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68 results for “landscape history”
Scaling landscape fire history in sagebrush: Wildfires not historically frequent in the main population of threatened Gunnison Sage-grouse
<p>The main population of ∼5,000 Threatened Gunnison sage-grouse (GUSG; Centrocercus minimus) in Colorado depends on sagebrush that are killed by wildfires, with recovery taking decades, so frequent fire is a threat, but did it occur historically? Early land surveys showed that the historical (preindustrial) fire rotation (FR), the expected period to burn area equal to a focal land area, was 90-143 years in GUSG ranges, which is not frequent fire (≤25 years). However, recent research, based on fire scars on trees at ten sites near sagebrush, suggested some frequent fire historically in the main population. That study was not spatial, essential to estimate FR, so spatial data were created in GIS with land-survey reconstructions, survey dates, fire-scar sites, Thiessen polygons around sites, and sagebrush. The previous study assumed fires that burned 2+ sites likely burned across sagebrush. Historical FRs were calculated several ways over a common period. A recovery estimate of FR was 90-135 years, a land-survey estimate 82-131 years, and three spatial scar-based estimates 93-107 years, showing agreement. However, comparing land-survey and fire-scar results showed that using fire scars spatially only 43% matched land surveys. Detailed analysis showed that 10 fire-scar sites were insufficient to detect historical fire sizes and distributions across the large 168,753 ha sagebrush area. An adequate historical fire reconstruction could require ∼45-60 fire-scar sites, making only ∼30,000 ha of sagebrush feasible. Using the two remaining methods, which cross-validate, showed frequent fire did not occur historically in the study area, as historical FRs were 82-135 years. </p>
Genome data and resources on the recombination landscape and population history of the harlequin fly
<p>This dataset contains phased vcf files of <em>Chironomus riparius, </em>ouput files of RepeatMasker, MELT, RepeatOBserver, MSMC2, iSMC and bedtools, such as supporting files. </p> <p>For further details also check the GitHub page: <a href="https://github.com/lpettrich/Crip_Recombination_PopHistory_Cla_2024" target="_blank" rel="noopener">https://github.com/lpettrich/Crip_Recombination_PopHistory_Cla_2024</a></p> <ul> <li><strong>phased-vcfs: </strong>Artificially phased vcf-files of five populations with four individuals each. Needed to generate multihetsep files. Input files for iSMC.<br> <ul> <li>Hesse in Germany = MG</li> <li>Rhône-Alpes in France = MF</li> <li>Lorraine in France = NMF</li> <li>Piemont in Italy = SI</li> <li>Andalusia in Spain = SS</li> </ul> </li> <li><strong>multihetsep-files: </strong>Created with msmc-tools. Input files for MSMC2. </li> <li><strong>RepeatMasker: </strong>Raw output of RepeatMasker run. Summary file and file with filtered <em>Cla</em>-element (a transposable element) included.<strong><br></strong></li> <li><strong>MELT: </strong>MELT ouput with added info on population and numbered insertions reflecting all 441 detected <em>Cla </em>insertions.<strong><br></strong></li> <li><strong>RepeatOBserver: </strong>Summary files on centromere predictions based on histograms and Shannon Diversity from RepeatOBserver. Genome-wise Shannon Diversity per chromosome included. <strong><br></strong></li> <li><strong>MSMC2: </strong>Raw ouput of combined cross-coalescence and mean values if MSMC2 per populations. <strong><br></strong></li> <li><strong>iSMC: </strong>Recombination rate rho in 10 kb windows and 100 kb windows along the genome. <strong><br></strong></li> <li><strong>bedtools closest ismc 10 kb: </strong>Bedtools closest analysis of the distance of the next <em>Cla</em>-element to the recombination rate rho in 10 kb windows.<strong><br></strong></li> <li><strong>bedtools closest ismc 100 kb: </strong>Bedtools closest analysis of the distance of the next <em>Cla</em>-element to the recombination rate rho in 100 kb windows.</li> <li><strong>input-files figures: </strong>Supporting files needed to create figures.<strong><br></strong></li> </ul>
Figure 7 in Diversity and life-history traits of wild bees (Insecta: Hymenoptera) in intensive agricultural landscapes in the Rolling Pampa, Argentina
Figure 7. Mean number of (a) above-ground nesting bee individuals, (b) floral specialist bee individuals, (c) oligolectic bee individuals and (d) oil-collecting bee individuals in cropped area (n = 28 points) and semi-natural area (n = 11 points). ns indicates a non-significant result. Asterisks indicate that means are significantly different (Wilcoxon rank sum test, ** = P <0.01). Bars show SEs.
