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Revisiting niche fundamentals with Tukey depth

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Revisiting niche fundamentals with Tukey depth. / Cerdeira, Jorge Orestes; Monteiro-Henriques, Tiago; João Martins, Maria; Silva, Pedro C.; Alagador, Diogo; Franco, Aldina M. A.; Campagnolo, Manuel L.; Arsénio, Pedro; Aguiar, Francisca C.; Cabeza, Mar.

In: Methods in Ecology and Evolution, Vol. 9, No. 12, 12.2018, p. 2349-2361.

Research output: Contribution to journalArticle

Harvard

Cerdeira, JO, Monteiro-Henriques, T, João Martins, M, Silva, PC, Alagador, D, Franco, AMA, Campagnolo, ML, Arsénio, P, Aguiar, FC & Cabeza, M 2018, 'Revisiting niche fundamentals with Tukey depth', Methods in Ecology and Evolution, vol. 9, no. 12, pp. 2349-2361. https://doi.org/10.1111/2041-210X.13074

APA

Cerdeira, J. O., Monteiro-Henriques, T., João Martins, M., Silva, P. C., Alagador, D., Franco, A. M. A., Campagnolo, M. L., Arsénio, P., Aguiar, F. C., & Cabeza, M. (2018). Revisiting niche fundamentals with Tukey depth. Methods in Ecology and Evolution, 9(12), 2349-2361. https://doi.org/10.1111/2041-210X.13074

Vancouver

Cerdeira JO, Monteiro-Henriques T, João Martins M, Silva PC, Alagador D, Franco AMA et al. Revisiting niche fundamentals with Tukey depth. Methods in Ecology and Evolution. 2018 Dec;9(12):2349-2361. https://doi.org/10.1111/2041-210X.13074

Author

Cerdeira, Jorge Orestes ; Monteiro-Henriques, Tiago ; João Martins, Maria ; Silva, Pedro C. ; Alagador, Diogo ; Franco, Aldina M. A. ; Campagnolo, Manuel L. ; Arsénio, Pedro ; Aguiar, Francisca C. ; Cabeza, Mar. / Revisiting niche fundamentals with Tukey depth. In: Methods in Ecology and Evolution. 2018 ; Vol. 9, No. 12. pp. 2349-2361.

Bibtex- Download

@article{be2adbdb8e2443c3abff336d9df85ff7,
title = "Revisiting niche fundamentals with Tukey depth",
abstract = "1. The first attempts to describe species ecological niches were simple geometric procedures that depict the niche boundaries directly from environmental data. The convex hull was one of such procedures, popular for its simplicity, clear ecological rational and precise definition of the niche. However, it lacked the ability to differentiate areas of the niche with different probabilities of occurrence according to environmental suitability. 2. We incorporate the Tukey depth, a mathematical tool to measure the centrality of a point within a cloud of points on a multidimensional space, in the convex hull approach to (i) propose a new procedure (CH-Tukey) to estimate species{\textquoteright} environmental suitability, and (ii) estimate niche overlap coherently. In addition to a clear ecological rational and simplicity the CHTukey procedure has a number of attractive features: use of presence-only data; independence from background data; invariance to scale; robustness to outliers; and the decomposition of the niche into a finite number of isosuitability levels, permitting the computation of consistent overlap indices. We illustrate the use of CH-Tukey, using occurrence data of the main Quercus species and subspecies from Western Mediterranean Europe, comparing its outputs with BIOCLIM and MAXENT. 3. Results showed distinct niche geometries among the different approaches. BIOCLIM produced rectilinear niches reflecting the assumption that ecological variables are independent in their action on the species. CHTukey, relaxing this assumption, adjusts niche outer boundary and the inner suitability levels to the known occurrences. MAXENT produced unbounded niche geometries, showing abrupt shifts in the species response to the environmental variables.4. The niche predictions obtained with geometric approaches, BIOCLIM and CH Tukey, are simpler but better aligned with Hutchinson{\textquoteright}s niche concept than those obtained with MAXENT, this latter showing ecologically implausible relationships with the environmental variables. CH-Tukey and the related overlap measures provide an adequate tool to explore niche properties and species-environment relationships.",
keywords = "depth functions, environmental envelope, geometric procedures, Hutchinsonian niche, niche modelling, niche overlap, Quercus species",
author = "Cerdeira, {Jorge Orestes} and Tiago Monteiro-Henriques and {Jo{\~a}o Martins}, Maria and Silva, {Pedro C.} and Diogo Alagador and Franco, {Aldina M. A.} and Campagnolo, {Manuel L.} and Pedro Ars{\'e}nio and Aguiar, {Francisca C.} and Mar Cabeza",
year = "2018",
month = dec,
doi = "10.1111/2041-210X.13074",
language = "English",
volume = "9",
pages = "2349--2361",
journal = "Methods in Ecology and Evolution",
issn = "2041-210X",
publisher = "Wiley",
number = "12",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Revisiting niche fundamentals with Tukey depth

AU - Cerdeira, Jorge Orestes

AU - Monteiro-Henriques, Tiago

AU - João Martins, Maria

AU - Silva, Pedro C.

