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299 results for “niche models”
Fig. 7 in Distribution of Tomicus destruens (Coleoptera: Scolytinae) mitochondrial lineages: phylogeographic insights and niche modelling
Fig. 7 Partial response curve results of GAM of diversity haplotype indices using mean values on areas of the environmental mean temperature of wettest quartet variable. a Exclusive haplotype ratio (Hex). b Standardized haplotype (Hst). c Haplotypic index (Hind). d Endemicity index (Eind).
Fig. 5 in Distribution of Tomicus destruens (Coleoptera: Scolytinae) mitochondrial lineages: phylogeographic insights and niche modelling
Fig. 5 Tests for niche identity applied to level 3 clades about the I and D metric. a Clade 3-1 vs clade 3-3. b Clade 3-1 vs clade 3-2. c Clade 3-2 vs clade 3-3. Black lines indicate the I observed overlap values and black dashed lines specify the D value
Fig. 2 a in Distribution of Tomicus destruens (Coleoptera: Scolytinae) mitochondrial lineages: phylogeographic insights and niche modelling
Fig. 2 a Statistical parsimony network of haplotypes of Tomicus destruens from the Mediterranean samples, of a 618 bp fragment of the mitochondrial genes cytochrome c oxidase I (COI) and II (COII) that flank the tRNAleu gene. Each line corresponds to a mutational step and each empty circle to a missing intermediate; boxes indicate nested clades
Fig. 6 a–d. Ecological niche models for H. fumariifolia populations. a in Refugia and geographic barriers of populations of the desert poppy, Hunnemannia fumariifolia (Papaveraceae)
Fig. 6 a–d. Ecological niche models for H. fumariifolia populations. a Prediction of suitable habitat in the current environment. b Prediction projected onto past climatic layers (LGM; CCSM). c Prediction under
Figure 2 in Presence of the crab-eating fox Cerdocyon thous in La Rioja, Argentina, and implications for its geographic and environmental niche modeling
Figure 2: Cerdocyon thous present environmental niche models result maps. (A) South model. (B) Detail of model (A) for the province of La Rioja. (C) Complete model. (D) Detail of model (C) for the province of La Rioja. The color gradient indicates the suitability values, where white represents minimum values (0–10 %) and red the maximum values (76–100 %), as detailed in the figure.
Figure 1 in Presence of the crab-eating fox Cerdocyon thous in La Rioja, Argentina, and implications for its geographic and environmental niche modeling
Figure 1: New records Cerdocyon thous in La Rioja. (A–C) Photograps taken near Huaco River (2020–2021). (D) C. thous skin collected by Parodi in 1929, deposited as MACN 29.882 and label information.
Figure 3 in Presence of the crab-eating fox Cerdocyon thous in La Rioja, Argentina, and implications for its geographic and environmental niche modeling
Figure 3: Cerdocyon thous past environmental niche models for result maps. (A) Last interglacial model. (B) Last glacial maximum model. (C) Middle Holocene model. The color gradient indicates the suitability values, where white represents minimum values (0–10 %) and red the maximum values (76–100 %), as detailed in the figure.
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.
