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opencc-by-4.0Jan 2017View details →

T a b l e 5 in Month-To-Month Variations In Densities And Dominance Of Birds Breeding In An Extensive Pine Forest

T a b l e 5. Recommended and highly recommended months for counting birds by means of line transect method in pine forests

opencc-by-4.0Jan 2017View details →

Fig. 1 in Possible Ways Of Development Of The Breeding Bird Communities Of The Lower Dnipro

Fig. 1. The active coastal erosion and the initial stage of formation of the sandy beach (the upper reaches of the Kakhovka Reservoir, 2012).

Fig. 12 in Breeding Bird Assemblage In A Mosaic Of Urbanized Habitats In A Cenral European City

Fig. 12. Distribution of occupied territories of Cuculus canorus, Oriolus oriolus, Phasianus colchicus and Dendrocopos major.

Fig. 7 in Breeding Bird Assemblage In A Mosaic Of Urbanized Habitats In A Cenral European City

Fig. 7. Distribution of occupied territories of Acrocephalus plustris, A. Arundinaceus and A. scirpaceus.

Fig. 4 in Breeding Bird Assemblage In A Mosaic Of Urbanized Habitats In A Cenral European City

Fig. 4. Distribution of occupied territories of Serinus Fig. 5. Distribution of occupied territories of serinus, Phylloscopus collybita, P. trochilus and Phoenicurus ochruros. P. sibilatrix.

Fig. 2 in Breeding Bird Assemblage In A Mosaic Of Urbanized Habitats In A Cenral European City

Fig. 2. Distribution of occupied territories of Sylvia Fig. 3. Distribution of occupied territories of Sylvia communis. curruca.

Fig. 1 in Breeding Bird Assemblage In A Mosaic Of Urbanized Habitats In A Cenral European City

Fig. 1. Location of the study area (surrounded with a broken line) in the city of Wroclaw: A — borders of the study area; B — rivers; C — main roads; D — loosely built-up areas; E —densely built-up areas.

opencc-by-4.0Nov 2014View details →

Fig. 3 in Spatial Patterns Of Bird Communities Of The Lower Dnieper Sands During The Breeding Season: Differentiation Factors

Fig. 3. The abundance (the mean number of individuals per sample) of campophilous and dendrophilous birds in groups of samples A (Clusters I–IV) and B (Clusters V–VI). N o t e. The central line represents median, the lower and upper limits of the rectangle — the first and third quartile respectively, "whiskers" — ± 1.5 of interquartile range; circles — outliers.

opencc-by-4.0Nov 2014View details →

Fig. 1 in Spatial Patterns Of Bird Communities Of The Lower Dnieper Sands During The Breeding Season: Differentiation Factors

Fig. 1. The scheme of the study area. Аrenas of Low-Dnieper Sands: A — Kakhovska; B — Kozachelaherska; C — Oleshkivska; D — Chalbaska; E — Zburivska; F — Ivanivska; G — Kinburn Peninsula. N o t e. The first and the last sample of each census route are marked by numbers; the numbering of samples is the same as in table 1.

opencc-by-4.0Nov 2014View details →

Fig. 4 in Spatial Patterns Of Bird Communities Of The Lower Dnieper Sands During The Breeding Season: Differentiation Factors

Fig. 4. The area ratio of different types of habitats on standard test plots in the groups of samples.

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Data from: Sex-dependent effects of parental age on offspring fitness in a cooperatively breeding bird

Parental age can have considerable effects on offspring phenotypes and health. However, intergenerational effects may also have longer-term effects on offspring fitness. Few studies have investigated parental age effects on offspring fitness in natural populations while also testing for sex- and environment-specific effects. Further, longitudinal parental age effects may be masked by population-level processes such as the selective disappearance of poor-quality individuals. Here, we used multi-generational data collected on individually marked Seychelles warblers (Acrocephalus sechellensis) to investigate the impact of maternal and paternal age on offspring lifespan and lifetime reproductive success. We found negative effects of maternal age on female offspring lifespan and lifetime reproductive success, which were driven by within-mother effects. There was no difference in annual reproductive output of females born to older versus younger mothers, suggesting that the differences in offspring lifetime reproductive success were driven by effects on offspring lifespan. In contrast, there was no association between paternal age and female offspring lifespan or either maternal or paternal age and male offspring lifespan. Lifetime reproductive success, but not annual reproductive success, of male offspring increased with maternal age, but this was driven by between-mother effects. No paternal age effects were found on female offspring's lifetime reproductive success but there was a positive between-father effect on male offspring's lifetime reproductive success. We did not find strong evidence for environment-dependent parental age effects. Our study provides evidence for parental age effects on the lifetime fitness of offspring and shows that such effects can be sex-dependent. These results add to the growing literature indicating the importance of intergenerational effects on long-term offspring performance and highlight that these effects can be an important driver of variation in longevity and fitness in the wild.

