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Figure 9 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446
Figure 9 Collage (application letters) of the procedure to request the recognition and incorporation of this Chiton articulatus mollusc into the National Fisheries Chart.
Vegetation growth and landscape genetics of Tillandsia lomas at its dry limits in the Atacama Desert shows fine-scale response to environmental parameters
<p>1. Ecosystems at its dry limits have been studied while focusing on species biology, fitness and interactions of biotic and abiotic parameters; however, the interactive effects of these parameters remain under-explored and, therefore, information is often lacking about the putative effect of global climate change on these ecosystems.</p> <p>2. Here, we conducted an analysis of the interplay of fine-scale landscape genetics and biotic and abiotic factors of terrestrial <i>Tillandsia</i> lomas in the hyperarid Atacama Desert, characterized by a fog-dependent vegetation type consisting of almost one single vascular plant species only.</p> <p>3. We showed that metapopulations of <i>Tillandsia landbeckii</i> are genetically connected over many hundreds of squarekilometres, and despite a large potential to propagate clonally genetic diversity is structured, regionally and locally. On landscape-level genetic diversity correlates well with fitness parameters such as growth, flowering and vegetation density, and we observed also fine-scaled correlation with a 3-D landscape model indicating a positive feedback with saisonal fog occurrence and availability. The various interdependies of biotic and abiotic factors also result in regular linear banding patterns of vegetation arranged orthogonally towards landscape slope. <i>Ex-situ</i> growth experiments indicate that <i>T. landbeckii</i> growths at optimal rates within this extreme, hyperarid environment, and we can extrapolate mean biomass production for this particular ecosystem.</p> <p>4. <i>Synthesis.</i> Our results suggest that the unique ecosystem of terrestrial <i>Tillandsia</i> lomas in the hyperarid Atacama Desert is an evolutionary balanced and fine-scaled system. Vegetation itself is built up by long-lived and persistent modules. We developed a descriptive model of the various interacting factors, thereby highlighting also a severe threat caused by global climate change.</p>
Data from: Temperature-driven colour lightness and body size variation scale to local assemblages of European Odonata but are modified by propensity for dispersal
<p>1. Previous macrophysiological studies suggested that temperature-driven colour lightness and body size variations strongly influence biogeographical patterns in ectotherms. However, these trait-environment relationships scale to local assemblages and the extent to which they can be modified by dispersal remains largely unexplored. We test whether the predictions of the thermal melanism hypothesis and the Bergmann's rule hold for local assemblages. We also assess whether these trait-environment relationships are more important for species adapted to less stable (lentic) habitats, due to their greater dispersal propensity compared to those adapted to stable (lotic) habitats.</p> <p>2. We quantified the colour lightness and body volume of 99 European dragon- and damselflies (Odonata) and combined these trait information with survey data for 518 local assemblages across Europe. Based on this continent-wide yet spatially explicit dataset, we tested for effects temperature and precipitation on the colour lightness and body volume of local assemblages and assessed differences in their relative importance and strength between lentic and lotic assemblages, while accounting for spatial and phylogenetic autocorrelation.</p> <p>3. The colour lightness of assemblages of odonates increased and body size decreased with increasing temperature. Trait-environment relationships in the average and phylogenetic predicted component were equally important for assemblages of both habitat types but were stronger in lentic assemblages when accounting for phylogenetic autocorrelation.</p> <p>4. Our results show that the mechanism underlying colour lightness and body size variations scale to local assemblages, indicating their general importance. These mechanisms were of equal evolutionary significance for lentic and lotic species, but higher dispersal ability seems to enable lentic species to cope better with historical climatic changes. The documented differences between lentic and lotic assemblages also highlight the importance of integrating interactions of thermal adaptations with proxies of the dispersal ability of species into trait-based models, for improving our understanding of climate-driven biological responses.</p>
