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Supplementary material for "Demographic assessment of reintroduced bearded vultures in the Alps: success in the core, challenges in the periphery"
<p><strong>Abstract</strong></p> <ol> <li> Regular assessment of reintroduced populations is essential to guide management and provide lessons for other reintroduction projects. Bearded vulture <em>Gypaetus barbatus</em> reintroduction in the Alps began in 1986 with the release of the first fledglings, the first successful reproduction was recorded in 1997, and the population has grown steadily since. A previous assessment suggested that no further releases would be required to establish a self-sustaining population from a demographic point of view. However, this conclusion was based on a small sample size and spatially homogeneous demographic rates of released individuals, which may differ from and be spatially variable among wild-hatched individuals.</li> <li>Using longitudinal data and breeding site survey data, we constructed an integrated population model to examine the demography of the entire Alpine population, spatially stratified into a core and a periphery. We performed retrospective population analyses to identify demographic reasons of spatial differences in population growth, and conducted population viability analyses to assess the impact of future threats and reintroduction options.</li> <li>In 2021, an estimated 173 (CRI: 149-199) females were present in the Alps, of which 65 (CRI: 63-67) were breeders. Adult survival and productivity were higher in the core than in the periphery, so the population grew more strongly in the core than in the periphery. Differences in adult survival contributed most to the differences in population growth between the two areas.</li> <li>The population viability analysis predicts that the Alpine population will double in 10 years but that an increase in the mortality hazard above 0.055 will lead to a population decline. Unlike the population in the core, the population in the periphery is dependent on further releases at this stage.</li> <li>Bearded vulture reintroductions in the Alps have succeeded in creating a self-sustaining population with higher reproductive success and similar survival probabilities to the autochthonous Pyrenean population. In general, management should focus on preventing further mortality risks. In the periphery, reducing current mortality and increasing reproductive success are essential to make the population independent of releases.</li> </ol> <p> </p> <p><strong>Readme</strong></p> <p>Data files and code for all analyses and figures presented in the paper. The two data files are provided in csv format (SightingData.csv, OccupancyData.csv). There are five code files written for R, but some the main analysis requires software JAGS. The main code (IPM_Code.txt) contains a description of the data, code for loading and managing the data, and for fitting the integrated population model. The other files contain custom written functions (Functions.txt), code for the density dependence test (DensityDependence_Code.txt), code for the retrospective analyses (tLTRE_Code.txt) and code for miscellaneous statistics and figure generation (Figure_Code.txt).</p>
Dataset: Global range dynamics of the Bearded Vulture (Gypaetus barbatus) from the Last Glacial Maxima to climate change scenarios
<p>This dataset consists of Bearded Vulture <em>Gypaetus barbatus </em>occurrence points which were used to develop a distribution model to study its suitable habitat of this species. Using these data, we modelled the current distribution of Bearded Vulture throughout its entire range and projected the Last Glacial Maxima (LGM), Mid-Holocene (MH) and future distribution under 2070s climate change scenarios. We compiled these data from the entire distribution range in Asia, Europe and Africa using different sources: freely accessible online resources including, eBird and GBIF repositories, published reports and grey literature and occurrence data collected by the authors in the field, mostly in Nepal.</p> <p> </p> <p> </p>
Figure 1 in Movement and home range of cinereous vulture Aegypius monachus during the wintering and summering periods in East Asia
Figure 1. Migration route of cinereous vultures (a) VK 1501, (b) VK 1502, (c) VK 1503, (d) VK 1504, (e) VK 1505, (f) VK 1506, (g) VK 1507, and (h) total birds tracked using the GPS-WCDMA-based transmitter in East Asia from January 2015 to March 2017.
Figure 3 in Turkey's largest Cinereous vulture population in a recently discovered breeding area in North-west Anatolia
Figure 3. Nest Tree DBH against Canopy Crown Class and Nest Tree Height, categorized by Canopy Crown Class (O: Dominant, 1: Intermediate, 2: Supressed).
Figure 2 in Turkey's largest Cinereous vulture population in a recently discovered breeding area in North-west Anatolia
Figure 2. Density of active nests of the cinereous vulture population at the Köroğlu Mountains, calculated within a grid of 1x1-km squares.
