Assessing the effect of sample bias correction in species distribution models

1. Open-source biodiversity databases contain a large number of species occurrence records but are often spatially biased; which affects the reliability of species distribution models based on these records. Sample bias correction techniques require data filtering which comes at the cost of record numbers, or require considerable additional sampling effort. Since independent data is rarely available, assessment of the correction technique often relies solely on performance metrics computed using subsets of the available – biased – data, which may prove misleading. 2. Here, we assess the extent to which an acknowledged sample bias correction technique is likely to improve models’ ability to predict species distributions in the absence of independent data. We assessed variation in model predictions induced by the aforementioned correction and model stochasticity; the variability between model replicates related to a random component (pseudo-absences sets and cross-validation subsets). We present, then, an index of the effect of correction relative to model stochasticity; the Relative Overlap Index (ROI). We investigated whether the ROI better represented the effect of correction than classic performance metrics (Boyce index, cAUC, AUC and TSS) and absolute overlap metrics (Schoener’s D, Pearson’s and Spearman’s correlation coefficients) when considering data related to 64 vertebrate species and 21 virtual species with a generated sample bias. 3. When based on absolute overlaps and cross-validation performance metrics, we found that correction produced no significant effects. When considering its effect relative to model stochasticity, the effect of correction was strong for most species at one of the three sites. The use of virtual species enabled us to verify that the correction technique improved both distribution predictions and the biological relevance of the selected variables at the specific site, when these were not correlated with sample bias patterns. 4. In the absence of additional independent data, the assessment of sample bias correction based on subsample data may be misleading. We propose to investigate both the biological relevance of environmental variables selected, and, the effect of sample bias correction based on its effect relative to model stochasticity. Accessibility maps Cross-validation Performance metrics Overlap Pseudo-absence selection Terrestrial vertebrates Variable selection Virtual speciespublishedVersio

Functional traits—not nativeness—shape the effects of large mammalian herbivores on plant communities

DATA AND MATERIALS AVAILABILITY : All data and the core analysis scripts are provided in Dryad (24).Large mammalian herbivores (megafauna) have experienced extinctions and declines since prehistory. Introduced megafauna have partly counteracted these losses yet are thought to have unusually negative effects on plants compared with native megafauna. Using a meta-analysis of 3995 plot-scale plant abundance and diversity responses from 221 studies, we found no evidence that megafauna impacts were shaped by nativeness, “invasiveness,” “feralness,” coevolutionary history, or functional and phylogenetic novelty. Nor was there evidence that introduced megafauna facilitate introduced plants more than native megafauna. Instead, we found strong evidence that functional traits shaped megafauna impacts, with larger-bodied and bulk-feeding megafauna promoting plant diversity. Our work suggests that trait-based ecology provides better insight into interactions between megafauna and plants than do concepts of nativeness.EDITOR'S SUMMARY : Large herbivores shape ecosystems by consuming vegetation, dispersing seeds, and creating disturbances. Due to extirpations of many large herbivorous mammals and the spread of others by people, many ecosystems host megaherbivores that did not coevolve with the local plant species. Lundgren et al. investigated whether introduced species therefore have stronger and more negative effects on plant abundance and diversity (see the Perspective by Buckley and Torsney). In their meta-analysis of more than 200 studies, they found no differences between introduced and native megaherbivore impacts or evidence for stronger impacts of functionally novel species. Instead, large-bodied herbivores and those with selective diets had a stronger effect on vegetation (e.g., grass feeders reducing graminoid diversity), suggesting a stronger role for species’ traits than origins in determining their impacts. —Bianca LopezVILLUM FONDEN; Danish National Research Foundation; and Independent Research Fund Denmark–Natural Sciences.https://www.science.org/journal/sciadvhj2024Mammal Research InstituteSDG-15:Life on lan

Developing Transdisciplinary Approaches to Sustainability Challenges: The Need to Model Socio-Environmental Systems in the Longue Durée

Human beings are an active component of every terrestrial ecosystem on Earth. Although our local impact on the evolution of these ecosystems has been undeniable and extensively documented, it remains unclear precisely how our activities are altering them, in part because ecosystems are dynamic systems structured by complex, non-linear feedback processes and cascading effects. We argue that it is only by studying human–environment interactions over timescales that greatly exceed the lifespan of any individual human (i.e., the deep past or longue durée), we can hope to fully understand such processes and their implications. In this article, we identify some of the key challenges faced in integrating long-term datasets with those of other areas of sustainability science, and suggest some useful ways forward. Specifically, we (a) highlight the potential of the historical sciences for sustainability science, (b) stress the need to integrate theoretical frameworks wherein humans are seen as inherently entangled with the environment, and (c) propose formal computational modelling as the ideal platform to overcome the challenges of transdisciplinary work across large, and multiple, geographical and temporal scales. Our goal is to provide a manifesto for an integrated scientific approach to the study of socio-ecological systems over the long term

