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14 results for “supplementary breeding”
Supplementary data: Breeding wheat for organic farming: can the high grain protein gene Gpc-B1 help to tackle challenges in view of end-use quality?
<p>Agronomic and quality data of organic wheat (<em>Triticum aestivum</em>), mean comparisons and supplementary figures related to the publication "Breeding wheat for organic farming: can the high grain protein gene Gpc-B1 help to tackle challenges in view of end-use quality?" by Grausgruber et al. (2024) published in the Journal of Cereal Science.</p>
Supplementary data for "Influence of prey availability on habitat selection during the non-breeding period in a resident bird of prey"
<p><strong>Abstract</strong></p> <p>Background: For resident birds of prey in the temperate zone, the cold non-breeding period can have strong impacts on survival and reproduction with implications for population dynamics. Therefore, the non-breeding period should receive the same attention as other parts of the annual life cycle. Birds of prey in intensively managed agricultural areas are repeatedly confronted with unpredictable, rapid changes in their habitat due to agricultural practices such as mowing, harvesting, and ploughing. Such a dynamic landscape likely affects prey distribution and availability and may even result in changes in habitat selection of the predator throughout the annual cycle.</p> <p>Methods: In the present study, we 1) quantified barn owl prey availability in different habitats across the annual cycle, 2) quantified the size and location of barn owl breeding and non-breeding home ranges using GPS-data, 3) assessed habitat selection in relation to prey availability during the non-breeding period, and 4) discussed differences in habitat selection during the non-breeding period to habitat selection during the breeding period.</p> <p>Results: The patchier prey distribution during the non-breeding period compared to the breeding period led to habitat selection towards grassland during the non-breeding period. The size of barn owl home ranges during breeding and non-breeding were similar, but there was a small shift in home range location which was more pronounced in females than males. The changes in prey availability led to a mainly grassland-oriented habitat selection during the non-breeding period. Further, our results showed the importance of biodiversity promotion areas and undisturbed field margins within the intensively managed agricultural landscape. </p> <p>Conclusions: We showed that different prey availability in habitat categories can lead to changes in habitat preference between the breeding and the non-breeding period. Given these results we show how important it is to maintain and enhance structural diversity in intensive agricultural landscapes, to effectively protect birds of prey specialised on small mammals. Hereafter we provide the datasets and R script to reproduce the resource selection functions.</p>
Supplementary material 1 from: Pontoppidan M, Nachman G (2013) Changes in behavioural responses to infrastructure affect local and regional connectivity – a simulation study on pond breeding amphibians. Nature Conservation 5: 13-28. https://doi.org/10.3897/natureconservation.5.4611
Full model description following the ODD-template suggested by Grimm et al. (2006, 2010) and model parameterisation. (doi: 10.3897/natureconservation.5.4611.app). File format: Adobe PDF document (pdf).:
Supplementary information for "Reassessment of French breeding bird population sizes using citizen science and accounting for species detectability"
<p>Reproducibility data for the manuscript "<em>Reassessment of French breeding bird population sizes using citizen science and accounting for species detectability</em>", it contains data and script for :</p> <ol> <li> <p>The R script <code>01_HDSfreq_Calibration.R</code> of the developed approach to estimate national breeding bird population size using Hierarchical Distance Sampling (HDS) and the secondary candidate set model selection method (Morin et al., 2020)</p> </li> <li> <p>The R script <code>02_pglmm_figures.R</code> for the calibration of the Phylogenetic Generalised Mixed Model (PGLMM) used in the manuscript to compare previous population size estimates to ones modelled using <code>01_HDSfreq_Calibration.R</code>, while accounting for species phylogenetic relatedness</p> </li> <li> <p>The R script <code>03_results_tables.R</code>, used to generate supplementary tables S2.1-3 and S6.1-2.