Multi-objective optimization data (large scale truss)
<p>The file contains data obtained from the multi-objective optimization of a large scale truss</p>
Dataset on Article: Multiple stressors determine river ecological status at the European scale: Towards an integrated understanding of river status deterioration
<p>The shape file contains the raw data from the Global Change Biology article "River types, hydrology, riparian land use, nutrients, toxic substances, ecological status, stressor interactions". </p> <p><strong>General Information</strong></p> <p>Name of the dataset: MultipleStress_RiverEcoStatus.shp</p> <p>Type of dataset: vector data (shape file)</p> <p>Number of polygons: 52.847</p> <p>Geographic Coordinate System: GCS_WGS_1984</p> <p> </p> <p><strong>Contact details</strong></p> <p>Metadata / scientific contact person:</p> <p> First, last name: Sebastian Birk</p> <p> Email: <a href="mailto:sebastian.birk@uni-due.de">sebastian.birk@uni-due.de</a></p> <p> Institution: University of Duisburg-Essen, Faculty of Biology, Institute of Aquatic Ecology</p> <p> Address: Universitätsstrasse 5</p> <p> Postal code, city: 45141 Essen</p> <p> Country: Germany</p> <p> Web address: <a href="https://www.uni-due.de/aquatic_ecology/">https://www.uni-due.de/aquatic_ecology/</a></p> <p><strong>Attribute description</strong></p> <p><strong>m_zhyd_1</strong></p> <ul> <li>Unique identifier of FEC (Functional Elementary Catchment)</li> <li>Data structure: character</li> </ul> <p><strong>mars_bt12</strong></p> <ul> <li>Broad river type aggregated</li> <li>Data structure: character</li> </ul> <p><strong>eco_stat_2</strong></p> <ul> <li>Ecological status (class)</li> <li>Data structure: character</li> </ul> <p><strong>eco_stat_n</strong></p> <ul> <li>Ecological status (numeric class)</li> <li>Data structure: integer</li> </ul> <p><strong>LoadTPArea</strong></p> <ul> <li>Total phosphorous riverine loading (unit: kg km<sup>-2</sup> a<sup>-1</sup>)</li> <li>Decimal separator: comma</li> <li>Data structure: double</li> </ul> <p><strong>LoadTN_Are</strong></p> <ul> <li>Total nitrogen riverine loading (unit: kg ha<sup>-1</sup> a<sup>-1</sup>)</li> <li>Decimal separator: comma</li> <li>Data structure: double</li> </ul> <p><strong>lu_r_urb</strong></p> <ul> <li>Percent urban land use in the riparian zone</li> <li>Decimal separator: comma</li> <li>Data structure: double</li> </ul> <p><strong>lu_r_agr</strong></p> <ul> <li>Percent agricultural land use in the riparian zone</li> <li>Decimal separator: comma</li> <li>Data structure: double</li> </ul> <p><strong>hy_maf_abs</strong></p> <ul> <li>Alteration of mean annual flow (ratio scale)</li> <li>Decimal separator: comma</li> <li>Data structure: double</li> </ul> <p><strong>hy_bfi_abs</strong></p> <ul> <li>Alteration of base flow (ratio scale)</li> <li>Decimal separator: comma</li> <li>Data structure: double</li> </ul> <p><strong>msPAFP5EC5</strong></p> <ul> <li>Multi-substance Potentially Affected Fraction of species (msPAF-EC<sub>50</sub> based on 95<sup>th</sup> percentile)</li> <li>Decimal separator: comma</li> <li>Data structure: double</li> </ul> <p><strong>Further information</strong></p> <p>For more details on the dataset, see</p> <p>(Manuscript accepted, wating for publication at the moment)<br> </p> <p><strong>Acknowledgements</strong></p> <p>This work was funded by the MARS project (Managing Aquatic ecosystems and water resources under multiple stress), funded by the European Union under the 7th Framework Programme, contract no. 603378.</p>
Trait-similarity and trait-hierarchy jointly determine fine-scale spatial associations of resident and invasive ant species
<p>Interspecific competition, a dominant process structuring ecological communities, is influenced by species' phenotypic differences. Limiting similarity theory holds that species with similar traits should compete intensely ("trait-similarity"). In contrast, competing theories including modern coexistence theory emphasize that species with traits conferring competitive advantages should outcompete others ("trait-hierarchy"). Either or both of these mechanisms may drive competitive exclusion, but their relative importance and interacting effects are rarely studied. Here, we explore empirically whether trait-similarity and trait-hierarchy can explain fine-scale spatial associations observed between invasive and native ant species in a tropical assemblage. We find that pairwise co-occurrences between the invasive red imported fire ant Solenopsis invicta and 28 other species across relatively homogenous grasslands can be explained largely by an interaction of trait-similarity and trait-hierarchy in a single morphological trait, relative pronotum width. Specifically, higher trait-hierarchy values are associated with negative co-occurrences; however, these effects are counteracted when species are increasingly dissimilar in their trait ranges. These findings are consistent with the notion that limiting similarity and competitive hierarchies are interactive rather than discrete mechanisms driving competitive exclusion.</p>
