Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
180
datasets available to search
ShareScore release 0.7.1
Dataset results
180 results for “range shift”
Range shifts in butternut, a rare, endangered tree, in response to past climate and modern conditions
<p><strong>Aim: </strong>Range shifts are a key process that determine species distributions and genetic patterns. A previous investigation reported that <em>Juglans cinerea</em> (butternut) has lower genetic diversity at higher latitudes, hypothesized to be the result of range shifts following the last glacial period. However, genetic patterns can also be impacted by modern ecogeographic conditions. Therefore, we re-investigate genetic patterns of butternut with additional northern population sampling, hindcasted species distribution models, and fossil pollen records to clarify the impact of glaciation on butternut.</p> <p><strong>Location:</strong> Eastern North America</p> <p><strong>Taxon:</strong> <em>Juglans cinerea </em>(L., Juglandaceae) (butternut)</p> <p><strong>Methods:</strong> Using 11 microsatellites, we examined range-wide spatial patterns of genetic diversity metrics (allelic richness, heterozygosity, FST) for previously studied butternut individuals and an additional 757 samples. We constructed hindcast species distribution models and mapped fossil pollen records to evaluate habitat suitability and evidence of species' presence throughout space and time.</p> <p><strong>Results:</strong> Contrary to previous work on butternut, we found that genetic diversity increased with distance to range edge, and previous latitudinal clines in diversity were likely due to a few outlier populations. Populations in New Brunswick, Canada were genetically distinct from other populations. At the Last Glacial Maximum, pollen records demonstrate butternut likely persisted near the glacial margin, and hindcast species distribution models identified suitable habitat in the southern United States and near Nova Scotia.</p> <p><strong>Main conclusions: </strong>Genetic patterns in butternut may be shaped by both glaciation and modern environmental conditions. Pollen records and hindcast species distribution models combined with genetic distinctiveness in New Brunswick suggest that butternut may have persisted in cryptic northern refugia. We suggest that thorough sampling across a species range and evaluating multiple lines of evidence are essential to understanding past species movements.</p>
Data from: Predicting range shifts of Davidia involucrata Ball. under future climate change
<p>Understanding and predicting how species will respond to climate change is crucial for biodiversity conservation. Here, we assessed future climate change impacts on the distribution of a rare and endangered plant species, Davidia involucrate in China, using the most recent global circulation models developed in the sixth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC6). We assessed the potential range shifts in this species by using an ensemble of species distribution models (SDMs). The ensemble SDMs exhibited high predictive ability and suggested that the temperature annual range, annual mean temperature, and precipitation of the driest month are the most influential predictors in shaping distribution patterns of this species. The projections of the ensemble SDMs also suggested that D. involucrate is very vulnerable to future climate change, with at least one-third of its suitable range expected to be lost in all future climate change scenarios and will shift to the northward of high-latitude regions. Similarly, at least one-fifthof the overlap area of the current nature reserve networks and projected suitable habitat is also expected to be lost. These findings suggest that it is of great importance to ensure that adaptive conservation management strategies are in place to mitigate the impacts of climate change on D. involucrate.</p>
Idiosyncratic shifts in life-history traits at species' geographic range edges
