scholarly journals Biomod2EZ - An R script suite for visualizing projected niche model ensembles and reporting statistical results

2017 ◽  
Author(s):  
Paul R. Sesink Clee ◽  
Stephen Woloszynek ◽  
Mary Katherine Gonder
Keyword(s):  
Graphical User Interface ◽  
Ecological Niche ◽  
Ecological Niche Modeling ◽  
R Package ◽  
Ecological Niche Models ◽  
Report Generation ◽  
Modeling Techniques ◽  
Model Ensembles ◽  
Statistical Results ◽  
Niche Models

AbstractBiomod2EZ is a suite of R scripts to use in conjunction with the Biomod2 R package by Thuiller et al. (2016) that is used to create ensemble ecological niche models using up to 11 different modeling techniques. Biomod2EZ adds to the functionality of Biomod2 (Thuiller et al. 2016) by incorporating a report generation feature, detailed script annotation, and sample dataset/tutorial to ease the transition from ecological niche modeling using a Graphical User Interface to the coding environment of the R framework (R Development Core Team, 2016).

scholarly journals kuenm: an R package for detailed development of ecological niche models using Maxent

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6281 ◽  
Author(s):  
Marlon E. Cobos ◽  
A. Townsend Peterson ◽  
Narayani Barve ◽  
Luis Osorio-Olvera
Keyword(s):  
Model Calibration ◽  
Ecological Niche ◽  
Ecological Niche Modeling ◽  
Statistical Significance ◽  
R Package ◽  
Model Complexity ◽  
Ecological Niche Models ◽  
Detailed Model ◽  
Analytical Tools ◽  
Niche Models

Background Ecological niche modeling is a set of analytical tools with applications in diverse disciplines, yet creating these models rigorously is now a challenging task. The calibration phase of these models is critical, but despite recent attempts at providing tools for performing this step, adequate detail is still missing. Here, we present the kuenm R package, a new set of tools for performing detailed development of ecological niche models using the platform Maxent in a reproducible way. Results This package takes advantage of the versatility of R and Maxent to enable detailed model calibration and selection, final model creation and evaluation, and extrapolation risk analysis. Best parameters for modeling are selected considering (1) statistical significance, (2) predictive power, and (3) model complexity. For final models, we enable multiple parameter sets and model transfers, making processing simpler. Users can also evaluate extrapolation risk in model transfers via mobility-oriented parity (MOP) metric. Discussion Use of this package allows robust processes of model calibration, facilitating creation of final models based on model significance, performance, and simplicity. Model transfers to multiple scenarios, also facilitated in this package, significantly reduce time invested in performing these tasks. Finally, efficient assessments of strict-extrapolation risks in model transfers via the MOP and MESS metrics help to prevent overinterpretation in model outcomes.

Species’ Invasions

2011 ◽  
Author(s):  
A. Townsend Peterson ◽  
Jorge Soberón ◽  
Richard G. Pearson ◽  
Robert P. Anderson ◽  
Enrique Martínez-Meyer ◽  
...  
Keyword(s):  
Ecological Niche ◽  
Ecological Niche Modeling ◽  
Biotic Interactions ◽  
Niche Modeling ◽  
Future Research ◽  
Ecological Niche Models ◽  
Species Invasions ◽  
Future Research Directions ◽  
Native And Introduced Ranges ◽  
Niche Models

This chapter discusses the use of ecological niche modeling to study species invasions, and more specifically to identify and understand genuine exceptions to ecological niche equivalency between native and introduced ranges of species. In addition, it examines the degree to which the geographic course of species’ invasions can be anticipated based on scenopoetic variables and biotic interactions. The chapter also reviews practical considerations that must be taken into account when exploring the utility of ecological niche models in understanding species’ invasions, such as using niche conservatism to predict likely changes in the distributional potential of invasive species under scenarios of changing environmental conditions. Finally, it describes caveats and limitations of the approach and outlines future research directions and challenges involved in the application of niche modeling ideas in species invasions.

scholarly journals Ecological Niche Models of Four Hard Tick Genera (Ixodidae) in Mexico

Animals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 649 ◽  
Author(s):  
Emilio Clarke-Crespo ◽  
Claudia N. Moreno-Arzate ◽  
Carlos A. López-González
Keyword(s):  
Ecological Niche ◽  
Ecological Niche Modeling ◽  
Distribution Patterns ◽  
Hard Tick ◽  
Ecological Niche Models ◽  
Generalist Species ◽  
Public Health Decision ◽  
Vector Borne Diseases ◽  
Temperature And Precipitation ◽  
Niche Models

