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385 results for “Conservation genetics”
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>
Lepidoptera genomics based on 88 chromosomal reference sequences informs population genetic parameters for conservation
<p>This repository contains (1) germline mutations called by the DeepVariant (v1.1.0) pipeline in VCF format; (2) rejected substitution scores calculated by the Genomic Evolutionary Rate Profiling (GERP++) software on each species and chromosome; and (3) the phylogenetic tree used as guide tree in the Cactus alignment.</p>
Figure 2 in Extant because important or important because extant? On the scientific importance and conservation of a genetically pure Sicilian population of the threatened Salmo cettii Rafinesque, 1810
Figure 2. – Individual Salmo cettii from Tellesimo Stream (for the morphological and phenotypical characteristics of Sicilian trout see: Duchi, 1988; Fruciano et al., 2014; Duchi, 2018).
Genetic diversity of wild and cultivated Coffea canephora in northeastern DR Congo and the implications for conservation - Additional Data
<p>List of wild and cultivated <em>Coffea canephora </em>accessions from northeastern Democratic Republic of the Congo included in Vanden Abeele et al. 2021 - American Journal of Botany, and the corresponding alleles for each of the 18 microsatellite markers (0 indicates missing alleles).</p>
FIG. 4 in Genetic diversity of Malagasy baobabs: implications for conservation
FIG. 4. — Observed nucleotide diversity PI (π) for the six Adansonia L. species endemic to Madagascar. Northern and southern populations of A. za Baill. are combined here. When distinguishing between geographic populations of A. za, nucleotide diversity was the same as combined for southern populations (π = 0.0029), but less for northern populations (π = 0.0026).
FIG. 3 in Genetic diversity of Malagasy baobabs: implications for conservation
FIG. 3. — Principal components analysis (PCA) of Malagasy Adansonia L. colored by species. Panels represent different PCA axes from: A, 2089 SNPs for all Malagasy Adansonia for axis 1 vs axis 2; B, axis 3 vs axis 4; C, 1873 SNPs for Longitubae taxa only for axis 1 vs axis 2; and D), axis 3 vs axis 4. Northern and southern populations of A. za Baill. labeled.
FIG. 2 in Genetic diversity of Malagasy baobabs: implications for conservation
FIG. 2. — SNP-based tree from 2089 biallelic SNPs as inferred by IQ-TREE. Values on the branches represent bootstrap support for the primary clades: A, broad scale relationships with monophyletic taxa collapsed and number of samples per clade indicated in parentheses; B, detailed phylogeny for the core Longitubae clade (A. perrieri Capuron, A. madagascariensis Baill., and A. za Baill.), with individual accessions mapped to their respective geographic localities in Madagascar (B). Adansonia za (Aza) accessions are listed in red; A. madagascariensis (Ama), in blue; and A. perrieri (Ape) accessions in yellow.
FIG. 1 in Genetic diversity of Malagasy baobabs: implications for conservation
FIG. 1. — Flowers of the six species of baobabs endemic to Madagascar: A, Adansonia grandidieri Baill.; B, A. madagascariensis Baill.; C, A. perrieri Capuron; D, A. rubrostipa Jum. & H. Perrier; E, A. suarezensis H. Perrier; F, A. za Baill. Photographs by David A. Baum and Nisa Karimi.
Figure 4 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.
Figure 4 Holotype of Andrias jiangxiensis sp. nov. (KIZ 037731) in preservative A–C: Holotype of A. jiangxiensis sp. nov., in dorsal (A), lateral (B), and ventral (C) views. D, E: Dorsal (D) and ventral (E) views of head of holotype of A. jiangxiensis sp. nov. F, G: Ventral view of the left hand (F) and left foot (G) of the holotype of A. jiangxiensis sp. nov. Photos by Chen-Qi Lu.
Figure 7 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.
Figure 7 The habitat of Andrias jiangxiensis sp. nov. in Daqi Mountain, Jing'an County, Jiangxi, China A, B: Summer (A) and winter (B) scene of 8–10 meters-wide stream with excellent vegetation coverage. C: Abreeding cave for A. jiangxiensis sp. nov. found in a backwater bay of the stream. Red arrow indicates the exit of the cave. D: Enlarged area near the exit of the cave. Dashed circles in cyan indicate six larvae of A. jiangxiensis sp. nov., and the ones in white indicate the co-occurring shrimps and fishes. Photos by Mu-Rong Yi.
Figure 3 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.
