COMPUTER PROGRAMS: <scp>d‐novl</scp>: a program to simulate overlap between two niche‐based distribution models

Stockman, Amy K.; Danell, Ryan M.; Bond, Jason E.

doi:10.1111/j.1471-8286.2007.01947.x

Cited by 9 publications

(4 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Peterson and Holt (2003) proposed the “niche differentiation index,” which asks how well an ENM from one species predicts the range(s) of other species relative to its own distribution; however, they did not suggest how this metric can be assessed statistically. Most recently, Stockman et al (2008) introduced a simulation‐based method that may be used to investigate patterns of niche overlap, but this method too is dependent on overly simplistic binary predictions.…”

Section: Methodsmentioning

confidence: 99%

Environmental Niche Equivalency Versus Conservatism: Quantitative Approaches to Niche Evolution

2008

View full text Add to dashboard Cite

Environmental niche models, which are generated by combining species occurrence data with environmental GIS data layers, are increasingly used to answer fundamental questions about niche evolution, speciation, and the accumulation of ecological diversity within clades. The question of whether environmental niches are conserved over evolutionary time scales has attracted considerable attention, but often produced conflicting conclusions. This conflict, however, may result from differences in how niche similarity is measured and the specific null hypothesis being tested. We develop new methods for quantifying niche overlap that rely on a traditional ecological measure and a metric from mathematical statistics. We reexamine a classic study of niche conservatism between sister species in several groups of Mexican animals, and, for the first time, address alternative definitions of "niche conservatism" within a single framework using consistent methods. As expected, we find that environmental niches of sister species are more similar than expected under three distinct null hypotheses, but that they are rarely identical. We demonstrate how our measures can be used in phylogenetic comparative analyses by reexamining niche divergence in an adaptive radiation of Cuban anoles. Our results show that environmental niche overlap is closely tied to geographic overlap, but not to phylogenetic distances, suggesting that niche conservatism has not constrained local communities in this group to consist of closely related species. We suggest various randomization tests that may prove useful in other areas of ecology and evolutionary biology.

show abstract

Section: Methodsmentioning

confidence: 99%

Environmental Niche Equivalency Versus Conservatism: Quantitative Approaches to Niche Evolution

2008

View full text Add to dashboard Cite

show abstract

“…Indeed, depending on the type of data at hand, there are several valuable alternatives for assessing niche similarity and overlap (e.g. Junker, Kuppler, Bathke, Schreyer, & Trutschnig, ; Peterson, Soberón, & Sánchez‐Cordero, ; Warren, Glor, & Turelli, ), such as methods based on simulations (Stockman, Danell, & Bond, ) or resampled geographical species distributions (Broennimann, Di Cola, & Guisan, ; Broennimann et al, ; Godsoe & Case, ). Although these other approaches certainly represent valuable alternatives to the default ones, it may be useful to calculate and report the default metrics too, to enhance and facilitate future meta‐analyses and comparisons.…”

Section: Discussionmentioning

confidence: 99%

Assessing similarity of n‐dimensional hypervolumes: Which metric to use?

Mammola

2019

Journal of Biogeography

View full text Add to dashboard Cite

Aim:The n-dimensional hypervolume framework (Glob. Ecol. Biogeogr. [2014] 23:595-609) implemented through the R package 'hypervolume' is being increasingly used in ecology and biogeography. This approach offers a reliable means for comparing the niche of two or more species, through the calculation of the intersection between hypervolumes in a multidimensional space, as well as different distance metrics (minimum and centroid distance) and niche similarity indexes based on volume ratios (Sørensen-Dice and Jaccard similarity). However, given that these metrics have conceptual differences, there is still no consensus on which one(s) should be routinely used in order to assess niche similarity. The aim of this study is to provide general guidance for constructing and comparing n-dimensional hypervolumes.Location: Virtual study site. Taxon: Virtual species.Method: First, the literature was screened to verify the usage of the different metrics in studies (2014-2018) relying on this method. Subsequently, a comparative analysis based on simulated morphological and bioclimatic traits was performed, taking into consideration different analytical dimensions, sample sizes and algorithms for hypervolume construction.Results: Literature survey revealed that there was no clear preference for one metric over the others in current studies relying on the n-dimensional hypervolume method.In simulated data, a high correlation among similarity and distance metrics was found for all datatypes considered. For most analytical scenarios, using at least one overlap and one distance metric would be therefore the most appropriate approach for assessing niche overlap. Yet, when hypervolumes are fully disjunct, similarity metrics become uninformative and calculating the two distance metrics is recommended.The sample size and the choice of algorithm and dimensionality can lead to significant variations in the overlap of hypervolumes in the hyperspace, and therefore should be carefully considered. Main conclusions: Best practise for constructing n-dimensional hypervolumes and assessing their similarity are drawn, representing a practical aid for scientists using the 'hypervolume' R package in their research. These recommendations apply to most datatypes and analytical scenarios. The R scripts published alongside this methodological study can be modified for performing large-scale analyses of species niches B I OS K E TCH Stefano Mammola is an ecologist whose scientific activity focuses primarily on the use of caves and other subterranean habitats as model systems in which to investigate an array of ecological processes. S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section at the end of the article. How to cite this article: Mammola S. Assessing similarity of n-dimensional hypervolumes: Which metric to use? J Biogeogr.

show abstract

“…Lineages whose DMs are completely or largely overlapping are considered to be ecologically interchangeable (Stockman and Bond, 2007). For each closed related lineage we performed 1000 simulations following Stockman et al (2008). Secondly, a PCA was performed using the extracted values of 19 climate variables (WorldClim 1.4; Hijmans et al, 2005) for each unique locality of each clade to examine the overall level of divergence in environmental space among the extant taxa.…”

Section: Ecological Niche Modelingmentioning

confidence: 99%

Delimiting species boundaries within the Neotropical bamboo Otatea (Poaceae: Bambusoideae) using molecular, morphological and ecological data

Ruíz-Sánchez

Sosa

2010

Molecular Phylogenetics and Evolution

View full text Add to dashboard Cite

COMPUTER PROGRAMS: d‐novl: a program to simulate overlap between two niche‐based distribution models

Cited by 9 publications

References 24 publications

Environmental Niche Equivalency Versus Conservatism: Quantitative Approaches to Niche Evolution

Environmental Niche Equivalency Versus Conservatism: Quantitative Approaches to Niche Evolution

Assessing similarity of n‐dimensional hypervolumes: Which metric to use?

Delimiting species boundaries within the Neotropical bamboo Otatea (Poaceae: Bambusoideae) using molecular, morphological and ecological data

Contact Info

Product

Resources

About