Reproducible results for: pmparser and PMDB: resources for large-scale, open studies of the biomedical literature
<p>The zip file contains all code and results. See the included readme.</p>
Similarity between agricultural and natural land covers shapes how biodiversity responds to agricultural expansion at landscape scales
<p><span>The impact of agriculture on biodiversity depends on the extent and types of agriculture and the degree to which agricultural land contrasts with the natural ecosystem. Most research on the latter comes from studies on the influence of different agricultural types within a single ecosystem with far less study on how the natural ecosystem context shapes the response of biodiversity to agricultural production. We used citizen science data from agricultural areas in Canada's Eastern Hardwood-Boreal (forest ecosystem, n=108 landscapes) and Prairie Pothole (prairie ecosystem, n=99) regions to examine how ecosystem context shapes the response of avian species diversity, functional diversity and abundance to the amount of arable crop and pastoral agriculture at landscape scales. Avian surveys were conducted along 8km transects of Breeding Bird Survey routes with land cover assembled within a 20km2 landscape around each transect. The amount of agriculture at which species diversity peaked differed between the forest (15%) and prairie (51%) ecosystems, indicating that fewer species tolerated the expansion of agriculture in the former. In both ecosystems, functional diversity initially increased with agriculture and peaked at higher amounts (forest: 42%, prairie: 77 %) than species diversity suggesting that functional redundancy was lost first as agriculture increased. Species turnover with increasing agriculture was primarily among functional groups in forest where a shift from a low to a high agriculture landscape led to a decline in the percent of the community represented by Neotropical migrants, insectivores, upper foliage gleaners and bark foragers, and an increase in the percent of the community represented by short-distance migrants, granivores, omnivores and ground gleaners. There were few distinct shifts in the percent of the community represented by different functional groups in the prairie ecosystem. Total abundance was the least sensitive measure examined in both ecosystems and indicated that species losses with agriculture are likely followed by numerical compensation from agriculture tolerant species. Our results highlight the importance of ecosystem context for understanding how biodiversity is affected by agricultural production with declines in diversity occurring at lower agricultural extents in ecosystems with lower similarity between natural and agricultural land covers. These findings allow for more specific conservation recommendations including managing for species intolerant to agriculture in prairie ecosystems and limiting the expansion of high contrast agriculture and the loss of semi-natural habitat, such as hedge rows, in historically forested ecosystems.</span></p>
Data from: Genetic data reveal fine-scale ecological segregation between larval plethodontid salamanders in replicate contact zones
<p>Contact zones present unique opportunities to investigate ecological divergence, reproductive barriers, and gene flow between species. The two-lined salamander (<em>Eurycea</em> <em>bislineata</em>) species complex is a group of semiaquatic plethodontid salamanders with a reticulate evolutionary history that reflects the reorganization of river drainage basins. Although evidence for widespread, ancient introgression suggests an absence of reproductive isolating mechanisms in the early evolutionary history of the group, modern contact zones reveal a broader diversity of outcomes—with some putative species pairs occurring in sympatry and others exhibiting narrow hybrid zones. Here, we used RADcap data to investigate gene flow and ecological divergence in replicate contact zones between two species in the Appalachian foothills. Our results demonstrate that gene flow between these species is absent or rare, and larvae show strong, fine-scale ecological segregation among riffles, runs, and pools in streams. These results reinforce the more ambiguous conclusions of previous studies that suggested the evolutionary distinctiveness of these two species and underscore the importance of ecological factors in shaping local distributions.</p>
