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opencc-zeroApr 2022View details →

Data from: Repeatability of adaptive radiation depends on spatial scale: regional versus global replicates of stickleback in lake versus stream habitats

The repeatability of adaptive radiation is expected to be scale dependent, with determinism decreasing as greater spatial separation among "replicates" leads to their increased genetic and ecological independence. Threespine stickleback (Gasterosteus aculeatus) provide an opportunity to test whether this expectation holds for the early stages of adaptive radiation -their diversification in freshwater ecosystems has been replicated many times. To better understand the repeatability of that adaptive radiation, we examined the influence of geographic scale on levels of parallel evolution by quantifying phenotypic and genetic divergence between lake and stream stickleback pairs sampled at regional (Vancouver Island) and global (North America and Europe) scales. We measured phenotypes known to show lake-stream divergence and used reduced representation genome-wide sequencing to estimate genetic divergence. We assessed the scale-dependence of parallel evolution by comparing effect sizes from multivariate models and also the direction and magnitude of lake-stream divergence vectors. At the phenotypic level, parallelism was greater at the regional than the global scale. At the genetic level, putative selected loci showed greater lake-stream parallelism at the regional than the global scale. Generally, the level of parallel evolution was low at both scales, except for some key univariate traits. Divergence vectors were often orthogonal, highlighting possible ecological and genetic constraints on parallel evolution at both scales. Overall, our results confirm that the repeatability of adaptive radiation decreases at increasing spatial scales. We suggest that greater environmental heterogeneity at larger scales imposes different selection regimes, thus generating lower repeatability of adaptive radiation at larger spatial scales.

opencc-by-4.0Jun 2022View details →

GPR-BMP-SPI: High spatial resolution multi-scale SPI datasets over China from January 1984 to December 2020

The datasets include standard precipitation index (SPI) at 1-month, 3-month, 6-month, 9-month and 12-month scales over the main terrestrial lands of China from January 1984 to December 2020. The SPI datasets were produced by blending the information from meteorological stations, and precipitation products, as well as topographical and geographical variables based on Gaussian process regression (GPR) models. The meteorological station data are from the China Meteorological Data Service Centre. Five precipitation products are used: (1) CHIRPS Daily: Climate Hazards Group InfraRed Precipitation With Station Data (Version 2.0 Final); (3) ERA5-Land Monthly Averaged by Hour of Day - ECMWF Climate Reanalysis; (3) FLDAS: Famine Early Warning Systems Network (FEWS NET) Land Data Assimilation System; (4) PERSIANN-CDR: Precipitation Estimation From Remotely Sensed Information Using Artificial Neural Networks-Climate Data Record; (5) TerraClimate: Monthly Climate and Climatic Water Balance for Global Terrestrial Surfaces. The maps of the difference of the confidence intervals (the upper prediction limit minus the lower prediction limit) at a significance level of 95% are also provided to show the spatial uncertainty of every single SPI map. The drought events were counted during 1984-2020 at annual and seasonal scales. The variables related to the drought events are presented in “Drought_Event.zip”. Reference: He, Q., Wang, M., Liu, K., Li, B., & Jiang, Z. (2023). Spatiotemporal analysis of meteorological drought across China based on the high-spatial-resolution multiscale SPI generated by machine learning. Weather and Climate Extremes, 40, 100567.

opencc-zeroJul 2022View details →

Long-term nitrogen fertilization alters arbuscular mycorrhizal fungi community phylogenetic structure in plant roots across fine spatial scales

