scholarly journals Estimating the fundamental niche: accounting for the uneven availability of existing climates

2021 ◽  
Author(s):  
L. Jiménez ◽  
J. Soberón
Keyword(s):  
Environmental Conditions ◽  
Ecological Niche Modeling ◽  
Worked Examples ◽  
Sampling Distribution ◽  
Normal Model ◽  
Native Range ◽  
Realized Niche ◽  
Fundamental Niche ◽  
Presence Data ◽  
Dispersal Abilities

AbstractIn the last years, studies that question important conceptual and methodological aspects in the field of ecological niche modeling (and species distribution modeling) have cast doubts on the validity of the existing methodologies. Particularly, it has been broadly discussed whether it is possible to estimate the fundamental niche of a species using presence data. Although it has being identified that the main limitation is that presence data come from the realized niche, which is a subset of the fundamental niche, most of the existing methods lack the ability to overcome it, and then, they fit objects that are more similar to the realized niche. To overcome this limitation, we propose to use the region that is accessible to the species (based on its dispersal abilities) to determine a sampling distribution in environmental space that allow us to quantify the likelihood of observing a particular environmental combination in a sample of presence points. We incorporate this sampling distribution into a multivariate normal model (Mahalanobis model) by creating a weight function that modifies the probabilities of observing an environmental combination in a sample of presences as a way to account for the uneven availability of environmental conditions. We show that the parameters of the modified, weighted-normal model can be approximated by a maximum likelihood estimation approach, and used to draw ellipsoids (confidence regions) that represent the shape of the fundamental niche of the species. We illustrate the application of our model with two worked examples: (i) using presence points of an invasive species and an accessible area that includes only its native range, to evaluate whether the fitted model predicts confirmed establishments of the species outside its native range, and (ii) using presence data of closely related species with known accessible areas to exhibit how the different dispersal abilities of the species constraint a classic Mahalanobis model. Taking into account the distribution of environmental conditions that are accessible to the species indeed affected the estimation of the ellipsoids used to model their fundamental niches.

scholarly journals Plant population and soil origin effects on rhizosphere nematode community composition of a range-expanding plant species and a native congener

Oecologia ◽  
2020 ◽  
Vol 194 (1-2) ◽  
pp. 237-250
Author(s):  
Rutger A. Wilschut ◽  
Kim J. H. Magnée ◽  
S. Geisen ◽  
W. H. van der Putten ◽  
O. Kostenko
Keyword(s):  
Plant Species ◽  
Plant Population ◽  
Enemy Release ◽  
Native Range ◽  
Centaurea Stoebe ◽  
Plant Populations ◽  
Range Theory ◽  
Dispersal Abilities ◽  
Population Effects ◽  
Root Feeding

Abstract Climate change causes species range expansions to higher latitudes and altitudes. It is expected that, due to differences in dispersal abilities between plants and soil biota, range-expanding plant species will become associated with a partly new belowground community in their expanded range. Theory on biological invasions predicts that outside their native range, range-expanding plant species may be released from specialist natural enemies, leading to the evolution of enhanced defence against generalist enemies. Here we tested the hypothesis that expanded range populations of the range-expanding plant species Centaurea stoebe accumulate fewer root-feeding nematodes than populations from the original range. Moreover, we examined whether Centaurea stoebe accumulates fewer root-feeding nematodes in expanded range soil than in original range soil. We grew plants from three expanded range and three original range populations of C. stoebe in soil from the original and from the new range. We compared nematode communities of C. stoebe with those of C. jacea, a congeneric species native to both ranges. Our results show that expanded range populations of C. stoebe did not accumulate fewer root-feeding nematodes than populations from the original range, but that C. stoebe, unlike C. jacea, accumulated fewest root-feeding nematodes in expanded range soil. Moreover, when we examined other nematode feeding groups, we found intra-specific plant population effects on all these groups. We conclude that range-expanding plant populations from the expanded range were not better defended against root-feeding nematodes than populations from the original range, but that C. stoebe might experience partial belowground enemy release.

scholarly journals Ecological niche modeling of Babesia sp infection in wildlife experimentally evaluated in questing Ixodes ricinus.