Figure4 in Population Status and Nesting Behavior of Red-Headed Vultures (Sarcogyps Calvus) at Dhorfirdi, Tanahun District, Nepal
Figure4. Change of shift during incubation by a pair of vultures alternately one after another and successfully hatching of the egg shown by (a) incubation by female parent (b) arrival of male parent in the nest (c) change of shift by flying away of the female parent (d) turning of egg by male parent after foraging (e) continue incubation by the male parent as the female parent moves away (e) hatching of egg into the juvenile S. calvus in the nest
Capture-recapture histories used in our paper "High long-term survival and asymmetric movements in a reintroduced metapopulation of cinereous vultures" published by Ecosphere
<p>These three datasets correspond to the capture-recapture histories used in the E-surge software (in the HEADED format) for both population models (Capture_recapture_histories_ALPS.txt for the Alps and Capture_recapture_histories_CAUSSES.txt for the Causses) and the metapopulation model (Capture_recapture_histories_METAPOPULATION.txt).</p> <p>Columns descriptor:</p> <ul> <li>H:O1 to H:O25 correspond to each occasion (i.e. year)</li> <li>S: correspond to the sample size (i.e. associated number of animals)</li> <li>RC: correspond to the Right Censoring ( -1 if the animal is removed at the last capture or 0 if no right censoring)</li> <li>$COV:Group correspond to the group to which the individual belongs</li> </ul> <p>Individuals were grouped by age (from the 1<sup>st</sup> year until ≥6<sup>th</sup> years), by release status (wild-born / hacking: released juveniles before fledging / aviary: released immatures, sub-adults or adults), by origin (Causses / Alps) and if a missing ring was replaced. All details for the groups are given in the Appendix B for both population models and in the Appendix C for the metapopulation model.</p>
Efficacy of an inflatable deterrent for reducing new world vulture human-wildlife conflict
<p>An excel data spreadsheet used to determine the efficacy of inflatable scarecrows in deterring new world vultures from human-wildlife conflict sites, an excel data spreadsheet that includes variable descriptions. An second excel data spreadsheet that was used to determine if there was vulture selection of specific vehicle types and color and an excel data spreadsheet that includes variable descriptions.</p>
Microsatellite genotypes of bearded vultures (Gypaetus barbatus)
<p>Multilocus microsatellite genotypes of 236 <em>Gypaetus barbatus </em>individuals. This first column contains the individual sample identity as provided in Supplementary Data 1 and subsequent columns are allele scores in single row format. Alleles are scored according to their molecular size (in base pairs); missing data is given as "0".</p>
Blood lead levels in an endangered vulture decline following changes in hunting activity
<p>Lead ammunition stands out as one of the most pervasive pollutants affecting wildlife. Its impact on bird populations has spurred efforts for the phase-out of leaded gunshots in several countries, although with varying scopes and applications. Ongoing and future policy changes require data to assess the effectiveness of adopted measures, particularly in the current context of biodiversity loss. Here, we assessed the long-term changes in blood lead (Pb) levels of Egyptian vultures from the Canary Islands, Spain, which have been severely affected by Pb poisoning over the past two decades. During this period, the reduction in hunting pressure and changes in legislation regarding firearms usage for small game hunting likely contributed to a decrease in environmental Pb availability. As anticipated, our results show a reduction in Pb levels, especially after the ban on wild rabbit hunting with shotguns since 2010. This effect was stronger in the preadult fraction of the vulture population. However, we still observed elevated blood Pb levels above the background and clinical thresholds in 5.6% and 1.5% of individuals, respectively. Our results highlight the positive impact of reducing the availability of Pb from ammunition sources on individual health. Nonetheless, the continued use of Pb gunshot remains an important source of poisoning, even lethal, mainly affecting adult individuals. This poses particular concerns for long-lived birds, compounding by potential chronic effects associated with Pb bioaccumulation. Our findings align with recent studies indicating insufficient reductions in Pb levels among European birds of prey, attributed to limited policy changes and their uneven implementation. We anticipated further reductions in Pb levels among Egyptian vultures with expanded restrictions on hunting practices, including a blanket ban on Pb shot usage across all small game species.</p>
Genomic and morphometric data used in a demographic study of Coragyps vultures
