Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
146
datasets available to search
ShareScore release 0.9.0
Dataset results
146 results for “species loss”
Data from: Loss of animal seed dispersal increases extinction risk in a tropical tree species due to pervasive negative density dependence across life stages
Overhunting in tropical forests reduces populations of vertebrate seed dispersers. If reduced seed dispersal has a negative impact on tree population viability, overhunting could lead to altered forest structure and dynamics, including decreased biodiversity. However, empirical data showing decreased animal-dispersed tree abundance in overhunted forests contradict demographic models which predict minimal sensitivity of tree population growth rate to early life stages. One resolution to this discrepancy is that seed dispersal determines spatial aggregation, which could have demographic consequences for all life stages. We tested the impact of dispersal loss on population viability of a tropical tree species, Miliusa horsfieldii, currently dispersed by an intact community of large mammals in a Thai forest. We evaluated the effect of spatial aggregation for all tree life stages, from seeds to adult trees, and constructed simulation models to compare population viability with and without animal-mediated seed dispersal. In simulated populations, disperser loss increased spatial aggregation by fourfold, leading to increased negative density dependence across the life cycle and a 10-fold increase in the probability of extinction. Given that the majority of tree species in tropical forests are animal-dispersed, overhunting will potentially result in forests that are fundamentally different from those existing now.
Data from: Non-random loss of phylogenetically distinct rare species degrades phylogenetic diversity in semi-natural grasslands
1. Although biodiversity loss is a critically important topic, our understanding of how both land abandonment and land-use intensification in semi-natural grasslands alters the community diversity and assembly mechanisms is very limited. Large-scale economic drivers of land-use change might inadvertently result in the loss of vulnerable species and reduce ecosystem services provisioning. 2. In this study, we assessed non-random community change by examining patterns of low-abundance species loss, and community assembly in semi-natural grasslands due to land abandonment and intensification in southwest Japan. We analyzed relationships between evolutionary distinctiveness and abundance for each species. In addition, we used metrics of species and phylogenetic diversity and phylogenetic structure to assess patterns of non-random biodiversity loss due to both abandoned and intensified land-use. 3. We demonstrated that low-abundance species were more evolutionarily distinct compared to high-abundance (i.e., dominant) species. Furthermore, land-use intensification resulted in further declines in low-abundance species, whereas land abandonment resulted in declines in all species, regardless of their initial abundance. 4. We found that both forms of land-use change (abandonment and intensification) resulted in non-random patterns of community change, with traditional land-use maintaining the highest biodiversity and land-use change coinciding with decreased species and phylogenetic diversity measures. Intensified land-use caused phylogenetic community structure to be more closely related than expected by chance, whereas the metrics of how distant species are from one another on average based on phylogenetic tree (i.e., mean pairwise phylogenetic distance) did not change from land abandonment. 5. Synthesis and applications. We show that the loss of phylogenetic diversity, and especially of low-abundance species with high value of phylogenetic distinctiveness, resulted in non-random community disassembly. Our results argue that in order to maintain biodiversity in these semi-natural grasslands, traditional management practices should be encouraged over intensification and simple abandonment. Government agencies should adopt policies or provide incentives that encourage the maintenance of traditional practices in rural Japan, and elsewhere where the combination of land consolidation and abandonment are important conservation issues.
Data from: Do correlated responses to multiple environmental changes exacerbate or mitigate species loss?
Biological communities face multiple global changes simultaneously, and predicting how they will respond remains a key challenge. Co-tolerance theory offers a framework for understanding how species-level responses to multiple stressors affect community properties. Co-tolerance theory predicts that positive correlations in species responses (i.e., species that are susceptible to one stressor are more likely to be highly susceptible to a second) lessen total species loss, essentially because species cannot be eliminated from a community twice. However, it is unclear whether several of the tenets of co-tolerance theory describe real-world communities, and what consequences result from such deviations. Here, we use an empirical dataset of bird community response to land-use change over a climate gradient to examine co-tolerance theory's tenet that environmental changes only harm species (not benefit them). We show that this tenet is not met, and then use simulations to examine how predictions of total species richness and community intactness vary when multiple environmental changes both harm and benefit particular species in the community. Finally, we conduct a sensitivity analysis, examining how the average species response to environmental change, as well as the variance among species, can further alter predictions. Overall, we find that predictions of co-tolerance theory can break down when communities contain species that benefit from some environmental changes. As a result, the presence of multiple environmental changes can either compound or mitigate species loss when species' responses are positively correlated, preventing a one-size-fits-all statement regarding the effects of correlated responses. This finding highlights the need to carefully consider the underlying mechanisms of community change when making policy assessments regarding the consequences of correlations of species responses to environmental impacts.
