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2,549 results for “Diversification”
A Novel Crop Shortlisting Method for Sustainable Agricultural Diversification Across EU (Italy)
<p>In order to shortlist possible options from a pool of 2700 crops, a crop-climate-soil matching ex-ercise was performed across Italian territory and crops with more than 70% suitability where chosen for further analysis. In the second phase, a multicriteria ranking index was employed to assign ranks to chosen crops of 4 main types; (i) cereals and pseudocereals, (ii) legumes, (iii) starchy roots/ tubers and (iv) vegetables. In order to provide a comprehensive analysis, major crops that are grown in the region where also included in the analysis. The results of evaluation of 4 major criteria (a) calorie and nutrition demand b) functions and uses c) availability and acces-sibility to their genomic material d) possession of adaptive traits, and e) physiological traits) re-vealed the potential for teff, faba bean, cowpea, green arrow arum, Jerusalem artichoke, Fig-leaved Gourd and Watercress. </p>
Dataset: Relation of pest insect-killing and soilborne pathogen-inhibition abilities to species diversification in environmental Pseudomonas protegens
<p>This dataset is related to "<em>Relation of pest insect-killing and soilborne pathogen-inhibition abilities to species diversification in environmental Pseudomonas protegens</em>" and contains all the data obtained from insect experiments and plant-pathogen inhibition assays, as well as the code used for phylogenetic and Biolog anaylsis. </p>
Carbon decomposition and nitrogen mineralization in Marsden agroecosystem diversification experiment, Iowa, 2021
This dataset contains measurements of soil carbon decomposition and nitrogen mineralization from 36 soils in the Marsden agroecosystem diversification experiment. Soil samples were collected in fall 2021 from a long-term experiment initiated in 2002 at Iowa State University's Marsden Farm. The dataset includes laboratory data on soil organic carbon (SOC) content, soil total nitrogen content, the carbon-to-nitrogen ratio of soil, time-series CO2 fluxes from SOC decomposition in a 13.5-month lab incubation, and soil nitrogen mineralization rates. It also provides model simulations of SOC decomposition from different carbon pools using three process-based models: the Agricultural version of the Integrated Biosphere Simulator (Agro-IBIS), CN-SIM, and the Microbial-ENzyme Decomposition (MEND) models.
Data for "Crop Diversification in Viticulture with Aromatic Plants: Effects of Intercropping on Grapevine Productivity in a Steep-Slope Vineyard in the Mosel Area, Germany"
<p>This dataset is corresponding to an open-access article named "Crop Diversification in Viticulture with Aromatic Plants: Effects of Intercropping on Grapevine Productivity in a Steep-Slope Vineyard in the Mosel Area, Germany" published in Agriculture (https://www.mdpi.com/2077-0472/11/2/95; <a href="https://doi.org/10.3390/agriculture11020095">https://doi.org/10.3390/agriculture11020095</a>), funded by the European Commission Horizon 2020 project Diverfarming [grant agreement 728003]. </p>
Inventory of tools and resources for crop diversification available for stakeholders
<p>The aim of the database is to give an overview of existing resources, tools and methods to promote crop diversification strategies (rotation, multiple cropping, intercropping) at different levels (including the value chain and territory levels). This version contains 143 resources.</p> <p>Each resource is described with a set of criteria: strategies used / described in the resource, purpose of the resource (what is an end-user doing with the resource), expected performances, area of validity, context of use, but also characteristics for use (cost, training, required time to collect data…).</p> <p>A toolbox was also designed to support end-users to navigate among this database and aims to help different type of end-users to identify interesting and adapted resources to foster crop diversification.</p> <p></p>
Evidence for Early Mesozoic diversification of Hypsimetopidae Nicholls, 1943 (Isopoda), with the description of a new genus from Andhra Pradesh and notes on threats to Indian cave environments
