Find research datasets worth reusing

openother-openOct 2021View details →

Data from: Extrapolating potential crop damage by insect pests based on land use data: examining inter-regional generality in agricultural landscapes_210907

DamagePrediction_data_2021_210907 Data from: Extrapolating potential crop damage by insect pests based on land use data: examining inter-regional generality in agricultural landscapes

Deepened snow cover mitigates soil carbon loss from intensive land use in a semi-arid temperate grassland

Carbon (C) loss due to soil erosion is a major issue in semi-arid grasslands. The extent of soil erosion is determined by soil properties and vegetation structure, especially during the non-growing season. In many Inner Mongolian grasslands, intensive land use, such as overgrazing and mowing, has severely reduced plant cover and damaged soil structure, which has exacerbated soil C loss by erosion. At the same time, increasing winter snowfall due to climate change is stimulating plant growth and altering plant composition. However, we do not know how changes in winter snow cover interact with land-use practices to regulate soil C loss due to erosion. Here, we conducted a six-year snow manipulation experiment under different land-use practices (control; moderately mowed, MM; heavily mowed, HM) to measure net changes in soil depth, soil C, plant biomass, and vegetation structure. After six years, soil C loss under ambient snow was three times greater in the MM and four times greater in the HM treatment compared with controls during non-growing season. However, deepened winter snow alleviated erosion-induced soil C loss by 14%, 47%, 16% in the controls, MM and HM treatments, respectively. The severity of soil C loss declined with increasing aboveground biomass (AGB), surface root biomass and vegetation structure. Vegetation structure and AGB explained more of the variation in soil C loss than surface root biomass, possibly because a complex canopy and plant cover increases overall surface roughness, thereby reducing soil C loss. Intensified land use reduced AGB, surface root biomass and vegetation structure, but deepened snow increased overall surface roughness by promoting AGB. Hence, our study demonstrates that deepened snow can alleviate soil C loss due to land use practices by promoting AGB.

Disentangling effects of climate and land use on biodiversity and ecosystem services – a multi-scale experimental design

1. Climate and land-use change are key drivers of environmental degradation in the Anthropocene, but too little is known about their interactive effects on biodiversity and ecosystem services. Long-term data on biodiversity trends are currently lacking. Furthermore, previous ecological studies have rarely considered climate and land use in a joint design, did not achieve variable independence or lost statistical power by not covering the full range of environmental gradients. 2. Here, we introduce a multi-scale space-for-time study design to disentangle effects of climate and land use on biodiversity and ecosystem services. The site selection approach coupled extensive GIS-based exploration and correlation heatmaps with a crossed and nested design covering regional, landscape and local scales. Its implementation in Bavaria (Germany) resulted in a set of study plots that maximize the potential range and independence of environmental variables at different spatial scales. 3. Stratifying the state of Bavaria into five climate zones (reference period 1981–2010) and three prevailing land-use types, i.e. near-natural, agriculture and urban, resulted in 60 study regions (5.8x5.8 km quadrants) covering a mean annual temperature gradient of 5.6–9.8 °C and a spatial extent of ~310x310 km. Within these regions, we nested 180 study plots located in contrasting local land-use types, i.e. forests, grasslands, arable land or settlement (local climate gradient 4.5–10 °C). This approach achieved low correlations between climate and land use (proportional cover) at the regional and landscape scale with |r≤0.33| and |r≤0.29|, respectively. Furthermore, using correlation heatmaps for local plot selection reduced potentially confounding relationships between landscape composition and configuration for plots located in forests, arable land and settlements. 4. The suggested design expands upon previous research in covering a significant range of environmental gradients and including a diversity of dominant land-use types at different scales within different climatic contexts. It allows independent assessment of the relative contribution of multi-scale climate and land use on biodiversity and ecosystem services. Understanding potential interdependencies among global change drivers is essential to develop effective restoration and mitigation strategies against biodiversity decline, especially in expectation of future climatic changes. Importantly, this study also provides a baseline for long-term ecological monitoring programs.

opencc-zeroDec 2020View details →

Unexpected cryptic species among streptophyte algae most distant to land plants

Streptophytes are one of the major groups of the green lineage (Chloroplastida or Viridiplantae). During one-billion-years of evolution, streptophytes have radiated into an astounding diversity of uni- and multicellular green algae as well as land plants. Most divergent from land plants is a clade formed by Mesostigmatophyceae, Spirotaenia spp., and Chlorokybophyceae. All three lineages are species-poor and the Chlorokybophyceae consist of a single described species, Chlorokybus atmophyticus. In this study, we used phylogenomic analyses to shed light into the diversity within Chlorokybus using a sampling of isolates across its known distribution. We uncovered a consistent deep genetic structure within the Chlorokybus isolates, which prompted us to formally extend the Chlorokybophyceae by describing four new species. Gene expression differences among Chlorokybus species suggest certain constitutive variability that might influence their response to environmental factors. Failure to account for this diversity can hamper comparative genomic studies aiming to understand the evolution of stress response across streptophytes. Our data highlight that future studies on the evolution of plant form and function can tap into an unknown diversity at key deep branches of the streptophytes.

