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139 results for “reconcilation”
A tectonic model reconciling evidence for the collisions between India, Eurasia and intra-oceanic arcs of the central-eastern Tethys
<p>2 February 2014<br>Version 1.2</p> <p>Supplement and plate model accompanying: <br>Gibbons, A., Zahirovic, S., Müller, R., Whittaker, J., and Yatheesh, V., 2015, A tectonic model reconciling evidence for the collisions between India, Eurasia and intra-oceanic arcs of the central-eastern Tethys: Gondwana Research FOCUS.</p> <p><strong>Gibbons_etal_2015_GR_PlateModel.zip</strong></p> <p>This directory contains four files:</p> <p>TPW_CK95G94_Rigid_Gibbons.rot - the Gibbons et al. global rotation model TPW_CK95G94_PP_Rigid_Gibbons.gpml - the Gibbons et al. global evolving topologies <br>CK95G94_Coastlines.gpmlz - Present-day coastlines with Plate ID assignments<br>CK95G94_StaticPolygons_Gibbons.gpmlz - Present-day block outlines </p> <p>To load these datasets in GPlates do the following:</p> <p>1. Open GPlates<br>2. Pull down the GPlates File menu and select the operation Open Feature Collection<br>3. Click all the files while holding down the shift key to select all files. All the files should be highlighted.<br>4. Click Open </p> <p>Alternatively, drag and drop the files onto the globe.<br> <br>Play around with the GPlates buttons to make an animation, select features, draw features, etc. For more information, read the GPlates manual which can be downloaded from <a href="https://www.gplates.org">www.gplates.org</a></p> <p><strong>Zahirovic_etal_2014_SE</strong></p> <p>This file provides a detailed description of all of the files that make up the data collection associated with the publication: Zahirovic, S., Seton, M., & Müller, R. D. (2014). The Cretaceous and Cenozoic tectonic evolution of Southeast Asia. Solid Earth, 5(1), 227-273. doi:<a href="https://doi.org/10.5194/se-5-227-2014" target="_blank" rel="noopener">10.5194/se-5-227-2014</a></p> <p>Any questions, please email: <br>Ana Gibbons <angi@statoil.com><br>Sabin Zahirovic <sabin.zahirovic@sydney.edu.au></p>
Data and statistical code for "Reconciling biodiversity with timber production and revenue via an intensive forest management experiment"
<p><strong>Abstract</strong></p> <p>Understanding how land-management intensification shapes the relationships between biodiversity, yield and economic benefit is critical for managing natural resources. Yet, manipulative experiments that test how herbicides affect these relationships are scarce, particularly in forest ecosystems where considerable time lags exist between harvest revenue and initial investments. We assessed these relationships by combining 7 years of biodiversity surveys (>800 taxa) and forecasts of timber yield and economic return from a replicated, large-scale experiment that manipulated herbicide application intensity in operational timber plantations. Herbicides reduced species richness across trophic groups (-18%), but responses by higher-level trophic groups were more variable (0–38% reduction) than plant responses (-40%). Financial discounting, a conventional economic method to standardize past and future cashflows, strongly modified biodiversity-revenue relationships caused by management intensity. Despite a projected 28% timber yield gain with herbicides, biodiversity-revenue tradeoffs were muted when opportunity costs were high (i.e., economic discount rates ≥7%). Although herbicides can drive biodiversity-yield tradeoffs, under certain conditions, financial discounting provides opportunities to reconcile biodiversity conservation with revenue.</p>
Reconciling supertramps, great speciators and relict species with the taxon cycle stages of a large island radiation (Aves: Campephagidae)
