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opencc-by-4.0Jan 2021View details →

Ecological niche modeling and first records from Namibia and Zimbabwe validate the amphi-equatorial distribution of Byrsinus pseudosyriacus (Hemiptera: Cydnidae) - Supplementary data

Byrsinus pseudosyriacus (Linnavuori, 1977), the most widely distributed Afrotropical species of the genus Byrsinus Fieber, 1860 known hitherto only from the Sudano-Eremian area is for the first time reported in two countries south of the Equator. The species potential distribution map was generated using the ecological niche modelling (ENM) methods that allowed this species to be regarded as amphi-equatorial in distribution.

opencc-zeroDec 2018View details →

Data from: A new null model approach to quantify performance and significance for ecological niche models of species distributions

Aim: Ecological niche modelling requires robust estimation of model performance and significance, but common evaluation approaches often yield biased estimates. Null models provide a solution but are rarely used in this field. We implemented an important modification to existing null-model tests, evaluating null models with the same withheld records that were used to evaluate the real model. We built and evaluated models across a range of modelling scenarios and for various performance measures using the algorithm Maxent and the monk parakeet (Myiopsitta monachus). Location: Native range in Southern America and global invasions predominantly in North/Central America and Europe Methods: We tested the ability of models built under 15 scenarios (five sets of calibration records and three settings that varied the level of model complexity) to predict spatially independent evaluation data in the invaded range (in effect, testing the models under spatial transfer). We quantified performance with measures of discriminatory ability and overfitting based on AUC and the omission error rate. We estimated null distributions of these measures and calculated effect size and significance. We determined how these estimates varied across modelling scenarios, comparing with two tests existing in the literature. Results: Performance varied starkly across modelling scenarios. As expected, the measures of overfitting agreed with each other and provided different information than that of discriminatory ability. However, high performance per se did not show strong association with high effect size and significance. Main Conclusions: Ecological niche models should be assessed with measures of effect size and significance based on appropriate null distributions, in contrast to several approaches existing in the literature. The proposed approach using independent evaluation data, implemented with our accompanying code, allows such estimates for either the same or a different region/time period, and it merits use and continued development.

opencc-by-4.0Jul 2023View details →

Supplementary material for "Analyzing potential niche shifts in alien pairs of mantis species (Insecta, Mantodea), with comments on the current taxonomic and ecological knowledge"

###Supplementary data for "Analyzing potential niche shifts in alien pairs of mantis species (Insecta, Mantodea), with comments on the current taxonomic and ecological knowledge"angui_intra: intra-species analyses for Tenodera angustipennis, with both complete and trimmed dataset.contrhierodula: intra-species analyses for the Hierodula species with controversial status (H. transcaucasica/H. tenuidentata). It includes analyses between H. transcaucasica and H. tenuidentata sensu stricto and the populations treated as separated species.hierodula_europe: inter-species analysis with the two Hierodula present in Europe.kendall: scripts and table used for calculating Kendall's rank correlation.pate_intra: intra-species analyses for Hierodula patellifera, with both complete and trimmed (no India, Nepal and Philippines points) datasets. There is also the analyses between Asian distribution and India, Nepal and Philippines pointssinensis_intra: intra-species analyses for Tenodera sinesis, with both complete and trimmed datasets.tenodera_europe: inter-species analysis with the two Tenodera present in North America, with both complete and trimmed datasets.####NOTEI did not include the raw presence points (the elaborated ones are together with the values in a csv file per each folder) and the wordlclim variables. For the latter, you can get them from the WorldClim website. If you want the raw presence points, I will give them on requestWARNING: AN ITALIAN LOCALE HAS BEEN USED FOR THIS ANALYSES; IF YOU HAVE ANY FORMAT ISSUE WITH THE CSV, CONSIDER USING THIS FOR IMPORTING INTO R: read_csv("namefile.csv", locale = locale(decimal_mark = ",", grouping_mark = ".")) IF THAT DOES NOT WORK, PLEASE CONTACT ME

opencc-zeroApr 2024View details →

Paleobiogeographic insights gained from ecological niche models: progress and continued challenges

