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337 results for “forest birds”
Bird species list for the Andrews Experimental Forest and Upper McKenzie River Basin, 1975 to 1995
This list quantifies bird species and indicates general abundance and habitat. The list covers the entire upper McKenzie River watershed with special reference to occurrence within the Andrews Forest. It represents the collective observations of many people over 20-plus years, but should not be viewed as either current or complete.
Valleywide Bird Survey, Hubbard Brook Experimental Forest, 1999-2016 (ongoing)
This data set includes bird point-count data collected during the breeding seasons (May-July) of 1999-2016 at 373 locations throughout Hubbard Brook Experimental Forest. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Calling activity of Birds in the White Mountain National Forest: Audio Recordings (2016 and 2018)
We collected 410 10-minute sound recordings of birds in and near the Hubbard Brook Experimental Forest in New Hampshire. Recordings, which encompassed most of the bird breeding season in each of two years, included 130,776 vocalizations from 46 taxa. In the associated publication, we report species lists, rarefaction curves, and vocalization descriptions. We also provide analyses of habitat associations, phenology, and spatial patterning in vocalization activity. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Calling activity of Birds in the White Mountain National Forest: Manifest of 99,778 acoustic recordings from bird plots in the Hubbard Brook Forest: 2016 - 2023
During 2016 - 2023, during the bird breeding season, we collected 99,778 files of bioacoustic recordings in and near the Hubbard Brook Experimental Forest in New Hampshire. Here, we provide a manifest of the sound files. Most files are one-hour recordings collected at 32 kHz and saved in FLAC format (~ 25 MB per file, ~ 13 TB total). Typical recording configuration was 05:00 - 08:00 and 17:30 - 20:30 local time. The full sound files have been saved in three respositories: two copies at Dartmouth College (Ayres lab) and one copy at the Macauley Library, Cornell Laboratory of Ornithology. The full sound files are available upon request. The file attributes within the manifest include date, start time, and recorder group: e.g., Main, 10ha, Oven, VW, AshBirch, and Ridge. Each recorder group had 5 - 20 recorders at plots separated by >100 m. Coordinates of each recorder are associated with plot names within metadata. The bird species expected to occur in these recordings are those from Holmes et al. (2021). These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station. Holmes, R., S. Sillett, and M. Hallworth. 2021. Bird species recorded within the Hubbard Brook Experimental Forest and vicinity (1963-2020; updated January 2021). ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/da6cbb1ed8142d52a9d72762983742d8 (Accessed 2024-10-24).
Data from: Habitat selection in transformed landscapes and the role of forest remnants and shade coffee in the conservation of resident birds
1. Biodiversity conservation in transformed landscapes is becoming increasingly important. However, most assessments of the value of modified habitats rely heavily on species presence and/or abundance, masking ecological processes such as habitat selection and phenomena like ecological traps, which may render species persistence uncertain. High species richness has been documented in tropical agroforestry systems but comparisons with native habitat remnants generally lack detailed information on species demography and habitat use. 2. We generated a multi-species, multi-measure framework to evaluate the role of habitat selection in the adaptation of species to transformed landscapes, and demonstrate that its use could affect how we value the contribution different land uses make to biodiversity conservation. 3. We analyzed seven years of capture-mark-recapture and observation data for twelve species of resident birds present in native forest remnants and shade coffee plantations in a mega-diverse region. We assessed whether species behaved adaptively by evaluating the correlation between measures of habitat preference (occurrence, abundance, fidelity, inter-seasonal variance and age) and performance (body condition, muscle, primary molt, breeding and juveniles) in forest and coffee, and generated hypotheses about their role in species persistence. 4. We documented adaptive habitat selection for seven species, non-ideal selection for four, and maladaptive selection for one. While many species showed equal-preference and/or equal performance in many traits, in general we found more evidence for birds preferring and/or performing better in forest than coffee, although relationships between our indicators and population adaptation need to be studied further before our proposed framework can be applied to more species and landscapes. 5. While shade coffee can act as a biodiversity-friendly matrix providing complementary or supplementary habitat to a wide range of resident bird species, protecting remnants of native vegetation is still of paramount importance for biodiversity conservation in agricultural landscapes. 28-Aug-2019
Digital repository for: Large-scale forest disturbance and associated management shape bird communities in Central European spruce forests
<p>Repository containing R-script and data to reproduce analysis and main figures on the effect of large-scale forest disturbance and associated pre- and post-disturbance management on bird communities in the Harz Mountains, Germany.