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233 results for “climatic niche”
Fig. 3 in Climatic Niche Conservatism and Ecological Diversification in the Holarctic Cold-Dwelling Butterfly Genus Erebia
Fig. 3. The relationships between climatic and elevation niche widths and niche position along the gradient of conditions occupied by the butterfly genus Erebia. The points correspond to the niche width (y-axis) and average value of a climate variable or elevation for individual species (x-axis).The best fit of generalized additive models (GAM) is shown by lines (separately for species of the European and the Asian clade). Statistical significance of the model fit is also shown. edf denotes the estimated degrees of freedom, which indicates the complexity of the nonlinear relationship (edf = 1 corresponds to a linear relationship).
Fig. 1 in Climatic Niche Conservatism and Ecological Diversification in the Holarctic Cold-Dwelling Butterfly Genus Erebia
Fig. 1. Phylogenetic relationships and divergence time estimates for the butterfly genus Erebia. The European clade diversified mainly in Europe, the Asian clade in Asia, although the geographic distribution of several species is not restricted to a single region (see Supp Fig. 3 [online only]). The full biogeographic reconstruction is shown in the Supp Figs. 3–5 (online only). Climatic PCA displays the distribution-based climatic data for all species of the European and the Asian clades.The polygons show the full extent of the conditions occupied by each clade (dotted lines) and the core 50% of the climatic niche (solid lines). The inset shows the correlation of individual bioclimatic variables with the first and second PCA axes.The bioclimatic variables (bio1, bio4, bio12, and bio15) displayed significant phylogenetic signal (Table 3).The European clade inhabits warmer, more humid, and less seasonal climate compared to the Asian clade.
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).
Worldclim 2.1 versus Worldclim 1.4: climatic niche and grid resolution affect between-version mismatches in habitat suitability models predictions across Europe
<p>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.</p>
Data from: Is adaptation to climate change really constrained in niche specialists?
Species with restricted distributions make up the vast majority of biodiversity. Recent evidence suggests that Drosophila species with restricted tropical distributions lack genetic variation in the key trait of desiccation resistance. It has therefore been predicted that tropically restricted species will be limited in their evolutionary response to future climatic changes and will face higher risks of extinction. However, these assessments have been made using extreme levels of desiccation stress (less than 10% relative humidity (RH)) that extend well beyond the changes projected for the wet tropics under climate change scenarios over the next 30 years. Here, we show that significant evolutionary responses to less extreme (35% RH) but more ecologically realistic levels of climatic change and desiccation stress are in fact possible in two species of rainforest restricted Drosophila. Evolution may indeed be an important means by which sensitive rainforest-restricted species are able to mitigate the effects of climate change.
Data from: Climatic niche lability but growth form conservatism in the African woody flora
<p><span>Climatic niche evolution during the diversification of tropical plants has received little attention in Africa. To address this, we characterized the climatic niche of >4000 tropical African woody species, distinguishing two broad bioclimatic groups (forest vs. savanna) and six subgroups. We quantified niche conservatism </span><span>versus</span><span> lability at the genus level and for higher clades, using a molecular phylogeny of >800 genera. Although niche stasis at speciation is prevalent, numerous clades individually cover vast climatic spaces suggesting a general ease in transcending ecological limits, especially across bioclimatic subgroups. </span><span>The forest biome was the main source of diversity, providing many lineages to savanna, but reverse shifts also occurred. </span><span>We identified clades that diversified in savanna after shifts from forest. </span><span>The forest-savanna transition was not consistently associated with a growth form change, though we found evolutionarily labile clades whose presence in forest or savanna is associated respectively with climbing or shrubby species diversification.</span></p>