The spatial distribution of individuals within ecological assemblages, and their associated traits and behaviors, are key determinants of ecosystem structure and function. Consequently, determining the spatial distribution of species, and how distributions influence patterns of species richness across ecosystems today and in the past, helps us understand what factors act as fundamental controls on biodiversity. Here, we explore how ecological niche modeling has contributed to understanding the spatiotemporal distribution of past biodiversity, and past ecological and evolutionary processes. We first perform a semi-quantitative literature review to capture studies that applied ecological niche models (ENMs) in the past, identifying 668 studies. We coded each study according to focal taxonomic groups and whether and how the study used fossil evidence, whether it relied on evidence or methods in addition to ENMs, and spatial scale and temporal intervals. We used trends in publication patterns across categories to anchor discussion of recent technical advances in niche modeling, focusing on paleobiogeographic ENM applications. We then explored the contributions of ENMs to paleobiogeography, with a particular focus on examining patterns and associated drivers of range dynamics; phylogeography and within-lineage dynamics; macroevolutionary patterns and processes, including niche change, speciation, and extinction; drivers of community assembly; and conservation paleobiogeography. Overall, ENMs are powerful tools for elucidating paleobiogeographic patterns. ENMs are most commonly used to understand Quaternary dynamics, but an increasing number of studies use ENMs to gain important insight into both ecological and evolutionary processes in pre-Quaternary times. Deeper integration with traits and phylogenies may further extend those insights.

Fig. 68 in The Phanaeus tridens species group (Coleoptera: Scarabaeoidea): a dung beetle group with genital morphological stasis but a changing ecological niche

Fig. 68. Predicted distribution of P. eximius Bates, 1887.

Fig. 66 in The Phanaeus tridens species group (Coleoptera: Scarabaeoidea): a dung beetle group with genital morphological stasis but a changing ecological niche

Fig. 66. Predicted distribution of P. furiosus Bates, 1887 and P. pseudofurcosus Balthasar, 1939.

Figs 8–9. Phanaeus balthasari Arnaud, 2001, stat. rev. 8 in The Phanaeus tridens species group (Coleoptera: Scarabaeoidea): a dung beetle group with genital morphological stasis but a changing ecological niche

Figs 8–9. Phanaeus balthasari Arnaud, 2001, stat. rev. 8 – male green phase; 9 – holotype

Fig. 67 in The Phanaeus tridens species group (Coleoptera: Scarabaeoidea): a dung beetle group with genital morphological stasis but a changing ecological niche

Fig. 67. Predicted distribution of P. nimrod Harold, 1863 and P. victoriae Moctezuma sp. nov.

opencc-by-4.0Mar 2015View details →

Fig. 5 in Using Ecological Niche Modeling For Biodiversity Conservation Guidance In The Western Podillya (Ukraine): Amphibians

Fig. 5. Summarized species richness map (see text for explanation).

opencc-zeroMay 2022View details →

Underlying microevolutionary processes parallel macroevolutionary patterns in ancient Neotropical Mountains - Ecological Niche Modeling and Corridors files

Aim Ancient climatic fluctuations are invoked as the main driving force that generates the astonishing biodiversity in ancient mountains. As a result, endemism and spatial turnover are usually high and few species are widespread among entire mountain ranges, precluding the understanding of origins of macroevolutionary patterns. Here, we used a species endemic to, but widespread in, one of the most species-rich ancient mountains on the globe to test how environmental changes acted on them and how their macroevolutionary patterns were shaped. Location Espinhaço Range, Eastern Brazil. Taxon Vriesea oligantha species complex (Bromeliaceae). Methods We compiled data for plastidial regions and nuclear microsatellites to assess genetic diversity, population structure, migration rates and phylogenetic relationships. Using temperature and precipitation variables we modeled suitable areas for the present and the past, estimating corridors between isolated populations. We also implemented Bayesian demographic analyses to estimate ancient populations dynamics. Finally, we tested if population structure is driven by isolation by environment or by distance using a Bayesian modeling approach. Results Our results showed that the intraspecific divergence events of V. oligantha are older than those associated with the latest Pleistocene climatic oscillations, supporting the view that Quaternary climatic fluctuations are key components for understanding its population differentiation processes. Species distribution modeling estimated corridors between populations in the past, as also shown in the demographic analyses, depicting a major spatial reorganization during colder climates. Besides, the high genetic structure estimated results from both models of isolation by distance and by environment. Main conclusions V. oligantha is a remarkable model to test the effects of climatic oscillations over the biological community, since this species originated in the early-Pleistocene, prevailing over several cycles of climatic fluctuations until today. The estimated demographic dynamics of V. oligantha agrees with the species-pump mechanism, suggesting it as the main cause of speciation within the Espinhaço Range. Moreover, the phylogeographic patterns of V. oligantha reflect previously recognized spatial and temporal macroevolutionary patterns in the Espinhaço Range, providing insights into how microevolutionary processes may have given rise to this astonishing mountain biodiversity.

