The Experts below are selected from a list of 44109 Experts worldwide ranked by ideXlab platform
Townsend A Peterson - One of the best experts on this subject based on the ideXlab platform.
-
a checklist for maximizing reproducibility of Ecological Niche models
Nature Ecology and Evolution, 2019Co-Authors: Xiao Feng, Daniel S Park, Cassondra Walker, Townsend A Peterson, Cory Merow, Monica PapesAbstract:Reporting specific modelling methods and metadata is essential to the reproducibility of Ecological studies, yet guidelines rarely exist regarding what information should be noted. Here, we address this issue for Ecological Niche modelling or species distribution modelling, a rapidly developing toolset in ecology used across many aspects of biodiversity science. Our quantitative review of the recent literature reveals a general lack of sufficient information to fully reproduce the work. Over two-thirds of the examined studies neglected to report the version or access date of the underlying data, and only half reported model parameters. To address this problem, we propose adopting a checklist to guide studies in reporting at least the minimum information necessary for Ecological Niche modelling reproducibility, offering a straightforward way to balance efficiency and accuracy. We encourage the Ecological Niche modelling community, as well as journal reviewers and editors, to utilize and further develop this framework to facilitate and improve the reproducibility of future work. The proposed checklist framework is generalizable to other areas of ecology, especially those utilizing biodiversity data, environmental data and statistical modelling, and could also be adopted by a broader array of disciplines. The authors evaluate the reproducibility of Ecological Niche modelling literature and provide a checklist of crucial items for more reproducible Ecological Niche models.
-
kuenm an r package for detailed development of Ecological Niche models using maxent
PeerJ, 2019Co-Authors: Marlon E Cobos, Townsend A Peterson, Narayani Barve, Luis OsorioolveraAbstract: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.
-
Ecological Niche modeling re examined a case study with the darwin s fox
Ecology and Evolution, 2018Co-Authors: Luis E Escobar, Huijie Qiao, Javier Cabello, Townsend A PetersonAbstract:: Many previous studies have attempted to assess Ecological Niche modeling performance using receiver operating characteristic (ROC) approaches, even though diverse problems with this metric have been pointed out in the literature. We explored different evaluation metrics based on independent testing data using the Darwin's Fox (Lycalopex fulvipes) as a detailed case in point. Six Ecological Niche models (ENMs; generalized linear models, boosted regression trees, Maxent, GARP, multivariable kernel density estimation, and NicheA) were explored and tested using six evaluation metrics (partial ROC, Akaike information criterion, omission rate, cumulative binomial probability), including two novel metrics to quantify model extrapolation versus interpolation (E-space index I) and extent of extrapolation versus Jaccard similarity (E-space index II). Different ENMs showed diverse and mixed performance, depending on the evaluation metric used. Because ENMs performed differently according to the evaluation metric employed, model selection should be based on the data available, assumptions necessary, and the particular research question. The typical ROC AUC evaluation approach should be discontinued when only presence data are available, and evaluations in environmental dimensions should be adopted as part of the toolkit of ENM researchers. Our results suggest that selecting Maxent ENM based solely on previous reports of its performance is a questionable practice. Instead, model comparisons, including diverse algorithms and parameterizations, should be the sine qua non for every study using Ecological Niche modeling. ENM evaluations should be developed using metrics that assess desired model characteristics instead of single measurement of fit between model and data. The metrics proposed herein that assess model performance in environmental space (i.e., E-space indices I and II) may complement current methods for ENM evaluation.
-
Ecological Niche structure and rangewide abundance patterns of species
Biology Letters, 2012Co-Authors: Enrique Martinezmeyer, Townsend A Peterson, Daniel Diazporras, Carlos YanezarenasAbstract:Spatial abundance patterns across species' ranges have attracted intense attention in macroecology and biogeography. One key hypothesis has been that abundance declines with geographical distance from the range centre, but tests of this idea have shown that the effect may occur indeed only in a minority of cases. We explore an alternative hypothesis: that species' abundances decline with distance from the centroid of the species' habitable conditions in environmental space (the Ecological Niche). We demonstrate consistent negative abundance–Ecological distance relationships across all 11 species analysed (turtles to wolves), and that relationships in environmental space are consistently stronger than relationships in geographical space.
