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

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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Ecological niche modeling as an effective tool to predict the distribution of freshwater organisms: The case of the Sabaleta Brycon henni (Eigenmann, 1913)

PLoS ONE ◽

10.1371/journal.pone.0247876 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0247876

Author(s):

Daniel Valencia-Rodríguez ◽

Luz Jiménez-Segura ◽

Carlos A. Rogéliz ◽

Juan L. Parra

Keyword(s):

Minimum Temperature ◽

Ecological Niche ◽

Potential Distribution ◽

Ecological Niche Modeling ◽

Predictive Accuracy ◽

National Level ◽

Ecological Niche Models ◽

Precipitation Seasonality ◽

Bioclimatic Variables ◽

Species Occurrences

Ecological niche models (ENMs) aim to recreate the relationships between species and the environments where they occur and allow us to identify unexplored areas in geography where these species might be present. These models have been successfully used in terrestrial organisms but their application in aquatic organisms is still scarce. Recent advances in the availability of species occurrences and environmental information particular to aquatic systems allow the evaluation of these models. This study aims to characterize the niche of the Sabaleta Brycon henni Eigenmann 1913, an endemic fish of the Colombian Andes, using ENMs to predict its geographical distribution across the Magdalena Basin. For this purpose, we used a set of environmental variables specific to freshwater systems in addition to the customary bioclimatic variables, and species’ occurrence data to model its potential distribution using the Maximum Entropy algorithm (MaxEnt). We evaluate the relative importance between these two sets of variables, the model’s performance, and its geographic overlap with the IUCN map. Both on-site (annual precipitation, minimum temperature of coldest month) and upstream variables (open waters, average minimum temperature of the coldest month and average precipitation seasonality) were included in the models with the highest predictive accuracy. With an area under the curve of 90%, 99% of the species occurrences and 68% of absences correctly predicted, our results support the good performance of ENMs to predict the potential distribution of the Sabaleta and the utility of this tool in conservation and decision-making at the national level.

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Ecological niche modeling, niche overlap, and good old Rabinowitz’s rarities applied to the conservation of gymnosperms in a global biodiversity hotspot

10.21203/rs.3.rs-809204/v1 ◽

2021 ◽

Author(s):

Paula Quiroga ◽

Cintia Souto

Keyword(s):

Habitat Suitability ◽

Ecological Niche ◽

Ecological Niche Modeling ◽

Niche Overlap ◽

Biodiversity Hotspot ◽

Conservation Priorities ◽

Ecological Niche Models ◽

Endemic Plant ◽

Key Species ◽

Global Biodiversity

Abstract ContextBiodiversity hotspots harbor 77% of endemic plant species. Patagonian Temperate Forest (PTF) is a biodiversity hotspot, but over the past centuries, has been over-exploited, fragmented and replaced with exotic species plantations, lately plus the threat of climate change. ObjectivesOur aim is to better understand patterns of habitat suitability and niche overlap of nine endemic gymnosperm species, key elements of the PTF, complementing traditional approaches of biodiversity conservation. MethodsUsing R packages and 3024 occurrence data, we deployed ecological niche models (ENM) in MaxEnt via KuENM, and classified species according to Rabinowitz’s types of rarity. We then overlapped their niches calculating Schoener's D index, and considered types of rarity in a spatial ecological context. Finally, we overlay high species’ suitability and protected areas and detect conservation priorities using GapAnalysis. ResultsWe generated simplified ENMs for nine Patagonian gymnosperms and found that most niches overlap, and only one species displayed a unique niche. Surprisingly, we found that three species have divergent suitability of habitats across the landscape. We showed that the rarer a species is the smaller niche volume tend to have, that six out of nine studied species have high conservation priority, and that there are conservation gaps in the PTF. ConclusionOur approach showed that there are unprotected suitable areas for native key species at high risk in Patagonian forests. Suggesting that integrating habitat-suitability models of multiple species, types of rarity, and niche overlap, can be a handy tool to identify potential conservation areas in global biodiversity hotspots.

