitable for relatively rare habitats (e.g. wetlands) while for common habitats (e.g. forests) the amount of the focal habitat is a better predictor. We used the Third Atlas of Breeding Birds in the Czech Republic as the source of species distribution data and CORINE Land Cover inventory as the source of the landcover information. To test our hypothesis, we fitted generalized linear models of 32 water and 32 forest bird species. Our results show that for water bird species, models using binary predictors (presence/absence of the habitat) performed better than models with continuous predictors (i.e. the amount of the habitat); for forest species, however, we observed the opposite. Thus, future studies using habitats as predictors of species occurrences should consider the prevalence of the habitat in the landscape, and the biological role of the habitat type in the particular species' life history. In addition, performing a preliminary comparison of the performance of the binary and continuous versions of habitat predictors (e.g. using information criteria) prior to modelling, during variable selection, can be beneficial. These are simple steps that will improve explanatory and predictive performance of models of species distributions in biogeography, community ecology, macroecology and ecological conservation

Double down on remote sensing for biodiversity estimation: a biological mindset

In the light of unprecedented planetary changes in biodiversity, real-time and accurate ecosystem and biodiversity assessments are becoming increasingly essential for informing policy and sustainable development. Biodiversity monitoring is a challenge, especially for large areas such as entire continents. Nowadays, spaceborne and airborne sensors provide information that incorporate wavelengths that cannot be seen nor imagined with the human eye. This is also now accomplished at unprecedented spatial resolutions, defined by the pixel size of images, achieving less than a meter for some satellite images and just millimeters for airborne imagery. Thanks to different modeling techniques, it is now possible to study functional diversity changes over different spatial and temporal scales. At the heart of this unifying framework are the “spectral species”—sets of pixels with a similar spectral signal—and their variability over space. The aim of this paper is to summarize the power of remote sensing for directly estimating plant species diversity, particularly focusing on the spectral species concept

Scientific maps should reach everyone: The cblindplot R package to let colour blind people visualise spatial patterns

Maps represent powerful tools to show the spatial variation of a variable in a straightforward manner. A crucial aspect in map rendering for its interpretation by users is the gamut of colours used for displaying data. One part of this problem is linked to the proportion of the human population that is colour blind and, therefore, highly sensitive to colour palette selection. The aim of this paper is to present the cblindplot R package and its founding function - cblind.plot() - which enables colour blind people to just enter an image in a coding workflow, simply set their colour blind deficiency type, and immediately get as output a colour blind friendly plot. We will first describe in detail colour blind problems, and then show a step by step example of the function being proposed. While examples exist to provide colour blind people with proper colour palettes, in such cases (i) the workflow include a separate import of the image and the application of a set of colour ramp palettes and (ii) albeit being well documented, there are many steps to be done before plotting an image with a colour blind friendly ramp palette. The function described in this paper, on the contrary, allows to (i) automatically call the image inside the function without any initial import step and (ii) explicitly refer to the colour blind deficiency type being experienced, to further automatically apply the proper colour ramp palette

Scale mismatches between predictor and response variables in species distribution modelling: A review of practices for appropriate grain selection

There is a lack of guidance on the choice of the spatial grain of predictor and response variables in species distribution models (SDM). This review summarizes the current state of the art with regard to the following points: (i) the effects of changing the resolution of predictor and response variables on model performance; (ii) the effect of conducting multi-grain versus single-grain analysis on model performance; and (iii) the role of land cover type and spatial autocorrelation in selecting the appropriate grain size. In the reviewed literature, we found that coarsening the resolution of the response variable typically leads to declining model performance. Therefore, we recommend aiming for finer resolutions unless there is a reason to do otherwise (e.g. expert knowledge of the ecological scale). We also found that so far, the improvements in model performance reported for multi-grain models have been relatively low and that useful predictions can be generated even from single-scale models. In addition, the use of high-resolution predictors improves model performance; however, there is only limited evidence on whether this applies to models with coarser-resolution response variables (e.g. 100 km2 and coarser). Low-resolution predictors are usually sufficient for species associated with fairly common environmental conditions but not for species associated with less common ones (e.g. common vs rare land cover category). This is because coarsening the resolution reduces variability within heterogeneous predictors and leads to underrepresentation of rare environments, which can lead to a decrease in model performance. Thus, assessing the spatial autocorrelation of the predictors at multiple grains can provide insights into the impacts of coarsening their resolution on model performance. Overall, we observed a lack of studies examining the simultaneous manipulation of the resolution of predictor and response variables. We stress the need to explicitly report the resolution of all predictor and response variables.Peer reviewe

WaterbirdData

Count, perimeter, and area of water bodies within mapping squares of Atlas of Breeding Birds in the Czech Republic 2001–2003. The values were derived from five datasets: clc - Corine Land Cover, gcl - Global Consensus Land Cover, giw - Global Inland Water, osm - Open Street Map, dib - Dibavod. IdSquare - ID of the atlas mapping square. PA - Presence/absence of the species (species name is included in the file name

Sensitivity analysis of parameters and contrasting performance of ground filtering algorithms with UAV photogrammetry-based and LiDAR point clouds