Ticks are vectors of a large number of pathogens of medical and veterinary importance, and in recent years, they have participated in the rise of multiple infectious outbreaks around the world. Studies have proposed that temperature and precipitation are the main variables that limit the geographical distribution of ticks. The analysis of environmental constraints with ecological niche modeling (ENM) techniques can improve our ability to identify suitable areas for emergence events. Algorithms used in this study showed different distributional patterns for each tick genera; the environmental suitability for Amblyomma includes warm and humid localities below 1000 m above the sea level, while Ixodes is mainly associated with ecosystems with high vegetation cover. Dermacentor and Rhipicephalus genus presented wider distribution patterns; the first includes species that are well adapted to resist desiccation, whereas the latter includes generalist species that are mostly associated with domestic hosts in Mexico. Ecological niche models have proven to be useful in estimating the geographic distribution of many taxa of ticks. Despite our limited knowledge of tick’s diversity, ENM can improve our understanding of the dynamics of vector-borne diseases and can assist public health decision-making processes.

Environmental Data

2011 ◽  
Author(s):  
A. Townsend Peterson ◽  
Jorge Soberón ◽  
Richard G. Pearson ◽  
Robert P. Anderson ◽  
Enrique Martínez-Meyer ◽  
...  
Keyword(s):  
Ecological Niche ◽  
Ecological Niche Modeling ◽  
Spatial Scales ◽  
Species Distributions ◽  
Niche Modeling ◽  
Environmental Data ◽  
Potential Utility ◽  
Ecological Niche Models ◽  
Ancillary Data ◽  
Niche Models

This chapter focuses on the conceptual and applied aspects of environmental data in the context of building and interpreting ecological niche models. It first examines how different suites of environmental factors may affect species distributions across a range of spatial scales before discussing which and how many variables are needed for ecological niche modeling. It then reviews the diverse sources of environmental datasets that are of potential utility in ecological niche modeling and concludes by considering a number of challenges involved in designing and choosing environmental data for ecological niche modeling. These challenges include data preparation, data quality, spatial extent, resolution in space and time, types of environmental data, and ancillary data.

scholarly journals ENMTML: An R package for a straightforward construction of complex ecological niche models

2020 ◽  
Vol 125 ◽  
pp. 104615 ◽  
Author(s):  
André Felipe Alves de Andrade ◽  
Santiago José Elías Velazco ◽  
Paulo De Marco Júnior
Keyword(s):  
Ecological Niche ◽  
R Package ◽  
Ecological Niche Models ◽  
Niche Models

Ecological niche modeling on the effect of climatic change and conservation of Ternstroemia lineata DC. (Ternstroemiaceae) in Mesoamerica

Botany ◽  
2012 ◽  
Vol 90 (7) ◽  
pp. 637-650 ◽  
Author(s):  
Isolda Luna-Vega ◽  
Othón Alcántara-Ayala ◽  
Raúl Contreras-Medina ◽  
César A. Ríos-Muñoz
Keyword(s):  
Climatic Change ◽  
Ecological Niche ◽  
Ecological Niche Modeling ◽  
Cloud Forest ◽  
Production Method ◽  
Emission Scenarios ◽  
Ecological Niche Models ◽  
Bioclimatic Modeling ◽  
Rule Set ◽  
Niche Models

A bioclimatic modeling of the tree Ternstroemia lineata DC. (Ternstroemiaceae) was undertaken. The genus itself is considered as diagnostic or characteristic of the Mexican cloud forest. Ternstroemia lineata has the broadest distribution of all species in this family in Mexico and northern Central America. This species consists of two subspecies, T. lineata subsp. lineata and T. lineata subsp. chalicophila (Loes.) B.M. Barthol. Ecological niche models for both subspecies were generated using the genetic algorithm for rule-set production method. The ecological models for the years 2020, 2050, and 2080 were obtained under the effects of global climatic change considering two emission scenarios (A2a and B2a). When climatic change values were introduced, the ecological niche representation for both subspecies contracted in such a way that they became almost lost throughout their entire geographical range. In both cases, predictions for all years in both scenarios contracted more than 90%. This species may not be able to adapt to modifications caused by climatic change to future conditions, so it is at risk of extinction in the immediate future.