-
species distribution modeling and Ecological Niche modeling getting the concepts right
Natureza & Conservacao, 2012Co-Authors: Townsend A Peterson, Jorge SoberonAbstract:We provide an overview of conceptual considerations in terminology related to Ecological Niche modeling and species distribution modeling, two near-synonymous (but not quite), relatively new tools in macroecology and biogeography. We show that a large majority of published studies taking advantage of these tools use terminology inappropriate to the biogeographic and Ecological basis on which their application is founded. We suggest that only via rigorous and appropriate terminology will these tools achieve their fullest potential.
A T Peterson - One of the best experts on this subject based on the ideXlab platform.
-
environmental data sets matter in Ecological Niche modelling an example with solenopsis invicta and solenopsis richteri
Global Ecology and Biogeography, 2007Co-Authors: A T Peterson, Yoshinori NakazawaAbstract:Aim In response to a recent paper suggesting the failure of Ecological Niche models to predict between native and introduced distributional areas of fire ants (Solenopsis invicta), we sought to assess methodological causes of this failure. Location Ecological Niche models were developed on the species’ native distributional area in South America, and projected globally. Methods We developed Ecological Niche models based on six different environmental data sets, and compared their respective abilities to anticipate the North American invasive distributional area of the species. Results We show that models based on the ‘bioclimatic variables’ of the WorldClim data set indeed fail to predict the full invasive potential of the species, but that models based on four other data sets could predict this potential correctly. Main conclusions The difference in predictive abilities appears to centre on the complexity of the environmental variables involved. These results emphasize important influences of environmental data sets on the generality and ability of Ecological Niche models to anticipate novel phenomena, and offer a simpler explanation for the lack of predictive ability among native and invaded distributional areas than that of Niche shifts.
-
conservatism of Ecological Niche characteristics in north american plant species over the pleistocene to recent transition
Journal of Biogeography, 2006Co-Authors: Enrique Martinezmeyer, A T PetersonAbstract:Aim To provide a test of the conservatism of a species’ Niche over the last 20,000 years by tracking the distribution of eight pollen taxa relative to climate type as they migrated across eastern North America following the Last Glacial Maximum (LGM). Location North America. Methods We drew taxon occurrence data from the North American pollen records in the Global Pollen Database, representing eight pollen types – all taxa for which ≥5 distinct geographic occurrences were available in both the present day and at the LGM (21,000 years ago ± 3000 years). These data were incorporated into Ecological Niche models based on present-day and LGM climatological summaries available from the Palaeoclimate Modelling Intercomparison Project to produce predicted potential geographic distributions for each species at present and at the LGM. The output for each time period was projected onto the ‘other’ time period, and tested using independent known occurrence information from that period. Results The result of our analyses was that all species tested showed general conservatism in Ecological characteristics over the climate changes associated with the Pleistocene-to-Recent transition. Main conclusions This analysis constitutes a further demonstration of general and pervasive conservatism in Ecological Niche characteristics over moderate periods of time despite profound changes in climate and environmental conditions. As such, our results reinforce the application of Ecological Niche modelling techniques to the reconstruction of Pleistocene biodiversity distribution patterns, and to project the future potential distribution range of species in the face of global-scale climatic changes.
Enrique Martinezmeyer - One of the best experts on this subject based on the ideXlab platform.
-
Ecological Niche structure and rangewide abundance patterns of species
Biology Letters, 2012Co-Authors: Enrique Martinezmeyer, Townsend A Peterson, Daniel Diazporras, Carlos YanezarenasAbstract:Spatial abundance patterns across species' ranges have attracted intense attention in macroecology and biogeography. One key hypothesis has been that abundance declines with geographical distance from the range centre, but tests of this idea have shown that the effect may occur indeed only in a minority of cases. We explore an alternative hypothesis: that species' abundances decline with distance from the centroid of the species' habitable conditions in environmental space (the Ecological Niche). We demonstrate consistent negative abundance–Ecological distance relationships across all 11 species analysed (turtles to wolves), and that relationships in environmental space are consistently stronger than relationships in geographical space.
