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76 results for “habitat loss”
Data and Code for "Why are generalists the 'winners' of habitat loss? Unveiling the process underlying specialist-generalist replacements in fragmented landscapes"
<p><span>Data and R-based workflow for the study "Why are generalists the ‘winners’ of habitat loss? Unveiling the process underlying specialist-generalist replacements in fragmented landscapes".</span></p>
"Agricultural trade and its impacts on cropland use and the global loss of species habitat." - Supplementary data
<p>This dataset and code is part of the following publication:<br> Schwarzmueller, F. & Kastner, T (2022), Agricultural trade and its impact on cropland use<br> and the global loss of species' habitats. Sustainability Science, doi: 10.1007/s11625-022-01138-7<br> </p> <p>There are three zip-folders accompanying this publication:</p> <p>Code.zip contains all the R-Scripts and input files neccessary for the calculation that were written by the authors.</p> <p>Data.zip contains the FAO-input data (as dowloaded in 2021). This exact data is not available anymore from the FAOSTAT website, which is why we included it in this repository.</p> <p>TradeMatrixFeed_import_dry_matter_1986-2013.zip contains the results from the calculation as shown in the paper.</p>
Proactive conservation to prevent habitat losses to agricultural expansion
<p>The projected loss of millions of square kilometres of natural ecosystems to meet future demand for food, animal feed, fibre, and bioenergy crops is likely to massively escalate threats to biodiversity. Reducing these threats requires a detailed knowledge of how and where they are likely to be most severe. We developed a geographically explicit model of future agricultural land clearance based on observed historic changes and combine the outputs with species-specific habitat preferences for 19,859 species of terrestrial vertebrates. We project that 87.7% of these species will lose habitat to agricultural expansion by 2050, with 1,280 species projected to lose ≥25% of their habitat. Proactive policies targeting how, where, and what food is produced could reduce these threats, with a combination of approaches potentially preventing almost all these losses while contributing to healthier human diets. As international biodiversity targets are set to be updated in 2021, these results highlight the importance of proactive efforts to safeguard biodiversity by reducing demand for agricultural land.</p>
Code and data for "Global warming generates predictable extinctions of warm- and cold-water marine benthic invertebrates via thermal habitat loss"
<pre>This repository contains the following information: Datasets S1 to S4 can all be loaded, manipulated, and analysed in R using script provided in Data S5 to obtain the results of the paper, Reddin et al. 2022, "Global warming generates predictable extinctions of warm and cold-water marine benthic invertebrates via thermal habitat loss". Data S1. (separate file) The original downloaded PaleoDB dataset. Data S2. (separate file) The pre-prepared dataset of occurrences. Data S3. (separate file) The finished environmental dataset. Data S4. (separate file) Additional environmental dataset. Data S5. (separate file) The R-code for the main analysis. Data S6. (compressed directory) Output data and code from the simulations. Table S7 (separate file). List of data source publications for PaleoDB data used in our study. Listed are the data source author list (ref_author), year (ref_pubyr), and reference number as appears in the PaleoDB (reference_no). </pre>
Global warming leads to habitat loss and genetic erosion of alpine biodiversity
<p><span><strong>Aim</strong>:</span><span> Species living on steep environmental gradients are expected to be especially sensitive to global climate change. Here, we combined genetic, ecological niche modelling and climatic niche comparisons to investigate the influence of climate on the biogeography of three alpine species with overlapping ranges.</span></p> <p><span><strong>Location</strong>:</span><span> Te Waipounamu (South Island) Aotearoa</span>–<span>New Zealand.</span></p> <p><span><strong>Taxon</strong>:</span><span> Endemic alpine-adapted Cataontopinae grasshoppers.</span></p> <p><span><strong>Methods</strong>:</span><span> We used niche modelling to estimate and project the potential niche of three focal species under past and future climate scenarios.</span><span> Vulnerability assessments were</span><span> performed using </span><span>niche factor analyses. Demographic trends and phylogeographic structure were investigated using samples from 15 mountain tops to generate mitochondrial DNA haplotype networks and population genetic statistics.