<p><strong>Aim</strong>: The taxon cycle concept provides a geographically explicit and testable set of hypotheses for exploring the evolutionary processes underlying the distribution of species in space and time. Here, we test taxon cycle predictions within a large avian island radiation, the core Campephagidae and explicitly integrate the concepts of 'supertramps', 'great speciators' and relictualization.</p> <p><strong>Location</strong>: The Indo-Pacific, Australia, Asia and Africa.</p> <p><strong>Taxon</strong>: Corvoid passerine birds.</p> <p><strong>Methods</strong>: We constructed a new time-calibrated molecular phylogeny of the core Campephagidae (cuckoo-shrikes, cicadabirds and trillers) using Bayesian phylogenetic methods. Ancestral range estimation methods and diversification rate analyses were used to explore the dispersal and diversification history of the group. We used an extensive dataset on wing morphology and range distributions to test for correlations between evolutionary age of species and dispersal capacity, diversification and distribution, while accounting for phylogenetic non-independence.</p> <p><strong>Results</strong>: The core Campephagidae represents an ecologically homogeneous radiation distributed across the Indo-Pacific, Australia, South-East Asia and Africa. Its members represent a continuum of dispersal abilities; some species are widespread and undifferentiated ('supertramps') or show strong differentiation of local populations ('great speciators'), and a few are endemic to single islands (relicts). We show that older species relative to younger species inhabit fewer and larger islands at higher elevations. The level of intraspecific variation measured as the number of subspecies also decreases with species age, and is highest in 'great speciators' with intermediate levels of dispersal abilities (as per hand-wing index).</p> <p><strong>Main conclusions</strong>: Based on trait correlations with species age, we infer phases of range expansion and contraction over millions of years (taxon cycles), within a single monophyletic group of birds. These observations demonstrate reconciliation of the concepts of 'supertramps', 'great speciators' and relictual paleo-endemics within the temporal stages of the taxon cycle.</p>
Genetic Architecture Reconciles Linkage and Association Studies of Complex Traits
<p>This (zipped) folder contains 3 sub-folders:</p> <p>#**********************************************************************************************************<br>The "bin" folder contains fuctions and gentic maps needed for analyes<br>bin \<br> predLink.R - function to predict linkage <br> sibREML_v0.1.1.R - function to run SibREML<br> sim-sib-array.R - script to simulate sib-pairs from parental haplotypes<br> Summarised_genetic_map_bcf.txt - genetic map per 0.5-cM long segments, based on map from bcftools <br> (BCFtools: https://samtools.github.io/bcftools/bcftools.html)<br> Summarised_genetic_map_OMNI.txt - genetic map per 0.5-cM long segments, based on OMNI map <br> (https://github.com/joepickrell/1000-genomes-genetic-maps/tree/master/interpolated_OMNI)<br>#**********************************************************************************************************</p> <p> </p> <p>#**********************************************************************************************************<br>The "SIM" folder contains the simulation pipeline (scripts 01-15) as well as IBD sharing and simulated phenotypes for Simulated sib-pairs.<br>SIM \<br> 01_sim-sib-array.sh *pre-run*<br> 02_bed_recode_bcf_map.sh *pre-run*<br> 03_make_merlin.R *pre-run*<br> 04_error_merlin.sh *pre-run*<br> 05_merlin_IBD.sh *pre-run*<br> 06_sample_causal_snps.R *pre-run*<br> 07_simulate_pheno.sh *pre-run*<br> 08_bhat_gwas.R *can be run using provided data* <br> 09_Linkage_VH.R *can be run using provided data* <br> 10_predLink.R *can be run using provided data*<br> 11_phi_hat.R *can be run using provided data*<br> 12_IBD_Mb.R *can be run using provided data*<br> 13_IBD_cM_recombrate_stratified.R *can be run using provided data*<br> 14_SibREML.R *can be run using provided data*<br> 15_SibREML_stratified_Q4.R *can be run using provided data*<br> causal_snps \ *provided causal SNPs*<br> IBD_results \ *provided IBD-probabilities for 1000 simulated sib-pairs*<br> Linkage_VH_results \ <br> pheno \ *provided simulated phenotypes (h2=1) for 8 genetic architectures*<br> Phi_hat_results.txt<br> predicted \<br> README<br> SibREML_results.txt<br> SibREML_stratified_Q4.txt</p> <p>The data can be used to run Linkage analysis, predict linkage, estimate phi_hat, <br>as well as estimate non-stratified and recombination rate stratified sib-heritability (h2_FS and c).