Supraspecific units in correlative niche modeling improves the prediction of geographic potential of biological invasions

Castaño-Quintero, Sandra; Escobar-Luján, Jazmín; Osorio‐Olvera, Luis; Peterson, A. Townsend; Chiappa‐Carrara, Xavier; Martínez‐Meyer, Enrique; Yáñez‐Arenas, Carlos

doi:10.7717/peerj.10454

Cited by 21 publications

(17 citation statements)

References 61 publications

(67 reference statements)

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“…Those studies that have reported their choice of parameter have used values of k = 0.95 ( Soberón, Peterson & Osorio-Olvera, 2018 ; Altamiranda-Saavedra et al, 2020 ; Castaño-Quintero et al, 2020 ), k = 0.975 ( Osorio-Olvera et al, 2020 ; Castaño-Quintero et al, 2020 ), and k = 0.99 ( Yañez-Arenas et al, 2018 ). These seem to be sensible choices based on the virtual experiments conducted here, as in comparison to the sample means and variance-covariance method, when k = 0.95 the MCD and MVE methods will not be too negatively affected by small sample sizes ( Fig.…”

Section: Discussionmentioning

confidence: 99%

“…1 ), we can see that both the MCD and MVE methods ignore the apparent outlier and produce measures of multivariate location and scatter that are focussed on where the data are more concentrated. Given the robustness of MCD and MVE methods to outliers resulting from errors in natural history observation data, it is perhaps no surprise that both methods have been adopted recently for ecological niche modelling ( Norris, Jackson & Betancourt, 2006 ; Liu, White & Newell, 2018 ; Soberón, Peterson & Osorio-Olvera, 2018 ; Yañez-Arenas et al, 2018 ; Qiao et al, 2019 ; Altamiranda-Saavedra et al, 2020 ; Osorio-Olvera et al, 2020 ; Castaño-Quintero et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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Mahalanobis distances for ecological niche modelling and outlier detection: implications of sample size, error, and bias for selecting and parameterising a multivariate location and scatter method

Etherington

2021

PeerJ

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The Mahalanobis distance is a statistical technique that has been used in statistics and data science for data classification and outlier detection, and in ecology to quantify species-environment relationships in habitat and ecological niche models. Mahalanobis distances are based on the location and scatter of a multivariate normal distribution, and can measure how distant any point in space is from the centre of this kind of distribution. Three different methods for calculating the multivariate location and scatter are commonly used: the sample mean and variance-covariance, the minimum covariance determinant, and the minimum volume ellipsoid. The minimum covariance determinant and minimum volume ellipsoid were developed to be robust to outliers by minimising the multivariate location and scatter for a subset of the full sample, with the proportion of the full sample forming the subset being controlled by a user-defined parameter. This outlier robustness means the minimum covariance determinant and the minimum volume ellipsoid are highly relevant for ecological niche analyses, which are usually based on natural history observations that are likely to contain errors. However, natural history observations will also contain extreme bias, to which the minimum covariance determinant and the minimum volume ellipsoid will also be sensitive. To provide guidance for selecting and parameterising a multivariate location and scatter method, a series of virtual ecological niche modelling experiments were conducted to demonstrate the performance of each multivariate location and scatter method under different levels of sample size, errors, and bias. The results show that there is no optimal modelling approach, and that choices need to be made based on the individual data and question. The sample mean and variance-covariance method will perform best on very small sample sizes if the data are free of error and bias. At larger sample sizes the minimum covariance determinant and minimum volume ellipsoid methods perform as well or better, but only if they are appropriately parameterised. Modellers who are more concerned about the prevalence of errors should retain a smaller proportion of the full data set, while modellers more concerned about the prevalence of bias should retain a larger proportion of the full data set. I conclude that Mahalanobis distances are a useful niche modelling technique, but only for questions relating to the fundamental niche of a species where the assumption of multivariate normality is reasonable. Users of the minimum covariance determinant and minimum volume ellipsoid methods must also clearly report their parameterisations so that the results can be interpreted correctly.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Mahalanobis distances for ecological niche modelling and outlier detection: implications of sample size, error, and bias for selecting and parameterising a multivariate location and scatter method

Etherington

2021

PeerJ

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“…This approach has been assessed under different taxonomic groups that explored the contribution of using supraspecific modelling units in niche construction showing that those modelling units improved the predictive ability of the ecological niche models. Specifically, by adding the occurrences of closer taxa reduced the omission rates considerably [ 30 ].…”

