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opencc-zeroAug 2020View details →

Genetic data improves niche model discrimination and alters the direction and magnitude of climate change forecasts

Ecological niche models (ENMs) have classically operated under the simplifying assumptions that there are no barriers to gene flow, species are genetically homogeneous (i.e., no population-specific local adaptation), and all individuals share the same niche. Yet, these assumptions are violated for most broadly distributed species. Here we incorporate genetic data from the widespread riparian tree species narrowleaf cottonwood (Populus angustifolia) to examine whether including intraspecific genetic variation can alter model performance and predictions of climate change impacts. We found that (1) P. angustifolia is differentiated into six genetic groups across its range from México to Canada, and (2) different populations occupy distinct climate niches representing unique ecotypes. Comparing model discriminatory power, (3) all genetically-informed ecological niche models (gENMs) outperformed the standard species-level ENM (3-14% increase in AUC; 1-23% increase in pROC). Furthermore, (4) gENMs predicted large differences among ecotypes in both the direction and magnitude of responses to climate change, and (5) revealed evidence of niche divergence, particularly for the Eastern Rocky Mountain ecotype. (6) Models also predicted progressively increasing fragmentation and decreasing overlap between ecotypes. Contact zones are often hotspots of diversity that are critical for supporting species' capacity to respond to present and future climate change, thus predicted reductions in connectivity among ecotypes is of conservation concern. We further examined the generality of our findings by comparing our model developed for a higher elevation Rocky Mountain species with a related desert riparian cottonwood, P. fremontii. Together our results suggest that incorporating intraspecific genetic information can improve model performance by addressing this important source of variance. gENMs bring an evolutionary perspective to niche modeling and provide a truly "adaptive management" approach to support conservation genetic management of species facing global change.

opencc-zeroDec 2020View details →

Supplementary material 1 from: Bustamante RO, Alves L, Goncalves E, Duarte M, Herrera I (2020) A classification system for predicting invasiveness using climatic niche traits and global distribution models: application to alien plant species in Chile. NeoBiota 63: 127-146. https://doi.org/10.3897/neobiota.63.50049

Table S1. Exotic species located in Quadrant 1 (see Figure 3) and impacts on biodiversity, agriculture and cattle raisng

opencc-zeroNov 2021View details →

Temporal variability is key to modelling the climatic niche

Aim: Niche-based species distribution models (SDMs) have become a ubiquitous tool in ecology and biogeography. These models relate species occurrences with the environmental conditions found at these sites. Climatic variables are the most commonly used environmental data, and are usually included in SDMs as averages of a reference period (30-50 years). In this study we analyze the impact of including inter-annual climatic variability on the estimation of species niches and predicted distributions when assessing plant demographic response to extreme climatic episodes. Location: Mediterranean basin, SE Iberian Peninsula. Methods: We first characterized species niches with inter-annual and average climate in the same environmental space. We then compare the respective capacities of climatic suitability obtained from averaged climate-based and from inter-annual variability-based niches to explain population demographic responses to extreme drought. Furthermore, we assessed the relative increase in niche size when including climatic variability for a set of Mediterranean species exhibiting a wide range of distribution areas. Results: We found that climatic suitability obtained from inter-annual variability-based niches showed higher explanatory capacity than average climate-based suitability, especially for populations living in climatically marginal conditions, although both niches quantifications significantly explained species demographic responses. In addition, species with restricted distribution ranges increased relatively more their niche space when considering climatic variability, probably because in widely distributed species spatial variability compensates for temporal variability. Main Conclusions: The common use of climatic averages when characterizing species niches could lead to underestimations of species distribution and misunderstanding of demographic behavior, with implications for conservation plans derived from SDMs, e.g. overestimations of species extinction risk under climate change, or underestimations of alien species invasion' risk. We highlight that including climatic variability in niche modelling can be particularly important when dealing with species with restricted distribution and populations at the margin of their species niche.

opencc-zeroFeb 2020View details →

Community science validates climate suitability projections from ecological niche modeling