A multi-species approach to manage effects of land cover and weather on upland game birds

Loss and degradation of grasslands in the Great Plains region has resulted in major declines in abundance of grassland bird species. To ensure future viability of grassland bird populations, it is crucial to evaluate specific effects of environmental factors among species to determine drivers of population decline and develop effective conservation strategies. We used threshold models to quantify effects of land cover and weather changes on lesser and greater prairie-chickens (Tympanuchus pallidicinctus and T. cupido, respectively), northern bobwhites (Colinus virginianus), and ring-necked pheasants (Phasianus colchicus). We demonstrated a novel approach for estimating landscape conditions needed to optimize abundance across multiple species at a variety of spatial scales. Abundance of all four species was highest following wet summers and dry winters. Prairie-chicken and ring-necked pheasant abundance was highest following cool winters, while northern bobwhite abundance was highest following warm winters. Greater prairie-chicken and northern bobwhite abundance was also highest following cooler summers. Optimal abundance of each species occurred in landscapes that represented a grassland and cropland mosaic, though prairie-chicken abundance was optimized in landscapes with more grassland and less edge habitat than northern bobwhites and ring-necked pheasants. Because these effects differed among species, managing for an optimal landscape for multiple species may not be the optimal scenario for any one species.

Data from: From microbes to mammals: pond biodiversity homogenization across different land-use types in an agricultural landscape

Local biodiversity patterns are expected to strongly reflect variation in topography, land use, dispersal boundaries, nutrient supplies, contaminant spread, management practices and other anthropogenic influences. In contrast, studies focusing on specific taxa revealed a biodiversity homogenization effect in areas subjected to long-term intensive industrial agriculture. We investigated whether land use affects biodiversity levels and community composition (α & β diversity) in 67 kettle holes (KH) representing small aquatic islands embedded in the patchwork matrix of a largely agricultural landscape comprising grassland, forest, and arable fields. These KH, similar to millions of standing water bodies of glacial origin, spread across northern Europe, Asia, and North America, are physico-chemically diverse, differ in the degree of coupling with their surroundings. We assessed biodiversity patterns of eukaryotes, Bacteria and Archaea in relation to environmental features of the KH, using deep-amplicon-sequencing of environmental DNA (eDNA). First, we asked whether deep sequencing of eDNA provides a representative picture of KH biodiversity across the Bacteria, Archaea, and Eukaryotes. Second, we investigated if and to what extent KH biodiversity is influenced by the surrounding land-use. Our data shows that deep eDNA amplicon sequencing is useful for in-depth assessments of cross-domain biodiversity comprising both micro- and macro-organisms, but, has limitations with respect to single-taxa conservation studies. Using this broad method, we show that sediment eDNA, integrating several years to decades, depicts the history of agricultural land-use intensification. The latter, coupled with landscape wide nutrient enrichment (including by atmospheric deposition), groundwater connectivity between KH and organismal (active and passive) dispersal in the tight network of ponds, resulted in a biodiversity homogenization in the KH water, levelling off today's detectable differences in KH biodiversity between land-use types.

Anthropogenic land‐use change shapes bird diversity along the eastern Himalayan altitudinal gradient

Globally, the conversion of natural forest into agricultural land and human settlement has altered avian diversity and structure often leading to functional and/or phylogenetic homogenisation. While the effects of land-use change on avian functional and phylogenetic diversity is well studied in the tropics, it is poorly understood and scarcely studied in the Himalayas, let alone in the eastern Himalayan bird communities. This dataset comprises observations of 336 bird species from a replicated point-count transect survey conducted between 2019 and 2020 in Bhutan. We used a multispecies occupancy model to estimate occupancy probability while accounting for detection probability. The detection-corrected z-matrix was used to calculate functional and phylogenetic diversity. Our study shows that bird community occupancy along the elevational gradient is negatively associated with human land use (agriculture and settlement). Bird assemblages were functionally and phylogenetically clustered at higher elevations. Agriculture and settlement harboured higher functional and phylogenetic diversity whereas forests had phylogenetically diverse communities within functionally convergent traits. The higher functional and phylogenetic diversity in agriculture and settlement suggests that bird diversity offers an opportunity for a broad range of ecosystem services. Protection of forests abutting human settlements and agriculture will help preserve higher phylogenetic diversity. We recommend that agricultural practices that safeguard and improve bird-friendly habitats should be promulgated. Educational programmes on the importance of the roles of birds should be implemented and integrating bird conservation with farm production will help conserve bird diversity in human-dominated landscapes. To enhance the conservation value of working landscapes in the Himalayas, avitourism can be explored further.