</p> </li> </ol> <ul> <li> <p>Column names are highlighted in italics.</p> </li> </ul> <h2>Data description</h2> <h5>A. BirdPhylo_Burleigh_et_al.tre</h5> <p>A phylogenetic tree from Burleigh et al., 2015. Phylogenetic distances are used as random effect for the PGLMM in script <code>02_pglmm_figures.R</code></p> <h5>B. Conservation_status.txt</h5> <p>A <code>.txt</code> file of the conservation status for France (<em>Statut_FR</em>) and Europe (<em>Statut_EU</em>) for the studied species retrieved from (UICN France et al., 2016). Only <em>Statut_FR</em> is used for the table S6.1.</p> <h5>C. FBBS_trends_20122023.txt</h5> <p>A <code>.txt</code> file containing species trend of the French Breeding Bird Survey data from 2012 to 2023.</p> <ul> <li> <p>Species names (English, French) associated with FBBS trend estimated using data collected from 2012 - 2023</p> </li> <li> <p><em>Hab_specialization</em>, determined from Julliard et al. 2006 approach</p> </li> <li> <p><em>infPrec, supPerc, estimate, se, pval</em> : Species trends over 2012-2023 period in % | lower and upper confidence intervals, mean, standard error and significance</p> </li> </ul> <h5>D. PrepData_HDS.RData</h5> <p>A file containing <code>.RData</code> environment required to run <code>01_HDSfreq_Calibration.R</code> script, it contains :</p> <ul> <li> <p><strong>ATLAS12</strong> : A dataframe with breeding status information from 2012 breeding bird atlas (used to restrict model prediction grid, in regard of 2012 known breeding locations)</p> </li> <li> <p><strong>ConcordTBL</strong> : A concordance table for species names (English, French and scientific notation)</p> </li> <li> <p><strong>EPOC_ODF</strong> : observation dataset, each line corresponds to detected individuals</p> <ul> <li> <p><em>UUID, Ref, ID_liste, ID, ID_place, Grid_10x10</em> : Columns used to identify observations, lists, sites, locations, 10x10 grids</p> </li> <li> <p><em>ID_species_Biolovision, Nom_espece, english_name, scientific_name</em> : Species ID and names</p> </li> <li> <p><em>Date, Day, Month, Year, Julian_date, Obs_hour, Hour_list, Complete_checklist, Commentary, Project_name, Scheme, Observer, List_time, List_diversity, List_abundance</em> : Lists and Observation related effort covariates and metadata</p> </li> <li> <p><em>X_Lambert93_m, Y_Lambert93_m</em> : Observation locations in <code>(crs = 2154)</code></p> </li> <li> <p><em>GPS_loc_observer</em> : Logical, TRUE : location of observers corresponds to true GPS information ; FALSE : observer's location approximated as the barycenter of observations</p> </li> <li> <p><em>X_barycentre_L93, Y_barycentre_L93</em> : Observers location in <code>(crs = 2154)</code></p> </li> <li> <p><em>Use_distance_sampling, Observation_distance_m, Distance_bin_logical, Distance_class_0_25, Distance_class_25_100, Distance_class_100_200, Distance_class_200_more</em> : Distance sampling related informations</p> </li> <li> <p><em>Abudance_brut, Estimate, Number, Nb_male_identified, Nb_female_identified, Nb_juvenile_identified, Nb_grounded, Nb_flying, Nb_auditory, Nb_NA</em> : Observation metadata, used in case of <em>a priori</em> filter over male detection.</p> </li> </ul> </li> <li> <p><strong>grid_pred_envvar</strong> : Prediction grid with environmental covariates, see appendix S3 of the manuscript, covering metropolitan France</p> </li> <li> <p><strong>grid_pred.sf</strong> : corresponding sf object</p> </li> <li> <p><strong>L93_10x10</strong> : sf object corresponding to 10x10 grid used in 2012 atlas</p> </li> <li> <p><strong>ObsVar_EPOCODF</strong> : dataframe specifying lists effort covariates</p> </li> <li> <p><strong>OCCU_EPOC_ODF</strong> : Environmental covariate agregated over lists</p> </li> <li> <p><strong>OCCU_EPOC_ODF_sites_envvar</strong> : Environmental covariate agregated over sites</p> </li> <li> <p><strong>table.pheno</strong> : species table specifying related phenology filter</p> </li> </ul> <h5>E. ReadOutput_HDSfreq_comparison.csv</h5> <p>A <code>.csv</code> table of species population size estimated using 2021-2023 EPOC-ODF data over areas determined as breeding in the 2012 atlas. <strong>Predictions were restrained over location known as breeding in 2012 for the sake of comparison.