opencc-zeroOct 2022View details →

opencc-by-4.0Apr 2024View details →

Ecosystem engineers spill-over of biodiversity: beavers affect breeding bird assemblage on wetland, but also on adjacent terrestrial habitats

Abundance of breeding bird species recorded on Eurasian beaver and reference sites in Poland (central Europe).

opencc-by-4.0Feb 2024View details →

Supplementary information for "Reassessment of French breeding bird population sizes using citizen science and accounting for species detectability"

Reproducibility data for the manuscript "Reassessment of French breeding bird population sizes using citizen science and accounting for species detectability", it contains data and script for : <ol> <li> 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) </li> <li> 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 </li> <li> The R script <code>03_results_tables.R</code>, used to generate supplementary tables S2.1-3 and S6.1-2. </li> </ol> <ul> <li> Column names are highlighted in italics. </li> </ul> <h2>Data description</h2> <h5>A. BirdPhylo_Burleigh_et_al.tre</h5> 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> <h5>B. Conservation_status.txt</h5> A <code>.txt</code> file of the conservation status for France (Statut_FR) and Europe (Statut_EU) for the studied species retrieved from (UICN France et al., 2016). Only Statut_FR is used for the table S6.1. <h5>C. FBBS_trends_20122023.txt</h5> A <code>.txt</code> file containing species trend of the French Breeding Bird Survey data from 2012 to 2023. <ul> <li> Species names (English, French) associated with FBBS trend estimated using data collected from 2012 - 2023 </li> <li> Hab_specialization, determined from Julliard et al. 2006 approach </li> <li> infPrec, supPerc, estimate, se, pval : Species trends over 2012-2023 period in % | lower and upper confidence intervals, mean, standard error and significance </li> </ul> <h5>D. PrepData_HDS.RData</h5> A file containing <code>.RData</code> environment required to run <code>01_HDSfreq_Calibration.R</code> script, it contains : <ul> <li> ATLAS12 : A dataframe with breeding status information from 2012 breeding bird atlas (used to restrict model prediction grid, in regard of 2012 known breeding locations) </li> <li> ConcordTBL : A concordance table for species names (English, French and scientific notation) </li> <li> EPOC_ODF : observation dataset, each line corresponds to detected individuals <ul> <li> UUID, Ref, ID_liste, ID, ID_place, Grid_10x10 : Columns used to identify observations, lists, sites, locations, 10x10 grids </li> <li> ID_species_Biolovision, Nom_espece, english_name, scientific_name : Species ID and names </li> <li> Date, Day, Month, Year, Julian_date, Obs_hour, Hour_list, Complete_checklist, Commentary, Project_name, Scheme, Observer, List_time, List_diversity, List_abundance : Lists and Observation related effort covariates and metadata </li> <li> X_Lambert93_m, Y_Lambert93_m : Observation locations in <code>(crs = 2154)</code> </li> <li> GPS_loc_observer : Logical, TRUE : location of observers corresponds to true GPS information ; FALSE : observer's location approximated as the barycenter of observations </li> <li> X_barycentre_L93, Y_barycentre_L93 : Observers location in <code>(crs = 2154)</code> </li> <li> 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 : Distance sampling related informations </li> <li> Abudance_brut, Estimate, Number, Nb_male_identified, Nb_female_identified, Nb_juvenile_identified, Nb_grounded, Nb_flying, Nb_auditory, Nb_NA : Observation metadata, used in case of a priori filter over male detection. </li> </ul> </li> <li> grid_pred_envvar : Prediction grid with environmental covariates, see appendix S3 of the manuscript, covering metropolitan France </li> <li> grid_pred.sf : corresponding sf object </li> <li> L93_10x10 : sf object corresponding to 10x10 grid used in 2012 atlas </li> <li> ObsVar_EPOCODF : dataframe specifying lists effort covariates </li> <li> OCCU_EPOC_ODF : Environmental covariate agregated over lists </li> <li> OCCU_EPOC_ODF_sites_envvar : Environmental covariate agregated over sites </li> <li> table.pheno : species table specifying related phenology filter </li> </ul> <h5>E. ReadOutput_HDSfreq_comparison.csv</h5> 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. Predictions were restrained over location known as breeding in 2012 for the sake of comparison. <ul> <li> HDS_estimUnfenced_XXX : average pop. size estimated with confidence interval before prediction post-treatment (describe in fig 2. of the manuscript) </li> <li> HDS_estim_ExtrapolFence_XXX : average pop. size estimated with confidence interval after prediction