Developing Transdisciplinary Approaches to Sustainability Challenges: The Need to Model Socio-Environmental Systems in the Longue Durée

Human beings are an active component of every terrestrial ecosystem on Earth. Although our local impact on the evolution of these ecosystems has been undeniable and extensively documented, it remains unclear precisely how our activities are altering them, in part because ecosystems are dynamic systems structured by complex, non-linear feedback processes and cascading effects. We argue that it is only by studying human–environment interactions over timescales that greatly exceed the lifespan of any individual human (i.e., the deep past or longue durée), we can hope to fully understand such processes and their implications. In this article, we identify some of the key challenges faced in integrating long-term datasets with those of other areas of sustainability science, and suggest some useful ways forward. Specifically, we (a) highlight the potential of the historical sciences for sustainability science, (b) stress the need to integrate theoretical frameworks wherein humans are seen as inherently entangled with the environment, and (c) propose formal computational modelling as the ideal platform to overcome the challenges of transdisciplinary work across large, and multiple, geographical and temporal scales. Our goal is to provide a manifesto for an integrated scientific approach to the study of socio-ecological systems over the long term

Reconstruction de la distribution et de l'abondance historiques des mammifères marins : établir un niveau de référence pour comprendre le passé, renseigner le présent et planifier l'avenir

Relevant baselines on the historical distribution and abundance of species are needed to support appropriate conservation targets for depleted species, but the full scale of cumulative human impacts on ecosystems is highly underestimated. In this project, I investigated the challenges and opportunities of combining historical data with analytical methods to improve these historical baselines. Occurrence data from archaeological, historical and industrial sources were reviewed for seven cetacean and three pinniped species, revealing range contractions and population depletions from prehistorical times to today. For five whale species, I used species distribution modelling to combine 19th Century whaling records with environmental data, to estimate pre-whaling distributions. For the highly depleted North Atlantic right whale, (Eubalaena glacialis), I obtained a detailed estimate of pre-whaling distribution and abundance by inferring from the historical distribution and abundance of its congeneric North Pacific right whale (E. japonica). These results suggest that the North Atlantic right whale occupies a small fraction of its historical range and that its current population represents <5% of its historical abundance, with implications for the management, monitoring and conservation targets of this species. More generally, these results emphasize the utility of considering historical data to understand the extent to which species have been impacted by humans, assess their current level of depletion, and inform the options available for their future recovery.La mise en place d'objectifs de conservation adéquats repose sur la définition d'états de référence appropriés pour la distribution et l'abondance des espèces. Cependant, l'étendue des impacts cumulés de l'homme sur les écosystèmes est aujourd'hui largement sous-estimée. Dans ce projet, je m'intéresse aux opportunités qu'offre l'utilisation de données historiques combinées à différentes méthodes analytiques pour définir ces états de référence ainsi qu'aux défis posés par ce type d'approche. Des données de présence ont été recueillies pour sept espèces de cétacés et trois espèces de pinnipèdes à partir de sources archéologiques, historiques et industrielles, révélant des réductions dans la distribution et l'abondance des espèces depuis la préhistoire à nos jours. Des modèles de distribution d'espèces ont été développés pour cinq espèces de cétacés, combinant des données de chasse baleinière du 19ème siècle à des variables environnementales afin d'estimer la distribution historique des espèces avant qu'elles n'aient été chassées. J'ai obtenu pour la baleine franche de l'Atlantique Nord (Eubalena glacialis) une estimation détaillée de sa distribution et de son abondance avant qu'elle ne soit exploitée, en extrapolant des connaissances sur la distribution et l'abondance d'une espèce congénérique, la baleine franche du Pacifique Nord (E. japonica). Ces résultats suggèrent que la baleine franche de l'Atlantique Nord occupe une portion réduite de sa distribution historique, et que son abondance actuelle ne représente qu'une infime portion (<5%) de son abondance passée. Plus généralement, ces résultats soulignent l'importance de considérer des données historiques pour comprendre le niveau d'impact par l'homme sur les espèces, évaluer leur niveau de déplétion et renseigner leur potentiel de rétablissement dans l'avenir

Reconstruction of marine mammals’ historical distribution and abundance : setting a baseline to understand the past, inform the present and plan the future