Implications of climate change for environmental niche overlap between five Cuscuta pest species and their two main host crop species
<p><span>Some parasitic plants are major pests in agriculture, but how this might be affected by climate change remains largely unknown. In this study, we assessed this for five generalist holoparasitic <em>Cuscuta </em>species (<em>Cuscuta approximata, C. australis, C. chinensis, C. europaea, C. japonica</em>) and two of their main Leguminosae host crop species (<em>Glycine max </em>and <em>Medicago sativa</em>). For each of the five <em>Cuscuta </em>species and the two crop species, we ran MaxEnt models, using climatic and soil variables to predict their potential current distributions and potential future distributions for 2070. We ran species distribution models for all seven species for multiple climate-change scenarios, and tested for changes in the overlap of suitable ranges of each crop with the five parasites. We found that annual mean temperature and isothermality are the main bioclimatic factors determining the suitable habitats of the <em>Cuscuta </em>species and their hosts. </span><span>For both host species, the marginally to optimally suitable area will increase by 2070 for all four RCP scenarios. For most of the <em>Cuscuta </em>species, the marginally to optimally suitable area will also increase. As the suitable area for both the hosts and the parasites will overall increase, Schoener's D, indicating the relative overlap in suitable area, will change only marginally. However, the absolute area of potential niche overlap may increase up to six-fold by 2070. Overall, our results indicate that larger parts of the globe will become suitable for both host species, but that they could also suffer from <em>Cuscuta </em>parasitism in larger parts of their suitable ranges.</span></p>
Genetic datasets, climatic conditions at sampled localities, and occurrence data to: Ice age-driven range shifts of diploids and expanding autotetraploids within a conserved niche (Grünig, Patsiou & Parisod, 2024, New Phytologist)
<div> <h3><strong>This repository includes</strong></h3> - An overview of the raw sequencing reads deposited in the European Nucleotide Archive (ENA) for the 370 individuals sampled in 17 diploid and 19 tetraploid field populations <div>- Scripts used to genotype diploids and autotetraploids samples of <em>Biscutella laevigata</em> from ddRADseq data</div> <div>- Input data (as vcf format) used in population genetic analyses</div> <div>- Scripts used to run the different genetic analyses</div> <div>- Dataset of extracted climatic conditions at sampled localities</div> <div>- Occurrence dataset used for the climatic niche modelling</div> <br> <h3><strong>Description of the data and file structure</strong></h3> <strong>00.ENA_samples_correspondance.txt: </strong>provides ENA project ID, run ID (i.e. raw fastq files), sample ID, and alias for each sample included in the study.<br> <div> </div> <div><strong>1.scripts_reads_to_vcf.zip:</strong> consists of the following:</div> - <strong>1.reads_to_vcf.md: </strong>md file with scripts documenting the read quality check, demultiplexing, mapping, SNP calling using GATK4, and filtering steps<br> <div>- Additional scripts called within <strong>1.reads_to_vcf.md</strong>:</div> <div>-- 1.3. Mapping: <strong>02_run_mapping_XXX.py</strong> and <strong>BWA-mem_bisc1_sg.py</strong> scripts</div> <div>-- 1.4.a. HaplotypeCaller: <strong>03_V1_gvcf.py</strong></div> <div>-- 1.4.b. GDBI + genotypeGVCF: <strong>03_V3_gdbi_genotype_per100scaf.py</strong></div> <br> <div><strong>2.datasets_genetics.tar.gz</strong> consists of the following</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30.vcf.gz</strong>: "Initial SNPs dataset" = biallelic SNPs fulfilling GATK quality hard filtering recommendations, present in at least 50% of samples. Genotypes with DP<15 for diploids and DP<30 for tetraploids are set to no-call. This vcf was used as basis for fastsimcoal dataset preparation, and as basis for subsequent selection of loci fulfilling requirements of each analysis. It includes 2246701 biallelic SNPs for 370 samples</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30_MD05_pruned.vcf.gz:</strong> subset of the "Initial SNPs dataset" retaining SNPs called in at least 50% of samples, and pruned for Linkage disequilibrium. This vcf includes 107574 biallelic SNPs for 370 samples and was used in the analysis of the proportion of diploids diagnostic alleles shared by tetraploids.