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.
102
datasets available to search
ShareScore release 0.9.0
Dataset results
102 results for “tree conservation”
Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
<p>Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all ~6000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our 'backbone-and-patch' approach to tree-building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (i) backbone relationships and ages among major lineages, using fossil node- or tip-dating; and (ii) species-level 'patch' phylogenies with non-overlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ('DNA-only' trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ('completed' trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (i) node ages are broadly concordant among studies, and (ii) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous 'supertree' approaches where unresolved nodes led to branch length artifacts. Credible sets of mammalian phylogenetic history are now available for download at <a href="http://vertlife.org/phylosubsets">http://vertlife.org/phylosubsets</a>, enabling investigations of long-standing questions in comparative biology.</p>
Tree mortality risks under climate change in Europe: assessment of silviculture practices and genetic conservation networks
<p>General context: Climate change can positively or negatively affect abiotic and biotic drivers of tree mortality. Process-based models integrating these climatic effects are only seldom used at species distribution scale.</p> <p>Objective: The main objective of this study was to investigate the multi-causal mortality risk of five major European forest tree species across their distribution range from an ecophysiological perspective, to quantify the impact of forest management practices on this risk and to identify threats on the genetic conservation network.</p> <p><br> Methods: We used the process-based ecophysiological model CASTANEA to simulate the mortality risk of \textit{Fagus sylvatica}, \textit{Quercus petraea}, \textit{Pinus sylvestris}, \textit{Pinus pinaster} and \textit{Picea abies} under current and future climate conditions, while considering local silviculture practices. The mortality risk was assessed by a composite risk index \textit{(CRIM)} integrating the risks of carbon starvation, hydraulic failure and frost damage. We took into account extreme climatic events with the \textit{CRIM$_{max}$}, computed as the maximum annual value of the \textit{CRIM}.</p> <p><br> Results: The physiological processes' contributions to \textit{CRIM} differed among species: it was mainly driven by hydraulic failure for \textit{P. sylvestris} and \textit{Q. petraea}, by frost damage for \textit{P. abies}, by carbon starvation for \textit{P. pinaster}, and by a combination of hydraulic failure and frost damage for \textit{F. sylvatica}. Under future climate, projection showed an increase of \textit{CRIM} for \textit{P. pinaster} but a decrease for \textit{P. abies}, \textit{Q. petraea} and \textit{F. sylvatica}, and little variation for \textit{P. sylvestris}. Under the harshest future climatic scenario, forest management decreased the mean \textit{CRIM} for \textit{P. sylvestris}, increased it for \textit{P. abies} and \textit{P. pinaster} and had no major impact for the two broadleaved species. By the year 2100, 38\% to 90\% of the conservation units are at extinction threat (\textit{CRIM$_{max}$}=1), depending on the species.</p> <p><br> Conclusions: Using a process-based ecophysiological model allowed us to disentangle the multiple drivers of tree mortality under current and future climate. Taking into account the positive effect of increased CO$_2$ on fertilization and water use efficiency, the average risks may increase or decrease in the future depending on species and sites. However, considering extreme climatic events, future projections are as pessimistic than those obtained with bioclimatic niche models.</p> <p> </p> <p>Abbreviation for column:</p> <p>X Longitude<br> Y Latitude<br> LAImax Leaf area index max reach<br> Nha Density per hectar<br> Vha Volume per hectar<br> NEE Net ecosystem exchange<br> NPP net primary production<br> Reco Respiration ecosystem<br> GPP Gross primary production<br> Etveg Evapotranspiration canopy<br> Etsol Evapotranspiration sol<br> TR tree transpiration<br> ETP evapotranspiration potentiel<br> BiomassOfReserves Biomass of reserve<br> rw ring width<br> dbh diameter at breast heast<br> height height<br> BBday Budburst date<br> rFD risk of frost<br> CRIM_max Maximum combined risk index of mortality reach<br> rNSC risk of carbon starvation<br> rPLC risk of embolism<br> rPLC_max Maximum risk of embolism reach<br> CRIM combined risk index of mortality<br> Climate Climatic model<br> rNSC_max maximum risk of carbon starvation reach<br> rFD_max Maximum risk of frost reach<br> Scenario_Sylvicol null means no silvulcture simulated<br> species species<br> Country Country<br> alt_watch altitude of climate simulated<br> grid_watch number of the pixel point of WATCH<br> grid_eurocordex number of the pixel point of Eurocordex<br> Pinus_sylvestris 0 abscence ; 1 presence<br> Fagus_sylvatica 0 abscence ; 1 presence<br> Quercus_petraea 0 abscence ; 1 presence<br> Picea_abies 0 abscence ; 1 presence<br> Pinus_pinaster 0 abscence ; 1 presence</p> <p> </p>
Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
Open the record for dataset details and reuse information.
Fig. 5 in Bird Diversity Differs Between Industrial Tree Plantations On Borneo: Implications For Conservation Planning
Fig. 5. Nonlinear multidimensional scaling of bird survey data pooled by point-transect. Vectors represent correlations between the ordination and habitat variables. Vectors and Pearson correlation coefficients are plotted for habitat variables with an r2> 0.200 for axis 1.