Figure 2 in Diversity and life-history traits of wild bees (Insecta: Hymenoptera) in intensive agricultural landscapes in the Rolling Pampa, Argentina
Figure 2. Semi-natural area of the study site: (a) semi-natural grassland; (b) the stream 'Arroyo Dulce' and its banks (Photos: Violette Le Féon).
Landscape composition and life-history traits influence bat movement and space use: analysis of 30 years of published telemetry data
<p>Using temperate bats, a group of particular conservation concern, we investigated how morphological traits, habitat specialization and environmental variables affect home range sizes and daily foraging movements, using a compilation of 30 years of published bat telemetry data in Northern America and Europe for the period 1988 – 2016.</p> <p>We compiled data on home range size and mean daily distance between roosts and foraging areas at both colony and individual levels from 166 studies of 3,129 radiotracked individuals of 49 bat species. We calculated multi-scale habitat composition and configuration in the surrounding landscapes of all studied roosts. Using mixed models, we examined the effects of habitat availability and spatial arrangement on bat movements, while accounting for body mass, aspect ratio, wing loading and habitat specialization.</p> <p>We found a significant effect of landscape composition on home range size and mean daily distance at both colony and individual levels. On average, home ranges were up to 42% smaller in the most habitat-diversified landscapes while mean daily distances were up to 30% shorter in the most forested landscapes. Bat home range size significantly increased with body mass, wing aspect ratio and wing loading, and decreased with habitat specialization.</p>
Data for: Holocene history of the landscape at the biogeographical and cultural crossroads between Central and Eastern Europe (Western Podillia, Ukraine)
<p><strong>Here, we publish the working data sheets for individual proxies (pollen, plant macrofossils, mollusc and geochemical composition), which was used for paleoecological diagrams in the paper Hájková et al. in Quaternary Science Reviews. </strong></p>
Landscape composition and life‐history traits influence bat movement and space use: Analysis of 30 years of published telemetry data
Open the record for dataset details and reuse information.
The effects of land-use history and the contemporary landscape on non-native plant invasion at local and regional scales in the French Broad Watersheds, 2007
Determining what factors explain the distribution of non-native invasive plants that can spread in forest-dominated landscapes could advance understanding of the invasion process and identify forest areas most susceptible to invasion. The researchers conducted roadside surveys to determine the presence and abundance of 15 non-native plant species known to invade forests in western North Carolina, USA. Prior to sampling, the researchers identified 15 non-native invasive plant species that were of concern in the study region. Generalized linear models were used to examine how contemporary and historic land use, landscape context, and topography influenced presence and abundance of the species at local and regional scales.