Quantifying niche similarity among new world seed plants--Species Distribution Models (SDMs) & associated metadata
<p>Niche shift and conservatism are often framed as mutually exclusive. However, both processes could contribute to biodiversity patterns. We tested this expectation by quantifying the degree of climatic niche similarity among New World seed plants.</p> <p>To incorporate the biological reality that species experience varied abiotic conditions across their range, we assembled distribution models and used these to characterize temperature, precipitation, and elevation niches for species as continuously-valued distributions. We then quantified niche similarity (distributional overlap) and identified statistically significant differences compared to a randomized null.</p> <p>The degree of niche similarity differed among climate variables, plant lineages, and at different phylogenetic scales. For example, ~17% of all seed plants were significantly different in elevational niche from their closest relative(s), whereas for precipitation, this value was only ~4%. Average niche similarity decreased with increasing phylogenetic distance, consistent with niche conservatism; however, variance in niche similarity among close relatives was large, such that there always existed niche differences equaling those among distantly related species.</p> <p>Our results suggest researchers should incorporate both niche shift and conservatism as important, scale-dependent factors shaping biodiversity patterns as these processes are not mutually exclusive, nor do they contribute equally to patterns among different plant lineages or niche variables.</p>
Presence, precipitation, and temperature data used to estimate eastern forest songbird historical distributions using climatic niche modeling
<p>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.</p>
Figure 1 in Distribution of the meadow lizard in Europe and its realized ecological niche model
Figure 1. Distribution map of the meadow lizard (Darevskia praticola) in south-eastern Europe given on an MGRS UTM 10 × 10 km grid scale. A small overview map shows the study region and the two separate parts of the meadow lizard distribution – separate geographic units and evolutionary lineages of the species (modified from Agasyan et al. 2009). Letters on the distribution map refer to the names of larger (100 × 100 km) MGRS squares. Occurrence records were compiled from a large literature survey and our own data (see Supplemental material 1) and classified on the map according to the time frame of the findings.
Figure 2 in Distribution of the meadow lizard in Europe and its realized ecological niche model
Figure 2. Habitat suitability maps for the meadow lizard (Darevskia praticola) in south-eastern Europe given separately for the low resolution (a) and the high resolution ecological niche model (b). Training points used for fitting the ecological niche models are represented with white dots, while the discarded occurrences are shown as '×' signs and placed for the overall visual representation of the model accuracy.
Figure 3 in Distribution of the meadow lizard in Europe and its realized ecological niche model
Figure 3. Examples showing details from the forest cover (Vegetation Continuous Fields layer) and the Maxent's habitat suitability map for the meadow lizard (Darevskia praticola). The maps show two localities: (a) a part of a fragmented forest area in southern Romania where the species occurs, and (b) an area near the Danube River along the border between Serbia and Romania, which is one of the places of greater habitat suitability for this species. The maps also show the difference between the low (upper images) and high (lower images) resolution of both the VCF layer and the habitat suitability.
Figure 3 in Potential geographic distribution niche modeling based on bioclimatic variables of three species of Temnomastax Rehn and Rehn, 1942 (Orthoptera: Eumastacidae)
Figure 3. Potential geographic distribution predicted by DOMAIN model to Temnomastax ricardoi Descamps, 1973 (blue), and Temnomastax tigris (Burr, 1899) (green). Darkest regions represent higher probabilities of occurrence than clearest regions. (■) Temnomastax ricardoi Descamps, 1973 records; (▲) Temnomastax tigris (Burr, 1899) records.
Figure 2 in Potential geographic distribution niche modeling based on bioclimatic variables of three species of Temnomastax Rehn and Rehn, 1942 (Orthoptera: Eumastacidae)
Figure 2. Potential geographic distribution predicted by DOMAIN model to Temnomastax hamus Rehn and Rehn, 1942 (green). Darkest regions represent higher probabilities of occurrence than clearest regions. On the left is marked the Andes in red, orange and yellow. (●) species records.
Figure 1 in Potential geographic distribution niche modeling based on bioclimatic variables of three species of Temnomastax Rehn and Rehn, 1942 (Orthoptera: Eumastacidae)
Figure 1. Male specimens of some studied species. (a) Temnomastax hamus Rehn and Rehn, 1942 from Minas Gerais, Brazil; (b) Temnomastax ricardoi Descamps, 1973 and (c) Temnomastax tigris (Burr, 1899) from Mato Grosso do Sul, Brazil (photos used with permission of the authors: Marcos Cesar Campis (a) and Paulo Robson de Souza (c).
Data from: The phylogeographic history of Megistostegium (Malvaceae) in the dry, spiny thickets of southwestern Madagascar using RAD-seq data and ecological niche modeling.