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Stefania Zanet ◽  
Ezio Ferroglio ◽  
Elena Battisti ◽  
Paolo Tizzani
Keyword(s):  
Ecological Niche Modeling ◽  
Roe Deer ◽  
Infection Prevalence ◽  
Tick Abundance ◽  
Preventive Actions ◽  
Presence Data ◽  
Alpine Chamois ◽  
Suitable Area ◽  
Reservoir Hosts ◽  
Babesia Spp

Tick-borne diseases and especially protozoa of the genus Babesia, are gaining increasing attention as emerging zoonotic pathogens. Zoonotic species like B. venatorum and B. microti have wild animals as main reservoir hosts. We propose a habitat suitability model for Babesia spp., as tool for institutions and policy makes to better understand the entity of Babesia presence, to improve diagnostic awareness and to optimize screening and preventive actions. The probability of presence of Babesia spp. was estimated using as presence data, wild ruminants positive by PCR to Babesia spp. which were correlated to environmental factors that can favor or limit vector and host availability. We developed three separate models to discriminate the different roles of Red deer and Roe deer and Alpine chamois in Babesia spp. epidemiology. A comprehensive model using all presence data from all ungulates species  was also developed. The overall suitable area for Babesia spp. in this simulation is of 3723 km2, which correspond to 15.51% of the background regional territory. The model developed was empirically validated assessing tick abundance in randomly chosen areas classified by the model as moderately or highly suitable for Babesia spp. Collected ticks were tested by PCR for Babesia spp. to confirm model predictions as infection prevalence with Babesia spp. was significantly higher in areas predicted as highly suitable compared to those classified by the model as moderately suitable for Babesia spp.  (X2=5.05 p<0.05, Odds Ratio OR= 2.12 CI95% 1.1-4.1).

scholarly journals Selective Native Plants of Oklahoma and Nearby States That Can Be a Nuisance to Occasionally Invasive

2021 ◽  
pp. 1-11
Author(s):  
Michael A. Schnelle
Keyword(s):  
Built Environment ◽  
Environmental Conditions ◽  
Prescribed Burning ◽  
Native Plants ◽  
Control Measures ◽  
Native Range ◽  
Native Flora ◽  
Sea Oats ◽  
Cornus Drummondii ◽  
Ornamental Species

Four ornamental species, lyreleaf salvia (Salvia lyrata), roughleaf dogwood (Cornus drummondii), northern sea oats (Chasmanthium latifolium), and cholla (Cylindropuntia imbricata), are all native to Oklahoma and nearby states. They all possess ornamental attributes and range from widespread to niche crops in the nursery industry and are also cultivated for their utilitarian, herbal, and miscellaneous merits. Their allure to customers and their ability to thrive in a myriad of environments is a major impetus for commercial growers and retailers to carry these species. However, their extraordinary ability to adapt to a plethora of environmental conditions, in the built environment or in their native range, also enables them to often outcompete neighboring flora. Their predisposition to be opportunistic, and ability to grow in challenging locations, sometimes results in their becoming a nuisance or even invasive (i.e., capable of displacing other native flora or fauna). Plants featured are described for their marketable attributes but also reviewed for control measures (e.g., herbicides, prescribed burning, improved grazing practices) when they grow in an aggressive manner.

scholarly journals Modeling Potential Habitat for Amblyomma Tick Species in California

Insects ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 201 ◽  
Author(s):  
Emily L. Pascoe ◽  
Matteo Marcantonio ◽  
Cyril Caminade ◽  
Janet E. Foley
Keyword(s):  
Tick Species ◽  
Ecological Niche Modeling ◽  
Amblyomma Americanum ◽  
Ecological Diversity ◽  
Amblyomma Cajennense ◽  
Potential Habitat ◽  
Online Databases ◽  
Presence Data ◽  
Amblyomma Ticks ◽  
Maxent Algorithm