<p>Anthropogenic changes drive shifts in species' geographic distributions and increase the occurrence of leading or trailing-edge marginal populations. Theoretical predictions and empirical observations indicate substantial changes in life-history traits in marginal populations, often involving dispersal and reproductive abilities. Using a common garden experiment, we studied the variation of life-history traits of populations sampled on spatial gradients extending from range-core to range-edge habitats for three expanding (miner's lettuce <em>Claytonia perfoliata</em>, Danish scurvygrass <em>Cochlearia</em> <em>danica</em>, and rock samphire <em>Crithmum</em> <em>maritimum</em>) and one receding plant species (dune pansy <em>Viola</em> <em>tricolor</em> subs. <em>curtisii</em>). We monitored life-history traits related to dispersal, phenology, survival, reproductive output, and selfing ability. Significant shifts in life-history traits between central and marginal populations strongly differed among species. Marginal populations of the three expanding species displayed modified seed weight in natura, suggesting increased dispersal abilities in leading-edge populations. Discarding unassessed maternal effects, this trait modification can be due to phenotypic plasticity or to genetic differentiation. In miner's lettuce, marginal expanding populations show advanced phenology and higher reproductive output, which may potentially influence their colonization ability. In rock samphire, life-history traits showed large intra- and inter-population variability that did not follow a core-to-edge geographic trend, except for seed size. Finally, the receding populations of the dune pansy displayed a shift towards a plant architecture maximizing survival but reducing individual reproductive success. Altogether, our results indicated a common trend for increased dispersal abilities in marginal populations of expanding species. However, shifts in species' distributions may drive idiosyncratic changes in other life-history traits, for which we observed no general evolutionary syndrome at range edges. These findings go along a stochastic view of trait evolution during range expansion and question how to draw predictive projections of species' distribution shifts under current global change.</p>
Supplementary material 1 from: Pérez-Luque AJ, Zamora R, Bonet FJ, Pérez-Pérez R (2015) Dataset of MIGRAME Project (Global Change, Altitudinal Range Shift and Colonization of Degraded Habitats in Mediterranean Mountains). PhytoKeys 56: 61-81. https://doi.org/10.3897/phytokeys.56.5482
Table S1: Explanation note: Information about transects of the project. Elevation in m a.s.l. Type: AM = Altitudinal migration; FO = Forest; MH = Marginal Habitat. Subtype: AC-e: Abandoned Cropland: edge; AC-i: Abandoned Cropland: inside; Pp-e: Pine plantations: edge; Pp-i: Pine plantations: inside; TE: Treeline Ecotone. Locality: CA = Robledal de Cáñar; SJ = Robledal de San Juan.
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 Interglacial refugia and range shifts of the alpine grasshopper Stenobothrus cotticus (Orthoptera: Acrididae: Gomphocerinae)
Fig. 3 Current distribution of Stenobothrus cotticus (white triangles) and S. rubicundulus (open circles) in Europe; S. rubicundulus further ranges to western Ukraine (not shown). For localities and corresponding references, see "Electronic Supplementary Material"
Fig. 1 in Species radiation in the Alps: multiple range shifts caused diversification in Ringlet butterflies in the European high mountains
Fig. 1 Sampling locations of all studied species, with Erebia cassioides arvernensis (grey circles), Erebia c. cassioides (black circles), Erebia c. neleus in the Balkan region (black-white circles), Erebia nivalis (white triangles), Erebia tyndarus (white circles) and Erebia ottomana (grey triangles) (a). The detailed map shows the distribution of the samples in the Alps (b). Given numbers coincide with other figures and tables
Data & code from: Simulated invasion suggests rapid evolution of biotic resistance to a range-shifting competitor
<p><strong>Abstract</strong></p> <p>Variable climate-change-driven range shifts will likely create novel species interactions. Most research has focused on how these interactions may impact expansion rates and adaptation of species on the move (range-shifting invaders). However, slower-moving (resident) species could also adapt to novel competitors. Here we construct populations of eight duckweed genotypes (<em>Lemna minor</em> = resident) from various localities near and beyond the range edge of a potential range-shifting competitor, <em>S. polyrhiza</em> (invader), and invade them with one genotype of <em>S. polyrhiza</em>. Following a 14-week invasion, we observed significant rapid evolution and phenotypic plasticity in the resident. Selection favoured genotypes with faster growth and smaller root-to-frond-area ratios. These changes led to slight reductions in invasibility, indicating weakly increased biotic resistance. This suggests that range-shifting species, even at low densities, may drive evolution, plasticity, and evolution of biotic resistance in resident competitors, which could feed back to influence the range expansion of the invader.