FIGURE 2 in A lost species or the loss of stripes? The case of Contomastix lizards from Cabo Polonio, Uruguay, with observations on C. lacertoides (Duméril & Bibron) and Cnemidophorus grandensis Cope (Squamata, Teiidae)
FIGURE 2. Uruguayan specimens of Contomastix lacertoides. On top, unvouchered adult male photographed while basking at La Palma, Rivera (orange color corresponds to parasitic mites); inset: detail of sexual color dimorphism in a male from Quebrada de los Cuervos, Treinta y Tres (MNHN 9460). Bottom, adult female from Quebrada de los Cuervos, (MNHN 9461, total length 196 mm).
FIGURE 8 in A lost species or the loss of stripes? The case of Contomastix lizards from Cabo Polonio, Uruguay, with observations on C. lacertoides (Duméril & Bibron) and Cnemidophorus grandensis Cope (Squamata, Teiidae)
FIGURE 8. On top, hyoid apparatus of Contomastix charrua ZVC-R 1266, paratype. Bottom, hyoid apparatus of topotypic C. lacertoides ZVC-R 1856. A and C are schematic representations as depicted by Cabrera and Carreira (2009); B and D are the corresponding hyoid preparations of Cabrera and Carreira (2009), photographed under a stereoscopic microscope (photos by CB). Notice in B the apparently fairly degraded right spicula of the second pair of ceratobranchials (arrow). Scale bars equals 5 mm.
FIGURE 1 in A lost species or the loss of stripes? The case of Contomastix lizards from Cabo Polonio, Uruguay, with observations on C. lacertoides (Duméril & Bibron) and Cnemidophorus grandensis Cope (Squamata, Teiidae)
FIGURE 1. Geographic distribution of Contomastix species from Argentina, Brazil and Uruguay, according to present study and published reports (Koslowsky 1898; Gudynas 1985; Cei & Martori 1991; Cei & Scrocchi 1991; Cei 1993; Federico 2000; Feltrim & Lema 2000; Pérez & Grassini 2001; Vrcibradic et al. 2004; Arias & Lobo 2005; Stahnke et al. 2006; Rholing et al. 2009; Caruccio et al. 2010; Cabrera et al. 2012). Closed circles, C. lacertoides (white circle, type locality Montevideo); open circle, C. charrua (type locality, Cabo Polonio); squares, C. leachei (white square, type locality, San Lorenzo); triangles, C. serrana (white triangle, type locality, Icho Cruz); pentagons, C. vacariensis (white pentagon, type locality, Vacaria). Abbreviations: BA, Buenos Aires Province; CB, Córdoba Province; ER, Entre Ríos Province; JU, Jujuy Province; RS, Rio Grande do Sul state; SA, Salta Province; SC, Santa Catarina state; SE, Santiago del Estero Province.
FIGURE 7 in A lost species or the loss of stripes? The case of Contomastix lizards from Cabo Polonio, Uruguay, with observations on C. lacertoides (Duméril & Bibron) and Cnemidophorus grandensis Cope (Squamata, Teiidae)
FIGURE 7. Left, ventral view of the head of a cleared and stained specimen of Contomastix lacertoides, MNHN 9462 (scale bar equals 5 mm). Right, X-ray image of the head of the holotype of Cnemidophorus grandensis ANSP 9593 in ventral view. Abbreviations: BH, basihyoid; CBI, first pair of ceratobranchials; CBII, second pair of ceratobranchials; EB, entoglossal bone; EH, epihyal; MA, mandible; PL, processus lingualis; TO, tongue; TR, trachea.
FIGURE 4 in A lost species or the loss of stripes? The case of Contomastix lizards from Cabo Polonio, Uruguay, with observations on C. lacertoides (Duméril & Bibron) and Cnemidophorus grandensis Cope (Squamata, Teiidae)
FIGURE 4. Ventral view of the head of adult Contomastix lizards (fixed specimens otherwise indicated). On top, C. lacertoides: A MCP 14453, B MCP 17758 (São Jerônimo, Rio Grande do Sul, Brazil); C MNHN 3189, D MNHN 3187 (Tambores, Tacuarembó). Middle, C. lacertoides from southeastern Uruguay: E MNHN 3185, F MNHN 5770 (Sierra de las Ánimas, Maldonado); G MNHN 9463 (in life), H MNHN 9464 (in life), (Quebrada de los Cuervos, Treinta y Tres). Bottom, C. lacertoides from southeastern Uruguay: I MNHN 3192 (Km 128, National Route #8, Lavalleja); C. charrua, J MNHN 3422 (paratype), K MNHN 3423, holotype (Cabo Polonio, Rocha); Cnemidophorus grandensis, L ANSP 9593, holotype (Rio Grande do Sul, Brazil).
