General Theory and Good Practices in Ecological Niche Modeling: A Basic Guide

Ecological niche modeling (ENM) and species distribution modeling (SDM) are sets of tools that allow the estimation of distributional areas on the basis of establishing relationships among known occurrences and environmental variables. These tools have a wide range of applications, particularly in biogeography, macroecology, and conservation biology, granting prediction of species potential distributional patterns in the present and dynamics of these areas in different periods or scenarios. Due to their relevance and practical applications, the usage of these methodologies has significantly increased throughout the years. Here, we provide a manual with the basic routines used in this field and a practical example of its implementation to promote good practices and guidance for new users

rangemap: An R Package to Explore Species' Geographic Ranges

Data exploration is a critical step in understanding patterns and biases in information about species’ geographic distributions. We present rangemap, an R package that implements tools to explore species’ ranges based on simple analyses and visualizations. The rangemap package uses species occurrence coordinates, spatial polygons, and raster layers as input data. Its analysis tools help to generate simple spatial polygons summarizing ranges based on distinct approaches, including spatial buffers, convex and concave (alpha) hulls, trend-surface analysis, and raster reclassification. Visualization tools included in the package help to produce simple, high-quality representations of occurrence data and figures summarizing resulting ranges in geographic and environmental spaces. Functions that create ranges also allow generating extents of occurrence (using convex hulls) and areas of occupancy according to IUCN criteria. A broad community of researchers and students could find in rangemap an interesting means by which to explore species’ geographic distributions

rangemap: An R Package to Explore Species' Geographic Ranges

Data exploration is a critical step in understanding patterns and biases in information about species’ geographic distributions. We present rangemap, an R package that implements tools to explore species’ ranges based on simple analyses and visualizations. The rangemap package uses species occurrence coordinates, spatial polygons, and raster layers as input data. Its analysis tools help to generate simple spatial polygons summarizing ranges based on distinct approaches, including spatial buffers, convex and concave (alpha) hulls, trend-surface analysis, and raster reclassification. Visualization tools included in the package help to produce simple, high-quality representations of occurrence data and figures summarizing resulting ranges in geographic and environmental spaces. Functions that create ranges also allow generating extents of occurrence (using convex hulls) and areas of occupancy according to IUCN criteria. A broad community of researchers and students could find in rangemap an interesting means by which to explore species’ geographic distributions

Regional anthropogenic disturbance and species-specific niche traits influence the invasiveness of European beetle species

Coleoptera are key elements of terrestrial trophic interactions and generate significant economic and ecological benefits, but their representatives also represent severe pest species. Understanding how invasive species operate is indispensable to identify and anticipate potential invasion areas. However, few studies have explored niche dynamics and drivers of invasions in this group. Here we examined niche dynamics across 54 invasive beetle species native to Europe and assessed whether factors such as human influence index, feeding habits, body size, and niche breadth are associated with the degree of invasion. The realized niches had low similarity in invasive and native ranges (i.e., invaded areas are climatically dissimilar to native ranges). This included a high degree of niche expansion in invaded areas but also environments occupied in the native ranges but unoccupied in the invasive range (unfilling), suggesting that altered species–climate relationships during invasion processes are common. Niche expansions showed positive association with small native niche breadth sizes and movements from highly disturbed native areas to less disturbed invaded ranges; unfilling was associated with invaded niche breadth size and frequency of species occurrence. Both were related to dissimilar realized climatic niches in invaded ranges. Colonization of invaded areas might be triggered by low quality resources in native areas. Unfilling levels might be related to the year of introduction and loss of biotic constraints present in their native distribution, leading to the use of different climatic spaces in the invasive areas. This idea is reinforced by larger invasive climatic niche breadth. Our results provide insight into patterns of invasive species, and initial holistic exploration towards the understanding of invasive species dynamics.journal articl

Inventory statistics meet big data: complications for estimating numbers of species

This work is licensed under a Creative Commons Attribution 4.0 International License.We point out complications inherent in biodiversity inventory metrics when applied to large-scale datasets. The number of units of inventory effort (e.g., days of inventory effort) in which a species is detected saturates, such that crucial numbers of detections of rare species approach zero. Any rare errors can then come to dominate species richness estimates, creating upward biases in estimates of species numbers. We document the problem via simulations of sampling from virtual biotas, illustrate its potential using a large empirical dataset (bird records from Cape May, NJ, USA), and outline the circumstances under which these problems may be expected to emerge

Effects of occurrence data density on conservation prioritization strategies

Place-prioritization analyses are a means by which researchers can translate information on the geographic distributions of species into quantitative prioritizations of areas for biodiversity conservation action. Although several robust algorithms are now available to support this sort of analysis, their vulnerability to biases deriving from incomplete and imbalanced distributional information is not well understood. In this contribution, we took a well-sampled group (i.e., Icteridae or New World blackbirds) in an intensively sampled region (the contiguous continental United States), and developed a set of pseudo-experimental manipulations of occurrence data density—in effect, we created situations in which data density was reduced 10- or 100-fold, and situations in which data density varied 100-fold from region to region. The effects were marked: priority areas for conservation shifted, appeared, and disappeared as a function of our manipulations. That is, differences in density of data can affect the position and complexity of areas of high conservation priority that are identified using distributional areas of species derived from ecological niche modeling. The effects of data density on prioritizations become more diffuse when considerations of existing protected areas and costs related to human intervention are taken into account, but changes are still manifested. Appropriate considerations of sampling density when constructing ecological niche models to identify distributional areas of species are key to preventing artifactual biases from entering into and affecting results of analyses of conservation priority