Fig. 4 in Bird Diversity Differs Between Industrial Tree Plantations On Borneo: Implications For Conservation Planning
Fig. 4. Plots of (A) species and (B) individual rates (from Fig. 1) versus number of species listed by www.birdlife.org (Table 1) per habitat type.
Fig. 1 in Bird Diversity Differs Between Industrial Tree Plantations On Borneo: Implications For Conservation Planning
Fig. 1. Map of forest occurrence in Borneo in 2005 (WWF-Malaysia, 2005) showing the localities of the Sarawak Planted Forest Project and Sabah Softwoods plantation.
Maps and R code from: Marginality indices for biodiversity conservation in forest trees
<p>This dataset provides the raster map of marginality indices for eight European tree species as described in the article "Marginality indices for biodiversity conservation in forest tree". It also provided the R code to compute the marginality indices.</p> <p>The eight species are the following:</p> <ul> <li><em>Abies alba</em> Mill. (silver fir)</li> <li><em>Fagus sylvatica</em> L. (European beech)</li> <li><em>Picea abies</em> (L.) H.Karst. (Norway spruce) </li> <li><em>Pinus halepensis</em> Mill. (Aleppo pine)</li> <li><em>Pinus nigra</em> J.F.Arnold (black pine)</li> <li><em>Pinus pinaster</em> Aiton (maritime pine) </li> <li><em>Pinus pinea</em> L. (stone pine)</li> <li><em>Pinus sylvestris</em> L. (Scots pine)</li> </ul> <p>For each species, a 7z archive of a multi-layered image of the raster maps of the marginality indices is given. Each image has 12 layers:</p> <ul> <li>Layer 1: distribution map of the species</li> <li>Layer 2: map of the probability of being marginal according to the Maxent model using eight marginality indices and countries as predictors</li> <li>Layer 3: map of the environmental marginality index, defined as the z-transform of the suitability of each location as predicted by a species distribution model using climatic variables as predictors</li> <li>Layer 4: map of the segmented distribution according to morphological spatial pattern analysis</li> <li>Layer 5: map of the area index</li> <li>Layer 6: map of the gravity index</li> <li>Layer 7: map of the centroid index</li> <li>Layer 8: map of the edge index</li> <li>Layer 9: map of the isolation index</li> <li>Layer 10: map of the second nearest core index</li> <li>Layer 11: map of the north/south index</li> <li>Layer 12: map of the east/west index</li> </ul>
Figure 1 in Description, biology and conservation of a new species of Australian tree frog (Amphibia: Anura: Hylidae: Litoria) and an assessment of the remaining populations of Litoria genimaculata Horst, 1883: systematic and conservation implications of an unusual speciation event
Figure 1. Distribution of Litoria myola sp. nov. (formerly termed iS) and the northern (N) and southern (S) lineages of Litoria genimaculata in the Wet Tropics, northeast Queensland. CT, Carbine Tableland; BMC, Black Mountain Corridor; LR, Lamb Range; BK, Bellenden Ker Range; AT, Atherton Tableland; MT, Malbon Thompson Range; GR, Graham Range.
Figure 2 in Description, biology and conservation of a new species of Australian tree frog (Amphibia: Anura: Hylidae: Litoria) and an assessment of the remaining populations of Litoria genimaculata Horst, 1883: systematic and conservation implications of an unusual speciation event
Figure 2. Litoria myola, sp. nov., males (A, a pale individual; B, a heavily marked individual), Kuranda, north-east Queensland.
Figure 3 in Description, biology and conservation of a new species of Australian tree frog (Amphibia: Anura: Hylidae: Litoria) and an assessment of the remaining populations of Litoria genimaculata Horst, 1883: systematic and conservation implications of an unusual speciation event
Figure 3. Spectrogram of the courtship call of Litoria myola sp. nov. (recorded at an air temperature of 25 °C). The spectrogram displays a single courtship call consisting of six notes ('tocs'). The degree of shading displays call intensity.
Figure 7 in Description, biology and conservation of a new species of Australian tree frog (Amphibia: Anura: Hylidae: Litoria) and an assessment of the remaining populations of Litoria genimaculata Horst, 1883: systematic and conservation implications of an unusual speciation event
Figure 7. Rainforest stream habitat, with rocky (A) and sandy (B) substrate, Kuranda, north-east Queensland. Litoria myola sp. nov. and Litoria genimaculata are present at both sites.