The Amblyomma genus of ticks comprises species that are aggressive human biters and vectors of pathogens. Numerous species in the genus are undergoing rapid range expansion. Amblyomma ticks have occasionally been introduced into California, but as yet, no established populations have been reported in the state. Because California has high ecological diversity and is a transport hub for potentially parasitized humans and animals, the risk of future Amblyomma establishment may be high. We used ecological niche modeling to predict areas in California suitable for four tick species that pose high risk to humans: Amblyomma americanum, Amblyomma maculatum, Amblyomma cajennense and Amblyomma mixtum. We collected presence data in the Americas for each species from the published literature and online databases. Twenty-three climatic and ecological variables were used in a MaxEnt algorithm to predict the distribution of each species. The minimum temperature of the coldest month was an important predictor for all four species due to high mortality of Amblyomma at low temperatures. Areas in California appear to be ecologically suitable for A. americanum, A. maculatum, and A. cajennense, but not A. mixtum. These findings could inform targeted surveillance prior to an invasion event, to allow mitigation actions to be quickly implemented.

scholarly journals Spatially Correlated Time Series and Ecological Niche Analysis of Cutaneous Leishmaniasis in Afghanistan

2016 ◽  
Author(s):  
Oyelola A. Adegboye ◽  
Majeed Adegboye
Keyword(s):  
Time Series ◽  
Cutaneous Leishmaniasis ◽  
Spatial Data ◽  
Ecological Niche ◽  
Ecological Niche Modeling ◽  
Multivariate Time Series ◽  
Steady Increase ◽  
Niche Modelling ◽  
Spatially Correlated ◽  
Presence Data

Leishmaniasis is the third most common vector-borne disease and a very important protozoan infection. Cutaneous leishmaniasis is one of the most common types of leishmaniasis infectious diseases with up to 2 million occurrences of new cases each year worldwide. A dynamic transmission multivariate time series model was applied to the data to account for overdispersion and evaluate the effects of three environmental layers as well as seasonality in the data. Furthermore, ecological niche modeling was used to investigate the geographical suitable conditions for cutaneous leishmaniasis using temperature, precipitation and altitude as environmental layers, together with the leishmaniasis presence data. A retrospective analysis of the cutaneous leishmaniasis spatial data in Afghanistan between 2003 and 2009 indicates a steady increase from 2003 to 2007, a small decrease in 2008, then another increase in 2009. An upward trend and regularly repeating patterns of highs and lows was observed related to the months of the year which suggests seasonality effect in the data. Two peaks were observed in the disease occurrence-- January to March and September to December -- which coincide with the cold period. Ecological niche modelling indicates that precipitation has the greatest contribution to the potential distribution of leishmaniasis.

scholarly journals Akaike information criteria and predictive geographical accuracy are not related in ecological niche modeling

2018 ◽  
Author(s):  
Julián A. Velasco ◽  
Constantino Gonzales-Salazar
Keyword(s):  
Ecological Niche ◽  
Ecological Niche Modeling ◽  
Information Criteria ◽  
Niche Modeling ◽  
Model Complexity ◽  
Classification Rate ◽  
Validation Metrics ◽  
Akaike Information Criteria ◽  
Presence Data ◽  
Virtual Species

AbstractAimEcological niche modeling (ENM) is an approach used to estimate species‘ presence given its environmental preferences. Model complexity in ENMs has increasingly gained relevance in the last years. In particular, in Maxent algorithm is captured using the Akaike Information Criteria (AIC) based on the number of parameters and likelihoods of continuous raw outputs. However, it is not clear whether best-selected models using AIC are the models with the highest classification rate of correct presences and absences. Here, we test for a link between model complexity and accuracy of geographical predictions of Maxent models.InnovationWe created a set of virtual species and generate true geographical predictions for each one. We build a set of Maxent models using presence data from each virtual species with different regularization and features schemes. We compared AICc values for each model with the scores of standard validation metrics (e.g., Kappa, TSS) and with the number of pixels correctly predicted as presences, absences or both.Main ConclusionsWe found that binary predictions (i.e., presence-absence maps) selected as best models for AIC tend to predict incorrectly sites as presences and absences using independent datasets. We suggest that information criteria as AIC should be avoided when users are interested in binary predictions. Future applications that capture model complexity in ENM applications should be evaluated using standard validation metrics.