<p class="MsoCommentText">The spiny thicket of southwestern Madagascar represents an extreme and ancient landscape with extraordinary levels of biodiversity and endemism. Few hypotheses exist for explaining speciation in the region and few plant studies have explored hypotheses for species diversification. Here we investigate three species in the endemic genus <i>Megistostegium </i>(Malvaceae) to evaluate phylogeographic structure and explore the roles of climate, soil and paleoclimate oscillations on population divergence and speciation throughout the region. We combine phylogenetic and phylogeographic inference of RADseq data with ecological niche modeling across space and time. Population structure is concurrent with major rivers in the region and we identify a new, potentially important biogeographic break coincident with several landscape features. Our data further suggests that niches occupied by species and populations differ substantially across their distribution. Paleodistribution modelling provide evidence that past climatic change could be responsible for the current distribution, population structure and maintenance of species in <i>Megistostegium.</i></p>
Ensemble Ecological Niche Models, in 2019 and across RCP 2.6, 4.5, and 8.5 scenarios in 2050 and 2100, of 1508 European Marine Species based on Ecological Niche Models developed with Artificial Neural Networks, Maximum Entropy, Support Vector Machines, and AquaMaps at 0.5° Resolution
<p>Ensemble Ecological Niche Models, in 2019 and across RCP 2.6, 4.5, and 8.5 scenarios in 2050 and 2100, of 1508 European marine species based on Ecological Niche Models developed with (i) Artificial Neural Networks, (ii) Maximum Entropy, (iii) Support Vector Machines, and (iv) AquaMaps at 0.5° Resolution. The data report, for each 0.5° cell, how many models (from 0 to 4) overcome a model-specific decision threshold to assess species presence in the cell.</p>
Data for: Habitat functionality: integrating environmental and geographic space in niche modelling for conservation planning
<p>Niche modelling is typically used to assess the effects of anthropogenic land use and climate change on species distributions and to inform spatial conservation planning. These models focus on the suitability of local biotic and abiotic conditions for a species in environmental space (E-space). Although movements also affect species occurrence, efforts to formally integrate geographic space (G-space) into niche modelling have been hindered by the lack of comprehensive theoretical frameworks. </p> <p>We propose the 'functional habitat' framework to define areas that are simultaneously of high-quality in E-space and functionally connected to other suitable habitat in G-space. Originating in metapopulation ecology, approaches have been developed to assess the amount of suitable connected habitat, based on the proximity between pairs of locations. Using network theory, which operates in topological space (T-space, defined by a network), we extended these metapopulation approaches to integrate movement constraints in G-space with niche modelling in E-space. </p> <p>We demonstrate the functional habitat framework using empirical data (GPS-tracking and population monitoring) throughout the European wild mountain reindeer (<em>Rangifer t. tarandus</em>) distribution range. We show that functional habitat outperforms traditional suitability in explaining the species' distribution. This approach integrates effects from habitat loss and fragmentation for spatial conservation planning and avoids overemphasizing small, inaccessible areas with locally suitable habitat. The functional habitat framework formally integrates biotic, abiotic, and movement constraints in niche modeling using network theory, thus opening a wide range of applications in spatial conservation planning.</p>
FIGURE 7 in Systematics and biogeography of Anoura cultrata (Mammalia, Chiroptera, Phyllostomidae): a morphometric, niche modeling, and genetic perspective, with a taxonomic reappraisal of the genus
FIGURE 7. Amendments to Clades 2 and 4 of the phylogeny of Calderón-Acevedo et al. (2022). Alphanumeric codes to the left of the equal signs are those used by these authors to label their samples (Aaeq = A. aequatoris; Acar = A. carishina; Acau = Anoura caudifer; Ageo = A. geoffroyi; Alat = A. latidens; Alui = A. luismanueli; and Aperu = A. peruana). Acronyms to the right of the equal signs are those of the museums in which the specimens are housed, except for JFD which are the collector's initials. These acronyms are followed by catalog or field numbers. Bold type indicates specimens whose taxonomic identifications are being challenged. Asterisks indicate specimens examined by JM. The species names to the right of brackets indicate the taxonomic identities assumed in our study. In the original tree (Calderón-Acevedo et al., 2022), all specimens in Clade 2 were deemed to be A. caudifer, and all specimens in the A. geoffroyi-A. peruana subclade of Clade 4 were deemed to be A. geoffroyi.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.