Geographic potential of the world’s largest hornet, Vespa mandarinia Smith (Hymenoptera: Vespidae), worldwide and particularly in North America

The Asian giant hornet (AGH, Vespa mandarinia) is the world’s largest hornet, occurring naturally in the Indomalayan region, where it is a voracious predator of pollinating insects including honey bees. In September 2019, a nest of Asian giant hornets was detected outside of Vancouver, British Columbia; multiple individuals were detected in British Columbia and Washington state in 2020; and another nest was found and eradicated in Washington state in November 2020, indicating that the AGH may have successfully wintered in North America. Because hornets tend to spread rapidly and become pests, reliable estimates of the potential invasive range of V. mandarinia in North America are needed to assess likely human and economic impacts, and to guide future eradication attempts. Here, we assess climatic suitability for AGH in North America, and suggest that, without control, this species could establish populations across the Pacific Northwest and much of eastern North America. Predicted suitable areas for AGH in North America overlap broadly with areas where honey production is highest, as well as with species-rich areas for native bumble bees and stingless bees of the genus Melipona in Mexico, highlighting the economic and environmental necessity of controlling this nascent invasion

Curso modelado de nicho ecológico, version 1.0

The suite of ideas, protocols, and software tools that has come to be known as “Ecological Niche Modeling” (ENM) — as well as those for the related “Species Distribution Modeling” (SDM)—has seen intensive exploration and research attention in recent decades. In spite of at least four syntheses, the field has grown so much in complexity that it is rather difficult to access for newcomers. Until now, accessibility to this field was achieved by in-person courses organized by universities or research centers, in some of which we have participated as instructors. However, the access to these specialized courses is limited, on one hand because they are not offered in all universities, and on the other because normally they are taught in English. To expand the access to a wider community of Spanish-speaking researchers, here we offer an entirely digital and free-of-charge course in Spanish, which was presented over 23 weeks via Internet in 2018. Although intrinsic Internet-related barriers may limit access to course materials, we have made them available in diverse formats (video, audio, pdf) in order to eliminate most of these problems.El conjunto de ideas, métodos y programas informáticos que se conoce como “Modelado de Nicho Ecológico” (MNE)—y el relacionado “Modelado de Distribución de Especies” (MDS)—han sido objeto de intensa exploración e investigación en las últimas décadas. A pesar de existir al menos cuatro síntesis publicadas, este campo ha crecido tanto en complejidad, que la formación de nuevos investigadores es difícil. Hasta ahora, dicha formación se ha hecho de manera presencial en cursos organizados por universidades o centros de investigación, de los que hemos formado parte como instructores. Sin embargo, el acceso a este tipo de cursos especializados es restringido, por un lado, porque los cursos no se ofrecen en todas las universidades, y por otro, porque normalmente se imparten en inglés. Para facilitar el acceso a una mayor comunidad de científicos de habla hispana, presentamos un curso en español, completamente digital y de acceso gratuito, que se realizó vía Internet durante 23 semanas consecutivas en 2018. Aunque las barreras intrínsecas al uso de Internet pueden dificultar la accesibilidad a los materiales del curso, hemos usado diversos formatos para la divulgación de los contenidos académicos (video, audio, pdf) con el objetivo de eliminar la mayor parte de estos problemas

Non-overlapping climatic niches and biogeographic barriers explain disjunct distributions of continental Urania moths

Larvae of Urania moths feed exclusively on Omphalea plants, which are widely distributed in the Neotropics. However, the distributions of the two Urania species in this region are disjunct. This distributional pattern could derive from the presence of the Andes, but it could also be related to differences in ecological niches, the presence of negative interactions, or the absence of conditions that can only be observed at a habitat level. We tested whether differences in the ecological niches of continental Urania moths play a role in their disjunct distribution. Using species records and climatic variables, we characterized the ecological niches of Urania moths and their host plants and analyzed the overlap of the moths' niches. Using ecoregions as a proxy of habitat-level environmental conditions, we explored the role of host plant availability on the moth distributions. Suitable conditions for the species were widespread, with a lack of suitability mostly restricted to the Andean highlands. The two moth distributions were closely related to that of their host plants. There was medium-high overlap of niche models when available conditions were considered; however, niche overlap was not found to be statistically significant. Our results corroborate the barrier effect of the Andes on the dispersal of these moths, but they also show that niche differences contribute to the disjunct distributions of U. fulgens and U. leilus. Furthermore, other non-climatic factors appear to play a crucial role in the disjunction of the species ranges in areas where overlapping suitable conditions are continuous. Our findings support speciation in Urania moths as allopatric and indicate that their disjunct distributions can be attributed to multiple factors. Other studies exploring the causes of similar distributional patterns should consider that a single factor may not be enough to explain such patterns