</span></p> <p><span><strong>Results</strong>:</span><span> Niche models and genetic data suggest suitable habitat for all three alpine species was more widespread and contiguous in the past than today. Demographic analyses indicate in situ survival rather than post-Pleistocene colonisation of current habitat. Population structuring and genetic divergence suggest that mountain uplift during the Pliocene and environmental barriers during Pleistocene glacial and interglacial stages shaped contemporary population structure of each species. Though geographically overlapping, niche analyses suggest these alpine species are not ecologically identical, and each shows similar but distinct responses to environmental change, but all will lose intraspecific diversity through population extinction.</span></p> <p><span><strong>Main</strong> <strong>conclusions</strong>:</span><span> Climatic, biological and geophysical factors controlled population structuring of three cold-adapted species during the Pleistocene with a legacy of spatially separate intraspecific lineages. Ecological niche models for each species emphasise distinct combinations of environmental proxies, but all are expected to experience severe habitat reduction during climate warming. Increased global temperatures drive available habitat to higher elevation resulting in population contractions, range shifts, habitat fragmentation, local extinctions, and genetic impoverishment. Despite alpine species not being ecologically identical, we predict all mountain biota will lose significant genetic diversity due to global warming.</span></p>
Data for: Extensive coral mortality and critical habitat loss following dredging and their association with remotely-sensed sediment plumes
<p>This work describes impacts to coral reefs surrounding the 2013-2015 dredging of the Port of Miami based on data collected before, during, and after dredging by Dial Cordy and Associates (DCA) on behalf of Great Lakes Dredge and Dock Company, the dredging contractors for the U.S. Army Corps of Engineers (USACE) and for the Port of Miami (Miami-Dade County). A front page for this repository can be accessed at <a href="http://jrcunning.github.io/pom-dredge">jrcunning.github.io/pom-dredge</a> containing rendered R Markdown detailing all analyses conducted as part of this work.</p>
Data from: Maintaining local adaptation is key for evolutionary rescue and long-term persistence of populations experiencing habitat loss and a changing environment
Open the record for dataset details and reuse information.
Proactive conservation to prevent habitat losses to agricultural expansion
Open the record for dataset details and reuse information.
Global warming leads to habitat loss and genetic erosion of alpine biodiversity
Open the record for dataset details and reuse information.
Habitat fragmentation affects plant-arthropod interactions through connectivity loss and edge effects
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Data from: Habitat loss in the restricted range of the endemic Ghanaian cichlid Limbochromis robertsi
<p>Remote sensing has become an integral and invaluable tool to inform biodiversity conservation and monitoring of habitat degradation and restoration over time. Despite the disproportionately high levels of biodiversity loss in freshwater ecosystems worldwide, ichthyofauna are commonly overlooked in favor of other keystone species. Freshwater fish, as indicators of overall aquatic ecosystem health can also be indicators of larger scale problems within an ecosystem. As a case study with multi-temporal, multi-resolution satellite imagery, we examined deforestation and forest fragmentation around the Atewa Forest Reserve, Ghana. Within small creeks, <i>Limbochromis robertsi</i>, a unique freshwater cichlid with an extremely limited distribution range can be found. Historically, the land cover in the area has undergone substantial deforestation for agriculture and artisanal small-scale mining. In the 1389 km<sup>2</sup> study area we found deforestation accelerated along with increased forest fragmentation in the 2014 – 2017 period (167.4 km<sup>2</sup> of deforestation) with the majority of the forest loss along the river and creek banks due to small-scale mining operations and increased agriculture. Field visits indicated a decrease in the total <i>L. robertsi</i> population by approximately 90% from the early 1990s to 2018. Its<i> </i>distribution has been reduced to higher elevations by anthropogenic habitat barriers at low elevations and the presence of predatory species. Loss of Riparian forest through land use and cover change to mining and agriculture contributes to the habitat degradation for these endemic species. The fine spatial and temporal scale studies required to assess habitat characteristics is not captured by global or continental scale datasets.</p>
Selective extinctions resulting from random habitat destruction lead to under‐estimates of local and regional biodiversity loss in a manipulative field experiment
