Find research datasets worth reusing

opencc-by-4.0May 2021View details →

Copernicus EMS fire activations delimitations (2012 - 2020) rasterised at 30m and aggregated per year and season

This dataset was created as part of the <a href="https://opendatascience.eu/">Geo-harmonizer project</a>, with the scope of making open data easier to access. It contains all the fire activations (forest fire, wild fire, wildfire) mapped by the<a href="https://emergency.copernicus.eu/mapping/list-of-activations-rapid"> Copernicus Emergency Rapid Mapping Service</a> between 2012 and 2020. To obtain these GeoTIFFs, the vector data packages from CEMS were individually downloaded, rasterized and mosaicked per year and season, resampled at 30-m and reprojected to <a href="https://epsg.io/3035">EPSG 3035: ETRS89-extended / LAEA Europe</a>. If no CEMS fire activation was identified in a specific year and season, the raster was not created. The rasters are provided as COG files, type=16Int, nodata value is 255. To allow an easier and faster search through all 2012 - 2020 CEMS fire activations, we have prepared a point vector layer (geojson) containing one point for each fire activation area of interest with the following attributes attached: CEMS identification number <ems_id>, area of interest defined by CEMS <ems_aoi>, URL link to the CEMS activation <ems_link>, year of the event <year_start>, <year_end> , <season> and the name of the <geo_harmonizer_raster> where the 30m rasterised delimitations of the burned areas of the corresponding fire activation can be found.  For any additional questions regarding the data please contact the author at codrina.ilie[at]terrasigna.com. The Copernicus Emergency Rapid Mapping Service data access policy is available <a href="https://emergency.copernicus.eu/mapping/sites/default/files/files/CopernicusEMS-Data_and_Dissemination_Policy.pdf">here</a>.

opencc-by-4.0May 2019View details →

Teleseismic P-wave Tomography Beneath the Pantanal, Paraná and Chaco-Paraná Basins, SE South America: Delimiting Lithospheric Blocks of the SW Gondwana Assemblage.

Tomographic data set for different depths (CSV-files with Longitude, Latitude anda Velocity Perturbation in percentage), Interpreted limit of the São Francisco Paleocontinent and the Abstract for the paper "Teleseismic P-wave Tomography Beneath the Pantanal, Paraná and Chaco-Paraná Basins, SE South America: Delimiting Lithospheric Blocks of the SW Gondwana Assemblage." submitted to Journal of Geophysical Research: Solid Earth.

opencc-by-4.0Jun 2019View details →

Delimiting the Neoproterozoic São Francisco Paleocontinental Block with P-wave travel-time tomography

Tomographic data set for different depths (CSV-files with Longitude, Latitude anda Velocity Perturbation in percentage), Interpreted limit of the São Francisco Paleocontinent and the Abstract for the paper "Delimiting the Neoproterozoic São Francisco paleocontinental block with P-wave travel-time tomography" accepted by Geophysical Journal International.

opencc-by-4.0Jul 2019View details →

FADN data on the support under the CAP delimited for LAU2 (NUTS2) regions in the EU Member States for the 2007-2013 programming period

Ready to use FADN dataset on the support under the CAP in 2007-2013 delimited for LAU2 (NUTS2) regions in the EU Member States. Investigation of the interaction between Cohesion and Rural Policies requires analysing comparable data. However, the CAP data are usually collected at the national level. The FADN database is the only data source for analysing the impact of agricultural policy instruments on the economic situation of farms. However, the regional breakdown of FADN data in some countries does not correspond to the NUTS2 breakdown for which cohesion policy is defined. The provided FADN data delimitation uses a methodology that takes into account the range of impact and features specific to a given region. Because the research shows a very strong relationship between the amount of support under the CAP and the number and size of farms on a given area, this criterion was used to delimit FADN data for particular LAU2 (NUTS2) regions, while maintaining the allocation to individual measures. FADN data aggregated (averaged) to the level of FADN regions and economic size classes were used. Each FADN region has been assigned a corresponding NUTS2 region (or regions) according to the classification in 2010 in which the full census of the farm structure survey was carried out. The delimitation of FADN data to NUTS2 regions was based on weights constructed on the basis of Eurostat data on utilised agricultural area and number of holdings in 2010. In each economic size class, each FADN region consisted of the sum of the NUTS2 regions weighted by the utilised agricultural area. The result of each FADN variable was the sum of its values in each economic size class, weighted by the total number of holdings in each class. This database has served as a basis for two articles, one validating the assumptions of the NUTS2 (LAU) delimitation of the FADN regions and the other using the database to compare synergies and trade-offs between cohesion policy and the common agricultural policy.