</strong></p> <ul> <li> <p><em>HDS_estimUnfenced_XXX</em> : average pop. size estimated with confidence interval before prediction post-treatment (describe in fig 2. of the manuscript)</p> </li> <li> <p><em>HDS_estim_ExtrapolFence_XXX</em> : average pop. size estimated with confidence interval after prediction post-treatment</p> </li> <li> <p><em>NB_data_calib</em> : Number of observations (distance data, not sites) used for calibration</p> </li> <li> <p><em>MALE_FILTERING</em> : (logical) indicating if female individuals could be detected in the same proportion of males during list recording. FALSE : we considered that estimated pop.size corresponded to the number of individuals leading to a division by 2 for the comparison with the previous atlas (in pairs). (cf . line 88-90 in <code>02_pglmm_figures.R</code>)</p> </li> <li> <p><em>EcartDTF_filtrage_maleOnly</em> : If MALE_FILTERING == T, proportion of the remaining data used for calibration after removal of list with individual tagged as female/juvenile (in %)</p> </li> <li> <p><em>Max_dist_breaks</em> : Maximal distance for detection function, after right-side truncation of 5%</p> </li> <li> <p><em>Chat</em> : Coefficient of overdisperion of the best model in the second candidate set</p> </li> <li> <p><em>MED_MEAN_Prob_Detect</em> (.._SE) : weighted averaged median of intercept from the availability state from HDS models, weigthed AICc-wise</p> </li> <li> <p><em>MED_MEAN_Density</em> : weighted averaged median of intercept from the abundance state from HDS models, weigthed AICc-wise</p> </li> <li> <p><em>Significant_phi/lambda</em> : Categorial (Significant/Near/Not), are availability/abundance intercepts significatively different from 0 (significant : alpha = 0.05, near : alpha = 0.1)</p> </li> <li> <p><em>KeyFun_used</em> : Key function used for distance sampling</p> </li> <li> <p><em>Mixtured_used</em> : Mixture used in the abundance state for HDS</p> </li> </ul> <h5>F. ReadOutput_HDSfreq_comparison_20212022.csv</h5> <p>A <code>.csv</code> table of species population size estimated using 2021-2022 EPOC-ODF data over areas determined as breeding in the 2012 atlas. Used for the robustness analysis of HDS estimated population size, see appendix S2 and table S2.2 of the manuscript.</p> <h5>G. ReadOutput_HDSfreq_EstimMetropole.csv</h5> <p>A <code>.csv</code> table of species population size estimated using 2021-2023 EPOC-ODF data over <strong>metropolitan France</strong>.</p> <ul> <li> <p><em>HDS_estimUnfenced_XXX</em> : average pop. size estimated with confidence interval before prediction post-treatment (describe in fig 2. of the manuscript)</p> </li> <li> <p><em>HDS_estim_ExtrapolFence_XXX</em> : average pop. size estimated with confidence interval after prediction post-treatment</p> </li> <li> <p><em>MALE_FILTERING</em> : (logical) indicating if female individuals could be detected in the same proportion of males during list recording. FALSE : we considered that estimated pop.size corresponded to the number of individuals leading to a division by 2 for conversion to pop. size in breeding pairs</p> </li> <li> <p><em>Chat</em> : Coefficient of overdisperion of the best model in the second candidate set</p> </li> <li> <p><em>KeyFun_used</em> : Key function used for distance sampling</p> </li> <li> <p><em>Mixtured_used</em> : Mixture used in the abundance state for HDS</p> </li> </ul> <h5>H. TABLE_SpeciesFilters_and_2012Estimates.txt</h5> <p>A <code>.txt </code>table containing species names (English, French and scientific notation), filters and 2012 French atlas pop. size estimates</p> <ul> <li> <p><em>debut_jour</em> : starting day of the month for phenology filter</p> </li> <li> <p><em>debut_mois</em> : starting month for phenology filter</p> </li> <li> <p><em>fin_jour</em> : ending day of the month for phenology filter</p> </li> <li> <p><em>fin_mois</em> : ending month for phenology filter</p> </li> <li> <p><em>Estim_low/up_Atlas2012</em> : Lower and Upper interval of estimated pop. size in 2012 (number in breeding pairs)</p> </li> <li> <p><em>gregarious</em> : logical (0,1) specifying if the species is considered gregarious during its breeding season</p> </li> </ul> <h5>I. sessionInfo_script_XX</h5> <p>User R session information, obtained from <code>sessionInfo()</code> R function, used for running R script.</p> <h2>Code</h2> <h5>A. <code>01_HDSfreq_Calibration.R</code></h5> <p>R script showcasing data formatting and model calibration of the HDS based upon frequentist aproach from <code>unmarked</code> R package. For more details of the model calibration approach, see appendix S4 of the manuscript.</p> <h5>B. <code>02_pglmm_figures.R</code></h5> <p>Script for the calibration of the PGLMM and generation of figure 5 of the manuscript.