<br>The README is provided within the folder. <br>#**********************************************************************************************************</p> <p> </p> <p>#**********************************************************************************************************<br>The "HT_BMI" folder contains data and scripts to predict linkage and estimate phi_hat for height and BMI.<br>HT_BMI \<br> 01_predLink_HT_BMI.R<br> 02_phi_hat_HT_BMI.R<br> gws_sumstats \ *provided summary GWAS summary statistics to predict linkage for height and BMI*<br> Linkage_results \ *provided linkage meta-analysis results for height and BMI from this study*<br> Phi_hat_results_HT_BMI.txt<br> PREDLINK_bmi.txt<br> PREDLINK_height.txt<br> README<br>The README is provided within the folder.<br>#**********************************************************************************************************</p> <p><strong> </strong></p>
Country-ocean-moisture-flows-reconciled-with-ERA5-reanalysis obtained processing Lagrangian moisture connections
<p>The dataset "Reconciled global atmospheric moisture flows between countries/oceans and subcontinents" presents tracked volumes of precipitation and evaporation reconciled with reanalysis data, closing the annual hydrological balance, and provides robust estimates of terrestrial moisture recycling and net moisture flows to support global water governance analysis.</p> <p>This repository is supplement to a study by De Petrillo & Fahrländer et al. (2025), which describes the development of the reconciliation framework, includes a perfromance analysis of the method and shows an exemplary case study on the published data. </p> <p>The atmospheric moisture flows are sourced from the UTrack atmospheric moisture flow dataset by Tuinenburg et al. (2020a) (dataset access: Tuinenburg et al., 2020b) and reconciled with ERA5 precipitation and evaporation data (Hersbach et al., 2020) on the mean annual basis in the period 2008-2017, by means of a post-processing framework, based on the Iterative Proportional Fitting (IPF) algorithm.</p> <p>NOTE: The final dataset is available in form of bilateral matrices (country/ocean and subcontinent/ocean) and in form of direct flows (flow edges). Supporting material to read the dataset is in the folder "List" . Processed ERA5 data (where the precipitation-evaporation annual balance is met) and input data to generate the figures are also available.</p> <p>References:</p> <p>De Petrillo, E., Fahrländer, S., Tuninetti, M., Andersen, L.S., Monaco, L., Ridolfi, L., Laio, F. (2025). Reconciling tracked atmospheric moisture flows to close the global freshwater cycle.<em> </em><em>Commun Earth Environ <strong>6</strong>, 347 (2025). </em><a href="https://doi.org/10.1038/s43247-025-02289-y">https://doi.org/10.1038/s43247-025-02289-y</a></p> <p>Tuinenburg, O. A., Theeuwen, J. J. E., & Staal, A. (2020a). High-resolution global atmospheric moisture connections from evaporation to precipitation. <em>Earth System Science Data</em>, <em>12</em>(4), 3177–3188. <a href="https://doi.org/10.5194/essd-12-3177-2020">https://doi.org/10.5194/essd-12-3177-2020</a></p> <p>Tuinenburg, O. A., Theeuwen, J. J. E., Staal, A. (2020b): Global evaporation to precipitation flows obtained with Lagrangian atmospheric moisture tracking. PANGAEA, <a href="https://github.com/ObbeTuinenburg/UTrack_global_database">https://doi.pangaea.de/10.1594/PANGAEA.912710</a></p> <p>Hersbach, H., Bell, B., Berrisford, P., Hirahara, S., Horányi, A., Muñoz‐Sabater, J., et al. (2020). The ERA5 global reanalysis. <em>Quarterly Journal of the Royal Meteorological Society</em>, <em>146</em>(730), 1999–2049. <a href="https://doi.org/10.1002/qj.3803">https://doi.org/10.1002/qj.3803</a></p> <p> </p> <p> </p>
Figure 7 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record
Figure 7. Cartoon to depict consensus relationships among Charadriiformes ('shorebirds') along with the holotype specimen of Morsoravis sedile, a new and exceptionally well-preserved fossil from Palaeocene–Lower Eocene deposits in Jutland, Denmark (1–2; G. J. Dyke, M. van Tuinen & D. M. Waterhouse, unpubl. data). The tree is based on various sources; see text for details. Scale bar = 10 mm.
