inst/shiny/modules/espace_nicheOv.md

In wallace: A Modular Platform for Reproducible Modeling of Species Niches and Distributions

Module: Niche Overlap

BACKGROUND

Quantifying niche differences between species has been a topic of interest in ecology for decades (e.g. Colwell and Futuyma 1971), originally with a focus on the consumption of depletable resources (i.e., related to the Eltonian niche). As an extension, quantifying niche differences along environmental gradients (i.e., related to Grinnellian and Hutchinsonian niches) using species occurrences became common in the late 1990s with the development of models of species niches and distributions (Guisan and Zimmermann 2000). Subsequently, Warren et al. 2008 developed a method based on niche models (and associated randomization tests) to quantify niche differences using pixel-by-pixel comparisons of predictions in geographic space. One potential drawback to this approach is that many pixels predicted as suitable by the model may not be occupied; although the models assume that species are at equilibrium with their environment, many factors (e.g., biotic interactions, dispersal limitations) might prevent these pixels from being occupied. Another drawback is that with a geographic approach, the measured niche overlap can vary depending on the extent and distribution of environmental gradients. This method is thus prone to overestimate overlap of realized niches. To avoid this potential bias, Broennimann et al. (2012) developed a similar quantification and associated randomization tests in environmental space, quantifying niche overlap in a defined environmental space using smoothed occurrence densities. This approach is implemented in this module.

IMPLEMENTATION

The niche overlap quantification is based on the occurrence and background densities in the available environmental space estimated in Module: Occurrence Density Grid. The metric overlap D (Schoener 1968) is calculated with the function ecospat.niche.overlap from the R package ecospat (Di Cola et al. 2017) and provides an overall index of niche overlap ranging from 0 to 1. A value of 1 is given when the ratio of density of occurrences to density of available environmental conditions (i.e., density of background) is exactly the same for both species in all pixels of environmental space. D is thus highly dependent on the delimitation of the background extent. To avoid results with problematic interpretations, it is important that the study extent which defines the environmental space encompass a region that has been accessible to the species over evolutionary time and does not include areas beyond important dispersal boundaries or other factors that violate distributional equilibrium (Anderson 2013; Barve et al. 2011).

Alternatively, to be independent of the study extent, niche overlap indices can be based on binary characterizations of niches (i.e., pixels represent presence/absence of the species). Note that in this case, however, the information about occurrence density is lost (i.e., any part of the niche is considered to have the same “quality”). Binary overlap (BinOv, BinOv1⊃2 and BinOv2⊂1) values are derived from the function ecospat.niche.dyn.index, originally developed to study niche changes in biological invasions (Guisan et al. 2014). BinOv measures the proportion of the overlap between the two species’ niches. BinOv2⊂1 measures the proportion of the niche of species 1 that overlaps with that of species 2. The plot on the left shows these indices in environmental space: the environmental conditions covered only by the niche of species 1 (blue), the environmental conditions covered only by the niche of species 2 (red), and the environmental conditions covered by both, or the niche overlap (purple). The histogram on the right shows the results of a niche similarity test. This test is analogous to the test presented by Warren et al. 2008, except that it corresponds to environmental rather than geographic space. In the test, both of the observed species niches are randomly shifted around the background extent, and these simulated “null” niche overlaps are calculated (gray). If the observed overlap (red) is higher than 95% of the simulated overlaps (p-value < 0.05), the test indicates the two species are more similar than random (one-tailed test).

Users can download a .png of the plots corresponding to the niche overlap and similarity tests.

REFERENCES

Barve, N., Barve, V., Jiménez-Valverde, A., Lira-Noriega, A., Maher, S.P., Peterson, A.T., Soberón, J., & Villalobos, F. (2011). The crucial role of the accessible area in ecological niche modeling and species distribution modeling. Ecological Modelling, 222(11), 1810–1819. DOI: 10.1016/j.ecolmodel.2011.02.011

Broennimann, O., Fitzpatrick, M.C., Pearman, P.B., Petitpierre, B., Pellissier, L., Yoccoz, N.G., Thuiller, W., Fortin, M.J., Randin, C., Zimmermann, N.E., Graham, C.H., & Guisan, A. (2012). Measuring ecological niche overlap from occurrence and spatial environmental data. Global Ecology and Biogeography, 21(4), 481-497. DOI: 10.1111/j.1466-8238.2011.00698.x

Broennimann, O., Di Cola V., & Guisan, A. (2016). ecospat: Spatial Ecology Miscellaneous Methods. R package version 2.1.1. CRAN

Colwell, R.K., & Futuyma, D.J. (1971). On the Measurement of Niche Breadth and Overlap. Ecology, 52(4), 567-576. DOI: 10.2307/1934144

Guisan, A., Petitpierre, B., Broennimann, O., Daehler, C., & Kueffer, C. (2014). Unifying niche shift studies: Insights from biological invasions. Trends in Ecology & Evolution, 29(5), 260–269. DOI: 10.1016/j.tree.2014.02.009

Guisan, A., & Zimmermann, N.E. (2000) Predictive habitat distribution models in ecology. Ecological Modelling, 135(2-3), 147-186. DOI: 10.1016/S0304-3800(00)00354-9

Schoener, T.W. (1968). Anolis lizards of Bimini: resource partitioning in a complex fauna. Ecology, 49(4), 704-726. DOI:10.2307/1935534

Warren, D.L., Glor, R.E., & Turelli, M. (2008). Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution, 62(11), 2868–2883. DOI: 10.1111/j.1558-5646.2008.00482.x

wallace documentation built on Sept. 11, 2024, 9:16 p.m.