FIGURE 3 in A lost species or the loss of stripes? The case of Contomastix lizards from Cabo Polonio, Uruguay, with observations on C. lacertoides (Duméril & Bibron) and Cnemidophorus grandensis Cope (Squamata, Teiidae)
FIGURE 3. Dorsal pattern of coloration in Contomastix lizards from Uruguay. On top, from left to right: C. lacertoides MNHN 5774, 5777 (Las Piedras, Artigas), MNHN 3196 (Pozo Hondo, Tacuarembó), MNHN 3190 (Tambores, Tacuarembó). Middle, from left to right: C. lacertoides MNHN 5767 (Aiguá, Lavalleja), MNHN 6222 (Route 8, km 162, Lavalleja), MNHN 5766, 5770 (Sierra de las Ánimas, Maldonado). Bottom, from left to right: C. lacertoides MNHN 3185 (Sierra de las Ánimas, Maldonado); C. charrua MNHN 3422, 3424, paratypes and MNHN 3423, holotype (Cabo Polonio, Rocha).
FIGURE 5 in A lost species or the loss of stripes? The case of Contomastix lizards from Cabo Polonio, Uruguay, with observations on C. lacertoides (Duméril & Bibron) and Cnemidophorus grandensis Cope (Squamata, Teiidae)
FIGURE 5. Paired dorsal and lateral views of the heads of: A Contomastix lacertoides (Quebrada de los Cuervos, Uruguay) MNHN 9464; B C. charrua MNHN 3424, paratype (Cabo Polonio, Uruguay); C Cnemidophorus grandensis ANSP 9593 (Rio Grande do Sul, Brazil).
Inverse priority effects: A role for historical contingency during species losses
<p>Communities worldwide are losing multiple species at an unprecedented rate, but how communities reassemble after these losses is often an open question. It is well established that the order and timing of species arrival during community assembly shapes forthcoming community composition and function. Yet, whether the order and timing of species losses can lead to divergent community trajectories remains largely unexplored. Here, we propose a novel framework that sets testable hypotheses on the effects of the order of species losses inverse priority effects and suggests its integration into the study of community assembly. We propose that the order of species losses within a community can generate alternative reassembly trajectories, and suggest mechanisms that may underlie these inverse priority effects. To formalize these concepts quantitatively, we used a three-species Lotka-Volterra competition model, enabling to investigate conditions in which the order of species losses can lead to divergent reassembly trajectories. The inverse priority effects framework proposed here promotes the systematic study of the dynamics of species losses from ecological communities, ultimately aimed to better understand community reassembly and guide management decisions in light of rapid global change.</p>
Variation in species' dispersal capacities amplifies effects of habitat loss and fragmentation on biodiversity loss
<p>Simulation data and model belonging to the manuscript '<span>Variation in species’ dispersal capacities amplifies effects of habitat loss and fragmentation on biodiversity loss</span>', by Monique de Jager and Edwin Pos. The folder 'Generated data' holds the generated simulation data. The folder 'Model' contains the 2-dimensional, semi-spatial, near-neutral, individual-based model. A description of the model can be found in the file 'README.md'. </p>
Intra-annual species gain overrides species loss in determining species richness in a typical steppe ecosystem after a decade of nitrogen enrichment
<p>Increasing deposition of atmospheric nitrogen (N) due to accelerated human activities is a threat to various ecosystems. However, there is a lack of long-term experimental evidence demonstrating the seasonal dynamics of plant species turnover that ultimately determine species richness in natural ecosystems under N enrichment. Moreover, the frequency of N addition also may affect species turnover in a community, but it is rarely studied.</p> <p>To assess the responses of a plant community to N addition, we manipulated the amounts (0-50 g N m<sup>-2</sup> year<sup>-1</sup>) and frequency (2 vs. 12 times year<sup>-1</sup>) of N addition in an Inner Mongolian typical steppe ecosystem in northern China for 12 consecutive years (2008-2020). We measured species richness and density of plant in the growing seasons (May-September) from 2018 to 2020, starting 10 years after the initial N addition treatment.</p> <p>Both species gain and species loss decreased with increasing amounts of N addition, resulting in a lower plant species turnover rate and greater similarity in the community between two adjacent months throughout the growing season. Species loss and species gain increased modestly under high N addition frequency. Species gain was more important than species loss in determining species richness after a decade of N application. In addition, plant density increased at high N amounts, mainly driven by enhanced clonal growth of the dominant species, <em>Leymus chinensis</em>.</p> <p><strong><em>Synthesis</em></strong>. Together, these results suggest that high levels of N deposition may suppress species richness due to aggravated soil chemical properties and may favor growth of a limited number of N-tolerant species compared to systems that experience low levels of N deposition. To conserve biodiversity and to facilitate restoration of degraded grassland ecosystems exposed to long-term N deposition, amelioration of the acidified soils induced by N deposition may be an important strategy to use.</p>
