modleR: a modular workflow to perform ecological niche modeling in R

AbstractEcological niche models (ENM) use the environmental variables associated with the currently known distribution of a species to model its ecological niche and project it into the geographic space. Widely used and misused, ENM has become a common tool for ecologists and decision-makers.Many ENM platforms have been developed over the years, first as standalone programs, later as packages within script-based programming languages and environments. The democratization of these programming tools and the advent of Open Science brought a growing concern regarding the reproducibility, transparency, robustness, portability, and interoperability in ENM workflows.ENM workflows have some core components that are replicated between projects. However, they have a large internal variation due to the variety of research questions and applications. Any ecological niche modeling platform should take into account this trade-off between stability and reproducibility on one hand, and flexibility and decision-making on the other.Here, we present modleR, a four-step workflow that wraps some of the common phases executed during an ecological niche model procedure. We have divided the process into (1) data setup, (2) model fitting and projection, (3) partition joining and (4) ensemble modeling (consensus between algorithms).modleR is highly adaptable and replicable depending on the user’s needs and is open to deeper internal parametrization. It can be used as a testing platform due to its consistent folder structure and its capacity to control some sources of variation while changing others. It can be run in interactive local sessions and in high-performance or high-throughput computational (HPC/HTC) platforms and parallelized by species or algorithms. It can also communicate with other tools in the field, allowing the user to enter and exit the workflow at any phase, and execute complementary routines outside the package. Finally, it records metadata and session information at each step, ensuring reproducibility beyond the use of script-based applications.

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Species’ Invasions

Ecological Niches and Geographic Distributions (MPB-49) ◽

10.23943/princeton/9780691136868.003.0013 ◽

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.

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Prediction of high CPT yielding ecotypes of Nothapodytes nimmoniana (Graham) Mabb. in Western Ghats using Ecological Niche Modeling

International Journal of Bio-Pharma Research ◽

10.21746/ijbpr.2018.7.12.1 ◽

2018 ◽

Vol 7 (12) ◽

pp. 2451-2458

Author(s):

Cordilea Hannah ◽

Joyce Sudandara Priya ◽

Kasthuri Bhai N.

Keyword(s):

Habitat Suitability ◽

Western Ghats ◽

Ecological Niche ◽

High Performance ◽

Ecological Niche Modeling ◽

Ecological Niche Models ◽

Natural Habitats ◽

Nothapodytes Nimmoniana ◽

Bioclimatic Variables ◽

Chemical Content

Camptothecin (CPT) is one of anticancer drug that is widely used for treating various cancers. In India, the drug is primarily sourced from natural habitats of the red listed species Nothapodytes nimmoniana. Ecological niche models are potential tools to define and predict the “ecological niche” of a species that exhibit ecological variations. The predicted ecological niche of a species indicates their survival fitness against Bioclimatic variables. The habitat suitability was predicted using Maxent for different ecotypes of Nothapodytes nimmoniana (Graham.) Mabb. In this study the synonymised populations of N. nimmoniana in the Western Ghats were cogitated as five different ecotypes. The predicted habitat suitability of different ecotypes were evaluated and correlated against CPT content using high performance thin layer chromatography. The study shows a significant positive correlation between the predicted habitat quality and chemical content. The ecotypes growing in sites predicted as highly suitable showed high content of camptothecin compared to those growing in poorly suitable sites. Thereby enabling precise identification of “chemical hot-spots” which will eventually establish a strong foot hold on monoculture of the species, an effort towards conservation.

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Environmental Data

Ecological Niches and Geographic Distributions (MPB-49) ◽

10.23943/princeton/9780691136868.003.0006 ◽

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.

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Geographic Distribution of Colombian Spittlebugs (Hemiptera: Cercopidae) via Ecological Niche Modeling: A Prediction for the Main Tropical Forages' Pest in the Neotropics

Frontiers in Sustainable Food Systems ◽

10.3389/fsufs.2021.725774 ◽

2021 ◽

Vol 5 ◽

Author(s):

Luis M. Hernández ◽

Paula Espitia ◽

David Florian ◽

Valheria Castiblanco ◽

Juan Andrés Cardoso ◽

...