post-treatment </li> <li> NB_data_calib : Number of observations (distance data, not sites) used for calibration </li> <li> MALE_FILTERING : (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>) </li> <li> EcartDTF_filtrage_maleOnly : If MALE_FILTERING == T, proportion of the remaining data used for calibration after removal of list with individual tagged as female/juvenile (in %) </li> <li> Max_dist_breaks : Maximal distance for detection function, after right-side truncation of 5% </li> <li> Chat : Coefficient of overdisperion of the best model in the second candidate set </li> <li> MED_MEAN_Prob_Detect (.._SE) : weighted averaged median of intercept from the availability state from HDS models, weigthed AICc-wise </li> <li> MED_MEAN_Density : weighted averaged median of intercept from the abundance state from HDS models, weigthed AICc-wise </li> <li> Significant_phi/lambda : Categorial (Significant/Near/Not), are availability/abundance intercepts significatively different from 0 (significant : alpha = 0.05, near : alpha = 0.1) </li> <li> KeyFun_used : Key function used for distance sampling </li> <li> Mixtured_used : Mixture used in the abundance state for HDS </li> </ul> <h5>F. ReadOutput_HDSfreq_comparison_20212022.csv</h5> 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. <h5>G. ReadOutput_HDSfreq_EstimMetropole.csv</h5> A <code>.csv</code> table of species population size estimated using 2021-2023 EPOC-ODF data over metropolitan France. <ul> <li> HDS_estimUnfenced_XXX : average pop. size estimated with confidence interval before prediction post-treatment (describe in fig 2. of the manuscript) </li> <li> HDS_estim_ExtrapolFence_XXX : average pop. size estimated with confidence interval after prediction post-treatment </li> <li> MALE_FILTERING : (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 </li> <li> Chat : Coefficient of overdisperion of the best model in the second candidate set </li> <li> KeyFun_used : Key function used for distance sampling </li> <li> Mixtured_used : Mixture used in the abundance state for HDS </li> </ul> <h5>H. TABLE_SpeciesFilters_and_2012Estimates.txt</h5> A <code>.txt </code>table containing species names (English, French and scientific notation), filters and 2012 French atlas pop. size estimates <ul> <li> debut_jour : starting day of the month for phenology filter </li> <li> debut_mois : starting month for phenology filter </li> <li> fin_jour : ending day of the month for phenology filter </li> <li> fin_mois : ending month for phenology filter </li> <li> Estim_low/up_Atlas2012 : Lower and Upper interval of estimated pop. size in 2012 (number in breeding pairs) </li> <li> gregarious : logical (0,1) specifying if the species is considered gregarious during its breeding season </li> </ul> <h5>I. sessionInfo_script_XX</h5> User R session information, obtained from <code>sessionInfo()</code> R function, used for running R script. <h2>Code</h2> <h5>A. <code>01_HDSfreq_Calibration.R</code></h5> 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. <h5>B. <code>02_pglmm_figures.R</code></h5> Script for the calibration of the PGLMM and generation of figure 5 of the manuscript. <h5>C. <code>03_results_tables.R</code></h5> Script to generate tables depicted in Appendices S2 (S2.1-3) and S6 (S6.1-2) <h5>D. <code>HDS_functions.R</code></h5> R script called in <code>01_HDSfreq_Calibration.R</code>, contains 2 functions: <ul> <li> <code>Try_HDS()</code> : Function implementing a try-catch permitting calibration of multiple species in a loop. <ul> <li> Species with non convergent models are skipped sending a notification to the user R interface. </li> <li> Used in all sub-candidate sets (i.e. "null", "p", "phi", "lambda") </li> <li> 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 </li> <li> Later part of the function hack the call of the unmarkedFit class, in order to accommodate from calibrating a gdistsamp using characters formulas </li> </ul> </li> <li> <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. </li> </ul> <h5>E. <code>dsmextra_modif_function.R</code></h5> 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. <h5>F. <code>misc_unmarked.R</code></h5> 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>). <h2>References</h2> Data was derived from the following sources: <ul> <li> 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> </li> </ul> Other sources : <ul> <li> 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> </li> <li> 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> </li> <li> UICN France, MNHN, LPO, SEOF, ONCFS, 2016. La Liste rouge des espèces menacées en France - Chapitre Oiseaux de France métropolitaine. Paris, France. </li> </ul>