dryad44/100

Data from: Species delimitation in endangered groundwater salamanders: implications for aquifer management and biodiversity conservation

Groundwater-dependent species are among the least-known components of global biodiversity, as well as some of the most vulnerable because of rapid groundwater depletion at regional and global scales. The karstic Edwards–Trinity aquifer system of west-central Texas is one of the most species-rich groundwater systems in the world, represented by dozens of endemic groundwater-obligate species with narrow, naturally fragmented distributions. Here, we examine how geomorphological and hydrogeological processes have driven population divergence and speciation in a radiation of salamanders (Eurycea) endemic to the Edwards–Trinity system using phylogenetic and population genetic analysis of genome-wide DNA sequence data. Results revealed complex patterns of isolation and reconnection driven by surface and subsurface hydrology, resulting in both adaptive and non-adaptive population divergence and speciation. Our results uncover new cryptic species diversity and refine the borders of several threatened and endangered species. The U.S. Endangered Species Act has been used to bring state regulation to unrestricted groundwater withdrawals in the Edwards (Balcones Fault Zone) Aquifer, where listed species are found. However, the Trinity and Edwards–Trinity (Plateau) aquifers harbor additional species with similarly small ranges that currently receive no protection from regulatory programs designed to prevent groundwater depletion. Based on regional climate models that predict increased air temperature, together with hydrologic models that project decreased springflow, we conclude that Edwards–Trinity salamanders and other co-distributed groundwater-dependent organisms are highly vulnerable to extinction within the next century.

opencc-zeroDec 2018View details →

opencc-by-4.0May 2023View details →

From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals

With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data is available due to the small number of currently available markers and obscures species boundaries. Difficulties in inferring gene trees and morphological incongruences further blur the study and conservation of these organisms. Yet, can genomics alone be used to delimit species? Here, focusing on the coral genus Pocillopora, whose colonies play key roles in Indo-Pacific reef ecosystems but have challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNP) were first used to resolve Pocillopora phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to other lines of evidence based on genetic, morphology, biogeography and symbiont associations. Out of 21 species hypotheses delimited by genomics, 13 were strongly supported by all approaches, while six could represent either undescribed species or nominal species that have been synonymised incorrectly. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine Pocillopora species boundaries, (2) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, (3) the requirement of molecular identification when species identity of colonies is absolutely necessary to interpret results, as morphology can blur species identification in the field, and (4) the need for a taxonomic revision of the genus Pocillopora. These results give new insights into the usefulness of multiple criteria for resolving Pocillopora, and more widely, scleractinian species boundaries, and will ultimately contribute to the taxonomic revision of this genus and the conservation of its species.   This deposit contains the data related to Oury N, Noël C, Mona S, Aurelle D, Magalon H (2023) From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals. Mol Phylogenet Evol 107803. doi:10.1016/j.ympev.2023.107803 See 0_README.txt for more content details.

dryad44/100

Data from: Species delimitation in endangered groundwater salamanders: implications for aquifer management and biodiversity conservation

Open the record for dataset details and reuse information.

publicJan 2019View details →

Fig. 12 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 12. Distribution map, face view, and lateral view of petiole of Rasopone JTL030 (worker, Panama, CASENT0633075), R. JTL037 (worker, Guatemala, CASENT0625283), R. mesoamericana (holotype worker), and R. JTL029 (worker, Panama, CASENT0633053). On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.