<p>Land-use change is a significant cause of anthropogenic extinctions, which are likely to continue and accelerate as habitat conversion proceeds in most biomes. One way to understand the effects of habitat loss on biodiversity is through improved tools for predicting the number and identity of species losses in response to habitat loss. There are relatively few methods for predicting extinctions and even fewer opportunities for rigorously assessing the quality of these predictions. In this paper we address these issues by applying a new method based on rarefaction to predict species losses after random, but aggregated, habitat loss. We compare predictions from three rarefaction models, individual-based, sample-based, and spatially-clustered, to those derived from a commonly-used extinction estimation method, the Species-Area Relationship (SAR). We apply each method to a mesocosm experiment, in which we aim to predict species richness and extinctions of arthropods immediately following 50% habitat loss. While each model produced strikingly accurate predictions of species richness immediately after the habitat loss disturbance, each model significantly underestimated the number of extinctions occurring at both the local (within-mesocosm) and regional (treatment-wide) scales. Despite the stochastic nature of our small-scale, short-term, and randomly applied habitat loss experiment, we found surprisingly clear evidence for extinction selectivity, for example when abundant species with low extinction probabilities were extirpated following habitat loss. The important role played by selective extinction even in this contrived experimental system suggests that ecologically driven, trait-based extinctions play an equally important role to stochastic extinction, even when the disturbance itself has no clear selectivity. As a result, neutrally stochastic null models such as the SAR and rarefaction are likely to underestimate extinctions caused by habitat loss. Nevertheless, given the difficulty of predicting extinctions, null models provide useful benchmarks for conservation planning by providing minimum estimates and probabilities of species extinctions.</p>
Caught in a bottleneck: habitat loss for woolly mammoths in central North America and the ice-free corridor during the last deglaciation
<p>The dataset is to describe the habitat structure and bioenergetic characteristics of woolly mammoths (<i><span>Mammuthus primigenius</span></i>) in North America during the last deglaciation between 15 and 10 ka. The habitat structure includes fractional woody cover (FWC) and net primary productivity (NPP) for 20 plant functional types (PFTs). NPP is based on the dynamic vegetation model LPJ-GUESS (LPJG). FWC is based on LPJ-GUESS and fossil pollen records in the Neotoma Paleoecology Database. The bioenergetic characteristics of woolly mammoths are the results of Niche Mapper, including metabolic rate, forage consumption, freshwater consumption, and other bioenergetic traits of individual woolly mammoths. These data were conducted at a temporal resolution of 100-year means of climate simulations every 1,000 years, from 15 to 10 ka. Simulations were run for all of North America except Alaska (10° – 80°N, 140° – 45°W) at a spatial resolution of 0.5°x0.5° grid latitude and longitude.</p>
Data from: Artificial refuges to combat habitat loss for an endangered marsupial predator: how do they measure up?
<p>One technique used to combat the growing global species extinction crisis has been to create artificial refuges—human-made replacements for natural refuges destroyed during habitat modification. However, there is limited knowledge of how closely artificial refuges replicate the natural refuges they seek to replace. Mining threatens many species worldwide through large-scale habitat modification, and artificial refuges have been proposed as a method to offset the resulting habitat loss. Here, we examined the microclimatic, physical, and biotic characteristics of natural dens occupied by the northern quoll (<i>Dasyurus hallucatus</i>)—an endangered marsupial threatened by habitat loss—and compared these to 1) superficially similar unoccupied crevices, and 2) artificial dens created by mining companies for northern quolls. Northern quolls occupied natural dens that were cooer and deeper than unoccupied crevices, likely to avoid lethal air temperatures as well as predators. Artificial dens provided similar thermal properties to occupied dens, but lacked key characteristics in having shallower den cavities, less complex surrounding habitat, increased feral cat visitation, and less small mammal prey compared to occupied dens. This study highlights the need to consider multiple facets when constructing artificial refuges, in order to avoid perverse outcomes, such as inadequate shelter, increased predation and food shortages.</p>
Data from: Landscape heterogeneity can partially offset negative effects of habitat loss on mammalian biodiversity in agroecosystems