Figure 6 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record
Figure 6. Cartoon to depict consensus relationships among Galliformes ('landfowl') along with some selected fossil material (based on Dyke, 2003b and Dyke et al., 2003): A, hypothesis for the phylogenetic positions of the Lower Eocene (c. 55 Mya) taxa Gallinuloides and Paraortygoides; B, fossil elements of Paraortygoides from the Lower Eocene London Clay Formation of England (see Dyke & Gulas, 2002); C, holotype specimen of Gallinuloides wyomingensis from the Lower Eocene Green River Formation of Wyoming (North America) (Dyke, 2003b). Scale bar = 10 mm.
Figure 5 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record
Figure 5. Cartoon depicting consensus phylogenetic relationships among Anseriformes ('waterfowl') (based on Livezey, 1997) (Presbyornithidae includes the taxa Presbyornis and Teviornis; see text for details) along with a selection of wellpreserved fossil taxa: A, holotype skull of Anatalavis oxfordi in lateral view from the Lower Eocene London Clay Formation (The Natural History Museum, London, Palaeontology Department Collections, BMNH PAL 5922) (see Dyke, 2001b); B, holotype coracoid of BMNH PAL 5922 in dorsal and medial views) (scale bars = 10 mm); C, holotype carpometacarpus of Teviornis gobiensis from the Late Cretaceous Nemegt Formation of Mongolia (Palaeontological Institute of the Russian Academy of Sciences, PIN 4499–1) in dorsal and ventral views (see Kurochkin et al., 2002). Scale bar = 10 mm.
Figure 4 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record
Figure 4. Phylogenetic relationships within Palaeognathae including the well-represented fossil taxa Palaeotis and Lithornis (see text for details): A, new specimen of Lithornis from the Palaeocene-Lower Eocene Fur Formation of Denmark (Dankrae Collections of the Geologisk Museum, Copenhagen, DK 330) encased in cement stone nodule; B, skull of DK 330 acid prepared in oblique lateral view; C, palate of Lithornis in ventral view (ba, basitemporal plate; de, dentary; pa, palatine; pt, pterygoid; vo, vomer); D, the phylogenetic placement of Lithornis and Palaeotis inferred from cladistic analysis of osteological characters (see G. J. Dyke & M. van Tuinen, unpubl. data for details of analysis and matrices).
Figure 3 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record
Figure 3. Seven possible definitions for the 'radiation of birds'. The true radiation of morphology observed in today's birds may have taken place as recently as points 6 or 7. Archaic ornithurines have not been found after the K–T boundary (black arrow). Although predicted from molecular clock analyses (dotted line; see text), little convincing evidence exists for neornithine fossils preceding the K–T boundary. The variation in number of species among traditional neornithine orders indicates that the 'radiation' was not equal across every major clade. Numbers refer to the following major evolutionary bird divergences: 1, diversification of Aves; 2, origin of Neornithes; 3, diversification of Neornithes; 4, origin of Neoaves; 5, origin of most orders (including 'Neoavian comb'); 6, diversification of most orders; 7, diversification of most families.