</p> <h5>C. <code>03_results_tables.R</code></h5> <p>Script to generate tables depicted in Appendices S2 (S2.1-3) and S6 (S6.1-2)</p> <h5>D. <code>HDS_functions.R</code></h5> <p>R script called in <code>01_HDSfreq_Calibration.R</code>, contains 2 functions:</p> <ul> <li> <p><code>Try_HDS()</code> : Function implementing a try-catch permitting calibration of multiple species in a loop.</p> <ul> <li> <p>Species with non convergent models are skipped sending a notification to the user R interface.</p> </li> <li> <p>Used in all sub-candidate sets (i.e. "null", "p", "phi", "lambda")</p> </li> <li> <p>When phase="ALL" corresponding to the second candidate set (i.e. ensemble of best model candidates, with delta_AIC <= 10, from previous sub-candidate sets), it permits the use of previous sub-candidates set coefficients as starting values, with <code>StartValues </code>argument</p> </li> <li> <p>Later part of the function hack the call of the unmarkedFit class, in order to accommodate from calibrating a gdistsamp using characters formulas</p> </li> </ul> </li> <li> <p><code>fitstats()</code> : Function from unmarked::parboot(), available with <code>help(parboot)</code>. Allow estimation of multiple goodness-of-git statistic (Freeman-Tukey, Chi-squared and Sum of Squared Estimate of errors) through parametric bootstrap. In the manuscript, only chi-squared metric is used.</p> </li> </ul> <h5>E. <code>dsmextra_modif_function.R</code></h5> <p>R script called in <code>01_HDSfreq_Calibration.R</code>. Miscellaneous adjustment of core function from <code>dsmextra </code>package (main change being the integration of tolerance argument (<code>tol</code>) in the chain of function.</p> <h5>F. <code>misc_unmarked.R</code></h5> <p>R script called in <code>01_HDSfreq_Calibration.R</code>. modify Setmethods for unmarked function, in particular for <code>unmarked::parboot</code>, allowing parallelization of parametric bootstrap with prior unmarked version (<code>unmarked < 1.3.0</code>).</p> <h2>References</h2> <p>Data was derived from the following sources:</p> <ul> <li> <p>Burleigh, J.G., Kimball, R.T., Braun, E.L., 2015. Building the avian tree of life using a large-scale, sparse supermatrix. Molecular Phylogenetics and Evolution 84, 53–63. <a href="https://doi.org/10.1016/j.ympev.2014.12.003">https://doi.org/10.1016/j.ympev.2014.12.003</a></p> </li> </ul> <p>Other sources :</p> <ul> <li> <p>Julliard, R., Clavel, J., Devictor, V., Jiguet, F., Couvet, D., 2006. Spatial segregation of specialists and generalists in bird communities. Ecology Letters 9, 1237–1244. <a href="https://doi.org/10.1111/j.1461-0248.2006.00977.x">https://doi.org/10.1111/j.1461-0248.2006.00977.x</a></p> </li> <li> <p>Morin, D.J., Yackulic, C.B., Diffendorfer, J.E., Lesmeister, D.B., Nielsen, C.K., Reid, J., Schauber, E.M., 2020. Is your ad hoc model selection strategy affecting your multimodel inference? Ecosphere 11, e02997. <a href="https://doi.org/10.1002/ecs2.2997">https://doi.org/10.1002/ecs2.2997</a></p> </li> <li> <p>UICN France, MNHN, LPO, SEOF, ONCFS, 2016. La Liste rouge des espèces menacées en France - Chapitre Oiseaux de France métropolitaine. Paris, France.</p> </li> </ul>
Supplementary files from: Improving inference and avoiding over-interpretation of hidden-state diversification models: Specialized plant breeding has no effect on diversification in frogs
<p>The hidden-state speciation and extinction (HiSSE) model helps avoid spurious results when testing whether a character affects diversification rates. However, care must be taken to optimally analyze models and interpret results. Recently, Tonini et al. (2020; TEA hereafter) studied anuran (frog and toad) diversification with HiSSE methods. They concluded that their focal state, breeding in phytotelmata, increases net diversification rates. Yet this conclusion is counterintuitive, because the state that purportedly increases net diversification rates is 14 times rarer among species than the alternative. Herein I revisit TEA's analyses and demonstrate problems with inferring model likelihoods, conducting post-hoc tests, and interpreting results. I also re-evaluate their top models and find that diverse strategies are necessary to reach the parameter values that maximize each model's likelihood. In contrast to TEA, I find no support for an effect of phytotelm breeding on net diversification rates in Neotropical anurans. In particular, even though the most highly supported models include the focal character, averaging parameter estimates over hidden states shows that the focal character does not influence diversification rates. Finally, I suggest ways to better analyze and interpret complex diversification models – both state-dependent and beyond – for future studies in other organisms.</p>
