New measures for assessing model equilibrium and prediction mismatch in species distribution models

Models based on species distributions are widely used and serve important purposes in ecology, biogeography and conservation. Their continuous predictions of environmental suitability are commonly converted into a binary classification of predicted (or potential) presences and absences, whose accuracy is then evaluated through a number of measures that have been the subject of recent reviews. We propose four additional measures that analyse observation-prediction mismatch from a different angle – namely, from the perspective of the predicted rather than the observed area – and add to the existing toolset of model evaluation methods. We explain how these measures can complete the view provided by the existing measures, allowing further insights into distribution model predictions. We also describe how they can be particularly useful when using models to forecast the spread of diseases or of invasive species and to predict modifications in species’ distributions under climate and land-use change

Impacts of climate change and species distribution modelling: future scenarios to endangered species in South Brazil.

2016

Patterns of Cactaceae species distribution in a protected area in the semiarid caatinga biome of North-Eastern Brazil.

2016

Spatial scale effects of sampling on the interpolation of species distribution models in the southwestern Amazon.

Knowledge of the geographical distribution of timber tree species in the Amazon is still scarce. This is especially true at the local level, thereby limiting natural resource management actions. Forest inventories are key sources of information on the occurrence of such species. However, areas with approved forest management plans are mostly located near access roads and the main industrial centers. The present study aimed to assess the spatial scale effects of forest inventories used as sources of occurrence data in the interpolation of potential species distribution models. The occurrence data of a group of six forest tree species were divided into four geographical areas during the modeling process. Several sampling schemes were then tested applying the maximum entropy algorithm, using the following predictor variables: elevation, slope, exposure, normalized difference vegetation index (NDVI) and height above the nearest drainage (HAND). The results revealed that using occurrence data from only one geographical area with unique environmental characteristics increased both model overfitting to input data and omission error rates. The use of a diagonal systematic sampling scheme and lower threshold values led to improved model performance. Forest inventories may be used to predict areas with a high probability of species occurrence, provided they are located in forest management plan regions representative of the environmental range of the model projection area.

Evidence of long-term changes in the distribution of key intertidal species

World Congress of Malacology, Ponta Delgada, July 22-28, 2013.

Predicting the distribution of forest tree species using topographic variables and vegetation index in eastern Acre, Brazil

Species distribution modeling has relevant implications for the studies of biodiversity, decision making about conservation and knowledge about ecological requirements of the species. The aim of this study was to evaluate if the use of forest inventories can improve the estimation of occurrence probability, identify the limits of the potential distribution and habitat preference of a group of timber tree species. The environmental predictor variables were: elevation, slope, aspect, normalized difference vegetation index (NDVI) and height above the nearest drainage (HAND). To estimate the distribution of species we used the maximum entropy method (Maxent). In comparison with a random distribution, using topographic variables and vegetation index as features, the Maxent method predicted with an average accuracy of 86% the geographical distribution of studied species. The altitude and NDVI were the most important variables. There were limitations to the interpolation of the models for non-sampled locations and that are outside of the elevation gradient associated with the occurrence data in approximately 7% of the basin area. Ceiba pentandra (samaúma), Castilla ulei (caucho) and Hura crepitans (assacu) is more likely to occur in nearby water course areas. Clarisia racemosa (guariúba), Amburana acreana (cerejeira), Aspidosperma macrocarpon (pereiro), Apuleia leiocarpa (cumaru cetim), Aspidosperma parvifolium (amarelão) and Astronium lecointei (aroeira) can also occur in upland forest and well drained soils. This modeling approach has potential for application on other tropical species still less studied, especially those that are under pressure from logging.

Anthropogenic influence on the distribution, abundance and diversity of sandfly species (Diptera: Phlebotominae: Psychodidae), vectors of cutaneous leishmaniasis in Panama

In Panama, species of the genus Lutzomyia are vectors of American cutaneous leishmaniasis (ACL). There is no recent ecological information that may be used to develop tools for the control of this disease. Thus, the goal of this study was to determine the composition, distribution and diversity of Lutzomyia species that serve as vectors of ACL. Sandfly sampling was conducted in forests, fragmented forests and rural environments, in locations with records of ACL. Lutzomyia gomezi, Lutzomyia panamensis and Lutzomyia trapidoi were the most widely distributed and prevalent species. Analysis of each sampling point showed that the species abundance and diversity were greatest at points located in the fragmented forest landscape. However, when the samples were grouped according to the landscape characteristics of the locations, there was a greater diversity of species in the rural environment locations. The Kruskal Wallis analysis of species abundance found that Lu. gomezi and Lu. trapidoi were associated with fragmented environments, while Lu. panamensis, Lutzomyia olmeca bicolor and Lutzomyia ylephiletor were associated with forested environments. Therefore, we suggest that human activity influences the distribution, composition and diversity of the vector species responsible for leishmaniasis in Panama.