opencc-zeroJun 2022View details →

Datafile - In situ adaptation and ecological release facilitate the occupied niche expansion of an invasive Madagascan day gecko in Florida

Aim To investigate whether the frequently advocated climate-matching species distribution modelling approach could predict the well-characterized colonization of Florida by the Madagascar giant day gecko Phelsuma grandis. Location Madagascar and Florida, USA. Methods To determine the climatic conditions associated with the native range of P. grandis, we used native-range presence-only records and Bioclim climatic data to build a Maxent species distribution model and projected the climatic thresholds of the native range onto Florida. We then built an analogous model using Florida presence-only data and projected it onto Madagascar. We constructed a third model using native-range presences for both P. grandis and the closely related parapatric species P. kochi. Results Despite performing well within the native range, our Madagascar Bioclim model failed to identify suitable climatic habitat currently occupied by P. grandis in Florida. The model constructed using Florida presences also failed to reflect the distribution in Madagascar by over-predicting distribution, especially in western areas occupied by P. kochi. The model built using the combined P. kochi/P. grandis dataset modestly improved the prediction of the range of P. grandis in Florida, thereby implying competitive exclusion of P. grandis by P. kochi from habitat within the former's fundamental niche. These findings thus suggest ecological release of P. grandis in Florida. However, because ecological release cannot fully explain the divergent occupied niches of P. grandis in Madagascar versus Florida, our findings also demonstrate some degree of in situ adaptation in Florida. Main conclusions Our models suggest that the discrepancy between the predicted and observed range of P. grandis in Florida is attributable to either in situ adaptation by P. grandis within Florida, or a combination of such in situ adaptation and competition with P. kochi in Madagascar. Our study demonstrates that climate-matching species distribution models can severely underpredict the establishment risk posed by non-native herpetofauna.

opencc-zeroJun 2024View details →

Data from: Too much of a good thing? Supplementing current species observations with fossil data to assess climate change vulnerability via ecological niche models

Ecological niche models (ENMs) are a powerful tool in ecological research and conservation planning. Since ENMs provide probability maps of suitable areas under environmental change, they may assist in designing conservation actions and addressing conservation priorities. However, ENMs are usually implemented by learning the species climatic preferences from their current geographic distribution, which leaves them vulnerable to the issue of niche truncation issues, as if comes with non-climatic limits to the current species distribution posed by e.g. anthropic activities and settlements, and is bound to assume that species are at equilibrium with their environments. These problems might be alleviated by the inclusion of fossil occurrences, which refer to moments during species evolution when such limits were absent, and a larger fraction of the species fundamental niche was probably explored. Here, we combined current and fossil occurrence data for 38 medium-large mammal species of conservation concern to assess the influence of the fossil record on ENM predictions under future climate change scenarios. We found that ignoring or including fossil data yields consistent trends in terms of predicted range increase/decrease. Yet, although adding fossil data invariably results in increased niche width, estimates of range change magnitude improved for just one half only of the species. These results suggest that most species might be in non-equilibrium with their environment, and that the inclusion of fossil data may be crucial to the better understanding of species climatic requirements, hence for designing effective conservation strategies.