Data from: Contrasting population structure and demographic history of cereal aphids in different environmental and agricultural landscapes
<p>Single Nucleotide Polymorphisms files and phylogonetic trees of S. miscanthi samples collected in China and S. avenae from the UK used to study the population genetics analyses of these species. These are:</p> <p>China_samples_vcf.zip: dataset of SNPs from S. miscanthi sampled in 10 populations of China obtained using FreeBayes (in vcf format).</p> <p>China_samples_vcf_filtered.zip: SNPs from S. miscanthi after filtering the file China_samples_vcf.zip using vcftools (max-missing 0.75, minDP 3, mac 3, minQ 30, remove-indels, thin 2000, max-missing 0.9, thin 5000). This file was used in all population genetic analyses of the Chinese populations in the paper, transforming to the appropriate formats.</p> <p>China_samples_SNPs.fas: fasta file of phased SNPs used to estimate the phylogeny of S. miscanthi haplotypes using RAxML.</p> <p>China_RAxML_phylogeny_newick.tre: RAxML phylogenetic tree in newick format obtained with China_samples_SNPs.fas.</p> <p>England_samples_vcf.zip: dataset of SNPs from S. avenae sampled in 12 populations of England obtained using FreeBayes (in vcf format).</p> <p>England_samples_vcf_filtered.zip: SNPs from S. avenae after filtering the file England_samples_vcf.zip using vcftools (max-missing 0.5, mac 3, minQ 30, minDP 3, max-missing 0.5, exclude individuals with 50% missing data, max-missing 0.75, remove-indels, thin 2000). This file was used in all population genetic analyses of the English populations in the paper, transforming the vcf to the corresponding formats.</p> <p>England_samples_SNPs.fas: fasta file of phased SNPs.</p> <p>England_samples_SNPs_polymorphic.fas: fasta file of phased SNPs used in the phylogenetic reconstruction of S. avenae haplotypes using RAxML. This file is the same as England_samples_SNPs.fas after removing sites which were not polymorphic (e.g. a site that contains N and T in different samples is not considered polymorphic for RAxML and has to be removed)</p> <p>England_RAxML_phylogeny_newick.tre: RAxML phylogenetic tree in newick format obtained with England_samples_SNPs_polymorphic.fas.</p>
Raster and original working data for the paper Holocene matters: landscape history accounts for current species richness of vascular plants in forests and grasslands of eastern Central Europe
<p>Aim: Current species-richness patterns are sometimes interpreted as a legacy of landscape history, but historical processes shaping the distribution of species during the Holocene are frequently omitted in biodiversity models. Here, we test their importance in modelling current species richness of vascular plants in forest and grassland vegetation.<br> Location: Western Carpathians and adjacent regions.<br> Taxon: Vascular plants.<br> Methods: Numbers of all species and of habitat specialists were extracted from plot records of forest and grassland vegetation. For each plot, environmental and historical data were derived from thematic maps. Historical data related to the persistence of (i) temperate taxa during the Late Glacial and Early Holocene, (ii) open-landscape taxa during the Middle Holocene, and (iii) taiga species during the Late Holocene were based on 112 fossil pollen profiles. Boosted regression trees were used to model spatial patterns in species richness.<br> Results: Historical variables always appeared among the best predictors of current species richness. In light forests, species richness highly mirrored both the Late Glacial (12.5% contribution) and Middle-Holocene (8.6%) landscape history. The latter factor became an important predictor also for species richness of steppe grasslands (8.3%) along with temperature seasonality (11.9%). Species richness of dark coniferous forests was best predicted by the Late-Holocene occurrence of taiga forests (14.8%), which had an even stronger effect on the richness of habitat specialists (20.5%). <br> Main conclusions: Landscape changes since the Last Glacial Maximum are important predictors of current plant species richness. The historical effects were found to be habitat-specific and, because they may interact with recent environmental conditions and anthropogenic pressures, they often show a non-linear relationship with species richness. We provide one possible direction of incorporating past landscape changes into the models of species richness.</p>
Data from: Landscape composition and life-history traits influence bat movement and space use: analysis of 30 years of published telemetry data