Climate change poses an intensifying threat to many bird species, and projections of future climate suitability provide insight into how species may shift their distributions in response. Climate suitability is characterized using ecological niche models (ENMs), which correlate species occurrence data with current environmental covariates and project future distributions using the modeled relationships together with climate predictions. Despite their widespread adoption, ENMs rely on several assumptions that are rarely validated in situ and can be highly sensitive to modeling decisions, precluding their reliability in conservation decision-making. Using data from a novel, large-scale community science program, we developed dynamic occupancy models to validate near-term climate suitability projections for bluebirds and nuthatches in summer and winter. We estimated occupancy, colonization, and extinction dynamics across species' ranges in the United States in relation to projected climate suitability in the 2020s, and used a Gibbs variable selection approach to quantify evidence of species-climate relationships. We also included a Bird Conservation Region strata-level random effect to examine among-strata variation in occupancy that may be attributable to land-use and ecoregional differences. Across species and seasons, we found strong evidence that initial occupancy and colonization were positively related to 2020 climate suitability, illustrating an independent validation of projections from ENMs across a large geographic area. Random strata effects revealed that occupancy probabilities were generally higher than average in core areas and lower than average in peripheral areas of species' ranges, and served as a first step in identifying spatial patterns of occupancy from these community science data. Our findings lend much-needed support to the use of ENM projections for addressing questions about potential climate-induced changes in species' occupancy dynamics. More broadly, our work highlights the value of community scientist observations for ground-truthing projections from statistical models and for refining our understanding of the processes shaping species' distributions under a changing climate.

opencc-zeroDec 2017View details →

Data from: Intraspecific niche models for ponderosa pine (Pinus ponderosa) suggest potential variability in population-level response to climate change.

Unique responses to climate change can occur across intraspecific levels, resulting in individualistic adaptation or movement patterns among populations within a given species. Thus, the need to model potential responses among genetically distinct populations within a species is increasingly recognized. However, predictive models of future distributions are regularly fit at the species level, often because intraspecific variation is unknown or is identified only within limited sample locations. In this study, we considered the role of intraspecific variation to shape the geographic distribution of ponderosa pine (Pinus ponderosa), an ecologically and economically important tree species in North America. Morphological and genetic variation across the distribution of ponderosa pine suggest the need to model intraspecific populations: the two varieties (var. ponderosa and var. scopulorum) and several haplotype groups within each variety have been shown to occupy unique climatic niches, suggesting populations have distinct evolutionary lineages adapted to different environmental conditions. We utilized a recently-available, geographically-widespread dataset of intraspecific variation (haplotypes) for ponderosa pine and a recently-devised lineage distance modeling approach to derive additional, likely intraspecific occurrence locations. We confirmed the relative uniqueness of each haplotype-climate relationship using a niche-overlap analysis, and developed ecological niche models (ENMs) to project the distribution for two varieties and eight haplotypes under future climate forecasts. Future projections of haplotype niche distributions generally revealed greater potential range loss than predicted for the varieties. This difference may reflect intraspecific responses of distinct evolutionary lineages. However, directional trends are generally consistent across intraspecific levels, and include a loss of distributional area and an upward shift in elevation. Our results demonstrate the utility in modeling intraspecific response to changing climate and they inform management and conservation strategies, by identifying haplotypes and geographic areas that may be most at risk, or most secure, under projected climate change.

Fig. 8 in Taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis; Boraginaceae) based on morphological, population genetic and climate-edaphic niche modelling data

Fig. 8. Myosotis antarctica subsp. traillii photographs and distribution map. (a) Habit. (b, d) Rosette leaf tips: (b) adaxial and (d) abaxial sides. (c) Flower. (e) Nutlets. (f) Map of georeferenced herbarium specimens observed by J. M. Prebble (35). Whie scale bars: 2 mm; black scale bars: 1 mm. Photo credits: a, e by J. M. Prebble (a: WELT SP100487, Tiwai Point, Southland, South Island; e: WELT SP104518, cultivated ex Mason Bay, Stewart Island). b, c © Te Papa by H. M. Meudt (b: WELT SP090544, Manihi Rd, Taranaki, North Island; c: WELT SP090629, Hukanui, Gisborne, North Island; d: WELT SP090631, Waipuna, Gisborne, North Island).

Fig. 2 in Taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis; Boraginaceae) based on morphological, population genetic and climate-edaphic niche modelling data

Fig. 2. Maps of MaxEnt niche models for pygmy Myosotis in New Zealand and southern South America. (a) Myosotis glauca (light blue circles). (b) M. pygmaea (green circles). (c, h) M. "Volcanic Plateau" (grey triangles). (d) M. brevis (yellow cir-cles). (e) M. drucei (dark blue circles; excluding individuals identified as M. "Volcanic Plateau"). (f) M. drucei (dark blue circles) + M. pygmaea (green circles) + M. "Volcanic Plateau" (grey triangles) (g) M. antarctica (pink circles; Chilean locations), note scale is the same as for maps of New Zealand. a–f use models based on the nine-layer model (see Table 1), whereas g and h are based on the sevenlayer model.