Result data from "Relative effects of land conversion and land-use intensity on terrestrial vertebrate diversity"

These tif files contain the raw results of the publication "Relative effects of land conversion and land-use intensity on terrestrial vertebrate diversity", i.e. the raw data used to create the species richness loss maps shown in the main text and Supplementary Information of the publication. Please cite the publication when using these data.

opencc-by-4.0Sep 2021View details →

Modeling the economic and environmental impacts of land scarcity under deep uncertainty

Code and input files for the Dolan et al. 2021 paper "Modeling the economic and environmental impacts of land scarcity under deep uncertainty"

Representing surface heterogeneity in land-atmosphere coupling in E3SMv1 single-column model over ARM SGP during summertime - E3SM SCM data and code

This dataset contains post-processed E3SM single-column model output and code used to produce the figures in the manuscript that we are targeting Geoscientific Model Development to submit.

Existing land uses constrain climate change mitigation potential of forest restoration in India

The datasets were developed as part of the publication "Existing land uses constrain climate change mitigation potential of forest restoration in India". Please refer to the manuscript for processing details. ForestBioclimaticEnvelop_ProjectionUTM is the bioclimatic envelope of forests developed. The data is in raster format (GeoTIFF 32bit Float) where pixel values = 1 represent the bioclimatic envelope of forests and remaning pixel values are NA. The spatial resolution is 60m in WGS 84 UTM 43N projection system. FinalOpportunity_AfterExclusions_ProjectionUTM is the feasible area of opportunity, after all exclusions of land uses and covers that cannot naturally regenerate to forests. The data is in raster format (GeoTIFF 32bit Float) where pixel values = 1 represent the bioclimatic envelope of forests and remaning pixel values are NA. The spatial resolution is 60m in WGS 84 UTM 43N projection system.

Dung beetle and mammal dung data across a land-use gradient in Sabah, Malaysia

Dung beetle and mammal dung baited pitfall trap data across a land-use gradient from primary tropical forest to plantations in Sabah, Malaysia from February to April 2018.  The dataset accompanies the following journal article: Li Yuen Chiew, Talya D. Hackett, Jedediah F. Brodie, Shu Woan Teoh, David F. R. P. Burslem, Glen Reynolds, Nicolas J. Deere, Charles S. Vairappan, Eleanor M. Slade. Tropical forest dung beetle-mammal dung interaction networks remain similar across an environmental disturbance gradient. Journal of Animal Ecology. This Project was funded under United Nations Development Programme (UNDP): Biodiversity Conservation in Multiple Use Forest Landscapes and the Global Environmental Facility, and co-financed by Sabah Forestry Department, Yayasan Sabah, and WWF.

opencc-zeroDec 2021View details →

Experimental evidence that novel land management interventions inspired by history enhance biodiversity

To address biodiversity declines within semi-natural habitats, land-management must cater for diverse taxonomic groups. Integrating our understanding of the ecological requirements of priority (rare, scarce or threatened) species through 'biodiversity auditing', with that of the intensity and complexity of historical land-use, encourages novel forms of management. Experimental confirmation is needed to establish whether this enhances biodiversity conservation relative to routine management. Biodiversity auditing and historical land-use of dry-open terrestrial habitats in Breckland (Eastern England) both encourage management incorporating ground-disturbance and spatio-temporal variability. To test biodiversity conservation outcomes, we developed 40 4-ha management complexes over three successive winters, of which 20 were shallow-cultivated (rotovation) and 20 deep-cultivated (ploughing), stratified across 3,850-ha of closed-sward dry grassland and lowland heathland (collectively 'dry grassland'). Complexes comprised four 1-ha sub-treatments: repeat-cultivation, first-time-cultivation, one-year-old fallow and two-year-old fallow. We examined responses of vascular plants; spiders; true bugs; ground, rove and 'other' beetles; bees and wasps; ants; and true flies on treatment complexes and 21 4-ha untreated controls. Sampling gave 132,251 invertebrates from 877 species and 28,846 plant observations from 167 species. Resampling and rarefaction analyses showed shallow- and deep-cultivation both doubled priority species richness (pooling sub-treatments within complexes) compared to controls. Priority spider, ground beetle, other beetle, and true bug richness were greater on both treatments than controls. Responses were strongest for those priority dry-open-habitat associated invertebrates initially predicted (by biodiversity auditing) to benefit from heavy physical-disturbance. Assemblage composition (pooling non-priority and priority species) varied between sub-treatments for plants, ants, true bugs, spiders, ground, rove and other beetles; but only one-year-old fallowed deep-cultivation increased priority richness across multiple taxa. Treatments produced similar biodiversity responses across various dry grassland 'habitats' that differed in plant composition, allowing simplified management guidance. Synthesis and applications. Our landscape-scale experiment confirmed the considerable biodiversity value of interventions inspired by history and informed by systematic multi-taxa analysis of ecological requirements across priority biota. Since assemblage composition varied between sub-treatments, providing heterogeneity in management will support the widest suite of species. Crucially, the intended recipients responded most strongly, suggesting biodiversity audits could successfully inform interventions within other systems.