scholarly journals Local Segregation of Realised Niches in Lizards

2020 ◽  
Vol 9 (12) ◽  
pp. 764
Author(s):  
Neftalí Sillero ◽  
Elena Argaña ◽  
Cátia Matos ◽  
Marc Franch ◽  
Antigoni Kaliontzopoulou ◽  
...  
Keyword(s):  
Environmental Variables ◽  
Ecological Niche ◽  
Species Coexistence ◽  
Niche Overlap ◽  
R Package ◽  
Abundant Species ◽  
Ecological Niche Models ◽  
Changes Over Time ◽  
Local Segregation ◽  
Niche Models

Species can occupy different realised niches when sharing the space with other congeneric species or when living in allopatry. Ecological niche models are powerful tools to analyse species niches and their changes over time and space. Analysing how species’ realised niches shift is paramount in ecology. Here, we examine the ecological realised niche of three species of wall lizards in six study areas: three areas where each species occurs alone; and three areas where they occur together in pairs. We compared the species’ realised niches and how they vary depending on species’ coexistence, by quantifying niche overlap between pairs of species or populations with the R package ecospat. For this, we considered three environmental variables (temperature, humidity, and wind speed) recorded at each lizard re-sighting location. Realised niches were very similar when comparing syntopic species occurring in the same study area. However, realised niches differed when comparing conspecific populations across areas. In each of the three areas of syntopy, the less abundant species shift its realised niche. Our study demonstrates that sympatry may shift species’ realised niche.

scholarly journals Supraspecific units in correlative niche modeling improves the prediction of geographic potential of biological invasions

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10454
Author(s):  
Sandra Castaño-Quintero ◽  
Jazmín Escobar-Luján ◽  
Luis Osorio-Olvera ◽  
A Townsend Peterson ◽  
Xavier Chiappa-Carrara ◽  
...  
Keyword(s):  
Invasive Species ◽  
Biological Invasions ◽  
Ecological Niche ◽  
Ecological Niche Modeling ◽  
Predictive Ability ◽  
Complete Characterization ◽  
Niche Modeling ◽  
Ecological Niche Models ◽  
Full Spectrum ◽  
Niche Models

Background Biological invasions rank among the most significant threats to biodiversity and ecosystems. Correlative ecological niche modeling is among the most frequently used tools with which to estimate potential distributions of invasive species. However, when areas accessible to the species across its native distribution do not represent the full spectrum of environmental conditions that the species can tolerate, correlative studies often underestimate fundamental niches. Methods Here, we explore the utility of supraspecific modeling units to improve the predictive ability of models focused on biological invasions. Taking into account phylogenetic relationships in correlative ecological niche models, we studied the invasion patterns of three species (Aedes aegypti, Pterois volitans and Oreochromis mossambicus). Results Use of supraspecific modeling units improved the predictive ability of correlative niche models in anticipating potential distributions of three invasive species. We demonstrated that integrating data on closely related species allowed a more complete characterization of fundamental niches. This approach could be used to model species with invasive potential but that have not yet invaded new regions.

Ecological niche modeling (ENM) of Leptoglossus clypealis a new potential global invader: following in the footsteps of Leptoglossus occidentalis?

2020 ◽  
pp. 1-12
Author(s):  
Leonela Olivera ◽  
Eugenia Minghetti ◽  
Sara I. Montemayor
Keyword(s):  
North America ◽  
Ecological Niche ◽  
Ecological Niche Modeling ◽  
Niche Breadth ◽  
Niche Modeling ◽  
Ecological Niche Models ◽  
Leptoglossus Occidentalis ◽  
Major Pest ◽  
Successful Establishment ◽  
Niche Models

Abstract The introduction of alien species is one of the main problems in conservation. Many successful invaders cause severe economic and ecological damage. Such is the case of Leptoglossus occidentalis, a phytophagous true bug native to North America, which has become a pest in Europe, Asia, Africa and South America. Within the genus, another species whose distributional range is expanding toward the east of North America is Leptoglossus clypealis. As climate determines the successful establishment of insects, the identification of climatically suitable areas for invasive species based on ecological niche models (ENMs) offers an excellent opportunity for preventing invasions. In this study, ENMs were built for both species and their native climatic niches were compared. Their niche breath was also measured. The climatic niches of both species are identical and the niche breadth of L. clypealis is broader than that of L. occidentalis. In view of the great ecological resemblance between these two species, we believe that L. clypealis could became a major pest thus it should be carefully monitored. The results of the present worldwide ENMs showed numerous regions with suitable conditions for the establishment of both species. The future ENMs exhibited a retraction in the suitable areas in North America, Europe and Asia.

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