<p><span><b>Aim: </b>Animal movement determines home range patterns, which in turn affect individual fitness, population dynamics and ecosystem functioning. Using temperate bats, a group of particular conservation concern, we investigated how morphological traits, habitat specialization and environmental variables affect home range sizes and daily foraging movements, using a compilation of 30 years of published bat telemetry data.</span></p> <p><span><b>Location</b>: Northern America and Europe.</span></p> <p><span><b>Time period</b>: 1988 – 2016.</span></p> <p><span><b>Major taxa studied</b>: Bats.</span></p> <p><span><b>Methods</b>: We compiled data on home range size and mean daily distance between roosts and foraging areas at both colony and individual levels from 166 studies of 3,129 radiotracked individuals of 49 bat species. We calculated multi-scale habitat composition and configuration in the surrounding landscapes of the 165 studied roosts. Using mixed models, we examined the effects of habitat availability and spatial arrangement on bat movements, while accounting for body mass, aspect ratio, wing loading and habitat specialization.</span></p> <p><span><b>Results:</b><i> </i>We found a significant effect of landscape composition on home range size and mean daily distance at both colony and individual levels. On average, home ranges were up to 42% smaller in the most habitat-diversified landscapes while mean daily distances were up to 30% shorter in the most forested landscapes. Bat home range size significantly increased with body mass, wing aspect ratio and wing loading, and decreased with habitat specialization.</span></p> <p><span><b>Main conclusions: </b>Promoting bat movements through the landscape surrounding roosts at large spatial scales is crucial for bat conservation. Forest loss and overall landscape homogenization lead temperate bats to fly farther to meet their ecological requirements, by increasing home range sizes and daily foraging distances. Both processes might be more detrimental for smaller, habitat-specialized bats, less able to travel increasingly longer distances to meet their diverse needs.</span></p>
Combining local ecological knowledge with camera traps to assess the link between African mammal life history traits and their occurrence in anthropogenic landscapes
<p>Understanding what influences species and trait composition is critical for predicting changes in communities driven by landscape transformation. </p> <p>We explored how life history traits are associated with the persistence of mammal species in human-dominated habitats within the Garden Route Biosphere Reserve, South Africa. We combined data from a camera trap and a local ecological knowledge-based survey in an integrated occupancy model to analyze species occurrence along a gradient of anthropogenic landscape transformation. </p> <p>Results confirmed that mammal occurrence in human-modified habitats was related to specific life history traits. Species with more specialist diets, as well as larger body mass species were more likely to stay in protected areas. Species with slow reproductive strategies occupied more natural areas. </p> <p>Our study also showed that combining different monitoring methods enabled us to increase spatial coverage and mammal sighting numbers. This approach fostered research participation by various stakeholders, an important step for co-designing wildlife-friendly anthropogenic spaces. </p> <p><strong>Synthesis and applications: </strong>Integrating data from a standard ecological protocol and structured participatory citizen knowledge allowed us to identify the species functional traits associated with mammal species occurrence in anthropogenic landscapes at a local scale. These results advocate for wisely combining methods, and will guide conservation orientated land-use planning towards the protection of natural habitats in the Garden Route Biosphere Reserve. This methodological approach will enable managers and conservationists to use data obtain from diverse protocols. This should catalyze the involvement of citizens in biodiversity monitoring and conservation.</p>
The ecological memory of fish assemblages in agroecosystems with different history of landscape changes
<p>Here, we presented the data (local, past and response) and R code (models_Zeni et al.) we used to investigate the relationship between past land use changes and instream habitat (explanatory variables) and fish biodiversity patterns (response variables) in streams from different regions in Brazil. </p>
Combining local ecological knowledge with camera traps to assess the link between African mammal life history traits and their occurrence in anthropogenic landscapes
Open the record for dataset details and reuse information.
Raster and original working data for the paper Holocene matters: landscape history accounts for current species richness of vascular plants in forests and grasslands of eastern Central Europe
Open the record for dataset details and reuse information.
Data from: Contrasting population structure and demographic history of cereal aphids in different environmental and agricultural landscapes
Open the record for dataset details and reuse information.
Data from: Landscape composition and life-history traits influence bat movement and space use: analysis of 30 years of published telemetry data
Open the record for dataset details and reuse information.