Purpose: Nitrogen deposition due to human activities is known to have a substantial impact on arbuscular mycorrhizal fungi (AMF) community in plant roots. However, the influence of elevated nitrogen on the phylogenetic structure of AMF across fine spatial scales, as well as the mechanisms behind such alterations, are remained poorly understood. Results: Nitrogen addition significantly increased the phylogenetic alpha diversity (diversity within a plot) and the 'within-treatment' phylogenetic beta diversity (dissimilarity among replicate plots) of AMF communities, which resulted in an increased 'within-treatment' phylogenetic gamma diversity (overall diversity among all the replicate plots within a treatment). These changes were caused by the relative abundance decline of a dominant genus (Glomus) and an increase in non-dominant genera. Mechanically, nitrogen addition affected phylogenetic alpha diversity mainly by influencing soil properties. Likewise, the increased 'within-treatment' dissimilarity of plant community composition and changes in soil properties caused by nitrogen addition and plot distance contributed to an increase in within-treatment phylogenetic beta diversity. Conclusions: We conclude that deterministic environmental filtering (both abiotic and biotic) and dispersal limitation effect played critical roles in AMF community assembly under global change scenarios. Insightfully, this study provides a mechanistic understanding of the response of AMF to nitrogen addition across fine scales.

opencc-zeroJul 2022View details →

Fine-scale spatial genetic structure in a locally abundant native bunchgrass (Achnatherum thurberianum) including distinct lineages revealed within seed transfer zones

Analyses of the factors shaping genetic variation in widespread plant species are important for understanding evolutionary history and local adaptation and have applied significance for guiding conservation and restoration decisions. Thurber's needlegrass (Achnatherum thurberianum) is a widespread, locally abundant grass that inhabits heterogeneous arid environments of western North America and is of restoration significance. It is a common component of shrubland steppe communities in the Great Basin Desert, where drought, fire, and invasive grasses have degraded natural communities. Using a reduced representation sequencing approach, we generated SNP data at 5,677 loci across 246 individuals from 17 A. thurberianum populations spanning five previously delineated seed zones from the western Great Basin. Analyses revealed pronounced population genetic structure, with individuals forming consistent geographical clusters across a variety of population genetic analyses and spatial scales. Low levels of genetic diversity within populations, as well as high population estimates of linkage disequilibrium and relatedness, were consistent with self-fertilization as a contributor to population differentiation. Variance partitioning and partial redundancy analysis (pRDA) indicated local adaptation to environment as additionally influencing the spatial distribution of genetic variation. The environmental variables driving these results were similar to those implicated in recent genecological work which inferred local adaptation for seed zone delineation. Our analyses also revealed a complex evolutionary history of A. thurberianum in the Great Basin, where previously delineated seed zones contain distantly related populations. Our results indicate evolutionary history, mating system, and differentiation across distinct geographic and environmental scales have shaped genetic variation in A. thurberianum and illustrate how numerous aspects of population genetic variation might require consideration for restoration planning.

opencc-zeroAug 2022View details →

Replication data and code for: Environmental discourse exhibits consistency and variation across spatial scales on Twitter

Social media platforms, such as Twitter, are an increasingly important source of information and are forums for discourse within and between interest groups. Research highlights how social media communities have amplified movements such as the Arab Spring, #MeToo, and Black Lives Matter. But environmental digital discourse remains underexplored. In the present article, we apply automated text analysis to 200,000 Twitter users in several countries following leading environmental nongovernmental organizations. Some issues such as public action to decarbonize society or species conservation were discussed more intensely than agriculture or marine conservation. Our results illustrate where environmental discourse diverges and converges on Twitter across countries, states, and characteristics, such as political ideology. Using the coterminous United States as a case study, we observed that the prominence of issues varies across states and, in some cases, covaries with political ideology across counties. Our findings show paths forward to characterizing environmental priorities across many issues at unprecedented scale and extent. In this repository, we provide data and code to reproduce the results in the main text of this manuscript. This replication code and dataset accompany this manuscript: https://doi.org/10.1093/biosci/biac051

opencc-zeroSep 2022View details →

Grassland bird population declines at three Breeding Bird Survey spatial scales in contrast to a large native prairie