openother-openDec 2021View details →

Data archive for paper "Machine Learning Emulation of Urban Land Surface Processes"

This archive contains models, data* (Overview), as well as the Singularity image to optionally rerun experiments described in "<a href="https://doi.org/10.1029/2021MS002744">Machine Learning Emulation of Urban Land Surface Processes</a>". Prerequisites <ul> <li>Linux or macOS with Bash shell.</li> <li><a href="https://sylabs.io/">Singularity</a> (tested with version 3.6.3-1.el8)</li> </ul> Please note that all steps require <a href="https://sylabs.io/">Singularity</a> to be installed on your system. If you are looking for information on how to install or use Singularity, please refer to the <a href="https://sylabs.io/docs">Singularity documentation</a>. Overview A general overview of the repository structure is given below. Due to licensing restrictions analysis and forcing data (*) cannot be included and need to be requested separately (see Initialization). Data derivatives (**) from either analysis or forcing, as well as intermediary data (***), are not included as they can be generated by rerunning experiments (see Usage). <pre><code>. ├── data │ ├── analysis* │ ├── forcing* │ ├── teb │ ├── utils │ ├── wps │ └── wrf ├── hpc ├── models │ ├── teb │ ├── unn │ ├── wps │ └── wrf-unn ├── notebooks ├── outputs │ ├── analysis** │ ├── benchmark*** │ ├── forcing** │ ├── kerastuner*** │ ├── notebooks │ ├── tabular │ ├── teb** │ ├── unn** │ ├── wps*** │ └── wrf ├── paper │ └── figures ├── singularity └── tools </code></pre> Initialization Forcing and analysis data need to be requested separately. The following directories should map to their respective data archives: <ul> <li><code>./data/analysis</code> -> <a href="http://doi.org/10.5281/zenodo.4678387">Grimmond et al. (2013)</a></li> <li><code>./data/forcing</code> -> <a href="http://doi.org/10.5281/zenodo.4679279">Grimmond et al. (2021)</a></li> </ul> Usage To rerun all experiments and reproduce results, run <code>tools/run_all.sh</code> from your command prompt. After completion, all results are saved in the <code>outputs</code> directory. Note that WRF simulations require high CPU time and may take hours or days to complete. Alternatively, if <a href="https://en.wikipedia.org/wiki/Portable_Batch_System">Portable Batch System (PBS)</a> is available on your system, the following helpers may be used instead: <pre><code>qsub hpc/submit_init.pbs qsub hpc/submit_tuner.pbs qsub hpc/submit_unn.pbs qsub hpc/submit_find_median_unn.pbs qsub hpc/submit_wrf.pbs qsub hpc/submit_postprocess.pbs qsub hpc/submit_benchmark.pbs </code></pre> Note that you may need to modify PBS helper scripts to suit your specific environment. Development notes See DEVELOP.md. License The source code developed for this work is licensed under MIT (<code>LICENSE_CODE.txt</code>). For licensing information of third-party software see licenses under the <code>models</code> directory. Data files in this archive, including the initial and boundary condition data from the European Centre for Medium-Range Weather Forecasts (<code>data/wps/ungrib</code>), are licensed under CC BY-NC 4.0 (<code>LICENSE_DATA.txt</code>).

opencc-by-4.0Oct 2021View details →

A new approach to simulate peat accumulation, degradation and stability in a global land surface scheme (JULES vn5.8_accumulate_soil) for northern and temperate peatlands