</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30_MD01_pruned.vcf.gz: </strong>subset of the "Initial SNPs dataset", retaining SNPs called in at least 90% of samples, and pruned for Linkage disequilibrium. This vcf includes 4444 biallelic SNPs for 370 samples and was used in the analyses of Population diversity and differentiation (SpaGeDi, GenoDive, PCA), and f3-statistics.</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30_MD0.1_pruned_MAC3rm.vcf.gz:</strong> subset of the "Initial SNPs dataset", retaining SNPs called in at least 90% of samples, pruned for Linkage disequilibrium, and with a minor allele count of 3. This vcf includes 2593 biallelic SNPs for 370 samples and was used in STRUCTURE analysis</div> <br><br> <div><strong>3.pres_2x.txt:</strong> list of the 128 diploid occurrences used in climatic niche modelling</div> <br> <div><strong>3.pres_4x_strat_reg.txt:</strong> list of the 924 tetraploid occurrences used in climatic niche modelling</div> <br> <div><strong>biscall_chelsa_ordered_noDEM.txt:</strong> climatic data extracted from the CHELSA dataset at sampled localities</div> <br> <div><strong>4.plot_GTfreqs.md:</strong> markdown file including scripts to plot allele and genotype frequencies</div> <br> <div> </div> <h3><strong>Sharing/Access information</strong></h3> Raw sequencing reads have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under the accession number PRJEB48869:<a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB48869"> https://www.ebi.ac.uk/ena/browser/view/PRJEB48869</a></div>
Fig. 3 in Climatic niche evolution in the Andean genus Menonvillea (Cremolobeae: Brassicaceae)
Fig. 3 Maximum clade credibility species tree (MCCT) estimated from nuclear ribosomal ITS and three chloroplast DNA regions (trnL-F, trnHpsbA, rps16 intron) using the multispecies coalescent method implement- ed in *BEAST, uncorrelated log-normal relaxed clock model, and two
Fig. 5 in Niche overlap and host specificity in parasitic Maculinea butterflies (Lepidoptera: Lycaenidae) as a measure for potential extinction risks under climate change
Fig. 5 Niche identity tests of Maculinea/Myrmica host associations under the A2a climate change scenario for 2080. The red arrow indicates the measured niche overlap between hosts and parasites
Fig. 3 in Niche overlap and host specificity in parasitic Maculinea butterflies (Lepidoptera: Lycaenidae) as a measure for potential extinction risks under climate change
Fig. 3 Niche identity tests of Maculinea/Myrmica host associations under current climate. The red arrow indicates the measured niche overlap between hosts and parasites derived from ENMs generated
Fig. 2 in Niche overlap and host specificity in parasitic Maculinea butterflies (Lepidoptera: Lycaenidae) as a measure for potential extinction risks under climate change
Fig. 2 Estimated potential distributions of Maculinea butterflies (light grey) and Myrmica ants (dark grey) under current climatic conditions show large geographic overlaps of the butterfly species with their respective main (red) and secondary hosts (orange)
Fig. 3 in Climate-induced shifts in the niche similarity of two related spadefoot toads (genus Pelobates)
Fig. 3 The potential distribution of P. fuscus and P. syriacus in: a present climate for the two species, b Last Interglacial climate, c Last Glacial Maximum MIROC Scenario, d Last Glacial Maximum CCSM Scenario, and e A1B scenario for 2080. The modeling extent merges the minimum convex polygons of the two species and an additional buffer zone of 335 km that includes all fossil records
Fig. 2 in Climate-induced shifts in the niche similarity of two related spadefoot toads (genus Pelobates)
Fig. 2 Modeling stages used in the present study for investigating the factors limiting the current range overlap and possible changes in the geographic ranges of the two species studied under future climate change scenarios
Fig. 7 in A novel method to calculate climatic niche similarity among species with restricted ranges-the case of terrestrial Lycian salamanders