Last species standing: loss of Pocilloporidae corals associated with coastal urbanization in a tropical city state
<p>DNA sequence alignment</p>
Fig. 2 in Major range loss predicted from lack of heat adaptability in an alpine Drosophila species
Fig. 2. Heat knock-down results for the three regimes (C, L, A) of two populations (Kaserstattalm, Pfitscherjoch). Colours indicate the temperature at which the flies were reared in the generation used for testing knock-down performance. Significances based on analyses of variance and Bonferroni post hoc tests (n = 875, alpha = 0.05) are indicated by lower-case letters. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
Fig. 4 in Major range loss predicted from lack of heat adaptability in an alpine Drosophila species
Fig. 4. Ecological niche modelling of habitable area of Drosophila nigrosparsa for pre-current, immanent, proximate, and distant future. (a) Multi-model consensus predictions of precurrent and future high emission scenarios (SRES A2 and RCP8.5). (b) PNO profiles for different time periods (pre-current, 2020s, 2030s, 2080s) scaled according to the suitable area based on the MTP (whole distribution area) and MTSS (core area) as well as histograms of frequencies of available altitude in the study region. For details, see Section 2.6 and Supporting Information S1.
Fig. 1 in Major range loss predicted from lack of heat adaptability in an alpine Drosophila species
Fig. 1. Overview of experiments. Years 2012–2016 with months abbreviated; G1-G20…generation number for selection regimes, L and A; controls C developed more slowly resulting in a difference of one generation at Generation 19 of the selection regimes; coll…collecting of flies in two populations, Kaserstattalm and Pfitscherjoch; breeding…flies were reared at a fluctuating ambient temperature mimicking natural daily conditions; red upward pointing arrow…increasing the ambient temperature by 0.5 ̊C for L and A; KD…artificial selection of A in heat knock-down tube; N14…founding of lines using fresh flies collected from the field in 2014 to test for possible laboratory adaptation; s… replicate lines from each regime were combined to create new synthetic lines to control for possible inbreeding effects; larv…assays of egg-to-adult viability and wing size in non-competitive and competitive situations; w…upscaling of lines and switches to the opposed rearing temperature (L and A switched to C rearing temperature; C to L = A rearing temperature) in addition to keeping the lines at the rearing temperatures corresponding to their regime; *…for evaluating progress in selection response, heat resistance was measured as knock-down temperature under gradual heating, and for safeguarding against unexpected loss of genetic diversity during the selection experiments, three polymorphic microsatellite loci were analysed; sim… simulating technical defect of climate chamber that occurred in previous generation for evaluating validity of data for that generation; horizontal bars denote replicate fly lines of the three regimes, i.e., C…control; L…laboratory natural selection (in Generation 14, one replicate each of L from Kaserstattalm and Pfitscherjoch were lost); A…artificial selection combined with laboratory natural selection; blue…fluctuating ambient temperature mimicking natural daily conditions (control temperature); red…increased ambient temperature (selection temperature). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
Fig. 3 in Major range loss predicted from lack of heat adaptability in an alpine Drosophila species
Fig. 3. Egg-to-adult viability and wing size under non-competitive and competitive situations. (a) Egg-to-adult viability of the three regimes (C, L, A) under regular larval density. Significances based on analyses of variance (n = 30). (b) Wing size of the three regimes separately for females and males under regular larval density. Significances based on analyses of variance (n = 374). (c) Inter-regime competition (increased larval density). Output proportion of C relative to L and A at end of experiment (adults) plotted against input proportion of C relative to L and A at beginning of experiment (eggs). Dashed line: theoretical 45̊ equilibrium line on which output proportion equals input proportion. Significance values based on Wilcoxon Signed-rank tests calculated separately for each output proportion by comparison with corresponding value of theoretical equilibrium line (n = 10 for all tests except for C against A at input ratio 0.25, for which n = 9). (d) Wing size at inter-regime competition of different ratios. Females are shown as solid lines, males as dashed lines. Significance values at alpha = 0.05 are indicated by lower-case letters (a, b) and * (c).