<p>Datafiles and scripts for https://doi.org/10.1093/jcbiol/ruac052</p> <p>Evidence for Early Mesozoic diversification of Hypsimetopidae Nicholls, 1943 (Isopoda), with the description of a new genus from Andhra Pradesh and notes on threats to Indian cave environments</p> <p>George D. F. Wilson1,2 and Shabuddin Shaik 3</p> <p>1 Saugatuck Natural History Laboratory, Saugatuck, MI, USA; gdfw@snhlab.com</p> <p>3 Department of Life Science, Central University of Karnataka, Kadaganchi, 585 367, India; shabu.biologist@gmail.com</p> <p>2 Corresponding author: George D. F. Wilson, P. O. Box 714, Saugatuck, Michigan 49453, USA. e-mail: gdfw@snhlab.com </p> <p>File List:</p> <p>Phreatoi20220525.nex <br> Mesquite data file that contains all data from the DELTA taxonomic database that were used for data presentation, organization, analysis, as well as trees resulting from all analyses. For Mesquite version 3.70; Maddison WP, Maddison DR. 2021. Mesquite: a modular system for evolutionary analysis. Version 3.6 University of British Columbia & Oregon State University., http://www.mesquiteproject.org/ <br> <br> The DELTA database is still being edited and changed so it is not included here<br> For DELTA, see website https://www.delta-intkey.com/<br> publications:<br> Dallwitz MJ. 1980. A general system for coding taxonomic descriptions. TAXON 29: 41-46.<br> Dallwitz MJ, Paine TA, Zurcher EJ. 2000. User's guide to the DELTA system: a general system for processing taxonomic descriptions. CSIRO: Canberra.</p> <p> <br> Phreatoi20220525.tnt - the TNT data file generated by Mesquite<br> Analyses were performed using TNT-64bit, version 1.5, Goloboff PA, Catalano SA. 2016. TNT version 1.5, including a full implementation of phylogenetic morphometrics. Cladistics 32: 221-238.<br> Note: TNT counts zero as a number so the first tree, taxon or k paramter is 0, the second is 1, the third is 2 and so on </p> <p>TNT Scripts were written or modified for this project by George D. F. Wilson. They were run using the console in Ubuntu 20.04 but should work using the console version of TNT in other operating systems available from http://www.lillo.org.ar/phylogeny/tnt/. I recommend using the console because it allows you do to multiple analysis with one script. </p> <p>Each script has a banner that explains what is being done. If this fails to appear the first time, enter n and restart the script</p> <p>These are easily modified in a text editor to change the analysis<br> -- tnt.run : standard run of tnt. <br> -- tnt-jacK.run : symmetric jackknife analysis with concavity parameter, select file, concavity and prob parameter <br> -- piwe_rangeK.run : A range of concavity parameters are selected at the beginning and run sequentially<br> -- setk_trans.run : Modified from setk.run by Salvador Arias, Instituto Miguel Lillo, San Miguel de Tucuman, Argentina<br> -- aquickie_bt1000.run : Modified from the standard script distributed with TNT with more iterations of jackknifing<br> <br> If you are new to using TNT, see the information available on http://www.lillo.org.ar/phylogeny/tnt/ as well as these articles:<br> Goloboff PA. 1993. Estimating character weights during tree search. Cladistics 9: 83-91.<br> Goloboff PA. 1997. Self-Weighted Optimization: Tree Searches and Character State Reconstructions under Implied Transformation Costs. Cladistics 13: 225-245.<br> Goloboff PA, Carpenter JM, Arias JS, Esquivel DRM. 2008. Weighting against homoplasy improves phylogenetic analysis of morphological data sets. Cladistics 24: 758-773.<br> Goloboff PA, Catalano SA. 2016. TNT version 1.5, including a full implementation of phylogenetic morphometrics. Cladistics 32: 221-238.<br> Goloboff PA, Farris JS. 2001. Methods for Quick Consensus Estimation. Cladistics 17: S26-S34.<br> Goloboff PA, Farris JS, Källersjö M, Oxelman B, Ramírez MJ, Szumik CA. 2003. Improvements to resampling measures of group support. Cladistics 19: 324-332.<br> Goloboff PA, Farris JS, Nixon KC. 2008. TNT, a free program for phylogenetic analysis. Cladistics 24: 774-786.</p>
Dataset for the article "Barriers and Opportunities for Sustainable Farming Practices and Crop Diversification Strategies in Mediterranean Cereal-Based Systems"
<p>Datasets from the surveys applied for the article "Barriers and Opportunities for Sustainable Farming Practices and Crop Diversification Strategies in Mediterranean Cereal-Based Systems" <a href="https://doi.org/10.3389/fenvs.2022.861225">https://doi.org/10.3389/fenvs.2022.861225</a></p>
Evolutionary dynamics of mycorrhizal symbiosis in land plant diversification - phylogenetic data
<p>This submission supplements the manuscript entitled <em>Evolutionary dynamics of mycorrhizal symbiosis in land plant diversification</em> by <strong>Frida A.A. Feijen, Rutger A. Vos, Jorinde Nuytinck & Vincent S.F.T. Merckx.</strong></p> <p>The contents of this submission are dating analysis results for rootings of the land plant topology. Contains the following files:</p> <ul> <li>*.log.gz BEAST logs</li> <li>*.trees.gz BEAST trees</li> <li>*.tiff screen dumps of tracer, showing the burn-in</li> <li>*.consensus.trees produced with treeannotator</li> </ul> <p><strong>For more information</strong>: https://github.com/naturalis/mycorrhiza/tree/v1.0.0</p>
Allopatric and sympatric diversification within roach (Rutilus rutilus) of large pre‐alpine lakes