Fig. 7 Mean of 100 Maxent SDMs computed with pooled species records of all Lyciasalamandra species omitting L. fazilae (a), L. flavimembris (b), and L. luschani (c). Areas climatically suitable for salamanders and suitable due to the presence of carstic limestone formations are indicated (dark greyMaxent values above the minimum training presence, black values above the minimum 10% training omission threshold). Areas climatically unsuitable to Lycian salamanders are indicated in light grey where carstic limestone formations are present and white where they are not
Fig. 5 in A novel method to calculate climatic niche similarity among species with restricted ranges-the case of terrestrial Lycian salamanders
Fig. 5 Relative position of species records in environmental niche space. Note the decreasing number of species records with decreasing temperature and precipitation. This pattern corroborates well field observations by Klewen (1991) and Steinfartz and Mutz (1998)
Fig. 2 Conceptual differences among proposed niche overlap analyses. Imagine a in A novel method to calculate climatic niche similarity among species with restricted ranges-the case of terrestrial Lycian salamanders
Fig. 2 Conceptual differences among proposed niche overlap analyses. Imagine a set of three species with different preferences along an environmental gradient. Using SDM projections, it is possible to derive for each species a probability distribution across the gradient. Comparing two species as proposed by Warren et al. (2008), the overlap (grey area in the middle panel) of their respective probability distributions in geographic space is computed (pair-wise niche overlap). In our jackknife approach, a probability distribution derived from all species records is compared to a probability distribution derived from all minus one species. The 1−the resulting overlap value reflects the relative contribution of the omitted species to the entire probability distribution (grey area in the lower panel) and can be used as measure to rank all species when omitting them iteratively. Note that these specific indices are comparable only across each method but not among the different approaches
Fig. 1 a in A novel method to calculate climatic niche similarity among species with restricted ranges-the case of terrestrial Lycian salamanders
Fig. 1 a Presence of carstic limestone formations (light grey) and species records used for species distribution modelling (SDM). White dots Lyciasalamandra antalyana, black dots L. atifi, black squares L. billae, grey squares L. fazilae, black triangles L. flavimembris, white triangles L. helverseni, grey triangles L. luschani. b Mean of 100 Maxent SDMs computed with pooled species records of all Lyciasalamandra species. c Maxent SDMs trained with all pooled records omitting L. helverseni. Areas climatically suitable for salamanders and also suitable due to the presence of carstic limestone formations are indicated. Dark grey Maxent values above the minimum training presence, black values above the minimum 10% training omission threshold. Areas climatically unsuitable to Lycian salamanders are indicated in light grey where carstic limestone formations are present and white where they are not
Fig. 6 in A novel method to calculate climatic niche similarity among species with restricted ranges-the case of terrestrial Lycian salamanders
Fig. 6 Mean of 100 Maxent SDMs computed with pooled species records of all Lyciasalamandra species omitting L. antalyana (a), L. atifi (b), and L. billae (c). Areas climatically suitable for salamanders and suitable due to the presence of carstic limestone formations are indicated (dark grey Maxent values above the minimum training presence, black values above the minimum 10% training omission threshold). Areas climatically unsuitable to Lycian Salamanders are indicated in light grey where carstic limestone formations are present and white where they are not
Figure 4 in First ecological assessment of the endangered Lichtenfelder's Tiger Gecko (Goniurosaurus lichtenfelderi) from northern Vietnam: micro-habitat and macro-climatic niche comparisons between island and mainland populations
Figure 4. (A) Substrate types between island and mainland populations of Goniurosaurus lichtenfelderi; (B) Number of observed individuals at positions (in or out) in different time intervals; (C) Elevations resided by island and mainland populations; (D) Distances from the observed animal to the near stream shore among four study areas.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.