AU - Alagador, Diogo

AU - Franco, Aldina M. A.

AU - Campagnolo, Manuel L.

AU - Arsénio, Pedro

AU - Aguiar, Francisca C.

AU - Cabeza, Mar

PY - 2018/12

Y1 - 2018/12

N2 - 1. The first attempts to describe species ecological niches were simple geometric procedures that depict the niche boundaries directly from environmental data. The convex hull was one of such procedures, popular for its simplicity, clear ecological rational and precise definition of the niche. However, it lacked the ability to differentiate areas of the niche with different probabilities of occurrence according to environmental suitability. 2. We incorporate the Tukey depth, a mathematical tool to measure the centrality of a point within a cloud of points on a multidimensional space, in the convex hull approach to (i) propose a new procedure (CH-Tukey) to estimate species’ environmental suitability, and (ii) estimate niche overlap coherently. In addition to a clear ecological rational and simplicity the CHTukey procedure has a number of attractive features: use of presence-only data; independence from background data; invariance to scale; robustness to outliers; and the decomposition of the niche into a finite number of isosuitability levels, permitting the computation of consistent overlap indices. We illustrate the use of CH-Tukey, using occurrence data of the main Quercus species and subspecies from Western Mediterranean Europe, comparing its outputs with BIOCLIM and MAXENT. 3. Results showed distinct niche geometries among the different approaches. BIOCLIM produced rectilinear niches reflecting the assumption that ecological variables are independent in their action on the species. CHTukey, relaxing this assumption, adjusts niche outer boundary and the inner suitability levels to the known occurrences. MAXENT produced unbounded niche geometries, showing abrupt shifts in the species response to the environmental variables.4. The niche predictions obtained with geometric approaches, BIOCLIM and CH Tukey, are simpler but better aligned with Hutchinson’s niche concept than those obtained with MAXENT, this latter showing ecologically implausible relationships with the environmental variables. CH-Tukey and the related overlap measures provide an adequate tool to explore niche properties and species-environment relationships.

AB - 1. The first attempts to describe species ecological niches were simple geometric procedures that depict the niche boundaries directly from environmental data. The convex hull was one of such procedures, popular for its simplicity, clear ecological rational and precise definition of the niche. However, it lacked the ability to differentiate areas of the niche with different probabilities of occurrence according to environmental suitability. 2. We incorporate the Tukey depth, a mathematical tool to measure the centrality of a point within a cloud of points on a multidimensional space, in the convex hull approach to (i) propose a new procedure (CH-Tukey) to estimate species’ environmental suitability, and (ii) estimate niche overlap coherently. In addition to a clear ecological rational and simplicity the CHTukey procedure has a number of attractive features: use of presence-only data; independence from background data; invariance to scale; robustness to outliers; and the decomposition of the niche into a finite number of isosuitability levels, permitting the computation of consistent overlap indices. We illustrate the use of CH-Tukey, using occurrence data of the main Quercus species and subspecies from Western Mediterranean Europe, comparing its outputs with BIOCLIM and MAXENT. 3. Results showed distinct niche geometries among the different approaches. BIOCLIM produced rectilinear niches reflecting the assumption that ecological variables are independent in their action on the species. CHTukey, relaxing this assumption, adjusts niche outer boundary and the inner suitability levels to the known occurrences. MAXENT produced unbounded niche geometries, showing abrupt shifts in the species response to the environmental variables.4. The niche predictions obtained with geometric approaches, BIOCLIM and CH Tukey, are simpler but better aligned with Hutchinson’s niche concept than those obtained with MAXENT, this latter showing ecologically implausible relationships with the environmental variables. CH-Tukey and the related overlap measures provide an adequate tool to explore niche properties and species-environment relationships.

KW - depth functions

KW - environmental envelope

KW - geometric procedures

KW - Hutchinsonian niche

KW - niche modelling

KW - niche overlap

KW - Quercus species

U2 - 10.1111/2041-210X.13074

DO - 10.1111/2041-210X.13074

M3 - Article

VL - 9

SP - 2349

EP - 2361

JO - Methods in Ecology and Evolution

JF - Methods in Ecology and Evolution

SN - 2041-210X

IS - 12

ER -

ID: 139436105