Most ground filtering algorithms are primarily designed for airborne LiDAR point cloud processing and their successful use in identifying ground points from photogrammetric point clouds remains questionable. We compared six ground filtering algorithms implemented in Metashape, ArcGIS, CloudCompare, LAStools, and PDAL. We used UAV photogrammetry-based (acquired under leaf-off conditions) and airborne LiDAR (leaf-on) point clouds of the same area to: (i) compare accuracy of generated DTMs; (ii) evaluate the effect of vegetation density and terrain slope on filtering accuracy; and (iii) assess which algorithm parameters have the greatest effect on the filtering accuracy. Our results show that the performance of filtering algorithms was affected by the point cloud type, terrain slope and vegetation cover. The results were generally better for LiDAR (RMSE 0.13–0.19 m) than for photogrammetric (RMSE 0.19–0.23 m) point clouds. The behavior in varying vegetation and terrain conditions was consistent for LiDAR point clouds. However, when applied on photogrammetric point clouds, the algorithms’ behavior was inconsistent, especially in areas of steep slope (except for the Progressive Triangulated Irregular Network in LAStools). Parameters related to the selection of the initial minimum elevation ground points were the most influential in all algorithms and point clouds

Use of TanDEM-X and SRTM-C Data for Detection of Deforestation Caused by Bark Beetle in Central European Mountains

The availability of global digital elevation models (DEMs) from multiple time points allows their combination for analysing vegetation changes. The combination of models (e.g., SRTM and TanDEM-X) can contain errors, which can, due to their synergistic effects, yield incorrect results. We used a high-resolution LiDAR-derived digital surface model (DSM) to evaluate the accuracy of canopy height estimates of the aforementioned global DEMs. In addition, we subtracted SRTM and TanDEM-X data at 90 and 30 m resolutions, respectively, to detect deforestation caused by bark beetle disturbance and evaluated the associations of their difference with terrain characteristics. The study areas covered three Central European mountain ranges and their surrounding areas: Bohemian Forest, Erzgebirge, and Giant Mountains. We found that vertical bias of SRTM and TanDEM-X, relative to the canopy height, is similar with negative values of up to −2.5 m and LE90s below 7.8 m in non-forest areas. In forests, the vertical bias of SRTM and TanDEM-X ranged from −0.5 to 4.1 m and LE90s from 7.2 to 11.0 m, respectively. The height differences between SRTM and TanDEM-X show moderate dependence on the slope and its orientation. LE90s for TDX-SRTM differences tended to be smaller for east-facing than for west-facing slopes, and varied, with aspect, by up to 1.5 m in non-forest areas and 3 m in forests, respectively. Finally, subtracting SRTM and NASA DEMs from TanDEM-X and Copernicus DEMs, respectively, successfully identified large areas of deforestation caused by hurricane Kyril in 2007 and a subsequent bark beetle disturbance in the Bohemian Forest. However, local errors in TanDEM-X, associated mainly with forest-covered west-facing slopes, resulted in erroneous identification of deforestation. Therefore, caution is needed when combining SRTM and TanDEM-X data in multitemporal studies in a mountain environment. Still, we can conclude that SRTM and TanDEM-X data represent suitable near global sources for the identification of deforestation in the period between the time points of their acquisition

Importance of data selection and filtering in species distribution models: A case study on the Cantabrian brown bear

Abstract Species distribution models (SDMs) are powerful tools in ecology and conservation. Choosing the right environmental drivers and filtering species' occurrences taking their biases into account are key factors to consider before modeling. In this case study, we address five common problems arising during the selection of input data for presence‐only SDMs on an example of a generalist species: the endangered Cantabrian brown bear. First, we focus on the selection of environmental variables that may drive its distribution, testing if climatic variables should be considered at a 1‐km analysis grain. Second, we investigate how filtering the species' data in view of (1) their collection procedures, (2) different time frames, (3) dispersal areas, and (4) subpopulations affects the performance and outputs of the models at three different spatial analysis grains (500 m, 1 km, and 5 km). Our results show that models with different input data yielded only minor differences in performance and behaved properly in terms of model validation, although coarsening the analysis grain deteriorated model performance. Still, the contribution of individual variables and the habitat suitability predictions differed among models. We show that a combination of limited data availability and poor selection of environmental variables can lead to inaccurate predictions. Specifically for the brown bear, we conclude that climatic variables should not be considered for exploring habitat suitability and that the best input data for modeling habitat suitability in the study area originate from (1) observations and traces from the (2) most recent period (2006–2019) in which the population is expanding, (3) not considering cells of dispersing bear occurrences and (4) modeling subpopulations independently (as they show distinct habitat preferences). In conclusion, SDMs can serve as a useful tool for generalist species including all available data; still, expert evaluation from the perspective of data suitability for the purpose of modeling and possible biases is recommended. This is especially important when the results are intended for management and conservation purposes at the local level, and for species that respond to the environment at coarse analysis grains

Modeling plant invasion on Mediterranean coastal landscapes: An integrative approach using remotely sensed data

Although many hypotheses explaining invasion success have been formulated, invasion drivers are usually tested in isolation. This work aims to analyze the combined influence of propagule pressure (P), abiotic (A) and biotic (B) factors (PAB) on determining the invasion process of an exotic plant taxon (Carpobrotus sp.) in Mediterranean coastal landscapes. Specifically, we used a binomial Generalized Additive Model for exploring the relation between the occurrence of the invasive species and a set of PAB proxy variables derived from high-resolution remote sensed imagery (LiDAR - Light Detection and Ranging - and orthophotos). We evaluated the predictive power of the model by computing the mean of the AUC scores obtained through a 5-fold cross-validation and visual inspection of the Hosmer-Lemeshow plot. The integrated PAB approach efficiently captured the different roles played by the drivers of invasion in affecting the presence of the species. Invasion does not proceed homogeneously across the coastal landscape, but is promoted wherever the combined action of the PAB factors is favorable for establishment of the invader. Moreover, the use of remotely sensed data allowed us to model the invader-landscape relationship on a large geographic extent and to highlight the coastal sectors that are most likely to be invaded in the future