Bioclimatic constraints to Andean cat distribution: a modelling application for rare species

AimTo identify the bioclimatic niche of the endangered Andean cat (Leopardus jacobita), one of the rarest and least known felids in the world, by developing a species distribution model.LocationSouth America, High Andes and Patagonian steppe. Peru, Bolivia, Chile, Argentina.MethodsWe used 108 Andean cat records to build the models, and 27 to test them, applying the Maxent algorithm to sets of uncorrelated bioclimatic variables from global databases, including elevation. We based our biogeographical interpretations on the examination of the predicted geographic range, the modelled response curves and latitudinal variations in climatic variables associated with the locality data.ResultsSimple bioclimatic models for Andean cats were highly predictive with only 3-4 explanatory variables. The climatic niche of the species was defined by extreme diurnal variations in temperature, cold minimum and moderate maximum temperatures, and aridity, characteristic not only of the Andean highlands but also of the Patagonian steppe. Argentina had the highest representation of suitable climates, and Chile the lowest. The most favourable conditions were centrally located and spanned across international boundaries. Discontinuities in suitable climatic conditions coincided with three biogeographical barriers associated with climatic or topographic transitions.Main conclusionsSimple bioclimatic models can produce useful predictions of suitable climatic conditions for rare species, including major biogeographical constraints. In our study case, these constraints are also known to affect the distribution of other Andean species and the genetic structure of Andean cat populations. We recommend surveys of areas with suitable climates and no Andean cat records, including the corridor connecting two core populations. The inclusion of landscape variables at finer scales, crucially the distribution of Andean cat prey, would contribute to refine our predictions for conservation applications.

Fire management, climate change and their interacting effects on birds in complex Mediterranean landscapes: dynamic distribution modelling of an early-successional species - the near-threatened Dartford Warbler (Sylvia undata)

The current challenge in a context of major environmental changes is to anticipate the responses of species to future landscape and climate scenarios. In the Mediterranean basin, climate change is one the most powerful driving forces of fire dynamics, with fire frequency and impact having markedly increased in recent years. Species distribution modelling plays a fundamental role in this challenge, but better integration of available ecological knowledge is needed to adequately guide conservation efforts. Here, we quantified changes in habitat suitability of an early-succession bird in Catalonia, the Dartford Warbler (Sylvia undata) ― globally evaluated as Near Threatened in the IUCN Red List. We assessed potential changes in species distributions between 2000 and 2050 under different fire management and climate change scenarios and described landscape dynamics using a spatially-explicit fire-succession model that simulates fire impacts in the landscape and post-fire regeneration (MEDFIRE model). Dartford Warbler occurrence data were acquired at two different spatial scales from: 1) the Atlas of European Breeding Birds (EBCC) and 2) Catalan Breeding Bird Atlas (CBBA). Habitat suitability was modelled using five widely-used modelling techniques in an ensemble forecasting framework. Our results indicated considerable habitat suitability losses (ranging between 47% and 57% in baseline scenarios), which were modulated to a large extent by fire regime changes derived from fire management policies and climate changes. Such result highlighted the need for taking the spatial interaction between climate changes, fire-mediated landscape dynamics and fire management policies into account for coherently anticipating habitat suitability changes of early succession bird species. We conclude that fire management programs need to be integrated into conservation plans to effectively preserve sparsely forested and early succession habitats and their associated species in the face of global environmental change.

Distribution of tree species in a geomorphological and pedological gradient of submontane semidecidual seasonal forest in the vicinity of Rio Doce state park, Minas Gerais