<p><span>The New World Vulture</span><span> [<em>Coragyps</em>] <em>occidentalis</em> (L. Miller, 1909) is one of many species that were extinct by the end of the Pleistocene. To understand its </span><span>evolutionary </span><span>history we sequenced the genome of a 14,000-year-old [<em>Coragyps</em>] <em>occidentalis</em> found associated with megaherbivores in the Peruvian Andes. <em>occidentalis</em> has been viewed as the ancestor, or possibly sister, to the extant Black Vulture <em>Coragyps atratus</em>, but </span><span>genomic data shows <em>occidentalis</em> to be deeply nested within the South American clade of<em> atratus</em>. <em>Coragyps atratus</em> inhabits lowlands, but the fossil record indicates that <em>occidentalis</em> mostly occupied high elevations. Our results suggest that<em> occidentalis</em> evolved from a population of <em>atratus</em> </span><span>in southwestern South America </span><span>that colonized the High Andes 300 to 400 kya. The morphological and morphometric differences </span><span>between <em>occidentalis</em> </span><span>and <em>atratus</em> may thus be explained by </span><span>ecological diversification following </span><span>the natural selection imposed by this new and extreme, high-elevation environment. The </span><span>sudden evolution of a population with significantly larger body size and different anatomical proportions than <em>atratus</em> thus constitutes an example of punctuated evolution. </span></p>
Microsatellite fragment sizing of South African Cape vulture (Gyps coprotheres)
<p>Microsatellite genoytping fragment sizing of <em>Gyps coprotheres</em> individuals collected in South Africa.</p>
Microsatellite genotypes of South African Cape vulture (Gyps coprotheres)
<p>Multilocus microsatellite genotypes of 605 <em>Gyps coprotheres</em> individuals. This first column contains the individual sample identity as provided in Supplementary Data 1 and subsequent columns are allele scores in single row format. Alleles are scored according to their molecular size (in base pairs); missing data is encoded as "0".</p>
Figure 2 in Heavy metal accumulation as a threat to the endangered Egyptian vulture (Neophron percnopterus L.) in Turkey
Figure 2. Distribution of As values for calamus and vane (Z= –2.49, P = 0.01).
Figure 1 in Heavy metal accumulation as a threat to the endangered Egyptian vulture (Neophron percnopterus L.) in Turkey
Figure 1. Study area and the sampled nests.
Figure 1 in Turkey's largest Cinereous vulture population in a recently discovered breeding area in North-west Anatolia
Figure 1. The study area indicating by red border.
Figure3 in Population Status and Nesting Behavior of Red-Headed Vultures (Sarcogyps Calvus) at Dhorfirdi, Tanahun District, Nepal
Figure3. Nesting behavior of S. calvus
Figure1 in Population Status and Nesting Behavior of Red-Headed Vultures (Sarcogyps Calvus) at Dhorfirdi, Tanahun District, Nepal
Figure1. Location map showing vulture sighted areas in MTR
Figure2 in Population Status and Nesting Behavior of Red-Headed Vultures (Sarcogyps Calvus) at Dhorfirdi, Tanahun District, Nepal
Figure2. Summer and winter vulture population
Effects of the environmental conditions and seasonality on a population survey of the Andean Condor Vultur gryphus in the tropical Andes
<p>Script, datasets, and other supplementary material in Márquez-Alvis et al. 2023 PeerJ.<br> <br> <strong>Background:</strong> Among the New World vultures, the Andean Condor is considered one of the most culturally and ecologically important species. However, their populations are declining over their entire distributional range. In response, conservation strategies have been implemented in many countries to reverse the increasing extinction risk of this species. The initiatives rely on extensive population surveys to gather basic information necessary to implement policies and to intervene efficiently. Still, there is a need to standardize the surveys based on seasonality and suitable environmental conditions throughout the species distribution. Here, we provide the first assessment of how daily temperature, rainfall, and seasonality influence surveys of Andean Condors on a communal roost in the central Peruvian Andes.</p> <p><strong>Methods:</strong> Using an autoregressive generalized linear model, we associated environmental variables with visual surveys of adult and young condors at three different times of the day and three times a week between June 2014 and March 2015.</p> <p><strong>Results:</strong> We found that both adults and young Andean Condors showed a threefold reduction in the use of the communal roost after the beginning of the rainy season. Colder and drier days (dry season) are preferable for surveying, as we expect the total number of condors using communal roosts to reduce under rainy (rainfall = -0.53 ± 0.16) and warmer days (temperature= - 0.04 ± 0.02) days. Therefore, the significant variation in the use of roosts across seasons and hours should be carefully accounted for in national surveys, at the risk of undermining the full potential of the communal roost surveys. Moreover, we also found a strong bias towards immatures (about 76%) in the adult:immature ratio and a remarkable absence of Andean Condors during the wet season. These results suggest that the species might be using other unknown communal roosts hierarchically. Such results provide key information for selecting priority areas for conservation and selecting the best time to survey this species in the tropical Andes. Finally, it may open a fruitful avenue for further research on the protection of the Andean Condor.</p>
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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.