Fig. 5 in Taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis; Boraginaceae) based on morphological, population genetic and climate-edaphic niche modelling data

Fig. 5. Myosotis glauca photographs and distribution map. (a) Habit. (b) Rosette leaves, adaxial and abaxial sides. (c) Calyces, left to right most to least mature. (d) Nutlets. (e) Map of georeferenced herbarium specimens observed by J. M. Prebble (16). White scale bars: 2 mm; black scale bar: 1 mm. Photo credits: all by J. M. Prebble (WELT SP093285, Nevis Valley, Otago).

Fig. 4 in Taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis; Boraginaceae) based on morphological, population genetic and climate-edaphic niche modelling data

Fig. 4. Myosotis brevis photographs and distribution map. (a) Habit. (b) Inflorescence showing cauline leaf abaxial side. (c) Inflorescence showing cauline leaf adaxial side, calyces, and flower. (d) Rosette leaf adaxial side showing colour morphs. (e) Flower. (f) Nutlet. (g) Map of georeferenced herbarium specimens observed by J. M. Prebble (25). White scale bars: 2 mm; black scale bar: 1 mm. Photo credits: a–e © Te Papa by H. M. Meudt (a: WELT SP090549, Te Ikaamaru Bay, Wellington; b, c: WELT SP090545, Ngawi, Wairarapa; d: WELT SP090543, Stent Road, Taranaki; e: WELT SP090550, Ohau Bay, Wellington); f by J. M. Prebble (WELT SP090543, cultivated ex Stent Road, Taranaki).

Fig. 7. Myosotis antarctica subsp. antarctica. Illustration reproduced from Bot. Antarct. Voy. I in Taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis; Boraginaceae) based on morphological, population genetic and climate-edaphic niche modelling data

Fig. 7. Myosotis antarctica subsp. antarctica. Illustration reproduced from Bot. Antarct. Voy. I. (Fl. Antarct.) Part I, plate 38 (Hooker 1844). Illustration by W. H. Fitch. This image is in the public domain, downloaded from the Biodiversity Heritage Library (https:// www.biodiversitylibrary.org/page/13448452#page/81/ mode/1up, accessed 8 June 2021). Draft pencil drawings for this figure are attached to the type specimen of M. antarctica (K0007878799; visible online at http:// apps.kew.org/herbcat/getImage.do?imageBarcode= K000787899, accessed 8 June 2021), which was collected by J. D. Hooker from Campbell Island.

Fig. 6 in Taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis; Boraginaceae) based on morphological, population genetic and climate-edaphic niche modelling data

Fig. 6. Myosotis antarctica subsp. antarctica photographs and distribution maps. (a, b) Habit. (c) Rosette leaves abaxial and adaxial sides. (d) Flower. (e) Nutlets. (f) Map of mainland New Zealand distribution based on georeferenced herbarium specimens observed by J. M. Prebble (163). (g) Map of Campbell Island distribution based on georeferenced herbarium specimens observed by J. M. Prebble (14). (h) Map of Chilean distribution based on georeferenced herbarium specimens observed by J. M. Prebble (2). White scale bars: 2 mm; black scale bars: 1 mm. Photo credits: a, c, e by J. M. Prebble (a: WELT SP102777, Mt Azimuth, Campbell Island; c: WELT SP093293, Port Hills, Canterbury, South Island E: WELT SP100466, cultivated ex Mt Peel, Western Nelson. South Island). b, d © Te Papa by H. M. Meudt (b: WELT SP106592, Matiri Range, Western Nelson, South Island; d: WELT SP107322, Mt Starveall, Western Nelson, South Island).

Fig. 3 in Taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis; Boraginaceae) based on morphological, population genetic and climate-edaphic niche modelling data

Fig. 3. Plots displaying (a, c) omission and commission values and (b, d) area under the receiving operating characteristic curve (AUC) for two pygmy forget-me-not taxa: (a, b) M. "Volcanic Plateau" and (c, d) M. drucei, modelled using MaxEnt and all nine environmental layers for the New Zealand extent.

Fig. 1. Maps displaying all 290 in Taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis; Boraginaceae) based on morphological, population genetic and climate-edaphic niche modelling data

Fig. 1. Maps displaying all 290 occurrence points used for Myosotis pygmy species group niche modelling (Supplementary Table S1). Maps, clockwise from top: World, New Zealand, Campbell Island, and southern South America. Colour represents a priori species: M. antarctica (pink circles); M. drucei (dark blue circles); M. pygmaea (green circles); M. brevis (yellow circles); M. glauca (light blue circles); M. "Volcanic Plateau" (grey triangles).

opencc-zeroDec 2022View details →

Worldclim 2.1 versus Worldclim 1.4: climatic niche and grid resolution affect between-version mismatches in habitat suitability models predictions across Europe