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

10.1101/2020.04.01.021105 ◽

2020 ◽

Author(s):

Andrea Sánchez-Tapia ◽

Sara Ribeiro Mortara ◽

Diogo Souza Bezerra Rocha ◽

Felipe Sodré Mendes Barros ◽

Guilherme Gall ◽

...

Keyword(s):

Programming Languages ◽

Ecological Niche ◽

High Performance ◽

Ecological Niche Modeling ◽

Model Fitting ◽

Open Science ◽

Niche Modeling ◽

Ecological Niche Models ◽

Geographic Space ◽

Core Components

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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Potential geographic distribution of the tiger mosquito Aedes albopictus (Skuse, 1894) (Diptera: Culicidae) in current and future conditions for Colombia

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0008212 ◽

2021 ◽

Vol 15 (5) ◽

pp. e0008212

Author(s):

Emmanuel Echeverry-Cárdenas ◽

Carolina López-Castañeda ◽

Juan D. Carvajal-Castro ◽

Oscar Alexander Aguirre-Obando

Keyword(s):

At Risk ◽

Aedes Albopictus ◽

Geographic Distribution ◽

Ecological Niche ◽

Ecological Niche Models ◽

Niche Modelling ◽

Continental Extension ◽

Bioclimatic Variables ◽

Valle Del Cauca ◽

Potential Geographic Distribution

In Colombia, little is known on the distribution of the Asian mosquito Aedes albopictus, main vector of dengue, chikungunya, and Zika in Asia and Oceania. Therefore, this work sought to estimate its current and future potential geographic distribution under the Representative Concentration Paths (RCP) 2.6 and 8.5 emission scenarios by 2050 and 2070, using ecological niche models. For this, predictions were made in MaxEnt, employing occurrences of A. albopictus from their native area and South America and bioclimatic variables of these places. We found that, from their invasion of Colombia to the most recent years, A. albopictus is present in 47% of the country, in peri-urban (20%), rural (23%), and urban (57%) areas between 0 and 1800 m, with Antioquia and Valle del Cauca being the departments with most of the records. Our ecological niche modelling for the currently suggests that A. albopictus is distributed in 96% of the Colombian continental surface up to 3000 m (p < 0.001) putting at risk at least 48 million of people that could be infected by the arboviruses that this species transmits. Additionally, by 2050 and 2070, under RCP 2.6 scenario, its distribution could cover to nearly 90% of continental extension up to 3100 m (≈55 million of people at risk), while under RCP 8.5 scenario, it could decrease below 60% of continental extension, but expand upward to 3200 m (< 38 million of people at risk). These results suggest that, currently in Colombia, A. albopictus is found throughout the country and climate change could diminish eventually its area of distribution, but increase its altitudinal range. In Colombia, surveillance and vector control programs must focus their attention on this vector to avoid complications in the national public health setting.

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

Animals ◽

10.3390/ani10040649 ◽

2020 ◽

Vol 10 (4) ◽

pp. 649 ◽

Cited By ~ 1

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.

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Novel insights into the historical biogeography of the streak-breasted scimitar babbler complex (Aves: Timaliidae: Pomatorhinus ruficollis complex)

Current Zoology ◽

10.1093/czoolo/61.5.910 ◽

2015 ◽

Vol 61 (5) ◽

pp. 910-921 ◽

Cited By ~ 4

Author(s):

Sushma Reddy ◽

Árpád S. Nyári

Keyword(s):