Supplementary data for "Genomic signatures of strawberry domestication and breeding" paper
<pre>############################################################################################ ## Supplementary data for "Genomic signatures of strawberry domestication and breeding" ## ## Author: Zhen Fan ## ## Date: 6/26/2023 ## ############################################################################################</pre> <p>Octoploid strawberry SNP map (SNP.vcf.gz) includes filtered SNP using 289 individuals.</p> <p>GWAS_raw.zip includes raw data, BLUE estimates, genotyping data and marker positions for GWAS study of fruit size and yield. </p>
Supplementary files from: Improving inference and avoiding over-interpretation of hidden-state diversification models: Specialized plant breeding has no effect on diversification in frogs
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Supplementary material 1 from: Studer A, Cardoso de Sousa M, Barcena Goyena B (2018) Breeding biology and nest success of Short-tailed Antthrush Chamaeza campanisona (Aves: Formicariidae) in the Atlantic rainforest of northeastern Brazil. Zoologia 35: 1-8. https://doi.org/10.3897/zoologia.35.e12906
Nests of Chamaeza campanisona found during the study period (1986–2016) with their respective characteristics : Data type: species data
Data from: The effects of supplementary food on the breeding performance of Eurasian reed warblers Acrocephalus scirpaceus; implications for climate change impacts
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Supplementary materials for: Female‐female aggression in a cooperatively breeding bird during the non‐breeding period: The behavioral strategy to maintain long‐term partnerships
<p>Social monogamy evolves in association with biparental care. However, males who tend to pursue multiple mating are expected to place less value on established partnerships, whereas females do the opposite to ensure males'participation in rearing offspring. Accordingly, selection is expected to favor paired females to behave aggressively towards females that approach their social mates. For species with long-term partnerships, female-female aggression commonly observed during the breeding period should also occur in the non-breeding period. We look at whether these expectations are held up by conducting a field experiment in Tibetan ground tits Pseudopodoces humilis, a cooperatively breeding bird that has lifetime monogamy and forms new pair bonds in winter. Paired but not unpaired females were more aggressive towards the same-sex than towards opposite-sex intruders experimentally introduced into the winter group territory, an indication that paired females may be protecting partnerships. Both paired and unpaired males, on the other hand, displayed aggression almost equally against intruders of both sexes, indicating a likely function in territory defense. Our work provides the first evidence for the female's role in maintaining long-term monogamy during the non-breeding period in birds, and contributes to the recent progress regarding intrasexual competition between females as a component of sexual selection.</p>
Supplementary material 2 from: Lang A, Dolek M, Lee MS, Freese-Hager A, Otto M (2020) Selection of non-target Lepidoptera species to test Bt maize effects in the laboratory: which species and how to breed them? BioRisk 15: 45-65. https://doi.org/10.3897/biorisk.15.59823
Review breeding information
Supplementary material 1 from: Lang A, Dolek M, Lee MS, Freese-Hager A, Otto M (2020) Selection of non-target Lepidoptera species to test Bt maize effects in the laboratory: which species and how to breed them? BioRisk 15: 45-65. https://doi.org/10.3897/biorisk.15.59823
Reference list: breeding and rearing Lepidoptera
Supplementary material 1 from: Herrera-Alva V, Catenazzi A, Aguilar-Puntriano C (2023) A new cryptic species of terrestrial breeding frog of the Pristimantis danae Group (Anura, Strabomantidae) from montane forests in Ayacucho, Peru. ZooKeys 1187: 1-29. https://doi.org/10.3897/zookeys.1187.104536
p-uncorrected distances of 591 pb including gaps of rRNA 16s gene
Supplementary materials for: Female‐female aggression in a cooperatively breeding bird during the non‐breeding period: The behavioral strategy to maintain long‐term partnerships
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.