The influence of climate on the distribution of taxa has been extensively investigated in the last two decades through Habitat Suitability Models (HSMs). In this context, the Worldclim database represents an invaluable data source as it provides worldwide climate surfaces for both historical and future time horizons. Thousands of HSMs-based papers have been published taking advantage of Worldclim 1.4, the first online version of this repository. In 2017, Worldclim 2.1 was released. Here, we evaluated spatially explicit prediction mismatch at continental scale, focusing on Europe, between HSMs fitted using climate surfaces from the two Worldclim versions (between-version differences). To this aim, we simulated occurrence probability and presence-absence across Europe of four virtual species (VS) with differing climate-occurrence relationships. For each VS, we fitted HSMs upon uncorrelated bioclimatic variables derived from each Worldclim version at three grid resolutions. For each factor combination, HSMs attaining sufficient discrimination performance on spatially independent test data were projected across Europe under current conditions and various future scenarios, and importance scores of the single variables were computed. HSMs failed in accurately retrieving the simulated climate-occurrence relationships for the climate-tolerant VS and the one occurring under a narrow combination of climatic conditions. Under current climate, noticeable between-version prediction mismatch emerged across most of Europe for these two VSs, whose simulated suitability mainly depended upon diurnal or yearly variability in temperature; differently, between-version differences were more clustered toward areas showing extreme values, like mountainous massifs or southern regions, for VSs responding to average temperature and precipitation trends. Under future climate, the chosen emission scenarios and Global Climate Models did not evidently influence between-version prediction discrepancies, while grid resolution synergistically interacted with VSs' niche characteristics in determining extent of such differences. Our findings could help in re-evaluating previous biodiversity-related works relying on geographical predictions from Worldclim-based HSMs.

opencc-zeroDec 2014View details →

Data from: Do ecological niche models accurately identify climatic determinants of species ranges?

Defining species' niches is central to understanding their distributions and is thus fundamental to basic ecology and climate change projections. Ecological niche models (ENMs) are a key component of making accurate projections and include descriptions of the niche in terms of both response curves and rankings of variable importance. In this study, we evaluate Maxent's ranking of environmental variables based on their importance in delimiting species' range boundaries by asking whether these same variables also govern annual recruitment based on long-term demographic studies. We found that Maxent-based assessments of variable importance in setting range boundaries in the California tiger salamander (Ambystoma californiense; CTS) correlate very well with how important those variables are in governing ongoing recruitment of CTS at the population level. This strong correlation suggests that Maxent's ranking of variable importance captures biologically realistic assessments of factors governing population persistence. However, this result holds only when Maxent models are built using best-practice procedures and variables are ranked based on permutation importance. Our study highlights the need for building high-quality niche models and provides encouraging evidence that when such models are built, they can reflect important aspects of a species' ecology.

opencc-zeroAug 2022View details →

Presence, precipitation, and temperature data used to estimate eastern forest songbird historical distributions using climatic niche modeling

Boundaries between vegetation types, known as ecotones, can be dynamic in response to climatic changes. The North American Great Plains includes a forest-grassland ecotone in the south-central United States that has expanded and contracted in recent decades in response to historical periods of drought and pluvial conditions. This dynamic region also marks a western distributional limit for many passerine birds that typically breed in forests of the eastern United States. To better understand the influence that variability can exert on broad-scale biodiversity, we explored historical longitudinal shifts in the western extent of breeding ranges of eastern forest songbirds in response to the variable climate of the southern Great Plains. We used climatic niche modeling to estimate current distributional limits of nine species of forest-breeding passerines from 30-year average climate conditions from 1980 to 2010. During this time the southern Great Plains experienced an unprecedented wet period without periodic multi-year droughts that characterized the region's long-term climate from the early 1900s. Species' climatic niche models were then projected onto two historical drought periods: 1952–1958 and 1966–1972. Threshold models for each of the three time periods revealed dramatic breeding range contraction and expansion along the forest-grassland ecotone. Precipitation was the most important climate variable defining breeding ranges of these nine eastern forest songbirds. Range limits extended farther west into southern Great Plains during the more recent pluvial conditions of 1980–2010 and contracted during historical drought periods. An independent dataset from BBS was used to validate 1966–1972 range limit projections. Periods of lower precipitation in the forest-grassland ecotone are likely responsible for limiting the western extent of eastern forest songbird breeding distributions. Projected increases in temperature and drought conditions in the southern Great Plains associated with climate change may reverse range expansions observed in the past 30 years.

publicAug 2020View details →

Genetic data improves niche model discrimination and alters the direction and magnitude of climate change forecasts

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publicOct 2015View details →

Data from: Do ecological niche models accurately identify climatic determinants of species ranges?

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publicFeb 2021View details →

Temporal variability is key to modelling the climatic niche

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