Data from: Mapping Tasmania's cultural landscapes: using habitat suitability modelling of archaeological sites as a landscape history tool
Aim: Understanding past distributions of people across the landscape is key to understanding how people used, affected and related to the natural environment. Here we use habitat suitability modelling to represent the landscape distribution of Tasmanian Aboriginal archaeological sites and assess the implications for patterns of past human activity. Location: Tasmania, Australia Methods: We developed a RandomForest 'habitat suitability' model of site records in the Tasmanian Aboriginal Heritage Register. We applied a best-effort bias correction, considered 31 predictor variables relating to climate, topography and resource proximity, and used a variable selection procedure to optimise the final model. Model uncertainty was assessed via bootstrapping and we ran an analogous MAXENT model as a cross-validation exercise. Results: The results from the RandomForest and MAXENT models are highly congruent. The strongest environmental predictors of site occurrence include distance to coast, elevation, soil clay content, topographic roughness and distance to inland water. The highest habitat suitability scores are distributed across a wide range of environments in central, northern and eastern Tasmania, including coastal areas, inland water body margins, and forests and savannas in the drier parts of Tasmania. With the exception of coastal areas much of western Tasmania has low habitat suitability scores, consistent with theories of low-density Holocene Tasmanian Aboriginal settlement in this region. Main conclusions: Our modelling suggests Tasmanian Aboriginal people occupied a heterogeneity of habitats but targeted coastal areas around the whole island, and drier, less steep, and/or open forest and savanna environments in the central lowlands. The western interior was identified as being rarely used by Aboriginal people in the Holocene, with the exception of isolated pockets of habitat; yet whether this is a true reflection of Aboriginal resource use demands increased archaeological surveys, particularly in the Tasmanian Wilderness World Heritage Area.
Data from: The influence of landscape, climate, and history on spatial genetic patterns in keystone plants (Azorella) on sub-Antarctic islands
The distribution of genetic variation in species is governed by factors that act differently across spatial scales. To tease apart the contribution of different processes, especially at intermediate spatial scales, it is useful to study simpler ecosystems such as those on sub-Antarctic oceanic islands. In this study, we characterize spatial genetic patterns of two keystone plant species, Azorella selago on sub-Antarctic Marion Island and Azorella macquariensis on sub-Antarctic Macquarie Island. Although both islands experience a similar climate and vegetation structure, they differ significantly in topography and geological history. We genotyped six microsatellites for 1149 individuals from 123 sites across Marion Island and 372 individuals from 42 sites across Macquarie Island. We tested for spatial patterns in genetic diversity, including correlation with elevation and vegetation type, and clines in different directional bearings. We also examined genetic differentiation within islands, isolation-by-distance with and without accounting for direction, and signals of demographic change. Marion Island was found to have a distinct northwest-southeast divide, with lower genetic diversity and more sites with signal of population expansion in the northwest. We attribute this to asymmetric seed dispersal by the dominant northwesterly winds, and to population persistence in a southwestern refugium during the last Glacial Maximum. No apparent spatial pattern, but greater genetic diversity and differentiation between sites, was found on Macquarie Island, which may be due to the narrow length of the island in the direction of the dominant winds and longer population persistence permitted by the lack of extensive glaciation on the island.
Data from: Colonization history, host distribution, anthropogenic influence and landscape features shape populations of white pine blister rust, an invasive alien tree pathogen
White pine blister rust is caused by the fungal pathogen Cronartium ribicola J.C. Fisch (Basidiomycota, Pucciniales). This invasive alien pathogen was introduced into North America at the beginning of the 20th century on pine seedlings imported from Europe and has caused serious economic and ecological impacts. In this study, we applied a population and landscape genetics approach to understand the patterns of introduction and colonization as well as population structure and migration of C. ribicola. We characterized 1,292 samples of C. ribicola from 66 geographic locations in North America using single nucleotide polymorphisms (SNPs) and evaluated the effect of landscape features, host distribution, and colonization history on the structure of these pathogen populations. We identified eastern and western genetic populations in North America that are strongly differentiated. Genetic diversity is two to five times higher in eastern populations than in western ones, which can be explained by the repeated accidental introductions of the pathogen into northeastern North America compared with a single documented introduction into western North America. These distinct genetic populations are maintained by a barrier to gene flow that corresponds to a region where host connectivity is interrupted. Furthermore, additional cryptic spatial differentiation was identified in western populations. This differentiation corresponds to landscape features, such as mountain ranges, and also to host connectivity. We also detected genetic differentiation between the pathogen populations in natural stands and plantations, an indication that anthropogenic movement of this pathogen still takes place. These results highlight the importance of monitoring this invasive alien tree pathogen to prevent admixture of eastern and western populations where different pathogen races occur.
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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.