Data from: Re-evaluation of the law of constant extinction for ruminants at different taxonomical scale
<p><span>The "law of constant extinction," proposed by Van Valen, states that long and short-lived taxa have equal chances of going extinct. This pattern of age-independent extinction was originally inferred using the fossil record of several different taxa and relied on survivorship curves built from the literal reading of the fossil record. Van Valen's seminal work was mostly done at higher taxonomic levels, hence its prevalence at the species level could not be directly inferred. The surprisingly few subsequent studies done at the species level have challenged the prevalence of age-independent extinction, but those have, for the most part, failed to explicitly incorporate inherent biases of the fossil record. Using a recent Bayesian framework that accounts for several of those biases, including the fact that very short-living lineages might never make to the record itself, we showed that Ruminantia species present age-dependent extinction, where extinction probability decreases with species age. An analysis at the genus level suggested age-independent extinction but further examination suggested that the pattern might be more complex than previously reported by Van Valen. Our results indicate that different taxonomic levels may present different extinction regimes, which could justify the development of new macroevolutionary theory and methods.</span></p>
Multiple-scale negative impacts of warming on ecosystem carbon use efficiency across the Tibetan Plateau grasslands
<div> <p><strong>Aim:</strong> Ecosystem carbon use efficiency (CUEe) is a core parameter of ecosystem process models, but its relationships with climate are still uncertain, especially for ecosystems with harsh environments. High inconsistencies in climate impacts on the CUEe have been reported among various spatial scales. The goal of this study was to examine whether warming promotes or restricts the CUEe and whether the CUEe responds to a warming gradient in a linear or nonlinear manner.</p> <p><strong>Location:</strong> Tibetan Plateau.</p> <p><strong>Time period:</strong> 2000-2018.</p> <p><strong>Major taxa studied: </strong>Alpine grassland ecosystem.</p> <p><strong>Methods: </strong>We integrated multiple-source data of carbon fluxes and CUEe, including warming experiments at a site scale, eddy covariance observations at a landscape scale and synthesized warming experiments and ecosystem process models at a regional scale. Next, we deployed a statistical model to examine the warming impacts on the CUEe across scales; the effects of biotic and abiotic factors on the CUEe and its components were summarized based on the results of Standardized Major Axis Tests and Routines, structural equation modeling and nonlinear models.</p> <p><strong>Results: </strong>This study reported a suppressive warming impact on the CUEe, which followed a nonlinear curve with severe inhibition in the high-level warming treatment. With a warming threshold of 1.5-2.0 °C, CUEe response patterns transitioned from no change to a significant decrease. The restriction effects can be ascribed to the joint adverse and asymmetric effects of warming on CUEe components under multiple-level warming. Warming-modified relationships among CUEe components and the nonlinear effects of biotic and abiotic factors led to the nonlinear responses of CUEe to warming.</p> <p><strong>Main conclusions: </strong>This study revealed suppressive and nonlinear effects of warming on the CUEe, including especially dramatic CUEe decreases with high-level warming. These findings are critical for optimizing model parameters and improving predictions of the carbon sequestration capacity of alpine grasslands.</p> </div>
How adaptive capacity shapes the Adapt, React, Cope Response to climate impacts: insights from small-scale fisheries