<p>Intensive, large-scale agriculture promotes the conversion of natural habitats and diversified crops into monocultures, decreasing both native vegetation cover and landscape heterogeneity, leading to landscape simplification. Yet, a key knowledge gap persists on the relative impacts of the loss of native vegetation and landscape heterogeneity on biodiversity. Addressing this gap is pressing to support policies that conciliate agricultural production and biodiversity conservation and to move forward some scientific controversies, as the "land sharing versus land sparing" and "habitat loss versus fragmentation" debates.<br>Through a hierarchical sampling design that maximized variation, while minimizing correlation, between landscape heterogeneity and native vegetation cover, we recorded the occurrence of medium and large-bodied mammals in native vegetation and agricultural areas of 55 landscapes in a global conservation hotspot and a key commodity production area – the Brazilian savanna, Cerrado. We compared simple, additive, and interactive models to investigate the effects of landscape heterogeneity and native vegetation cover on richness and composition of native and invasive mammals. <br>Native and invasive mammal communities were affected by both native vegetation cover and landscape heterogeneity, although the effects of the first was stronger than the later. Both aspects had positive effects on native species richness and negative on invasive species richness, indicating that the loss of native vegetation and the reduction in landscape heterogeneity lead to biotic homogenization. Yet, while landscape heterogeneity benefited most native species, the direction of its effect varied among invasive species and depended on native vegetation cover.<br>Synthesis and applications: Besides reducing habitat loss, avoiding landscape homogenization is key for conciliating agricultural production and biodiversity conservation, pointing to the relevance of policies encouraging crop diversification. As increasing landscape heterogeneity can in part compensate the negative effects of losing native habitat on biodiversity in agroecosystems, policies can gain feasibility by adjusting the balance between native vegetation cover and landscape heterogeneity according to what best suits local restraints and demands.</p>
Wind energy development can lead to guild-specific habitat loss in boreal forest bats
<p>Forest management rarely considers protecting bats in Fennoscandian regions although all species rely on forest habitat at some point in their annual cycle. This issue is especially evident as wind parks have increasingly been developed inside Fennoscandian forests, against the advice of international bat conservation guidelines. In this study, we aimed to describe and explain bat community dynamics at a Norwegian wind park located in a boreal forest, especially to understand potential avoidance or attraction effects. The bat community was sampled acoustically and described using foraging guilds (short, medium, and long-range echolocators; SRE, MRE, LRE) as well as behavior (commuting, feeding and social calls). Sampling was undertaken at two locations per turbine: (i) the turbine pad and (ii) a paired natural habitat at ground level, as well as from a meteorological tower. We used a recently developed method for camera trapping nocturnal flying insects synchronously with bat acoustic activity. Our results reveal trends in feeding and general bat activity across foraging guilds in relation to insect availability, habitat type, wind, temperature, and seasonality. We show how seasonal patterns in behavior across guilds were affected by habitat type, temperature, and wind. We found that SRE commuting and especially feeding activity was highest in natural habitats, whereas LRE overall activity at habitats more season dependent. We found that nocturnal insect availability was positively correlated with total bat feeding activity throughout the night. Our results provide evidence for both direct and indirect risks to bat communities by wind parks: SRE bat habitat is lost to wind energy infrastructure and LRE bat may have an increased risk of fatality. Our findings provide important insights on seasonal and spatial variability in bat activity, which can inform standardizing monitoring of bats acoustically in boreal forests, at wind parks, and in combination with non-invasive insect monitoring.</p>
Data for: Climate warming and projected loss of thermal habitat volume in lake populations of brook trout
<p>We applied an ensemble of climate warming models and the seasonal temperature profile model for lakes (STM) to assess changes in brook trout thermal habitat volume (THV) among lakes (N=100) within a large, protected area under two climate warming scenarios, RCP 4.5 and RCP 8.5. Brook trout thermal habitat was defined as 9-17°C. Climate warming projections for the balance of this century, regardless of RCP category, will result in the loss of brook trout habitat in lakes that range widely in size. THV loss will be most extensive in lakes that are relatively shallow given their surface area. By 2071-2100 under RCP 4.5, the 90<sup>th</sup> percentile of THV loss = 31% vs. 63% under RCP 8.5. By the century's end under RCP 8.5, the protected area landscape will be a matrix of lakes with some serving as climate refugia (with reduced THV) and others having severe reductions in THV (>90<sup>th</sup> percentile THV loss).</p>