scholarly journals Cryptococcus neoformans Mates on Pigeon Guano: Implications for the Realized Ecological Niche and Globalization

2007 ◽  
Vol 6 (6) ◽  
pp. 949-959 ◽  
Author(s):  
Kirsten Nielsen ◽  
Anna L. De Obaldia ◽  
Joseph Heitman
Keyword(s):  
Cryptococcus Neoformans ◽  
Growth And Development ◽  
Ecological Niche ◽  
Ecological Niches ◽  
Brown Pigment ◽  
Pathogenic Yeast ◽  
Realized Niche ◽  
Fundamental Niche ◽  
Physical Conditions ◽  
Resource Requirements

ABSTRACT The ecological niche that a species can occupy is determined by its resource requirements and the physical conditions necessary for survival. The niche to which an organism is most highly adapted is the realized niche, whereas the complete range of habitats that an organism can occupy represents the fundamental niche. The growth and development of Cryptococcus neoformans and Cryptococcus gattii on pigeon guano were examined to determine whether these two species occupy the same or different ecological niches. C. neoformans is a cosmopolitan pathogenic yeast that infects predominantly immunocompromised individuals, exists in two varieties (grubii [serotype A] and neoformans [serotype D]), and is commonly isolated from pigeon guano worldwide. By contrast, C. gattii often infects immunocompetent individuals and is associated with geographically restricted environments, most notably, eucalyptus trees. Pigeon guano supported the growth of both species, and a brown pigment related to melanin, a key virulence factor, was produced. C. neoformans exhibited prolific mating on pigeon guano, whereas C. gattii did not. The observations that C. neoformans completes the life cycle on pigeon guano but that C. gattii does not indicates that pigeon guano could represent the realized ecological niche for C. neoformans. Because C. gattii grows on pigeon guano but cannot sexually reproduce, pigeon guano represents a fundamental but not a realized niche for C. gattii. Based on these studies, we hypothesize that an ancestral Cryptococcus strain gained the ability to sexually reproduce in pigeon guano and then swept the globe.

scholarly journals Biogeografía del tomate Solanum lycopersicum var. cerasiforme (Solanaceae) en su centro de origen (sur de América) y de domesticación (México)

2019 ◽  
Vol 67 (4) ◽  
Author(s):  
Gino Delices ◽  
Raúl Otto ◽  
Rosalia Nuñez Pastrana ◽  
Pablo Andrés Meza ◽  
Ricardo Serna-Lagunez ◽  
...  
Keyword(s):  
South America ◽  
Solanum Lycopersicum ◽  
Environmental Conditions ◽  
Ecological Niche ◽  
Ecological Niche Modeling ◽  
New Records ◽  
The State ◽  
Niche Modeling ◽  
Climatic Variables ◽  
Tomato Production

The understanding geography and ecology role in the distribution of Solanum lycopersicum var. cerasiforme is essential for knowledge of areas with potential for tomato production and conservation. In the present work, we analyzed the environmental conditions of the center of origin of the species in South America and we compared them with records in Mexico, particularly in the state of Veracruz, tomato domestication region. We used eight climatic variables predictors and the latitude and longitude data of the species collections registered in literature and database to run two models, the first one for the south of America and the second one for Mexico. We evaluated the models by using the partial ROC method; we conducted a niche similarity and equivalency test to compare both models. We carried out a fieldwork to observe new records of the species and register the environmental conditions in which they growth. The main climatic variables of temperature were the most important for the ecological niche modeling of South America and the ecological niche modeling of Mexico. The models performed very well cause the partial roc test showed significant value for both models1.86 y 1.71 (p<0.0001). Based on our fieldwork, we registered 27 new records, we can find wild tomatoes between 14 and 2 100 amsl in areas with a range of temperature average 19-24 ºC and annual average precipitation 1 166-2 260 mm. Finally, we find out that there is climatic differentiation between South America and Mexico (most areas of the state of Veracruz) for the species.

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