Ecological Niche ◽

Ecological Niche Modeling ◽

Southern China ◽

Hainan Island ◽

Central China ◽

Integrative Approach ◽

Suitable Habitat ◽

Ecological Niche Models ◽

Last Interglacial ◽

History Of

Abstract The Streak-breasted Scimitar Babblers of the Pomatorhinus ruficollis species complex are found in most of the forested habitats across southern and eastern Asia. The diversification history of this group is obscured by high plumage variation across populations and conflicting genetic signal across loci. We combined genetic and geographic data from several recent studies to investigate how these species diversified across China using both phylogenetic and ecological niche modeling analyses. These two lines of evidence are consistent in showing that two well-sampled species, P. reconditus and P. nigrostellatus, in central and southern China respectively, likely experienced a history of isolation and expansion as suitable habitat contracted during the last interglacial and expanded in patchy extent during the glacial maximum. The genetic analysis showed that populations of P. nigrostellatus on Hainan Island are very similar to the ones in nearby mainland southern China. We recovered two well-supported clades within P. reconditus that were not geographically structured with both containing individuals from the same localities across central China. This phylogenetic result corresponded to the ecological niche models that showed expansion from refugia since the last interglacial. This study illustrates the value of using an integrative approach and detailed geographic sampling to help understand the recent diversification of birds in China.

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Geographic shifts in Aedes aegypti habitat suitability in Ecuador using larval surveillance data and ecological niche modeling: Implications of climate change for public health vector control

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0007322 ◽

2019 ◽

Vol 13 (4) ◽

pp. e0007322 ◽

Cited By ~ 9

Author(s):

Catherine A. Lippi ◽

Anna M. Stewart-Ibarra ◽

M. E. Franklin Bajaña Loor ◽

Jose E. Dueñas Zambrano ◽

Nelson A. Espinoza Lopez ◽

...

Keyword(s):

Public Health ◽

Climate Change ◽

Aedes Aegypti ◽

Vector Control ◽

Habitat Suitability ◽

Ecological Niche ◽

Ecological Niche Modeling ◽

Niche Modeling ◽

Surveillance Data

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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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Ecological niche modelling to estimate the distribution of Culicoides, potential vectors of bluetongue virus in Senegal

BMC Ecology ◽

10.1186/s12898-019-0261-9 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 3

Author(s):

Mamadou Ciss ◽

Biram Biteye ◽

Assane Gueye Fall ◽

Moussa Fall ◽

Marie Cicille Ba Gahn ◽

...

Keyword(s):

Bluetongue Virus ◽

Ecological Niche ◽

Morbidity And Mortality ◽

Maximum Temperature ◽

High Morbidity ◽

Ecological Niche Models ◽

Niche Modelling ◽

Boosted Regression Tree ◽

Bioclimatic Variables ◽

Suitable Habitats

Abstract Background Vector-borne diseases are among the leading causes of morbidity and mortality in humans and animals. In the Afrotropical region, some are transmitted by Culicoides, such as Akabane, bluetongue, epizootic haemorrhagic fever and African horse sickness viruses. Bluetongue virus infection has an enormous impact on ruminant production, due to its high morbidity and mortality rates. Methods A nationwide Culicoides trapping campaign was organized at the end of the 2012 rainy season in Senegal. A Maximum Entropy approach (MaxEnt), Boosted Regression Tree (BRT) method and Ecological Niche Factor Analysis (ENFA) were used to develop a predictive spatial model for the distribution of Culicoides, using bio-climatic variables, livestock densities and altitude. Results The altitude, maximum temperature of the warmest month, precipitation of the warmest quarter, mean temperature of the wettest quarter, temperature seasonality, precipitation of the wettest quarter and livestock density were among the most important factors to predict suitable habitats of Culicoides. Culicoides occurrences were, in most of the cases, positively correlated to precipitation variables and livestock densities; and negatively correlated to the altitude and temperature indices. The Niayes area and the Groundnut basin were the most suitable habitats predicted. Conclusion We present ecological niche models for different Culicoides species, namely C. imicola, C. oxystoma, C. enderleini and C. miombo, potential vectors of bluetongue virus, on a nationwide scale in Senegal. Through our modelling approach, we were able to determine the effect of bioclimatic variables on Culicoides habitats and were able to generate maps for the occurrence of Culicoides species. This information will be helpful in developing risk maps for disease outbreaks.

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