Habitat loss shapes the structure and species roles in mutualistic seed dispersal networks
<p>This dataset has the variables used in the paper "Habitat loss shapes the structure and species roles in tropical seed dispersal networks" as well as the script to perform the analysis.</p>
From nature reserve to mosaic management: improving matrix survival, not permeability, benefits regional populations under habitat loss and fragmentation
<p>Although matrix improvement in fragmented landscapes is a promising conservation measure, matrix permeability (willingness of an organism to enter the matrix) and movement survival in the matrix are usually aggregated. Consequently, it is unknown which matrix property needs to be improved. It also remains unclear whether matrix upgrading from dispersal passage to providing reproduction opportunities has large conservation benefits and whether there are interactive effects between habitat and matrix management.</p> <p>We examined matrix effects on regional populations across a gradient of habitat loss and fragmentation using simulation experiments that integrated demographic processes and movement modeling based on circuit theory. We separately modified the levels of matrix permeability and movement survival to evaluate their individual effects. We also altered the amount and configuration of not only habitat but also improved matrix to assess their effects on population vital rates (size, survival and density).</p> <p>In binary landscapes comprising habitat and unimproved matrix, matrix movement survival had larger effects on population vital rates than matrix permeability. Increasing movement survival increased vital rates, yet, increasing matrix permeability decreased vital rates. Increased permeability required corresponding increased movement survival to offset potential negative population outcomes.</p> <p>When subsets of the matrix functioning as dispersal passage only (where no reproduction opportunities existed) were improved, increasing matrix permeability but holding movement survival constant reduced all vital rates, especially with increasing habitat fragmentation. In contrast, when movement survival increased, vital rates increased given strong habitat fragmentation. The benefits of upgrading dispersal passage to provide reproduction opportunities for population survival were greatest when habitat amount was moderate. We also found synergetic effects between amounts of habitat and improved matrix, and the benefits of matrix improvement were promoted when improvement was achieved in a spatially aggregated manner.</p> <p><em>Synthesis and applications</em>: Matrix improvement and connectivity modeling aimed at increasing movement survival will likely bring larger conservation benefits than those for improving permeability alone. Buffering and connecting habitat remnants with improved matrix could provide benefits as long as movement survival is increased. Simultaneous implementation of habitat management and matrix improvement would yield synergistic conservation benefits.</p>
Pearson correlation tests for environmental variables, Student t-test for range shift and comparisons for habitat loss in 2070
<p><span>Habitat loss and shifts associated with climate change threaten global biodiversity, with impacts likely to be most pronounced at high latitudes. With the disappearance of the tundra breeding habitats, migratory shorebirds that breed at these high latitudes are likely to be even more vulnerable to climate change than those in temperate regions. We examined this idea using new distributional information on two subspecies of Black-tailed Godwits <em>Limosa limosa</em> in Asia: the northerly, bog-breeding <em>L. l. bohaii</em> and the more southerly, steppe-breeding <em>L. l. melanuroides</em>. Based on breeding locations of tagged and molecularly assayed birds, we modelled the current breeding distributions of the two subspecies with species distribution models, tested those models for robustness, and then used them to predict climatically suitable breeding ranges in 2070 according to bioclimatic variables and different climate change scenarios. Our models were robust and showed that climate change is expected to push bohaii into the northern rim of the Eurasian continent. <em>Melanuroides</em> is also expected to shift northward, stopping in the Yablonovyy and </span><span>Stanovoy Ranges</span><span>, and breeding elevation is expected to increase.</span> <span>Climatically suitable breeding habitat ranges would shrink to 16% and 11% of the currently estimated ranges of <em>bohaii</em> and <em>melanuroides</em>, respectively. Overall, this study provides the first predictions for the future distributions of two little-known Black-tailed Godwit subspecies and highlights the importance of factoring in shifts in bird distribution when designing climate-proof conservation strategies.</span></p>
ScienceDex guides
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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.