Revisiting niche fundamentals with Tukey depth

Cerdeira, J. Orestes; Monteiro‐Henriques, Tiago; Martins, Maria João; Silva, Pedro C.; Alagador, Diogo; Franco, Aldina M. A.; Campagnolo, Manuel L.; Arsénio, Pedro; Aguiar, Francisca C.; Cabeza, Mar

doi:10.1111/2041-210x.13074

Cited by 12 publications

(14 citation statements)

References 49 publications

(62 reference statements)

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“…Our approach measuring overlap is by no means restricted to a plane. While measures of multidimensional overlap exist (see, e.g., an alternative approach of a multivariate index of niche overlap based on Tukey depth in Cerdeira et al 2018), it is unclear how the resulting indices can be compared to a 2‐dimensional index of geographic overlap, as overlap mathematically decreases with higher dimensionality. A first step is thus to reduce the ecological space to two dimensions, for instance, focusing on the first two axes of a multivariate analysis, which typically account for most of the information (Dallas et al 2017), at the expense of a more difficult interpretation.…”

Section: Discussionmentioning

confidence: 99%

Joint seasonality in geographic and ecological spaces, illustrated with a partially migratory bird

Basille

Watling²,

Romañach

et al. 2020

Ecosphere

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Citation: Basille, M., J. Watling, S. Romañach and R. Borkhataria. 2020. Joint seasonality in geographic and ecological spaces, illustrated with a partially migratory bird. Ecosphere 11(5):Abstract. As most species live in seasonal environments, considering varying conditions is essential to understand species dynamics in both geographic and ecological spaces. Both resident and migratory species need to contend with seasonality and balance settling in favorable areas with tracking favorable environmental conditions during the year. We present an exploratory framework to jointly investigate a species' niche in geographic and ecological spaces, applied to wood storks (Mycteria americana), which are partially migratory wading birds, in the southeastern United States. We concurrently described monthly geographic distributions and climatic niches based on temperature and precipitation. Geographic distributions of wood storks were more similar throughout the year than were climatic niches, suggesting that birds stay within specific areas seasonally, rather than tracking areas of similar climate. However, wood storks expressed consistent selection of warm areas during the winter, and wet areas during the summer, indicating that the selection of seasonal ranges may be directly related to environmental conditions across the entire range. Our flexible framework, which simultaneously considered geographic and ecological spaces, suggested that tracking climate alone did not explain seasonal distributions of wood storks in breeding and non-breeding areas.

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Section: Discussionmentioning

confidence: 99%

Joint seasonality in geographic and ecological spaces, illustrated with a partially migratory bird

Basille

Watling²,

Romañach

et al. 2020

Ecosphere

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“…While measures of multi-dimensional overlap exist (see for instance an alternative approach of a multivariate index of niche overlap based on Tukey depth in Cerdeira et al, 2018), it is unclear how the resulting indexes can be compared to a 2-dimensional index of geographic overlap, as overlap mathematically decreases with higher dimensionality. A first step is thus to reduce the ecological space to two dimensions, using multivariate analyses, and focus on the first two axes of the analysis, which typically account for most of the information (see e.g.…”

Section: Discussionmentioning

confidence: 99%

Joint seasonality in geographic and ecological spaces, illustrated with a partially migratory bird