This is the data (model output from JULES and observational data) used in the paper "A new approach to simulate peat accumulation, degradation and stability in a global land surface scheme (JULES vn5.8_accumulate_soil) for northern and temperate peatlands" for the resubmitted version after review of the discussion paper in Geoscientific Model Development Discussions (2021) https://doi.org/10.5194/gmd-2021-263. R code is provided that will recreate all of the plots in the paper using the data provided. These data include outputs from the JULES model including developments to represent peat accumulation, and observational data of peat properties (most are taken from other sources: references provided therein).

opencc-zeroJan 2022View details →

Leaf economics in a three‐dimensional environment: Testing leaf trait responses in vascular epiphytes to land use, climate, and tree zone

1. The study of functional traits offers predictive power for community ecology. Particularly in cases where individual species are difficult to study, known properties of trait spectra, such as the leaf economics spectrum (LES), and trait-environment relationships can provide crucial generalizable information that can contribute to forecasts of distributional shifts in response to the abiotic effects of climate and land use changes. 2. Vascular epiphytes have been proposed as indicators of environmental change, but we know little about the ecology of most species. Key functional trait assumptions are based on terrestrial plants; testing these in epiphytes verifies their universality and will inform applying functional traits in predicting epiphyte responses to climate and land use change. 3. In this study, we use functional traits from 37 vascular epiphyte species from forests and shade coffee farms at two sites in northern Nicaragua. We compare correlations among traits and intraspecific trait variances with those of terrestrial plants and among epiphyte taxonomic groups. We also test trait responses to environmental differences between sites and land use types, and within zones of the tree. 4. We find that epiphyte leaf traits fall toward the slower end of the LES, but with about one-third lower leaf nitrogen per change in specific leaf area (SLA) relative to terrestrial herbaceous plants. Bromeliads show less relationship between these traits than other epiphyte groups and also deviate in other trait interrelationships, suggesting unique leaf construction. 5. Trait-environment relationships varied most strongly along vertical gradients within trees, but some traits, including SLA and carbon isotope ratio, also responded to land use and site differences. 6. We present evidence that trait relationships established for terrestrial plants appear to translate to epiphytes, but identify some possible caveats. Strong trait response to vertical gradients within trees suggests that within-canopy shifts could provide resilience to climate and land use changes for some epiphyte species.

opencc-by-4.0Jan 2022View details →

Dataset for a manuscript entitled Variation in CO2 and CH4 Fluxes Among Land Cover Types in Heterogeneous Arctic Tundra in Northeastern Siberia

Dataset for the manuscript Variation in CO2 and CH4 Fluxes Among Land Cover Types in Heterogeneous Arctic Tundra in Northeastern Siberia authored by Sari Juutinen, Mika Aurela, Juha-Pekka Tuovinen, Viktor Ivakhov, Maiju Linkosalmi, Aleksi Räsänen, Tarmo Virtanen, Juha Mikola, Johanna Nyman, Emmi Vähä, Marina Loskutova, Alexander Makshtas, and Tuomas Laurila Dataset consists of CO2 and CH4 flux data measured mainly using chamber method in arctic tundra

opencc-zeroJan 2022View details →

Data from: Diversity of land snail tribe Helicini (Gastropoda: Stylommatophora: Helicidae): where do we stand after 20 years of sequencing mitochondrial markers?

Sequences of mitochondrial genes revolutionized the understanding of animal diversity and continue to be an important tool in biodiversity research. In the tribe Helicini, a prominent group of the western Palaearctic land snail fauna, mitochondrial data accumulating since the 2000s helped to newly delimit genera, inform species-level taxonomy, and reconstruct past range dynamics. We combined the published data with own unpublished sequences and provide a detailed overview of what they revealed about the diversity of the group. The delimitation of Helix is revised by placing Helix godetiana back in the genus and new synonymies are suggested within the genera Codringtonia and Helix. The spatial distribution of intraspecific mitochondrial lineages of several species is shown for the first time. Comparisons between species reveal considerable variation in distribution patterns of intraspecific lineages, from broad postglacial distributions to regions with a fine-scale pattern of allopatric lineage replacement. To provide a baseline for further research and information for anyone re-using the data, we thoroughly discuss the gaps in the current dataset, focusing on both taxonomic and geographic coverage. Thanks to the wealth of data already amassed and the relative ease with which they can be obtained, mitochondrial sequences remain an important source of information on intraspecific diversity over large areas and taxa.

Data repository - Substitution of ruminant meat with microbial protein in forward-looking global land-use scenarios towards 2050

This repository contains model-based scenario results of a study on substituting ruminant meat with microbial protein in human diets by 2050. The scenario data has been generated with the global multi-regional open-source land-use modelling framework MAgPIE 4.3.4: https://github.com/magpiemodel/magpie/releases/tag/v4.3.4 https://zenodo.org/record/4730378