opencc-zeroJul 2024View details →

Modeling data and R code for Chrysodeixis chalcites ecological niche

The golden twin-spot moth, Chrysodeixis chalcites Esper (Lepidoptera: Noctuidae), is a polyphagous, polyvoltine crop pest occurring natively from northern Europe to Mediterranean Africa and the Canary Islands. Larvae feed on a wide variety of naturally occurring plants as well as soybean and other legume crops, short staple cotton, tomato, potato, peppers, tobacco, and banana. Chrysodeixis chalcites has been recorded in agricultural lands in the Ontario peninsula in eastern Canada and in northern counties of Indiana, USA. Given the strong potential for C. chalcites to invade USA crop lands, it is important to identify environments most likely to sustain growing populations of this pest. Though C. chalcites is native to Europe and North Africa, it has invaded sub-Saharan Africa. Using occurrence data form the native and invaded ranges, and environmental predictors including bioclimatic conditions and human disturbance, we trained three ecological niche models to estimate an ensemble prediction of environmental suitability in the contiguous US. Because human impact is potentially a confounding predictor, models were trained both with and without it. High environmental suitability was projected for the Atlantic coast from New England to Florida, the Gulf coast, the lower Midwest, and the Pacific coast and Central Valley of California.

opencc-by-4.0Apr 2018View details →

Figure 7 in Analysis of the spatial organization of Vallonia pulchella (Muller, 1774) ecological niche in Technosols (Nikopol manganese ore basin, Ukraine)

Figure 7. Results of MADIFA-mapping of Vallonia pulchella ecological niche.

opencc-zeroSep 2021View details →

Predicting species abundance by implementing the ecological niche theory

Species are not uniformly distributed across the landscape. For every species, there should be few favoured sites where abundance is high and many other sites of lower suitability where abundance is low. Consequently, local abundance could be thought of as a natural expression of species response to local conditions. The correlation between abundance and environmental suitability has been well documented, and a recent meta-analysis has suggested that this relationship could be a generality. Despite the importance and potential implication of the abundance-suitability relationship, its predictive power for meaningful extrapolations has been surprisingly poorly explored. In this study, we showed how a highly predictable trend can be extracted from the abundance-suitability relationship, accurately predicting the variation in species abundance at a high spatial resolution. We produced high-quality environmental suitability estimations for 50 endemic species to the Australian Wet Tropics. Environmental suitability derived from species distribution models was related to observed abundance estimated using data from 29 years of uninterrupted monitoring effort. We used the fitted relationship to accurately predict abundance at a fine scale across the species range. Our results showed that the abundance-suitability relationship was strong for endemic species in the Australian Wet Tropics. The predictive power of our models was high, explaining, on average, 55% of the deviance across taxa. Despite interspecific variation in the strength of the abundance-suitability relationship associated with potential intrinsic estimation biases, our approach provides a powerful tool for predicting abundance across the species range at a fine scale. The potential for robust abundance predictions from occurrence-based species distribution models shown in this study are numerous, and it could have a significant impact in enhancing species conservation and management decisions.

opencc-zeroJan 2023View details →

Ecological niches of epiphyllous bryophytes along afrotropical elevation gradient

Understanding multiple environmental drivers governing tropical organisms' distribution and ecological niches is crucial for predicting their responses to ongoing rapid deforestation. While macroclimatic effects via energy and water availability are well predicted, less is known about locally modulating factors such as canopy structure, light and edaphic conditions. Here we show that minimum temperatures and ambient humidity drive the abundance and richness of leaf-inhabiting epiphyllous bryophytes across a 4-km elevation gradient on Mount Cameroon, West Africa, separating epiphyll-rich rainforests (0–2200 m) from epihyll-poor fire-driven afromontane savanna (2300–4000 m). However, local factors contribute more than half to the total abundance and richness variation, either directly (light) or indirectly (edaphic conditions) via their effects on host plant composition. The most abundant epiphyllous communities occur in vertically stratified upland rainforests between 600 and 1100 m elevation, where N-fixing tree legumes dominate. Their canopy is relatively sparse, due to nutrient-poor soils leached by high rainfall, leaving room for the development of diverse subcanopy tree and understory shrub and herb layers with epiphyll-rich communities. Vertically homogenous lowland rainforests on fertile soils below 500 m, with dense overstory and shaded and species-poor understory, have less developed epiphylls, as do seasonally dry montane forests between 2000 and 2300 m, or elephant fragmented forests between 1200 and 1600 m. We conclude that high temperature and humidity together with a vertically stratified canopy support epiphylls, whereas precipitation seasonality, disturbed vegetation with unstable microclimate, or dense, unstratified canopy discourage the development of epiphyllous communities. Our study illustrates that ecological niches of epiphyllous bryophytes are shaped by a complex interplay of multiple drivers, knowledge of which is essential for more realistic predictions of the impacts of current accelerated habitat loss on species distribution and diversity changes in the tropics.