Section: Methodsmentioning

confidence: 99%

Presence and potential distribution of malaria-infected New World primates of Costa Rica

Chaves

Dolz

Ibarra-Cerdeña

et al. 2022

Malar J

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Background In South and Central America, Plasmodium malariae/Plasmodium brasilianum, Plasmodium vivax, Plasmodium simium, and Plasmodium falciparum has been reported in New World primates (NWP). Specifically in Costa Rica, the presence of monkeys positive to P. malariae/P brasilianum has been identified in both captivity and in the wild. The aim of the present study was to determine the presence of P. brasilianum, P. falciparum, and P. vivax, and the potential distribution of these parasites-infecting NWP from Costa Rica. Methods The locations with PCR (Polymerase Chain Reaction) positive results and bioclimatic predictors were used to construct ecological niche models based on a modelling environment that uses the Maxent algorithm, named kuenm, capable to manage diverse settings to better estimate the potential distributions and uncertainty indices of the potential distribution. Results PCR analysis for the Plasmodium presence was conducted in 384 samples of four primates (Howler monkey [n = 130], White-face monkey [n = 132], Squirrel monkey [n = 50], and red spider monkey [n = 72]), from across Costa Rica. Three Plasmodium species were detected in all primate species (P. falciparum, P. malariae/P. brasilianum, and P. vivax). Overall, the infection prevalence was 8.9%, but each Plasmodium species ranged 2.1–3.4%. The niche model approach showed that the Pacific and the Atlantic coastal regions of Costa Rica presented suitable climatic conditions for parasite infections. However, the central pacific coast has a more trustable prediction for malaria in primates. Conclusions The results indicate that the regions with higher suitability for Plasmodium transmission in NWP coincide with regions where most human cases have been reported. These regions were also previously identified as areas with high suitability for vector species, suggesting that enzootic and epizootic cycles occur.

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“…2019; Castaño‐Quintero et al . 2020), particularly when working with fossil taxa (e.g. Waterson et al .…”

Section: Methodsmentioning

confidence: 99%

An Appalachian population of neochoristoderes (Diapsida, Choristodera) elucidated using fossil evidence and ecological niche modelling

et al. 2021

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Four neochoristoderan vertebral centra are described from the latest Cretaceous of New Jersey, USA. One specimen was recovered from the basal transgressive lag of the Navesink Formation in the area of Holmdel, New Jersey, and two others were recovered nearby and probably were derived from the same horizon. The fourth was recovered from the Marshalltown sequence in the vicinity of the Ellisdale Dinosaur Site. These vertebrae expand the geographical range of Late Cretaceous neochoristoderes in North America by over 2000 km further east, and represent the first neochoristoderan remains from the Atlantic coastal plain. To discern whether neochoristodere remains are to be expected in New Jersey, and elucidate why neochoristoderes are apparently so rare in Appalachia, we implemented ecological niche modelling to predict the range of suitable habitat for Champsosaurus, the only known genus of Late Cretaceous neochoristoderes. We found that in Appalachia, the ideal habitat of Champsosaurus probably existed slightly further north and west than the Atlantic coastal plain, and New Jersey is probably on or near the margin of this suitable habitat space. These results suggest that the occurrence of neochoristoderes in New Jersey is consistent with the habitat requirements of known Late Cretaceous neochoristoderes. These vertebrae may therefore represent the southern margin of a population of neochoristoderes that lived further inland, where latest Cretaceous sediments are not preserved. The continued recovery of material from Late Cretaceous deposits along the Atlantic coast, and review of existing collections, is encouraged to clarify the true distribution of neochoristoderes in Appalachia.

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Supraspecific units in correlative niche modeling improves the prediction of geographic potential of biological invasions

Cited by 21 publications

References 61 publications

Mahalanobis distances for ecological niche modelling and outlier detection: implications of sample size, error, and bias for selecting and parameterising a multivariate location and scatter method

Mahalanobis distances for ecological niche modelling and outlier detection: implications of sample size, error, and bias for selecting and parameterising a multivariate location and scatter method

Presence and potential distribution of malaria-infected New World primates of Costa Rica

An Appalachian population of neochoristoderes (Diapsida, Choristodera) elucidated using fossil evidence and ecological niche modelling

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