<p>As the impacts of climate change on human society accelerate, coastal communities are vulnerable to changing environmental conditions. The capacity of communities and households to respond to these changes (i.e., their adaptive capacity) will determine the impacts of climate and co-occurring stressors. To date, empirical evidence linking theoretical measures of adaptive capacity to community and household responses remains limited. Here we conduct a global meta-analysis examining how metrics of adaptive capacity translate to human responses to change (Adapt, React, Cope Response) in 22 small-scale fishing case studies from 20 countries (n=191 responses). Using both thematic and Qualitative Comparative Analysis, we evaluate how responses to climate, environmental, and social change were influenced by domains of adaptive capacity. Our findings show that adaptive responses at the community level only occurred in situations where the community had Access to Assets, in combination with other domains including Diversity and Flexibility, Learning and Knowledge, and Natural Capital. In contrast, Access to Assets was nonessential for adaptive responses at the household level. Adaptive households demonstrated Diversity and Flexibility when supported by strong Governance or Institutions and were able often able to substitute Learning and Knowledge and Natural Capital with one another. Standardized metrics of adaptive capacity are essential to designing effective policies promoting resilience in natural resource-dependent communities and understanding how social and ecological aspects of communities interact to influence responses. Our framework describes how small-scale fishing communities and households respond to environmental changes and can inform policies that support vulnerable populations.</p>
Observations of Short-Period Ion-Scale Current Sheet Flapping
<p>Additional data.</p>
Data from: Metacommunity structure of stream insects across three hierarchical spatial scales
<p>A major challenge in community ecology is to understand the underlying factors driving metacommunity (i.e. a set of local communities connected through species dispersal) dynamics. However, little is known about the effects of varying spatial scale on the relative importance of environmental and spatial (i.e. dispersal related) factors in shaping metacommunities and on the relevance of different dispersal pathways. Using a hierarchy of insect metacommunities at three spatial scales (a small, within-stream scale, intermediate, among-stream scale, and large, among-sub-basin scale), we assessed whether the relative importance of environmental and spatial factors shaping metacommunity structure varies predictably across spatial scales, and tested how the importance of different dispersal routes vary across spatial scales. We also studied if different dispersal ability groups differ in the balance between environmental and spatial control. Variation partitioning showed that environmental factors relative to spatial factors were more important for community composition at the within-stream scale. In contrast, spatial factors (i.e. eigenvectors from Moran's eigenvector maps) relative to environmental factors were more important at the among-sub-basin scale. These results indicate that environmental filtering is likely to be more important at the smallest scale with highest connectivity, while dispersal limitation seems to be more important at the largest scale with lowest connectivity. Community variation at the among-stream and among-sub-basin scales were strongly explained by geographical and topographical distances, indicating that overland pathways might be the main dispersal route at the larger scales among more isolated sites. The relative effect of environmental and spatial factors on insect communities varied between low and high dispersal ability groups; this variation was inconsistent among three hierarchical scales. In sum, our study indicates that spatial scale, connectivity and dispersal ability jointly shape stream metacommunities.</p>
Supplementary material 3 from: Manjarrés-Hernández A, Guisande C, García-Roselló E, Heine J, Pelayo-Villamil P, Pérez-Costas E, González-Vilas L, González-Dacosta J, R. Duque S, Granado-Lorencio C, Lobo JM (2021) Predicting the effects of climate change on future freshwater fish diversity at global scale. Nature Conservation 43: 1-24. https://doi.org/10.3897/natureconservation.43.58997
Appendix 2
Supplementary material 4 from: Manjarrés-Hernández A, Guisande C, García-Roselló E, Heine J, Pelayo-Villamil P, Pérez-Costas E, González-Vilas L, González-Dacosta J, R. Duque S, Granado-Lorencio C, Lobo JM (2021) Predicting the effects of climate change on future freshwater fish diversity at global scale. Nature Conservation 43: 1-24. https://doi.org/10.3897/natureconservation.43.58997
Appendix 3
Supplementary material 1 from: Manjarrés-Hernández A, Guisande C, García-Roselló E, Heine J, Pelayo-Villamil P, Pérez-Costas E, González-Vilas L, González-Dacosta J, R. Duque S, Granado-Lorencio C, Lobo JM (2021) Predicting the effects of climate change on future freshwater fish diversity at global scale. Nature Conservation 43: 1-24. https://doi.org/10.3897/natureconservation.43.58997