La mise en place d'objectifs de conservation adéquats repose sur la définition d'états de référence appropriés pour la distribution et l'abondance des espèces. Cependant, l'étendue des impacts cumulés de l'homme sur les écosystèmes est aujourd'hui largement sous-estimée. Dans ce projet, je m'intéresse aux opportunités qu'offre l'utilisation de données historiques combinées à différentes méthodes analytiques pour définir ces états de référence ainsi qu'aux défis posés par ce type d'approche. Des données de présence ont été recueillies pour sept espèces de cétacés et trois espèces de pinnipèdes à partir de sources archéologiques, historiques et industrielles, révélant des réductions dans la distribution et l'abondance des espèces depuis la préhistoire à nos jours. Des modèles de distribution d'espèces ont été développés pour cinq espèces de cétacés, combinant des données de chasse baleinière du 19ème siècle à des variables environnementales afin d'estimer la distribution historique des espèces avant qu'elles n'aient été chassées. J'ai obtenu pour la baleine franche de l'Atlantique Nord (Eubalena glacialis) une estimation détaillée de sa distribution et de son abondance avant qu'elle ne soit exploitée, en extrapolant des connaissances sur la distribution et l'abondance d'une espèce congénérique, la baleine franche du Pacifique Nord (E. japonica). Ces résultats suggèrent que la baleine franche de l'Atlantique Nord occupe une portion réduite de sa distribution historique, et que son abondance actuelle ne représente qu'une infime portion (<5%) de son abondance passée. Plus généralement, ces résultats soulignent l'importance de considérer des données historiques pour comprendre le niveau d'impact par l'homme sur les espèces, évaluer leur niveau de déplétion et renseigner leur potentiel de rétablissement dans l'avenir.Relevant baselines on the historical distribution and abundance of species are needed to support appropriate conservation targets for depleted species, but the full scale of cumulative human impacts on ecosystems is highly underestimated. In this project, I investigated the challenges and opportunities of combining historical data with analytical methods to improve these historical baselines. Occurrence data from archaeological, historical and industrial sources were reviewed for seven cetacean and three pinniped species, revealing range contractions and population depletions from prehistorical times to today. For five whale species, I used species distribution modelling to combine 19th Century whaling records with environmental data, to estimate pre-whaling distributions. For the highly depleted North Atlantic right whale, (Eubalaena glacialis), I obtained a detailed estimate of pre-whaling distribution and abundance by inferring from the historical distribution and abundance of its congeneric North Pacific right whale (E. japonica). These results suggest that the North Atlantic right whale occupies a small fraction of its historical range and that its current population represents <5% of its historical abundance, with implications for the management, monitoring and conservation targets of this species. More generally, these results emphasize the utility of considering historical data to understand the extent to which species have been impacted by humans, assess their current level of depletion, and inform the options available for their future recovery

Pre-human impact baselines of South African mammal biogeography

Relevant baselines on the historical distribution of species are needed to support appropriate conservation targets for depleted species. In South Africa, over-hunting and loss of habitat largely altered the composition and distribution of the large mammal fauna, especially since the start of the colonial period. Using modern ecological data therefore has the risk of considerably underestimating the full scale of anthropogenic impacts on biodiversity. By extending the timeline usually considered in ecology, long-term archives can provide novel insights into changing species distributions through time and represent a unique opportunity to better inform regional environmental management. Here, we use a large dataset of past distribution records for medium- to large-sized terrestrial mammals in South Africa, assembled from sources of the early historical period (late 1400s to the 1920s) to reconstruct the historical extent of occurrence and extinction dynamics for &gt;30 large mammal species. We evidence local extinctions and changes in community composition since the early historical period. The biogeography of population loss is consistent with a response to the demographic expansion of European colonists spreading from the south-western part of South Africa. These results contribute to novel baselines for conservation and provide a strengthened evidence-base for understanding long-term faunal responses to human pressures. These findings also allow the "shifted baselines" around modern mammal distributions to be identified, providing an avenue for new analyses of large mammal biogeographic patterns for this region.peerReviewe

Ancient whale exploitation in the Mediterranean: species matters

International audienceHow did ancient communities around the Mediterranean exploit the presence of whales in their seas? Given that the whales currently present in the region are seldom found near the coast, it seems probable that ancient whale exploitation would have been restricted to stranded animals. The authors explore, however, the possibility that additional species migrated seasonally through the Strait of Gibraltar to visit coastal calving grounds, which could have supported an organised whaling industry. Classical literature provides a number of descriptions suggestive of coastal encounters with whales. New methods of whale bone identification will shed light on which species were previously present in the Mediterranean and thus on the probability of ancient whaling. This article is one of two on ancient whaling in the current issue, and should be read in conjunction with that by Darío Bernal-Casasola and colleagues