<p>This is the data for the study entitled "Allopatric and sympatric diversification within roach (<em>Rutilus rutilus</em>) of large pre‐alpine lakes" published in the Journal of Evolutionary Biology <a href="https://doi.org/10.1111/jeb.13502">https://doi.org/10.1111/jeb.13502 .</a></p> <p>The dataset consists of three files:</p> <p><strong>Morphology.txt </strong></p> <p>Morphology data from seven Swiss lakes. Given are the individual ID, the respective lake, the habitat classification, grouped habitat classification, length of each fish (mm), and the raw x and y coordinates for 11 landmarks.</p> <p>Geometric morphometric landmarks were set as follow:</p> <p>1) anterior tip of snout, 2) anterior tip of lower jaw, 3) anterior, and 4) posterior point of operculum, 5) junction where the dorsolateral part of the head and body fuse, anterior insertion points of the 6) pectoral, 7) pelvic, and 8) anal fin, 9) ventral and 10) dorsal junction of the caudal peduncle and tail, 11) anterior insertion of the dorsal fin.</p> <p> </p> <p><strong>Stable_isotopes.txt </strong></p> <p>Morphology data from five Swiss lakes. Given are the individual ID, lake, baseline corrected delta 13C values.</p> <p> </p> <p><strong>Stable_isotopes_baselines.txt </strong></p> <p>Morphology data from five Swiss lakes. Given are the lake, the tissue used, delta 13C values.</p> <p> </p>
Experimental result to investigate the influence of user's tweets and diversification on serendipitous research paper recommendations
<p>This is a raw dataset of the experiment result to investigate the influence of user's tweets and diversification on serendipitous research paper recommendations.</p> <p> </p>
Supporting Data: Phylogeny of Arbacia Gray, 1835 (Echinoidea) reveals diversification patterns in the Atlantic and Pacific Oceans.
<p>This dataset contains:</p> <ol> <li>Appendix S1, metadata asociated with the specimens (collection localities, specimen numbers)</li> <li>The aligned sequence files for each marker: COI_fasta, 16S_fasta, CR_fasta</li> <li>The concatenated sequence file COI + 16S + CRA + 28S Arbacia_supermatrix_fasta and the partition file partitions_concat</li> <li>The Bayesian trees for COI, 16S, CRA, and the supermatrix: BI_tree_16S, BI_tree_COI, BI_tree_CR, BI_tree_Arbacia_supermatrix</li> <li>The ML tree of the supermatrix: ML_tree_Arbacia_supermatrix</li> <li>Appendix S2, which includes various information on the primers used, PCR cycles, etc.</li> <li>Appendix S3, which includes the index calculations for each marker.</li> </ol>
Comparative metabolomics of fruits and leaves in a hyperdiverse lineage suggests fruits are a key incubator of phytochemical diversification
<p>Data files, chromatograms, and metadata for the Frontiers in Plant Science article "Comparative metabolomics of fruits and leaves in a hyperdiverse lineage suggests fruits are a key incubator of phytochemical diversification" . </p> <p>doi: 10.3389/fpls.2021.693739</p>
Data and code: Kuipers et al. (2023) Land use diversification may mitigate on-site land use impacts on mammal popultions and assemblages. Global Change Biology
<p>Zip folder conaining the data and code that support the findings of <em>Kuipers et al. (2023) Land use diversification may mitigate on-site land use impacts on mammal popultions and assemblages. Global Change Biology.</em></p> <p>The <em>Data_code.zip</em> folder contains four subfolders with the following files:</p> <ul> <li>Data_raw <ul> <li>AgriDiv_data.csv</li> <li>AgriDiv_metadata.docx</li> <li>Species_data.csv</li> <li>Species_metadata.docx</li> <li>Landscape_data.csv</li> <li>Landscape_metadata.docx</li> </ul> </li> <li>Data_derived <ul> <li>RIA_RSR_effect_sizes.csv</li> <li>MSA_effect_sizes.csv</li> </ul> </li> <li>Data_output <ul> <li>Response_estimation.csv</li> </ul> </li> <li>R_scripts <ul> <li>01_Effect_size_calculation.R</li> <li>02_Null_model_analysis.R</li> <li>03_Model_selection.R</li> <li>04_Model_analysis.R</li> <li>05_Response_estimation.R</li> <li>06_Figures.R</li> <li>README.md</li> </ul> </li> </ul>
Code and data: Exploring congruent diversification histories with flexibility and parsimony