Grassland biomes in North America are threatened by agricultural intensification with implications for grassland associated bird populations via habitat loss, alteration, pesticide use and declining landscape heterogeneity. Despite decades of conservation concern, steep declines of North American grassland bird populations continue. Key to optimizing conservation effort is understanding how land-use practices, such as agriculture, across the annual cycle affects population status. Determining the relative influence of impacts on grassland bird declines is difficult given that the most robust estimates of population trends, the North American Breeding Bird Survey (BBS), are from surveys throughout agriculturally dominated regions. Our goal was to explore whether agriculture during the breeding season is a major driver of grassland bird declines. We derived trends for 16 grassland bird species spanning 23 years (1994-2016) at a large (459 km2), native prairie site, Suffield National Wildlife Area (SNWA) in Alberta, Canada. We compared those trends to the BBS across three spatial scales, a regional monitoring scheme with higher than average native grass cover (GBM), BCR 11 - Canada (Canada) and all of BCR 11 (BCR 11). Trends measured as annual percent change and credible interval varied greatly among species and survey strata. Across all species, declines were greatest for Canada (-1.3%, CI: -2.8, 0.0) and BCR 11 (-1.9%, CI: -3.2, -0.6). This contrasts with positive mean trends for GBM routes (1.0%, CI: -0.4, 2.3) and the SNWA data (1.7%, CI: 0.3, 3.3). Six of 16 species at SNWA were increasing with one decreasing. Five species increased at GBM and four declined. Canada had 10 species declines and three increases and BCR 11 had 10 declines and no increases. None of six grassland obligate species declined at SNWA, two declined at GBM, and all six declined over the two larger BBS strata. Our results showing fewer negative population trends at a large native grassland site compared to BBS at three spatial scales across the North American prairies support the prediction that agricultural intensification on breeding grounds is a major driver of declining populations and protection of remaining native grasslands should remain a key component of grassland bird conservation efforts.

Fig. 1 in Multi-Criteria Decision Analysis as a tool to extract fishing footprints: application to small scale fisheries and implications for management in the context of the Maritime Spatial Planning Directive

Fig. 1: Map of the study area.

opencc-zeroJun 2024View details →

Data from: Positive spatial and temporal density-dependence drive early reproductive economy-of-scale effects of masting in a European old-growth forest community

Masting, the spatial synchronization of interannual variation in seed production, can enhance reproductive efficiency through positive density-dependent processes (DD) that result in economies of scale (EOS), such as decreased pollen limitation and predator satiation in years of high reproduction. While the general occurrence of such EOS effects has been documented for masting species, few studies simultaneously investigated how spatial and temporal variation in reproduction affects pollination and predation. Furthermore, it is unclear whether the same mechanisms apply to co-occurring species with different levels of conspecific density, pollen limitation, and seed defenses. Here, we use a long-term data set with high spatial resolution of seed production of European beech (Fagus sylvatica), Norway spruce (Picea abies), and silver fir (Abies alba) in a primeval montane forest to investigate the relationship between reproductive effort, pollination efficiency, and predispersal predation by insects. We found that, along the temporal axis, the proportion of sound (fertilized and unpredated) seeds correlated positively with annual seed production over the 14-year study period in all three species, most strongly in beech and only weakly in silver fir. Moreover, the results show that in beech, spatial seed density interacts with plot-wide annual seed rain to enhance DD effects on seed predation, suggesting additive effects of synchronous reproduction on fitness benefits. Synthesis: For both pollination and predispersal predation in beech and spruce, the strongest DD effects occur at low levels of reproduction and quickly reach asymptotes at higher levels, suggesting the presence of thresholds in different EOS mechanisms. As variability and synchrony in mast-seeding are expected to decline with climate change, EOS effects driven by DD may remain stable until the threshold is reached, at which sudden declines would result in devastating effects on the availability of viable seeds for germination and recruitment.

Fig. 6 in Multi-Criteria Decision Analysis as a tool to extract fishing footprints: application to small scale fisheries and implications for management in the context of the Maritime Spatial Planning Directive

Fig. 6: Scatterplot matrices for Large (A) and Linear (B) FM functions.