Data for the paper entitled "Accessibility maps as a tool to predict sampling bias in historical biodiversity occurrence records"

This collection regroups data used in the paper "Accessibility maps as a tool to predict sampling bias in historical biodiversity occurrence records" by S. Monsarrat, A. Boshoff and G. Kerley.<div><br></div><div>Data description:</div><div><b>xy_histrecords: </b>Large mammal occurrence records collected from historical written sources in South Africa in the period 1497-1920. See details in the paper. Format: text file with 3 columns (X, Y, Year)</div><div><br></div><div><b>raster_hist records</b>: <strong> </strong>Large mammal occurrence records collected from historical written sources in South Africa in the period 1497-1920. Format: 0.1°x0.1° raster grid.</div><div><div>extent: 15, 35, -38, -20 (xmin, xmax, ymin, ymax)</div><div>coord. ref.: +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0 </div></div><div><br></div><div><b>cities_table</b>: 2 columns table with the coordinates of pre-1900 european settlements in South Africa, based on Floyd’s chronological order of town establishment in South Africa <a>(Floyd, 1960).</a></div><div><br></div><div><b>biome_ras: </b>0.1°x0.1°<strong> r</strong>aster grid of south african biomes, from the 2012 Vegetation Map of South Africa, Lesotho and Swaziland <a>(Mucina & Rutherford, 2006; South African National Biodiversity Institute, 2012).</a></div><div><a><div>extent: 15, 35, -38, -20 (xmin, xmax, ymin, ymax)</div><div>coord. ref.: +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0 </div></a></div><div><strong> </strong><br></div><div><b>max_temp:</b> 0.01°x0.01°<strong> r</strong>aster grid of maximum summer temperature, in °C, averaged over the period 1960-1990, obtained from WorldClim (Fick & Hijmans, 2017).</div><div><div>extent: 15, 35, -38, -20 (xmin, xmax, ymin, ymax)</div><div>coord. ref.: +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0 </div></div><div><br></div><div><b>mean_prec:</b> 0.01°x0.01°<strong> r</strong>aster grid of mean annual precipitation, in mm, averaged over the period 1960-1990, obtained from WorldClim (Fick & Hijmans, 2017).<br><b> </b></div><div><div>extent: 15, 35, -38, -20 (xmin, xmax, ymin, ymax)</div><div>coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0 </div></div><div> </div><div><br></div><div><b>NPP:</b> 0.1°x0.1°<strong> r</strong>aster grid of mean annual net primary productivity, in g C/m²/year, obtained from MODIS MOD17 Gross/Net Primary Production Project of the Numerical Terradynamic Simulation Group <a>(Zhao <i>et al.</i>, 2005).</a></div><div><a><div>extent: 15, 35, -38, -20 (xmin, xmax, ymin, ymax)</div><div>coord. ref.: +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0 </div><div><br></div></a><div><a><b>SPI</b>: </a><a></a><a><div>0.1°x0.1°<strong> r</strong>aster grid of the Settlement Proximity Index (SPI). See detail in the paper.</div></a><br></div><div><a><div><div>extent: 15, 35, -38, -20 (xmin, xmax, ymin, ymax)</div><div>coord. ref.: +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0 </div></div></a><div><a></a><a>(also provided: SPI built with different sizes of kernel widths <i>h_s</i> and <i>h_w</i>and with a triangular kernel instead of a gaussian (see Appendix S4))</a></div></div></div><div><a></a><div><a><b><br></b></a></div><div><a><b>WPI</b>: </a><a>0.1°x0.1°<strong> r</strong>aster grid of the Water Proximity Index (SPI). See details in the paper.</a></div></div><div><a></a><a><div><div>extent: 15, 35, -38, -20 (xmin, xmax, ymin, ymax)</div><div>coord. ref.: +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0 </div><div>(also provided: WPI built with different sizes of kernel widths <i>h_s</i> and <i>h_w</i>and with a triangular kernel instead of a gaussian (see Appendix S4))</div><div><br></div><div><b>Study Area</b>: ESRI shapefile of the study area.</div><div>class: SpatialPolygonsDataFrame<br></div><div>coord. ref. : +proj=tmerc +lat_0=0 +lon_0=21 +k=1 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0<br></div></div></a></div

R code for the paper entitled "Accessibility maps as a tool to predict sampling bias in historical biodiversity occurrence records"

This file contains the R code for the analyses in the paper entitled "Accessibility maps as a tool to predict sampling bias in historical biodiversity occurrence records", by S. Monsarrat, A. Boshoff and G. Kerle