Appendix 1
Supplementary material 2 from: Manjarrés-Hernández A, Guisande C, García-Roselló E, Heine J, Pelayo-Villamil P, Pérez-Costas E, González-Vilas L, González-Dacosta J, R. Duque S, Granado-Lorencio C, Lobo JM (2021) Predicting the effects of climate change on future freshwater fish diversity at global scale. Nature Conservation 43: 1-24. https://doi.org/10.3897/natureconservation.43.58997
Table S1
Data from: Private land conservation has landscape-scale benefits for wildlife in agroecosystems
Private lands contain much of the world's biodiversity. Conservation of private land, especially agricultural land, is urgent yet challenging because of the diverse priorities of landowners. Local effects of farmland conservation programmes have been evaluated thoroughly, but population-level response to these programmes may depend on effects that extend beyond targeted land parcels. We investigated the landscape-scale effects of a grassland conservation initiative, the Conservation Reserve Enhancement Program (CREP), on a socially and economically important gamebird, the Northern Bobwhite (Colinus virginianus). Barriers to assessing population-level response to conservation include determining the spatial scale at which a species responds to environmental change (the scale of effect) and untangling density-dependent processes. We performed point counts over 6 years at 247 sites with similar local CREP density but varying landscape-scale CREP density. We used an open-population distance sampling model to evaluate population response to landscape-level CREP density and to forecast population densities under differing re-enrollment scenarios. Our model included kernel smoothing techniques to estimate scale of effect and an estimator of the strength of density dependence. Density dependence moderated the effectiveness of the CREP, but overall populations responded positively to increasing landscape-scale CREP density. We estimated that at least 5% of the landscape needs to be in CREP to meet population density goals of 0.25 bobwhite/ha. Conservatively, we recommend 10% of the landscape to be in CREP. Our percent cover recommendations are based on a distance-weighted average of CREP around focal sites. Landscape-scale effects diminished with distance. For example, assuming all else is equal, a CREP field 3000 m away had 88% less of an effect on local abundance than a field 1000 m away. Fields farther than 5000 m away had no effect on local abundance. Synthesis and applications. Our study underscores the importance of a landscape-scale approach to farmland conservation. Benefits of these programmes can extend beyond the local scale, but their importance to local populations diminishes with distance. Estimating the relationship between increasing distance and the utility of conservation land to local populations could provide land managers a practical framework in which to target land enrollment to maximize biodiversity outcomes.
Data from: Scale dependencies and generalism in host use shape virus prevalence
Processes that generate the distribution of pathogens and their interactions with hosts are not insensitive to changes in spatial scale. Spatial scales and species traits are often selected intentionally, based on practical considerations, ignoring biases that the scale and type of observation may introduce. Specifically, these biases might change the interpretation of disease-diversity relationships that are reported as either 'dilution' or 'amplification' effects. Here, we combine field data of a host-pathogen community with empirical models to test the effects that i) spatial scale and ii) host range have on the relationship between plant-virus infection prevalence and diversity. We show that prevalence-diversity relationships are scale dependent, and can produce opposite effects associated with different habitats at sub-ecosystem scales. The total number of host species of each virus reflected generalism at the ecosystem scale. However, plasticity in host-range resembled habitat-specific specialisation and also changed model predictions. We show that habitat heterogeneity, ignored at larger (ecosystem) spatial scales, influences pathogen distributions. Hence, understanding disease distributions and the evolution of pathogens requires reconciling specific hypotheses of the study with an appropriate spatial scale, or scales, and consideration of traits, such as host range, that might strongly contribute to biotic interactions.
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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.