Fig. 8 in Multi-Criteria Decision Analysis as a tool to extract fishing footprints: application to small scale fisheries and implications for management in the context of the Maritime Spatial Planning Directive

Fig. 8: High values of the FP c index as estimated by Local Moran's I test.

Fig. 5 in Multi-Criteria Decision Analysis as a tool to extract fishing footprints: application to small scale fisheries and implications for management in the context of the Maritime Spatial Planning Directive

Fig. 5: Spatial representation of coastal vessels activity indexes (Ac).

Fig. 4 in Multi-Criteria Decision Analysis as a tool to extract fishing footprints: application to small scale fisheries and implications for management in the context of the Maritime Spatial Planning Directive

Fig. 4: Spatial representation of the Coastal fishery suitability index (Sc).

Fig. 3 in Multi-Criteria Decision Analysis as a tool to extract fishing footprints: application to small scale fisheries and implications for management in the context of the Maritime Spatial Planning Directive

Fig. 3: Spatial representation of the criteria ranking taken into account in MCDA.

opencc-by-4.0Feb 2019View details →

Data used in manuscript Spatial modelling of local-scale biogenic and anthropogenic carbon dioxide emissions in Helsinki

This data set includes data used to develop and evaluate carbon dioxide emission modelling component in the Surface Urban Energy and Water balance Scheme (SUEWS). The data files are: <ol> <li>CO2_Model_Parameter_Fitting.zip contains m-files (Matlab) used to calculate parameters for photosynthesis modelling <ul> <li>F_pho_data.mat includes meteorological and EC data used to fit photosynthesis model parameters in Kumpula</li> <li>FitKumpulaData.m calculates the model parameters in Kumpula</li> <li>FitViikkiData.m calculates the model parameters in Viikki</li> <li>Other m-files needed by the above two codes</li> </ul> </li> <li>Data.zip contains measured data used to develop and evaluate SUEWS <ul> <li>KumpulaData2012.txt and TorniData2012.txt include eddy covariance data measured at the two sites in Helsinki</li> <li>SMEARIII_meteorology_2016MM_30.m meteorological data used to fit model parameters in Viikki street trees (see 00 ReadMe_SMEARIII_Meteorology.TXT for details)</li> <li>Viikki_SWC_2016.txt measured soil moisture from Viikki in 2016</li> <li>Kumpula_2016_HH_RLAI6_Output.out is SPP output used to fit model parameters in Viikki street trees</li> </ul> </li> <li>SUEWS_EC_Site_Model_runs: SUEWS input and output files for Kumpula and Torni model runs</li> <li>SpatialRun_input.zip: SUEWS input files for the spatial model run</li> <li>spatmatHel_final.mat: SUEWS output files for spatial model run in mat-format</li> </ol>

opencc-by-4.0Dec 2018View details →

Agriculture erases climate constraints on soil nematode communities across large spatial scales

Data supporting "Agriculture erases climate constraints on soil nematode communities across large spatial scales".

opencc-by-4.0Dec 2008View details →

Fig. 1 in Distribution of carabid beetles in agroecosystems across spatial scales - A review

Fig. 1. Nested relations between the spatial levels (after Ettema, Wardle (2002), with changes).

opencc-by-4.0Jun 2021View details →

Data set for the article "Recently photoassimilated Carbon and fungus-delivered Nitrogen are spatially correlated at the cellular scale in the ectomycorrhizal tissue of Fagus sylvatica"