Figure 3 Genetic distinctiveness of CGS from clade U2 found in Jing'an County, Jiangxi, China A: Asimplified phylogeny based on COI of mtDNA modified from Yan et al. (2018), in which clade U2 represents haplotypes found in Jing'an County, Jiangxi. The clade to which A. davidianus belongs remains uncertain. Clade Dindicates the haplotypes of A. sligoi according to the analyses by Turvey et al. (2019). B: Maximum Likelihood (ML) network based on genomic SNPs for six clades. Light purple background marks the 28 individuals of clade U2. C, D: PcoA plots based on genomic SNPs for six clades. E: Genetic clustering (K=2–8, best K=7) based on genomic SNPs from six clades by ADMIXTURE analysis. Asterisks label 18 wild-caught individuals including larvae, juveniles, and adults from Daqi Mountain, diamonds in light purple indicate 10 farm-bred individuals. Colors in all figures correspond with the mtDNA clades.
Figure 2 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.
Figure 2 Results of field-monitoring surveys in Daqi Mountain, Jiangxi Jiulingshan National Nature Reserve (Sep. 2020–Mar. 2022) A: Capture per person-hour of juveniles and adults during Sep. 2020–Mar. 2022. B, C: Activity periods of newborn larvae displayed by capture per person-hour in 2021 and 2022.
Figure 6 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.
Figure 6 Ontogenetic variation in coloration pattern A: Coloration of dorsum with spotted pattern in a juvenile with body length of ~20 cm. B: Coloration of dorsum having larger patch patterns in an adult with body length over 50 cm. Photos by Mu-Rong Yi.
Figure 5 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.
Figure 5 The holotype of Andrias jiangxiensis sp. nov. (KIZ 037731) in life A–C: Coloration of dorsum of whole body (A), head (B), and enlarged view (C) of left periocular area. Photos by Chen-Qi Lu.
Figure 1 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.
Figure 1 Map of survey localities in Jing'an County, northwest of Jiangxi, China The west part of black dashed line displays the historical distribution areas of CGS, upstream of River Liao. Red dashed line circles Daqi Mountain, which is closed to the public. Grey triangles indicate 16 sites surveyed without detection of individuals, while the red triangle and red line display the searching sites with detections.
FIGURE 1 in Genetic diversity in two threatened species of guitarfish (Elasmobranchii: Rhinobatidae) from the Brazilian and Argentinian coasts: an alert for conservation
FIGURE 1 | Median-joining network of mtCR haplotypes for A. Pseudobatos horkelii and B. Pseudobatos percellens. Haplotypes are represented by circles with size proportional to frequency in the total sample. All hatch marks correspond to one mutation. Samples from northern Argentina (AR), Torrinha/RS (RS), Florianópolis/SC (SC), Pontal do Paraná/PR (PR), Cananéia/ SP (SP1), Mongaguá/SP (SP2), Santos/SP (SP3), Rio de Janeiro/RJ(RJ).
FIGURE 2 in Genetic diversity in two threatened species of guitarfish (Elasmobranchii: Rhinobatidae) from the Brazilian and Argentinian coasts: an alert for conservation
FIGURE 2 | Graph of the Bayesian analysis of population structure of mtCR for A. Pseudobatos horkelii and B. Pseudobatos percellens. Samples from northern Argentina (AR), Torrinha/RS (RS), Florianópolis/SC (SC), Pontal do Paraná/PR (PR), Cananéia/ SP (SP1), Mongaguá/SP (SP2), Santos/SP (SP3), Rio de Janeiro/RJ(RJ).
FIGURE 5 in Genetic diversity and aquaculture conservation for a threatened Neotropical catfish
FIGURE 5 | Candidates breeding pairs in the three hatcheries, Bebedouro (BEB), Paulo Afonso (PA) and Itiúba (IT), assessed by Coancestry (Lynch & Li estimator).
FIGURE 3 in Genetic diversity and aquaculture conservation for a threatened Neotropical catfish
FIGURE 3 | Scatterplot of the Discriminant Analysis of Principal Components (DAPC) of Lophiosilurus alexandri genotypes from captive broodstocks (Bebedouro, Paulo Afonso, and Itiúba (clusters 1, 3, and 5) and wild samples taken from two stretches of the São Francisco River (upper (cluster 2) and submiddle (cluster 4). Clusters are shown by different colors and inertia ellipses, while dots represent individuals. Eigenvalues of the analysis are displayed in inset.
FIGURE 4 in Genetic diversity and aquaculture conservation for a threatened Neotropical catfish
FIGURE 4 | Relatedness estimators Wang (RW) and Lynch & Li (RLL) calculated for A. the three full-sib families (■ FS1, ■ FS2 and ■ FS3) and B. for the wild samples (■ upper and ■ submiddle São Francisco River stretches) of Lophiosilurus alexandri.
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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.