Fig. 2 Phylogenetic tree representing relationships within Discodorididae. The latter contains about 400 species and 40 in A warning for ecologists and conservation biologists using species checklists: How the European marine fauna 'lost' all of its 16 Discodoris species (Mollusca: Gastropoda)
Fig. 2 Phylogenetic tree representing relationships within Discodorididae. The latter contains about 400 species and 40 genera, only some of which are mentioned here, with special emphasis on the genera that contain species originally described in Discodoris. Tree terminal taxa are labeled with the specific epithet followed by the generic name of the original combination in parenthesis. The current generic names are given on the right side of the braces indicating the (few) species per genus mentioned. Assignment of a generic name to a clade is based on a type species that belongs to that clade (e.g., Discodoris boholiensis is the type species of Discodoris). All genera correspond to clades, with the exception of "Montereina", a metaphyletic group at the base of Discodorididae for which no autapomorphic, diagnostic features could be found. For additional information on phylogenetic analyses, authorship of species names, etc., see Dayrat (2010a)
Fig. 2 in Syzygium setosum (Myrtaceae), a rare and endangered peat swamp tree in Southeast Asia: lectotypification, conservation status and a new record in Sumatra
Fig. 2. – Geographical distribution of Syzygium setosum (King) I.M. Turner. Extant populations of the taxon are represented by black solid circles, while likely extinct populations are represented by white circles.
Fig. 1 in Syzygium setosum (Myrtaceae), a rare and endangered peat swamp tree in Southeast Asia: lectotypification, conservation status and a new record in Sumatra
Fig. 1. – Syzygium setosum (King) I.M. Turner. A. Base of trunk showing the buttress; B. Close-up of the flush trunk showing pale cream inner bark and pale to dark cream sapwood; C. Close-up of a twig showing reddish-brown erect bristly hairs; D. Leafy branch showing opposite leaf arrangement; E. Adaxial (upper) leaf surface; F. Abaxial (lower) leaf surface; G. Immature terminal and axillary inflorescences; H. Mature inflorescences showing open flowers; I. Close-up of open flowers; J. Close-up of an infructescence; K. Apical view of a fruit; L. Seeds (left) and inner part of the carpel (right); M. Longitudinal section of a fruit. [Randi GB-052, BO] [Photos: A. Randi]
Data from: Native shade trees aid bird conservation in tea plantations in southern India
<p>In the Western Ghats, India, we study how different intensities of tea cultivation influence birds. We compared bird communities in conventional monoculture tea and mixed-shade tea plantations, both of which use agrochemicals, with organic tea plantations, a rainforest fragment, and continuous rainforest within the Anamalai Tiger Reserve. In 225 point count surveys, overall bird species richness and abundance were lowest in conventional tea and up to 33% higher in organic tea. Mixed-shade tea had 40% higher species richness (including 15 canopy and 4 shrub and mid-storey species – primarily frugivores, nectarivores and insectivores), and 83% higher bird abundance than conventional tea, with a greater proportion of forest-affiliated birds and similarity in species composition with forest sites. The rainforest fragment and continuous rainforest had a higher proportion, richness and abundance of forest-affiliated birds and fewer open-country birds, unlike tea plantations where the pattern was reversed. Habitat associations of 62 bird species in indicator species analysis revealed similar patterns. Thus organic tea is better than conventional tea for birds, but mixed-shade tea is even better, although still poorer than forests. Retaining or promoting native shade trees in tea plantations will increase bird diversity and abundance, including of forest-affiliated species and support landscape-level bird conservation.</p>
Figure 4 in Ecologically-sustainable tree monocultures contribute to conservation of an Araucaria Forest endemic frog
Figure 4. Mean (¡SE) number of food items per stomach in each habitat. FO, Araucaria Forest; PA, Araucaria angustifolia plantation; PP, Pinus plantation; PE, Eucalyptus plantation.
Figure 5 in Ecologically-sustainable tree monocultures contribute to conservation of an Araucaria Forest endemic frog
Figure 5. Rarefaction curves of Physalaemus lisei diet, relating taxonomic richness to the number of individuals in each habitat. FO, Araucaria Forest; PA, Araucaria angustifolia plantation; PP, Pinus plantation; PE, Eucalyptus plantation. The vertical lines comprise the 95% confidence intervals.
Figure 3 in Ecologically-sustainable tree monocultures contribute to conservation of an Araucaria Forest endemic frog
Figure 3. Diet composition of Physalaemus lisei (black bars) in relation to the taxonomic composition of pitfall traps (white bars). Dotted line delimits the feeding niche of P. lisei.
Figure 2 in Ecologically-sustainable tree monocultures contribute to conservation of an Araucaria Forest endemic frog
Figure 2. Body mass (g) distribution of Physalaemus lisei captured in the São Francisco de Paula National Forest, southern Brazil. (A) Temporal variation in body mass (g) distribution between October 2003 and April 2005; (B) among-habitat variation in body mass distribution. Horizontal line represents the median; the box delimits the first and third quartile; the vertical lines delimit the maximum and minimum values, except for the outliers that are represented by asterisks. FO, Araucaria Forest; PA, Araucaria angustifolia plantation; PP, Pinus plantation; PE, Eucalyptus plantation.
Figure 1 in Ecologically-sustainable tree monocultures contribute to conservation of an Araucaria Forest endemic frog
Figure 1. Number of individuals of Physalaemus lisei captured in the São Francisco de Paula National Forest, southern Brazil. (A) Temporal dynamic between October 2003 and April 2005; (B) among-habitat variation in the mean (¡SE) number of captures. FO, Araucaria Forest; PA, Araucaria angustifolia plantation; PP, Pinus plantation; PE, Eucalyptus plantation.
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.