<p>This repository contains the code and data for the article "Exploring congruent diversification histories with flexibility and parsimony" (abstract bellow).</p> <p>Data :</p> <ul> <li><strong>4705sp_mammal-time.tree</strong>: Species-level calibrated mammalian phylogeny from <em>Alvarez-Carretero et al. </em>(<a href="https://doi.org/10.6084/m9.figshare.14885691">https://doi.org/10.6084/m9.figshare.14885691</a>)</li> <li><strong>mammals_samplingfraction.csv</strong> : Clade-specific sampling fractions from <em>Quintero et al.</em>(<a href="https://www.biorxiv.org/content/10.1101/2022.08.09.503355v1.full">https://www.biorxiv.org/content/10.1101/2022.08.09.503355v1.full</a>).</li> </ul> <p>Code :</p> <ul> <li><strong>CRABS-v1.1.0.9004.zip</strong>: Archived version of the CRABS package with our extension.</li> <li><strong>Mammalian_rates_EBD_HSMRF.rev</strong>: <em>Rev</em> script for the mammalian diversification analysis in RevBayes with regularized priors on diversification rates.</li> <li><strong>Mammalian_rates_EBD_independent.rev</strong>: <em>Rev</em> script for the mammalian diversification analysis in RevBayes with independent diversification rates at each interval.</li> <li><strong>Mammals_proccess_RevBayes_outputs.Rmd</strong>: R notebook for processing the outputs from the RevBayes mammalian diversification analysis, plotting the rates through time, and saving the median trajectories used for further analyses.</li> <li><strong>Exploring_congruent_diversification_histories_with_flexibility_and_parsimony.Rmd</strong>: R notebook for comparing the initial CRABS features and our new extensions. It enables replicating the figures in the article.</li> </ul> <p>Outputs :</p> <ul> <li><strong>output_inferredIntervals_fixedRhp_HSMRF.zip</strong> & <strong>output_inferredIntervals_fixedRhp_independent.zip</strong>: The raw traces from the RevBayes analysis, and the resulting median rate trajectories that are used to construct the congruence class illustrated in the article.</li> </ul> <p><br> Abstract</p> <ol> <li>Using phylogenies of present-day species to estimate diversification rate trajectories -- speciation and extinction rates over time -- is a challenging task due to non-identifiability issues. Given a phylogeny, there exists an infinite set of trajectories that result in the same likelihood; this set has been coined a congruence class. Previous work has developed approaches for sampling trajectories within a given congruence class, with the aim to assess the extent to which congruent scenarios can vary from one another. Based on this sampling approach, it has been suggested that rapid changes in speciation or extinction rates are conserved across the class. Reaching such conclusions requires to sample the broadest possible set of distinct trajectories.</li> <li>We introduce a new method for exploring congruence classes, that we implement in the R package CRABS. Whereas existing methods constrain either the speciation rate or the extinction rate trajectory, ours provides more flexibility by sampling congruent speciation and extinction rate trajectories simultaneously. This allows covering a more representative set of distinct diversification rate trajectories. We also implement a filtering step that allows selecting the most parsimonious trajectories within a class.</li> <li>We demonstrate the utility of our new sampling strategy using a simulated scenario. Next, we apply our approach to the study of mammalian diversification history. We show that rapid changes in speciation and extinction rates need not be conserved across a congruence class, but that selecting the most parsimonious trajectories shrinks the class to concordant scenarios.</li> <li>Our approach opens new avenues both to truly explore the myriad of potential diversification histories consistent with a given phylogeny, embracing the uncertainty inherent to phylogenetic diversification models, and to select among these different histories. This should help refining our inference of diversification trajectories from extant data.</li> </ol>
DNA metabarcoding and spatial modelling link diet diversification with distribution homogeneity in European bats
<p>Inferences of the interactions between species’ ecological niches and spatial distribution have been historically based on simple metrics such as low-resolution dietary breadth and range size, which might have impeded the identification of meaningful links between niche features and spatial patterns. We analysed the relationship between dietary niche breadth and spatial distribution features of European bats, by combining continent-wide DNA metabarcoding of faecal samples with species distribution modelling. Our results show that while range size is not correlated with dietary features of bats, the homogeneity of the spatial distribution of species exhibits a strong correlation with dietary breadth. We also found that dietary breadth is correlated with bats’ hunting flexibility. However, these two patterns only stand when the phylogenetic relations between prey are accounted for when measuring dietary breadth. Our results suggest that the capacity to exploit different prey types enables species to thrive in more distinct environments and therefore exhibit more homogeneous distributions within their ranges.</p>
Valuing diversification benefits through intercropping in Mediterranean agroecosystems: A choice experiment approach.