Fig. 13 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 13. Distribution map, face view, and lateral view of petiole of Rasopone cubitalis (holotype worker), R. titanis (worker, Mexico, Chiapas, MCZ-ENT00716640), R. breviscapa (holotype queen), and R. rupinicola (worker, Colombia, face view MCZ-ENT00716589, petiole CASENT0217567). On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.

Fig. 11 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 11. Distribution map, face view, and lateral view of petiole of Rasopone ferruginea (worker, Nicaragua, CASENT0644264), R. JTL040 (worker, Colombia, MCZ-ENT00716609), R. JTL041 (worker, Colombia, MCZ-ENT00716614), and R. costaricensis form a (worker, Costa Rica, INB0003659312). On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality (type locality for R. ferruginea is 'Mexico').

Fig. 8 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 8. Distribution map, face view, and lateral view of petiole of Rasopone lunaris (worker, Brazil, Minas Gerais CASENT0644556), R. guatemalensis (holotype worker), R. costaricensis form c (worker, Costa Rica, INB0003659307), and R. JTL027 (worker, Panama, CASENT0633216). On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.

Fig. 7 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 7. Distribution map, face view, and lateral view of petiole of Rasopone MAS010 (worker, Costa Rica, 08COSTA-1723), R. cryptergates (worker, Costa Rica, INB0003660648), R. JTL042 (worker, Colombia, MCZ-ENT00716611), and R. JTL034 (worker, Mexico, CASENT0640282). On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.

Fig. 2 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 2. Phylogeny of Rasopone, Mayaponera, and selected outgroup taxa, inferred using the program IQ-TREE and 1,802 UCE loci. Node support values (ultrafast bootstrap/SH-like) <100/100 are depicted with red dots. Terminal names show original, morphology-based species assignments and depict morphological convergence across clades. The 'EX#' code in terminal names indicate unique extraction codes that link specimens to specimen data in provided tables. Simopelta andersoni, a distant outgroup, is not shown in the figure. Images depict workers of Rasopone ferruginea (Nicaragua, CASENT0644264), Mayponera becculata (Peru, CASENT0374638, modified from AntWeb, credit Michele Esposito), and Mayaponera constricta (Bolivia, CASENT0249137, modified from AntWeb, credit Ryan Perry).

Fig. 1 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 1. Characteristics of Rasopone species. (A) Habitus. (B) Scale-like petiole, showing definitions of petiole height (PTH) and petiole length (PTL), and the distinctive shape of the sternite. (C) Petiolar node intermediate between scale-like and cuboidal. (D) Cuboidal petiolar node. (E) Anterior clypeal margin truncate, with angulate lateral lobes. (F) Anterior clypeal margin sinuous, with rounded lateral lobes.

Fig. 6 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 6. Distribution map, face view, and lateral view of petiole of Rasopone pluviselva (holotype worker), R. minuta (worker, Mexico, Chiapas, CASENT0609834), R. JTL043 (worker, Ecuador, MCZ-ENT00716620), and R. JTL048 (worker, French Guiana, CASENT0645961). On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.

Fig. 4 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 4. Dealate queen of Rasopone ferruginea (Nicaragua, CASENT0624181). Scale bars are 0.5 mm for face view, 1.0 mm for dorsal and lateral views.

Fig. 5 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 5. Male of Rasopone mesoamericana sp. nov. (Nicaragua, CASENT0627722). Scale bars are 0.5 mm for face view, 1.0 mm for dorsal and lateral views.

Fig. 3. Phylogenetic relationships among a in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

Fig. 3. Phylogenetic relationships among a curated set of COI barcode sequences for Rasopone. Black samples were sequenced for UCEs. Red samples were downloaded from the BOLD database.The tree was inferred using IQ-TREE with the data partitioned by codon position. Black circles on nodes indicate high support, which we define as ≥95% ultrafast bootstrap support and ≥95% SH-like branch support.Terminal names match taxonomic changes proposed in paper and provide useful sample identifiers (e.g., extraction codes [EX#] or BOLD process IDs).A complete, unpruned COI tree is available in Supp Fig. S1 (online only).