Figure 2 in Notes on the breeding biology of birds in riverine floodplains of western Amazonia

Figure 2. Plain-winged Antshrike Thamnophilus schistaceus fledgling, Rondônia, Brazil, June 2018 (Tomaz Nascimento de Melo)

Figure 6 in Notes on the breeding biology of birds in riverine floodplains of western Amazonia

Figure 6. Nest and eggs of Euler's Flycatcher Lathrotriccus euleri in a dried cocoa Theobroma cacao fruit (Malvaceae), Rondônia, Brazil, September 2017 (Tomaz Nascimento de Melo)

Figure 5 in Notes on the breeding biology of birds in riverine floodplains of western Amazonia

Figure 5. Nest of Spotted Tody-Flycatcher Todirostrum maculatum constructed on the root of a Capsiandra sp. (Fabaceae) near the Madeira River, Rondônia, Brazil, July 2018 (Tomaz Nascimento de Melo)

Figure 4 in Notes on the breeding biology of birds in riverine floodplains of western Amazonia

Figure 4. Nest of Specked Spinetail Cranioleuca gutturata in floodplain várzea forest, Rondônia, Brazil, June 2018 (Tomaz Nascimento de Melo)

Figure 1 in Notes on the breeding biology of birds in riverine floodplains of western Amazonia

Figure 1. White-bearded Hermit Phaethornis hispidus nest with two nestlings, Rondônia, Brazil, June 2018 (Tomaz Nascimento de Melo)

opencc-zeroJun 2024View details →

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Data from: Coordination of care reduces conflict and predation risk in a cooperatively breeding bird

When two or more individuals cooperate to provision a shared brood, each carer may be able to maximize their payoffs by coordinating provisioning in relation to what others are doing. This investment 'game' is not simply a matter of how much to invest, but also of the relative timing of investment. Recent studies propose that temporal coordination of care in the forms of alternation (i.e. turn-taking) and synchrony (i.e. provisioning together) function to mitigate conflict between carers and reduce brood predation risk, respectively. Such coordination is widespread in biparental and cooperatively breeding birds, yet the fitness consequences have rarely been empirically tested. Here, we use a long-term study of long-tailed tits Aegithalos caudatus, a facultative cooperatively breeding bird with active coordination of care, to assess the support for these hypothesized functions for coordination of provisioning visits. First, we found evidence that turn-taking mitigates conflict between carers because, in cooperative groups, provisioning rates and offspring recruitment increased with the level of active alternation exhibited by carers, and with the associated increase in provisioning rate parity between carers. In contrast, offspring recruitment did not increase with alternation in biparental nests, although it was positively correlated with parity of provisioning between carers, which is predicted to result from conflict mitigation. Secondly, synchronous nest visits were associated with a reduced probability of nest predation and thus increased brood survival, especially when provisioning rates were high. We attribute this effect to synchrony reducing carer activity near the nest. We conclude that temporal coordination of provisioning visits in the forms of alternation and synchrony both confer fitness benefits on carers, and despite being intrinsically linked, these different kinds of coordination appear to serve different functions.