The objective of this study was to test the hypothesis that the distribution of tree species in a fragment of submontane seasonal semideciduous forest, a buffer zone in the Parque Estadual do Rio Doce, Minas Gerais, is influenced by geomorphological and weather and soil variables, therefore it can represent a source of information for the restoration of degraded areas where environmental conditions are similar to those of the study area. A detailed soil survey was conducted in the area by sampling three soil profiles per slope segment, totaling 12 profiles. To sample the topsoil, four composite samples were collected from the 10-20 cm layers in each topographic range totaling 16 composite samples. In the low ramp and the lower and upper concave slopes, the texture ranged from clay to sandy-clay. The soil and topographic gradient was characterized by changes in the soil physical-chemical properties. The soil in the 10-20 cm sampled layer was sandier, slightly more fertile and less acid in the low ramp than the clayer soil, nutrient-poor and highly acid soil at the top. The soil conditions in the lower and upper slope of the sampled layers, in turn, were intermediate. The P levels were limiting in all soils. The species distribution along the topographic gradient was associated with variations in chemical fertility, acidity and soil texture. The distribution of Pera leandri, Astronium fraxinifolium, Pouteria torta, Machaerium brasiliense and Myrcia rufipes was correlated with high aluminum levels and to low soil fertility and these species may be indicated for restoration of degraded areas on hillsides and hilltops in regions where environmental conditions are similar. The distribution of Pouteria venosa, Apuleia leiocarpa and Acacia polyphylla was correlated with the less acid and more fertile soil in the environment of the low ramps, indicating the potential for the restoration of similar areas.

Effects of global climate changes on geographical distribution patterns of economically important plant species in cerrado

Different climate models, modeling methods and carbon emission scenarios were used in this paper to evaluate the effects of future climate changes on geographical distribution of species of economic and cultural importance across the Cerrado biome. As the results of several studies have shown, there are still many uncertainties associated with these projections, although bioclimatic models are still widely used and effective method to evaluate the consequences for biodiversity of these climate changes. In this article, it was found that 90% of these uncertainties are related to methods of modeling, although, regardless of the uncertainties, the results revealed that the studied species will reduce about 78% of their geographic distribution in Cerrado. For an effective work on the conservation of these species, many studies still need to be carried out, although it is already possible to observe that climate change will have a strong influence on the pattern of distribution of these species.

Spatio-temporal segregation and size distribution of fish assemblages as related to non-native species occurrence in the middle rio Doce Valley, MG, Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Oral distribution of Candida species and presence of oral lesions in Brazilian leprosy patients under multidrug therapy

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Environmental factors influencing the distribution of three species within the genus Persephona Leach, 1817 (Crustacea, Decapoda, Leucosiidae) in two regions on the northern coast of Sao Paulo State, Brazil

Patterns of spatio-temporal distribution of Brachyura are determined by the interaction among life history traits, inter and intraspecific relationships, as well as by the variation of abiotic factors. This study aimed to characterize patterns of spatio-temporal distribution of Persephona lichtensteinii, Persephona mediterranea and Persephona punctata in two regions of the northern coast of Sao Paulo State, southeastern region of Brazil. Collections were done monthly from July 2001 to June 2003 in Caraguatatuba and Ubatuba, using a shrimp fishery boat equipped with double-rig nets. The patterns of species distribution were tested by means of redundancy analysis (RDA) and generalized linear mixed models (GLMM) in relation to the recorded environmental factors (BT: bottom temperature, BS: bottom salinity, OM: organic matter and granulometry (Phi)). The most influent environmental factor over the species distribution was the Phi, and the ascendant order of influence was P. lichtensteinii, P. punctata and P. mediterranea. The greater abundance of P. mediterranea showed a conservative pattern of distribution for the genus in the sampled region. The greater occurrence of P. punctata and P. lichtensteinii, in distinct transects than those occupied by P. mediterranea, seems to be a strategy to avoid competition among congeneric species, which is related to the substratum specificity.

Distribution models for mountain plant species: The value of elevation

The climatic conditions of mountain habitats are greatly influenced by topography. Large differences in microclimate occur with small changes in elevation, and this complex interaction is an important determinant of mountain plant distributions. In spite of this, elevation is not often considered as a relevant predictor in species distribution models (SDMs) for mountain plants. Here, we evaluated the importance of including elevation as a predictor in SDMs for mountain plant species. We generated two sets of SDMs for each of 73 plant species that occur in the Pacific Northwest of North America; one set of models included elevation as a predictor variable and the other set did not. AUC scores indicated that omitting elevation as a predictor resulted in a negligible reduction of model performance. However, further analysis revealed that the omission of elevation resulted in large over-predictions of species' niche breadths-this effect was most pronounced for species that occupy the highest elevations. In addition, the inclusion of elevation as a predictor constrained the effects of other predictors that superficially affected the outcome of the models generated without elevation. Our results demonstrate that the inclusion of elevation as a predictor variable improves the quality of SDMs for high-elevation plant species. Because of the negligible AUC score penalty for over-predicting niche breadth, our results support the notion that AUC scores alone should not be used as a measure of model quality. More generally, our results illustrate the importance of selecting biologically relevant predictor variables when constructing SDMs.