This dataset contains data that support the manuscript Mayerhofer et al (2021) "Recently photoassimilated Carbon and fungus-delivered Nitrogen are spatially correlated at the cellular scale in the ectomycorrhizal tissue of Fagus sylvatica", The New Phytologist, DOI:10.1111/nph.17591 It contains the following data: (1) NanoSIMS imaging data, which was used for Fig. 4-7, is provided in NanoSIMS_control_root_tip.zip and NanoSIMS_labelled_root_tip.zip. Each zip-files contains: <ul> <li>the original NanoSIMS images (.im)</li> <li>their related checkfiles (.chk_im)</li> <li>ROIs description (.rois.zip)</li> </ul> of the unlabelled control and the labelled root tip section, respectively. ".im" and ".chk_im" are the original image data aquisition files from the NanoSIMS instrument. "rois.zip" files describe selected regions of interests and were created utilizing the OpenMIMS plugin (Center for Nano Imaging, https://nano.bwh.harvard.edu/MIMSsoftware) for the image analysis software ImageJ (National Institutes of Health, Bethesda, MD, USA). (2) Means and standard deviations of all measured elements and isotopes of each region of interest, as obtained via the .rois.zip files from the NanoSIMS images, are reported in NanoSIMS_ROI_data.csv (used for Fig.7). (3) Linescan_data.csv contains data used for Fig. 8. (4) IRMS_roots_data.csv contains data of root segments and mycorrhizal root tips analysed with isotope-ratio mass spectrometry (EA-IRMS) (used for Fig. 2) Description of column meanings from csv data files can be found in the according "_description" files.

opencc-zeroSep 2021View details →

Data and codes to replicate the analysis in: The spatial ecology of conflicts: Unravelling patterns of wildlife damage at multiple scales

Human encroachment into natural habitats is typically followed by conflicts derived from wildlife damages to agriculture and livestock. Spatial risk modelling is a useful tool to gain understanding of wildlife damage and mitigate conflicts. Although resource selection is a hierarchical process operating at multiple scales, risk models usually fail to address more than one scale, which can result in the misidentification of the underlying processes. Here, we addressed the multi-scale nature of wildlife damage occurrence by considering ecological and management correlates interacting from household to landscape scales. We studied brown bear (Ursus arctos) damage to apiaries in the North-eastern Carpathians as our model system. Using generalized additive models, we found that brown bear tendency to avoid humans and the habitat preferences of bears and beekeepers determine the risk of bear damage at multiple scales. Damage risk at fine scales increased when the broad landscape context also favoured damages. Furthermore, integrated-scale risk maps resulted in more accurate predictions than single-scale models. Our results suggest that principles of resource selection by animals can be used to understand the occurrence of damages and help mitigate conflicts in a proactive and preventive manner.

opencc-zeroOct 2022View details →

Limited seed dispersal shapes fine-scale spatial genetic structure in a Neotropical dioecious large-seeded palm

Seed and pollen dispersal contribute to gene flow and shape the genetic patterns of plants over fine spatial scales. We inferred fine-scale spatial genetic structure (FSGS) and estimated realized dispersal distances in Phytelephas aequatorialis, a Neotropical dioecious large-seeded palm. We aimed to explore how seed and pollen dispersal shape this genetic pattern in a focal population. For this purpose, we genotyped 138 seedlings and 99 adults with 20 newly developed microsatellite markers. We tested if rodent-mediated seed dispersal has a stronger influence than insect-mediated pollen dispersal in shaping FSGS. We also tested if pollen dispersal was influenced by the density of male palms around mother palms in order to further explore this ecological process in large-seeded plants. Rodent-mediated dispersal of these large seeds occurred mostly over short distances (mean 34.76 ± 34.06 m) while pollen dispersal distances were two times higher (mean 67.91 ± 38.29 m). The spatial extent of FSGS up to 35 m and the fact that seed dispersal did not increase the distance at which male alleles disperse suggest that spatially limited seed dispersal is the main factor shaping FSGS and contributes only marginally to gene flow within the population. Pollen dispersal distances depended on the density of male palms, decreasing when individuals show a clumped distribution and increasing when they are scattered. Our results show that limited seed dispersal mediated by rodents shapes FSGS in P. aequatorialis, while more extensive pollen dispersal accounts for a larger contribution to gene flow and may maintain high genetic diversity.