SDM results for 10,590 tree species from "Regional uniqueness of tree species composition and response to forest loss and climate change"
<p>Output from species distribution models (SDMs) with geographic constraints to estimate the spatial distribution of tree species at the global level at a 30-arc second resolution, presented in the publication "Regional uniqueness of tree species composition and response to forest loss and climate change". </p> <h2>Data</h2> <p>This file contains the results for 10,590 tree species. The results for each species are contained in a directory with the species name connected by an underscore. For most species, the directory contains several .tif files that make up the tiles of the distribution maps for that species and a metadata file. The .tif files can be merged with the gdal_merge.py function to obtain a single .tif file per species (see example below). For some species, the directory contains a single .tif file which does not require merging. In all cases, the .tif files contain 9 bands that correspond to the predicted species distribution using climatic variables corresponding to various climate projections from Chelsa 2.1.</p> <h3>Band order</h3> <ol> <li>covariates_1981_2010: average of historical climate measurements from 1981 to 2010</li> <li>covariates_2011_2040_ssp126: average future climate projection for 2011-2040 under shared socioeconomic pathway (SSP) 1.26</li> <li>covariates_2011_2040_ssp370: average future climate projection for 2011-2040 under SSP 3.70</li> <li>covariates_2011_2040_ssp585: average future climate projection for 2011-2040 under SSP 5.85</li> <li>covariates_2041_2070_ssp126: average future climate projection for 2041-2070 under SSP 1.26</li> <li>covariates_2041_2070_ssp370: average future climate projection for 2041-2070 under SSP 3.70</li> <li>covariates_2041_2070_ssp585: average future climate projection for 2041-2070 under SSP 5.85</li> <li>covariates_2071_2100_ssp126: average future climate projection for 2071-2100 under SSP 1.26</li> <li>covariates_2071_2100_ssp370: average future climate projection for 2071-2100 under SSP 3.70</li> <li>covariates_2071_2100_ssp585: average future climate projection for 2071-2100 under SSP 5.85</li> </ol> <h3>Metadata</h3> <p>The metadata contains more information about the bands, as well as the following species-level properties:</p> <ul> <li>nobs: number of spatially distinct occurrence records used in model training</li> <li>precision: precision of binarised model output computed through 3-fold cross-validation</li> <li>threshold: threshold used to binarise probabilistic model output, determined as the threshold maximizing the true skill statistic (TSS) during 3-fold cross-validation</li> <li>f1: F1 score of binarised model output computed through 3-fold cross-validation</li> <li>auc: area under the ROC curve (AUC) of model output computed through 3-fold cross-validation</li> <li>prevalence: prevalence of presences (ie. occurrences records) throughout the training data which consisted of occurrence records and pseudo-absences</li> <li>tss: TSS of binarised model output computed through 3-fold cross-validation</li> <li>recall: recall of binarised model output computed through 3-fold cross-validation</li> <li>nativeness_info: indicates whether reported native countries were available for this species (possible values: "yes" or "no", should be "yes" for all species included)</li> <li>npa: number of pseudo-absences used in model training</li> <li>system:index: species name </li> </ul> <h3>Merging example</h3> <p>For example, the directory Abarema_barbouriana contains files Abarema_barbouriana_0.tif, Abarema_barbouriana_2.tif, ..., Abarema_barbouriana_9.tif and metadata.json. The tiles can be merged with the command "gdal_merge.py -o Abarema_barbouriana_merged.tif Abarema_barbouriana/Abarema_barbouriana_*.tif".</p>
FIGURE 1 in Faunal survey, endemism and possible species loss of Scarabaeinae (Coleoptera: Scarabaeidae) in the western slopes of the moist South Western Ghats, South India
FIGURE 1. Ecoregions in the western slopes of the moist south Western Ghats and regions of local endemism.
ScienceDex guides
Understand access before you commit
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.