opencc-zeroMay 2023View details →

Data from: Integrating ecological niche and hydrological connectivity models to assess the impacts of hydropower plants on an endemic and imperiled freshwater turtle

We built this dataset to assess the impacts of hydropower plants on the distribution of an endemic and imperiled freshwater turtle with very unique ecological requirements, the Williams' side-necked turtle (Phrynops williamsi). To prevent and mitigate impacts, we prioritized sites for species conservation by classifying planned HPP locations according to their predicted adverse effects on species distribution. The dataset has two files: i) species occurrence records and ii) hydropower plant data. The first dataset was fully built by the authors and the second was modified from the Brazilian Electricity Regulatory Agency (ANEEL) georeferenced data system.

opencc-zeroJun 2023View details →

Fine-scale intraspecific niche partitioning in a highly mobile, marine megafauna species: implications for ecology and conservation

A species may partition its realized ecological niche along bionomic and/or scenopoetic axes due to intraspecific competition for limited resources. How partitioning manifests depends on resource needs and availability by and for the partitioning groups. Here we demonstrate the utility of analyzing short- and long-term stable carbon and nitrogen isotope ratios from imperiled marine megafauna to elucidate realized niche partitioning in these species. We captured 113 loggerhead (Caretta caretta) sea turtles at a high-use area near Crystal River, Florida, between 2016–2022, comprising 53 subadults, 10 adult males, and 50 adult females. Isotopic analyses indicated that loggerheads partition their realized ecological niche by life stage, along a scenopoetic axis. Most adults likely forage and reside in shallow areas of the study site, with most subadults displaying habitat switching between deeper locations to forage and shallower locations to rest. Some subadults, like adults, also forage and reside in shallow areas, and may display behaviors to avoid intraspecific competition. Analysis of stable isotopes with different turnover rates was critical for this characterization of intraspecific niche partitioning in loggerhead turtles, which has direct implications for ongoing research and conservation efforts for this and other imperiled species.

opencc-zeroJun 2023View details →

Organismal effects of heat in a fixed ecological niche: Implications on the role of behavioral buffering in our changing world

Increasingly frequent and intense heatwaves generate new challenges for many organisms. Our understanding of the ecological predictors of thermal vulnerability is improving, yet, at least in endotherms, we are still only beginning to understand one critical component of predicting resilience: exactly how do wild animals cope with sub-lethal heat? In wild endotherms, most prior work focuses on one or a few traits, leaving uncertainty about organismal consequences of heatwaves. Here, we experimentally generated a 2.8 °C heatwave for free-living nestling tree swallows (Tachycineta bicolor). Over a week-long period coinciding with the peak of post-natal growth, we quantified a suite of traits to test the hypotheses that (a) behavioral or (b) physiological responses may be sufficient for coping with inescapable heat. Heat-exposed nestlings increased panting and decreased huddling, but treatment effects on panting dissipated over time, even though heat-induced temperatures remained elevated. Physiologically, we found no effects of heat on: gene expression of three heat shock proteins in blood, muscle, and three brain regions; secretion of circulating corticosterone at baseline or in response to handling; and telomere length. Moreover, heat had a positive effect on growth and a marginal, but not significant, positive effect on subsequent recruitment. These results suggest that nestlings were generally buffered from deleterious effects of heat, with one exception: heat-exposed nestlings exhibited lower gene expression for superoxide dismutase, a key antioxidant defense. Despite this one apparent cost, our thorough organismal investigation indicates general resilience to a heatwave that may, in part, stem from behavioral buffering and acclimation. Our approach provides a mechanistic framework that we hope will improve understanding of species persistence in the face of climate change.