-
conservatism of Ecological Niche characteristics in north american plant species over the pleistocene to recent transition
Journal of Biogeography, 2006Co-Authors: Enrique Martinezmeyer, A T PetersonAbstract:Aim To provide a test of the conservatism of a species’ Niche over the last 20,000 years by tracking the distribution of eight pollen taxa relative to climate type as they migrated across eastern North America following the Last Glacial Maximum (LGM). Location North America. Methods We drew taxon occurrence data from the North American pollen records in the Global Pollen Database, representing eight pollen types – all taxa for which ≥5 distinct geographic occurrences were available in both the present day and at the LGM (21,000 years ago ± 3000 years). These data were incorporated into Ecological Niche models based on present-day and LGM climatological summaries available from the Palaeoclimate Modelling Intercomparison Project to produce predicted potential geographic distributions for each species at present and at the LGM. The output for each time period was projected onto the ‘other’ time period, and tested using independent known occurrence information from that period. Results The result of our analyses was that all species tested showed general conservatism in Ecological characteristics over the climate changes associated with the Pleistocene-to-Recent transition. Main conclusions This analysis constitutes a further demonstration of general and pervasive conservatism in Ecological Niche characteristics over moderate periods of time despite profound changes in climate and environmental conditions. As such, our results reinforce the application of Ecological Niche modelling techniques to the reconstruction of Pleistocene biodiversity distribution patterns, and to project the future potential distribution range of species in the face of global-scale climatic changes.
Joseph J Apodaca - One of the best experts on this subject based on the ideXlab platform.
-
adding more ecology into species delimitation Ecological Niche models and phylogeography help define cryptic species in the black salamander aneides flavipunctatus
Systematic Biology, 2007Co-Authors: Leslie J Rissler, Joseph J ApodacaAbstract:Being able to efficiently and accurately delimit species is one of the most basic and important aspects of systematics because species are the fundamental unit of analysis in biogeography, ecology, and conservation. We present a rationale and approach for combining Ecological Niche modeling, spatially explicit analyses of environmental data, and phylogenetics in species delimitation, and we use our methodology in an empirical example focusing on Aneides flavipunctatus, the black salamander (Caudata: Plethodontidae), in California. We assess the relationships between genetic, environmental, and geographic distance among populations. We use 11 climatic variables and point locality data from public databases to create Ecological Niche models. The suitability of potential contact zones between parapatric lineages is also assessed using the data from Ecological Niche modeling. Phylogenetic analyses of portions of the mitochondrial genome reveal morphologically cryptic mitochondrial lineages in this species. In addition, we find that patterns of genetic divergence are strongly associated with divergence in the Ecological Niche. Our work demonstrates the ease and utility of using spatial analyses of environmental data and phylogenetics in species delimitation, especially for groups displaying fine-scaled endemism and cryptic species. (Aneides; California; Maxent; Niche modeling; salamanders; species delimitation.)
Yoshinori Nakazawa - One of the best experts on this subject based on the ideXlab platform.
-
environmental data sets matter in Ecological Niche modelling an example with solenopsis invicta and solenopsis richteri
Global Ecology and Biogeography, 2007Co-Authors: A T Peterson, Yoshinori NakazawaAbstract:Aim In response to a recent paper suggesting the failure of Ecological Niche models to predict between native and introduced distributional areas of fire ants (Solenopsis invicta), we sought to assess methodological causes of this failure. Location Ecological Niche models were developed on the species’ native distributional area in South America, and projected globally. Methods We developed Ecological Niche models based on six different environmental data sets, and compared their respective abilities to anticipate the North American invasive distributional area of the species. Results We show that models based on the ‘bioclimatic variables’ of the WorldClim data set indeed fail to predict the full invasive potential of the species, but that models based on four other data sets could predict this potential correctly. Main conclusions The difference in predictive abilities appears to centre on the complexity of the environmental variables involved. These results emphasize important influences of environmental data sets on the generality and ability of Ecological Niche models to anticipate novel phenomena, and offer a simpler explanation for the lack of predictive ability among native and invaded distributional areas than that of Niche shifts.