Keyword(s):

Geographic Distribution ◽

Ecological Niche ◽

Ecological Niche Modeling ◽

Niche Modeling ◽

Economic Losses ◽

Economic Damage ◽

Extensive Literature ◽

Design Strategies ◽

Ecological Niche Models ◽

Global Biodiversity Information Facility

Spittlebugs (Hemiptera: Cercopidae) are the main tropical pests in Central and South America of cultivated pastures. We aimed to estimate the potential distribution of Aeneolamia varia, A. lepidior, A. reducta, Prosapia simulans, Zulia carbonaria, and Z. pubescens throughout the Neotropics using ecological niche modeling. These six insect species are common in Colombia and cause large economic losses. Records of these species, prior to the year 2000, were compiled from human observations, specimens from CIAT Arthropod Reference Collection (CIATARC), Global Biodiversity Information Facility (GBIF), speciesLink (splink), and an extensive literature review. Different ecological niche models (ENMs) were generated for each species: Maximum Entropy (MaxEnt), generalized linear (GLM), multivariate adaptive regression spline (MARS), and random forest model (RF). Bioclimatic datasets were obtained from WorldClim and the 19 available variables were used as predictors. Future changes in the potential geographical distribution were simulated in ENMs generated based on climate change projections for 2050 in two scenarios: optimistic and pessimistic. The results suggest that (i) Colombian spittlebugs impose an important threat to Urochloa production in different South American countries, (ii) each spittlebug species has a unique geographic distribution pattern, (iii) in the future the six species are likely to invade new geographic areas even in an optimistic scenario, (iv) A. lepidior and A. reducta showed a higher number of suitable habitats across Colombia, Venezuela, Brazil, Peru, and Ecuador, where predicted risk is more severe. Our data will allow to (i) monitor the dispersion of these spittlebug species, (ii) design strategies for integrated spittlebug management that include resistant cultivars adoption to mitigate potential economic damage, and (iii) implement regulatory actions to prevent their introduction and spread in geographic areas where the species are not yet found.

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

PeerJ ◽

10.7717/peerj.10454 ◽

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.

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

Bulletin of Entomological Research ◽

10.1017/s0007485320000656 ◽

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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Discovering Biodiversity

Ecological Niches and Geographic Distributions (MPB-49) ◽

10.23943/princeton/9780691136868.003.0011 ◽

2011 ◽

Author(s):

A. Townsend Peterson ◽

Jorge Soberón ◽

Richard G. Pearson ◽

Robert P. Anderson ◽

Enrique Martínez-Meyer ◽

...

Keyword(s):

Ecological Niche ◽

Ecological Niche Modeling ◽

Niche Modeling ◽

Niche Conservatism ◽

Conceptual Basis ◽

Ecological Niche Models ◽

Species Limits ◽

As Species ◽

Unknown Species ◽

Niche Models

This chapter discusses the conceptual basis of using ecological niche modeling for discovering new elements of biodiversity. More specifically, it examines the use of ecological niche models to guide searches for and discovery of unknown populations of species as well as species limits. It also explains how niche conservatism provides some degree of predictability across related taxa and makes the use of niche models for discovering biodiversity possible. For applications focused on discovery of unknown species, the chapter shows that niche conservatism is necessary if predictions of likely distributional areas are to prove realistic. Finally, it reviews practical considerations that must be taken into account in applications of ecological niche models oriented at discovering biodiversity, along with the caveats and limitations of such applications.

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Ecological-niche modeling of genetically distinct populations revealed Kersting’s groundnut [Macrotyloma geocarpum (Harms) Maréchal et Baudet] as a resilient orphan crop to present and future climates

10.21203/rs.3.rs-763341/v1 ◽

2021 ◽

Author(s):

Mariam Coulibaly ◽

Rodrigue Idohou ◽

Félicien Akohoue ◽

Andrew Townsend Peterson ◽

Mahamadou Sawadogo ◽

...

Keyword(s):

Ecological Niche ◽

Food Systems ◽

Ecological Niche Modeling ◽

Smallholder Farmers ◽

Niche Modeling ◽

Ecological Niche Models ◽

Agricultural Adaptation ◽

Genetic Groups ◽

Macrotyloma Geocarpum ◽

Kersting’S Groundnut

Abstract Orphan legume crops play an important role in smallholder farmers’ food systems. Though less documented, they have the potential to contribute to adequate nutrition in vulnerable communities. Unfortunately, data are scarce about the potential of those crops to withstand current and future climate variations. Using Macrotyloma geocarpum as an example, we used genetically informed ecological niche models to explore the role of ecology on the current and future distributions of genetic populations of Kersting’s groundnut. Three main conclusions emerged: i) the models had good predictive power, indicating that M. geocarpum’s distribution was correlated with both climatic and soil layers; ii) identity and similarity tests revealed that the two genetic groups while overlapping, are each, locally adapted and display differences in climate suitability; iii) by integrating the genetic information in niche modeling, niches projections show divergence in the response of the species and genetic populations to ongoing climate change. This study highlights the importance of incorporating genetic data into ENM approaches to obtain a finer information of species’ future distribution, and explores the implications for agricultural adaptation, with a particular focus on identifying priority actions in orphan crops conservation and breeding.

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