<p>This data set contains information from a choice experiment survey developed to value the socio-economic benefits of intercropping practices in Mediterranean agroecosystems.</p> <p>These data correspond to the open-access article "Valuing diversification benefits through intercropping in Mediterranean agroecosystems: A choice experiment approach" published in Ecological Economics. (<a href="https://doi.org/10.1016/j.ecolecon.2020.106593">https://doi.org/10.1016/j.ecolecon.2020.106593</a>), funded by he European Commission Horizon 2020 project Diverfarming [grant agreement 728003]. </p>
FIG. 6 in L'apport du registre paléogène d'Amazonie sur la diversification initiale des Caviomorpha (Hystricognathi, Rodentia): implications phylogénétiques, macroévolutives et paléobiogéographiques
FIG. 6. — Consensus strict de l'AG1 (Fig. 5) et indices de Bremer aux noeuds. Les taxons en gras sont les espèces découvertes dans le Paléogène de Contamana (Éocène et Oligocène) et à Tarapoto/Shapaja. Le code couleur est le même que celui de la Figure 3.
FIG. 3 in L'apport du registre paléogène d'Amazonie sur la diversification initiale des Caviomorpha (Hystricognathi, Rodentia): implications phylogénétiques, macroévolutives et paléobiogéographiques
FIG. 3. — Arbre de contrainte employé pour les AG1-AG9, basé sur des données moléculaires. Modifié d'après Upham & Patterson (2015: 77, fig. 3). Les quatre super-familles de caviomorphes sont différenciées par des couleurs: Cavioidea (rouge), Chinchilloidea (bleu), Erehizontoidea (orange) et Octodontoidea (violet).
Fig. 7 in The changing course of the Amazon River in the Neogene: center stage for Neotropical diversification
Fig. 7. Growth of mega-wetlands in northern South America. Geological time scale at top. Eustatic sea-level estimates from Zachos et al. (2001). Area estimates of for Atlantic and Caribbean draining mega-wetlands from paleogeographic reconstructions in Wesselingh, Hoorn (2010) and Hoorn et al. (2017), and for the Orinoco basin by Jaramillo et al. (2017). Caribbeandraining Andean foreland basins in orange; Atlantic-draining basins contributing to transcontinental Amazon in yellow. Areas estimated using ImageJ (Abràmoff et al., 2004). Curves smoothed using a third-order Bezier Spline.
Data from: Exploring rainforest diversification using demographic model testing in the African foam-nest treefrog (Chiromantis rufescens)
Aim: Species with wide distributions spanning the African Guinean and Congolian rainforests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rainforest species, the African Foam-nest Treefrog (Chiromantis rufescens). Location: Guinean and Congolian rainforests, West and Central Africa. Taxon: Chiromantis rufescens. Methods: We collected mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data for 130 samples of Chiromantis rufescens. After estimating population structure and inferring species trees using coalescent methods, we tested demographic models to evaluate alternative population divergence histories that varied with respect to gene flow, population size change, and periods of isolation and secondary contact. Species distribution models were used to identify regions of climatic stability that could have served as forest refugia since the Last Interglacial. Results: Population structure within Chiromantis rufescens resembles the major biogeographic regions of the Guinean and Congolian forests. Coalescent-based phylogenetic analyses provide strong support for an early divergence between the western Upper Guinean forest and the remaining populations. Demographic inferences support diversification models with gene flow and population size changes even in cases where contemporary populations are currently allopatric, which provides support for forest refugia and barrier models. Species distribution models suggest that forest refugia were available for each of the populations throughout the Pleistocene. Main conclusions: Considering historical demography is essential for understanding population diversification, especially in complex landscapes such as those found in the Guineo-Congolian forest. Population demographic inferences help connect patterns of genetic variation to diversification model predictions. The diversification history of Chiromantis rufescens was shaped by a variety of processes, including vicariance from river barriers, forest fragmentation, and adaptive evolution along environmental gradients.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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