Figure 1 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record
Figure 1. Summary cladogram to show the phylogenetic relationships at the base of Neornithes (based on Cracraft et al., 2004). Despite advances in the use of genetic data to resolve the phylogenetic relationships of birds, differences between data sets remain and have led to conflict with regard to the interrelationships of clades within Neoaves. The part of this tree to the right-hand side (relationships within Neoaves) has often been referred to as the 'neoavian comb' (Cracraft et al., 2004).
Reconciling the onshore/offshore stratigraphy of the Canning Basin and implications for petroleum prospectivity supplementary material
<p>In this paper, figures 4 and 6 were made to a smaller scaler for improved visuals; however, this resulted in the extent of some units being left out of the figure. The supplementary material here includes the full extent of figures 4 and 6 so readers can identify where each unit was mapped in this study.</p>
Reconciling supertramps, great speciators and relict species with the taxon cycle stages of a large island radiation (Aves: Campephagidae)
Open the record for dataset details and reuse information.
Data for the publication "Reconciling compensating errors between precipitation constraints and the energy budget in a climate model"
<p>These data are a set of 6yr simulations using the MIROC6-SPRINTARS global aerosol-climate model with different treatments (diagnostic and prognostic) of precipitation under the present-day (PD, aerosol emission at the year 2000) and preindustrial (PI, aerosol emission at the year 1850) conditions.<br> The data are used in the manuscript entitled "Reconciling compensating errors between<br> precipitation constraints and the energy budget in a climate model".</p>
Data from: Extending full protection inside existing marine protected areas or reducing fishing effort outside can reconcile conservation and fisheries goals
<p>1. Most fish stocks worldwide are fished at maximum sustainable yield (MSY) or overfished, as many fisheries management strategies have failed to achieve sustainable fishing. Identifying effective fisheries management strategies has now become urgent.</p> <p>2. Here, we developed a spatially-explicit metapopulation model accounting for population connectivity in the north-western Mediterranean Sea, and parameterized it for three ecologically and economically important coastal fish species: the white seabream <i>Diplodus sargus</i>, the two-banded seabream <i>Diplodus vulgaris</i> and the dusky grouper <i>Epinephelus marginatus</i>.</p> <p>3. We used the model to assess how stock biomass and catches respond to changes in fishing mortality rate (<i>F</i>) and in the size of fully protected areas within the existing system of multiple-use marine protected areas (MPAs). For each species, we estimated MSY and the corresponding values of stock biomass (<i>B</i><sub>MSY</sub>) and fishing mortality rate (<i>F</i><sub>MSY</sub>), providing crucial reference points for the assessment of fisheries management.</p> <p>4. <i>D. sargus</i> is currently in low overfishing, while <i>D. vulgaris</i> and <i>E. marginatus</i> are in high overfishing. Stock recovery to <i>B</i><sub>MSY</sub> for the last two species requires a reduction of current <i>F</i> around 50%. This would guarantee an increase in both stock biomass (around 50 and 75% for <i>D. vulgaris</i> and <i>E. marginatus</i>, respectively) and catch (around 15 and 30%) after a transient time of ~15–30 years. Alternatively, doubling the size of fully protected areas over fishable areas within the existing network of MPAs would lead to positive conservation effects for all three species without substantially affecting the overall productivity of the fishery and the total economic value of the catch.</p> <p>5. <i>Synthesis and applications.</i> We provide the first assessment of stock status for three coastal species in the north-western Mediterranean and evaluate the ecological and fisheries outcomes of different management strategies. Extending full protection inside existing multiple-use marine protected areas or reducing fishing effort outside can deliver both conservation and fisheries benefits.</p>
Dataset from paper: "Mind the Gap: Reconciling tropical forest carbon flux estimates from Earth Observation and National Reporting requires transparency"
<p>This repository contains the processed data used in the publication of Heinrich et al., 2023 (Mind the Gap: Reconciling tropical forest carbon flux estimates from Earth Observation and National Reporting requires transparency). Carbon Balance and Management: https://cbmjournal.biomedcentral.com/articles/10.1186/s13021-023-00240-2 </p><p>When using this data, full reference to the raw data publications and the publication Heinrich et al., 2023 must be made.</p><p>The raw datasets used in this study are all available from their original sources.</p><p> </p>