</p> <p><strong>Methods</strong></p> <p>This dataset repository contains the analysis scripts/ R markdown files and collected data from "Simulated invasion suggests rapid evolution of biotic resistance to a range-shifting competitor" by Emma Menchions and Amy Angert. The collected data includes frond counts for <em>L. minor</em> and <em>S. polyrhiza </em>in the experimental populations, images (experimental populations and sampled rafts), as well as measurements on frond area, root length, and the number of fronds per raft on duckweed rafts sampled from experimental and control populations. </p> <p><strong>Usage notes</strong></p> <p>See the README files in the repository. </p> <p> </p>
Data from: Evidence of large-scale range shift in the distribution of a Palaearctic migrant in Africa
Aim: Long-distance Palaearctic migrant birds are declining at a faster rate than short-distance migrant or resident species. This is often attributed to changes on their non-breeding grounds and along their migratory routes. The European Honey-buzzard (Pernis apivorus) is a scarce migrant in southern Africa that is declining globally. This study assessed the distribution and abundance of honey-buzzards in southern Africa over the past four decades and compared it to trends in the East African population to examine possible drivers of population expansion in southern Africa. Location Southern and East Africa Methods European Honey-buzzard reporting data were collected from a variety of sources including citizen science databases (1983-2017). In addition, records of all other southern African vagrants (including ten other regularly occurring species) were gathered to account for changes in birdwatching effort in the sub-region. To assess the effect of forest loss on honey-buzzard abundance, rolling correlations were performed using forest cover in East Africa and number of honey-buzzard records in both sub-regions. Results European Honey-buzzard records in southern Africa have increased over five times more than other regularly occurring vagrant species and almost 40 times more than honey-buzzard in Tanzania, where the population has remained stable. Loss of forested area in East Africa was correlated with an increase in European Honey-buzzard records in southern Africa. Main conclusions We suggest that the European Honey-buzzard shift in wintering range may be driven by a decline in suitable habitat further north in Africa amongst other possible reasons. This effect may have been amplified by an increase in appropriate habitat across southern Africa brought about by anthropogenic changes to vegetation such as increased tree cover in urban areas. This study further highlights the importance of using African distributional data banks to understand the effects of global change on Palaearctic migrant bird species.
Data from: Sex-specific shifts in morphology and colour pattern polymorphism during range expansion of an invasive lizard
Aim: Human-assisted range expansion of animals to new environments can lead to phenotypic shifts over ecological timescales.We investigated whether phenotypic changes are sex-specific using an invasive lizard (Lampropholis delicata). Location: Pacific region (Hawaiian Islands, Lord Howe Island, New Zealand, eastern Australia) Methods: Using our knowledge of theintroduction history of L. delicata, we examined museum specimens of individuals collected across the native and introduced range to determine whether shifts in morphologyor colour pattern polymorphism had occurred during its range expansion, and if so, whether they differed between the sexes. Results: Sexual dimorphism in both size and shape was documented within the native range of the delicate skink. However, during range expansion, phenotypic shifts were observed in shape, but not size. In two of the three invasive populations, these phenotypic shifts were sex-specific. In the Hawaiian Islands, changes in shape were driven by males, whereas in New Zealand it was due to shifts in females.Similarly, changes in the frequency of a colour pattern polymorphism, a mid-lateral stripe shown to have sex-specific impacts on fitness (positive in females, negative in males), occurred following colonisation of the Hawaiian Islands and Lord Howe Island. In Hawaii, the incidence of the polymorphism increased over time in females, and decreased in males. Main conclusions: Phenotypic shifts during the range expansion of invasive species may be sex-specific, and are potentially related to the degree of realised niche shift that has occurred between the source and introduced range.