Basille

Watling

Romañach

et al. 2019

Preprint

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As most species live in seasonal environments, considering varying 5 conditions is essential to understand species dynamics in both geographic and ecological 6 spaces. Both resident and migratory species need to contend with seasonality, and balance 7 settling in favorable areas with tracking favorable environmental conditions during the 8 year. We present an exploratory framework to jointly investigate a species' niche in 9 geographic and ecological spaces, applied to wood storks (Mycteria americana), which are 10 partially migratory wading birds, in the southeastern U.S. We concurrently described 11 monthly geographic distributions and climatic niches based on temperature and 12 precipitation. Geographic distributions of wood storks were more similar throughout the 13 year than climatic niches were, suggesting that birds stay within specific areas seasonally, 14 rather than tracking areas of similar climate. However, wood storks expressed consistent 15 selection of warm areas during the winter, and wet areas during the summer, indicating 16 that the selection of seasonal ranges may be directly related to environmental conditions 17 across the entire range. Our flexible framework, which simultaneously considered 18 geographic and ecological spaces, suggested that tracking climate alone did not explain 19 seasonal distributions of wood storks in breeding and non-breeding areas. 20 Key words: climatic niche, ecological niche, kernel overlap, range, wood stork 21 3 BASILLE ET AL. Submitted to Ecosphere 45 et al. (2015) estimated overlap between breeding and non-breeding niches of warblers, 46 while Gómez et al. (2016) investigated seasonal niche overlap of passerine birds. 47 100December 2011, and the tags collected a total of 445,638 GPS locations, which is more 101 than 7,000 locations per individual on average (7, 306 ± 6, 036). We defined the study area 102 SEASONALITY IN CLIMATIC NICHE 6by the coastline to the South (i.e., all land masses), and by the limit of a convex hull 103 around all GPS locations to the North (see the study area limits in Fig. 1). 104 We first grouped all GPS data by month across all years to define monthly ranges. To 105 account for variability in number of locations among individuals, and the fact that 106 individual wood storks are a random sample of the population, we sampled 5,000 GPS 107 locations in each month by 1) removing individuals with fewer than 100 locations in a 108 given month, and 2) sampling 5,000 random individual wood storks (with replacement) 109 and 1 random location for each of the 5,000 sampled individuals. We thus compiled 60,000 110 random locations for the population, evenly distributed throughout the year. 111In climatic space, the wood stork niche was described by average monthly temperature 112 and precipitation using climate rasters from the Climate Research Unit (CRU) data set, 113 available at a resolution of approximately 10 arc-min (New et al. 2002). A previous 114 analysis (Watling et al. 2012) showed that variables describing monthly climate (e.g....

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“…An unfavorable feature of the CH is that its topology is strongly influenced by peripheral observations, making it very sensitive to outliers. Furthermore, the CH approach does not identify suitability levels that could occur internally (Cerdeira et al, 2018), the fitted hypervolume is fixed and unique, so it does not distinguish among different confidence levels (Blonder et al, 2014). However, this approach has the advantage of being distribution-free, or non-parametric, because no assumption about the statistical distribution of the data is assumed.…”

Section: Introductionmentioning

confidence: 99%

A new method to estimate the ecological niche throughn-dimensional hypervolumes that combines convex hulls and elliptical envelopes

Carrasco

Lisón

Jiménez³

et al. 2022

Preprint

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Methods that estimate the niche of a species by calculating a convex hull or an elliptical envelope have become popular due to their simplicity and interpretation, given Hutchinson’s conception of the niche as an n-dimensional hypervolume.It is well known that convex hulls are sensitive to outliers and do not have the ability to differentiate between regions of low and high concentration of presences, while the elliptical envelopes may contain large regions of niche space that are not relevant for the species. Thus, when the goal is to estimate the realized niche of the species, both methods may overestimate the niche.We present a methodology that combines both the convex hull and the elliptical envelope methods producing an n-dimensional hypervolume that better fits the observed density of species presences, making it a better candidate to model the realized niche. Our method, called the CHE approach, allows defining regions of iso-suitability as a function of the significance levels inherited from the method (Mahalanobis distance model, minimum covariance determinant, or minimum volume ellipsoid) used to fit an initial elliptical envelope from which we then discard regions not relevant for the species by calculating a convex hull.We applied the CHE approach to a case study of twenty-five species of bats present in the Iberian Peninsula, fitting a hypervolume for each species and comparing them to both the convex hulls and elliptical envelopes obtained with the same data and different values of n. We show that as the number of variables used to define the niche space increases, both the convex hull and elliptical envelope models produce overly large hypervolumes, while the size of the hypervolume fitted with the CHE approach remains stable. As a consequence, similarity measures that account for the niche overlap among different species may be inflated when using convex hulls or elliptical envelopes to model the niche; something that does not occur under the CHE approach.

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Revisiting niche fundamentals with Tukey depth

Cited by 12 publications

References 49 publications

Joint seasonality in geographic and ecological spaces, illustrated with a partially migratory bird

Joint seasonality in geographic and ecological spaces, illustrated with a partially migratory bird

Joint seasonality in geographic and ecological spaces, illustrated with a partially migratory bird

A new method to estimate the ecological niche throughn-dimensional hypervolumes that combines convex hulls and elliptical envelopes

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