Reconciling community-level responses of wild bees to highly anthropized landscapes
<p>Data and source code for the analyses described in the manuscript.</p>
Data from: Darwin's naturalization conundrum reconciled by changes of species interactions
<p>Although phylogenetic distance between native and exotic species has a close link with their interactions, it is still unclear how environmental stresses and species interactions influence the relationship between phylogenetic distance and biological invasions. Here we assessed the effect of invader-native phylogenetic distance on the growth of the invader (<em>Symphyotrichum subulatum</em>) under three levels of drought (no, moderate or intensive drought). Under no drought, interspecific competition between close relatives was the dominant process, and native communities more closely related to the invader showed higher resistance to invasion, supporting Darwin's naturalization hypothesis. In contrast, under intensive drought, facilitation between close relatives by mutualism with arbuscular mycorrhizal fungi (AMF) became more important, and the invader became more successful in their more closely related native communities, supporting the pre-adaptation hypothesis. The colonization rate of AMF of the invader was higher in more closely related native communities regardless of the drought treatment, but it was only positively related to invader biomass under intensive drought. Therefore, the shift of species interactions from competition to facilitation may be ascribed to the promotion of AMF to invasion occurring under intensive drought, which leads to the effect of closely related natives on the invader shifting from negative to positive. Our results provide a new angle to resolve Darwin's naturalization conundrum from the change of species interactions along a stress gradient, and provide important clues for invasion management when species interactions change in response to global climatic change.</p>
Updating splits, lumps, and shuffles: Reconciling GenBank names with standardized avian taxonomies
Abstract Biodiversity research has advanced by testing expectations of ecological and evolutionary hypotheses through the linking of large-scale genetic, distributional, and trait datasets. The rise of molecular systematics over the past 30 years has resulted in a wealth of DNA sequences from around the globe. Yet, advances in molecular systematics also have created taxonomic instability, as new estimates of evolutionary relationships and interpretations of species limits have required widespread scientific name changes. Taxonomic instability, colloquially "splits, lumps, and shuffles," presents logistical challenges to large-scale biodiversity research because (1) the same species or sets of populations may be listed under different names in different data sources, or (2) the same name may apply to different sets of populations representing different taxonomic concepts. Consequently, distributional and trait data are often difficult to link directly to primary DNA sequence data without extensive and time-consuming curation. Here, we present RANT: Reconciliation of Avian NCBI Taxonomy. RANT applies taxonomic reconciliation to standardize avian taxon names in use in NCBI GenBank, a primary source of genetic data, to a widely used and regularly updated avian taxonomy: eBird/Clements. Of 14,341 avian species/subspecies names in GenBank, 11,031 directly matched an eBird/Clements; these link to more than 6 million nucleotide sequences. For the remaining unmatched avian names in GenBank, we used Avibase's system of taxonomic concepts, taxonomic descriptions in Cornell's Birds of the World, and DNA sequence metadata to identify corresponding eBird/Clements names. Reconciled names linked to more than 600,000 nucleotide sequences, ~9% of all avian sequences on GenBank. Nearly 10% of eBird/Clements names had nucleotide sequences listed under 2 or more GenBank names. Our taxonomic reconciliation is a first step towards rigorous and open-source curation of avian GenBank sequences and is available at GitHub, where it can be updated to correspond to future annual eBird/Clements taxonomic updates.
Model runs - Reconciling the EU forest, biodiversity, and climate strategies
<p>These are the model runs for the paper "Reconciling the EU forest, biodiversity, and climate strategies" published in Global Change Biology in 2024, by Gregor et al.</p> <p>The data can be used to re-run the optimizations.</p>
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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.