Staying in situ or shifting range under ongoing climate change: A case of an endemic herb in the Himalaya-Hengduan Mountains across elevational gradients
<p><span><strong>Aim</strong>:</span><span> How species respond to ongoing climate change has been a hot research topic, especially with the controversy in shifting range (movement) or persisting in local habitat (<em>in situ</em>) as the primary response. Assessing the relative roles of range shifts, phenotypic plasticity and genetic adaptation helps us predict the evolutionary fate of species. We aim to explore the evolutionary strategies of plants under climate change from a keystone herb in alpine ecosystems, <em>Mirabilis</em> <em>himalaica</em>, along its elevational gradient.</span></p> <p><span><strong>Location</strong>:</span><span> Himalaya-Hengduan Mountains, China.</span></p> <p><span><strong>Methods</strong>: </span><span>We combined evidence from population genomics and ecological data in both space and time to investigate the state of "staying" or "moving". We identified migration events by assessing historical and contemporary gene flow, and changes in species distribution. Morphological variation was compared by measuring five traits using specimen data. Moreover, we explored climate-driven genetic variation and local selection regimes acting on populations in the alpine landscape along an elevational gradient.</span></p> <p><span><strong>Results</strong>: </span><span>Our results argue that staying <em>in situ</em> by morphological variation and local genetic evolution rather than range shifting plays an important role in <em>M</em>. <em>himalaica</em> response to climate change. We first found trace evidence of upward or climatic-driven shifting along an elevational gradient, although asymmetric gene flow was restricted within microenvironments of mid-elevational populations. Furthermore, morphological variation comparisons revealed clinal variation, as resource allocation showed a declining pattern in vegetative growth but increased reproductive growth with increasing elevation. Outlier tests and environment association analyses indicated adaptative loci primarily related to thermal-driven selection and continuous adaptations to high elevation in the Himalaya-Hengduan Mountains. </span></p> <p><span><strong>Main conclusions</strong>:</span><span> Our findings show <em>M</em>. <em>himalaica</em> may persist in local habitats rather than shifting range under climate change, exhibiting a low risk of genomic vulnerability in current habitats. This study has important implications for improving our understanding of the evolutionary response in alpine </span><span>plants to climate change.</span></p>
Osmanthus plastid genome sequence for: Plastid genomes reveal evolutionary shifts in elevational range and flowering time of Osmanthus (Oleaceae)
<p><span>Species of <em>Osmanthus</em> are economically important ornamental trees, yet information regarding their plastid genomes (plastomes) has rarely been reported, thus hindering taxonomic and evolutionary studies of this small but enigmatic genus. Here, we performed comparative genomics and evolutionary analyses on plastomes of 16 of the 28 currently accepted species, with 11 plastomes newly sequenced. Phylogenetic studies identified four main lineages within the genus that are here designated: 'Caucasian <em>Osmanthus</em>' (corresponding to <em>O</em>. <em>decorus</em>), '<em>Siphosmanthus</em>' (corresponding to <em>O</em>. sect. <em>Siphosmanthus</em>), '<em>O</em>. <em>serrulatus</em> + <em>O</em>. <em>yunnanensis</em>', and 'Core <em>Osmanthus</em>' (corresponding to <em>O</em>. sect. <em>Osmanthus</em> + <em>O</em>. sect. <em>Linocieroides</em>). Molecular clock analysis suggested that <em>Osmanthus</em> split from its sister clade c. 15.83 Ma. The estimated crown ages of the lineages were the following: genus <em>Osmanthus</em> at 12.66 Ma; '<em>Siphosmanthus</em>' clade at 5.85 Ma; '<em>O. serrulatus </em>+<em> O. yunnanensis</em>' at 4.89 Ma; 'Core <em>Osmanthus</em>' clade at 6.2 Ma. Ancestral state reconstructions and trait mapping showed that ancestors of <em>Osmanthus</em> were spring-flowering and originated at lower elevations. Phylogenetic principal component analysis clearly distinguished spring-flowering species from autumn-flowering species, suggesting that flowering time differentiation is related to the difference in ecological niches. Nucleotide substitution rates of 80 common genes showed a slow evolutionary pace and low nucleotide variations, all genes being subjected to purifying selection.</span></p>
Data from: Vegetation structure mediates a shift in predator avoidance behavior in a range-edge population
Open the record for dataset details and reuse information.
Data from: Evidence for shifts to faster growth strategies in the new ranges of invasive alien plants
Open the record for dataset details and reuse information.
Data from: Local adaptation primes cold-edge populations for range expansion but not warming-induced range shifts
Open the record for dataset details and reuse information.
Data from: Effects of contemporary shifts of range margins on patterns of genetic structure and mating system in two coastal plant species
Open the record for dataset details and reuse information.
Evolution of Castanea in North America: RADseq and ecological modeling reveal a history of radiation, range shifts, and disease
Open the record for dataset details and reuse information.
Data from: Northwest range shifts and shorter wintering period of an Arctic seabird in response to four decades of changing ocean climate
Open the record for dataset details and reuse information.
Data from: Tests of species-specific models reveal the importance of drought in postglacial range shifts of a Mediterranean-climate tree: insights from integrative distributional, demographic and coalescent modelling and ABC model selection
Open the record for dataset details and reuse information.
Data from: Cold temperature extremes during spring do not limit the range shift of Mediterranean pines into regions with intermittent frost
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
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.