</p> <p>R-script includes:</p> <ul> <li>indicator species analysis (R package indicspecies; Cáceres & Legendre, 2009)</li> <li>non-metric multidimensional scaling (R package vegan; Oksanen et al., 2016)</li> <li>rarefaction- and extrapolation of Hill numbers (R package iNEXT; Hsieh et al., 2019)</li> <li>multi-species community distance sampling (R package sp Abundance; Doser et al., 2023)</li> </ul> <p>Attached files:</p> <ul> <li><strong>bird_data_Graser_et_al.csv </strong>(row data of bird species point counts per distance category)</li> <li><strong>bird_data_abundance_100_Graser_et_al.csv </strong>(abundance of species per sampling site, summed up over all four sampling repeats only considering detected individuals up to 100 m around the sampling point)</li> <li><strong>siteCovs_Graser_et_al.csv</strong> (environmental variables for each sampling point)</li> <li><strong>A_species_matrix_100_new_Graser_et_al.csv</strong> (species-site matrix of <strong>bark-beetle disturbance, unlogged </strong>sites for rarefaction and extrapolation, species number summed up over all four sampling repeats only considering detected individuals up to 100 m around the sampling point)</li> <li><strong>B_species_matrix_100_new_Graser_et_al.csv </strong>(species-site matrix of <strong>windthrow disturbance, unlogged </strong>sites for rarefaction and extrapolation, species number summed up over all four sampling repeats only considering detected individuals up to 100 m around the sampling point)</li> <li><strong>C_species_matrix_100_new_Graser_et_al.csv </strong>(species-site matrix of <strong>bark-beetle/windthrow disturbance, underplanted, unlogged </strong>sites for rarefaction and extrapolation, species number summed up over all four sampling repeats only considering detected individuals up to 100 m around the sampling point)</li> <li><strong>D_species_matrix_100_new_Graser_et_al.csv </strong>(species-site matrix of <strong>bark-beetle /windthrow disturbance, salvage-unlogged </strong>sites for rarefaction and extrapolation, species number summed up over all four sampling repeats only considering detected individuals up to 100 m around the sampling point)</li> <li><strong>E_species_matrix_100_new_Graser_et_al.csv </strong>(species-site matrix of <strong>bark-beetle /windthrow disturbance, underplanted, salvage-unlogged </strong>sites for rarefaction and extrapolation, summed up over all four sampling repeats only considering detected individuals up to 100 m around the sampling point)</li> <li><strong> F_species_matrix_100_new_Graser_et_al.cs</strong>v (species-site matrix of <strong>mature spruce plantation </strong>sites for rarefaction and extrapolation, species number summed up over all four sampling repeats only considering detected individuals up to 100 m around the sampling point)</li> <li><strong>msHDS_bird_data_management_model_Graser_et_al.rds</strong> (R-data set for multi-species community distance sampling of the effect of different pre- and post-disturbance management groups)</li> <li><strong>msHDS_bird_data_stand_age_model_Graser_et_al.rds </strong>(R-data set for multi-species community distance sampling of the effect of post-disturbance forest succession)</li> </ul> <p>A more detailed description of the data can be found in the README.txt document.</p> <p><span>References:</span></p> <p><span>Cáceres, M. D., & Legendre, P. (2009). </span><span>Associations between species and groups of sites: Indices and statistical inference. <em>Ecology</em>, <em>90</em>(12), 3566–3574. https://doi.org/10.1890/08-1823.1</span></p> <p><span>Doser, J. W., Finley, A. O., Kéry, M., & Zipkin, E. F. (2023). spAbundance: An R package for single‐species and multi‐species spatially explicit abundance models. <em>Methods in Ecology and Evolution</em>, <em>15</em>(6), 1024–1033. https://doi.org/10.1111/2041-210X.14332</span></p> <p><span>Hsieh, T. C., Ma, K. H., & Chao, A. (2019). <em>iNEXT-package: Interpolation and extrapolation for species diversity</em>. https://cran.r-project.org/web/packages/iNEXT/vignettes/Introduction.html</span></p> <p><span>Oksanen, J., Blanchet, F. G., Kindt, R., Legendre, P., O’hara, R. B., Simpson, G. L., Solymos, P., Stevens, M. H. H., Wagner, H., Minchin, P. R., Gavin, L., & Henry, H. (2016). Vegan: Community ecology package. R package version 1.17-4. <em>Http://CRAN. R-Project. </em></span><em><span>Org/Package=vegan</span></em><span>.</span></p> <p></p> <p></p>
Simulated treatment effects on bird communities inform landscape‐scale dry conifer forest management
<p>Human land use and climate change have increased forest density and wildfire risk in dry conifer forests of western North America, threatening various ecosystem services, including habitat for wildlife. Government policy supports active management to restore historical structure and ecological function. Information on potential contributions of restoration to wildlife habitat can allow assessment of tradeoffs with other ecological benefits when prioritizing treatments. We predicted avian responses to simulated treatments representing alternative scenarios to inform landscape‐scale forest management planning along the Colorado Front Range. We used data from the Integrated Monitoring in Bird Conservation Regions program to inform a hierarchical multispecies occupancy model relating species occupancy and richness with canopy cover at two spatial scales. We then simulated changes in canopy cover (remotely sensed in 2018) under three alternative scenarios, (1) a "fuels reduction" scenario representing landscape‐wide 30% reduction in canopy cover, (2) a "restoration" scenario representing more nuanced, spatially variable treatments targeting historical conditions, and (3) a reference, no‐change scenario. Model predictions showed areas of potential gains and losses for species richness, richness of ponderosa pine forest habitat specialists, and the ratio of specialists to generalists at two (1 km<sup>2</sup> and 250 m<sup>2</sup>) spatial scales. Under both fuels reduction and restoration scenarios, we projected greater gains than losses for species richness. Surprisingly, despite restoration more explicitly targeting ecologically relevant historical conditions, fuels reduction benefited bird species richness over a greater spatial extent than restoration, particularly in the lower montane life zone. These benefits reflected generally positive species associations with moderate canopy cover promoted more consistently under the fuels reduction scenario. In practice, contemporary forest management is likely to lie somewhere between the fuels reduction and restoration scenarios represented here. Therefore, our results inform where and how active forest management can best support avian diversity. Although our study raises questions regarding the value of including landscape‐scale heterogeneity as a management objective, we do not question the value of targeting finer-scale heterogeneity (i.e., stand and treatment level). Rather, our results combined with those from previous work clarify the scale at which targeting structural heterogeneity and historical reference conditions can promote particular ecosystem services.</p>
Data from: The extreme rainfall gradient of the Cape Horn Biosphere Reserve and its impact on forest bird richness. Biodiversity and Conservation
<p><strong>Description of dataset</strong></p> <p>This dataset contains information about forest bird species richness and climatic variables in 61 sample sites of the Cape Horn Biosphere Reserve. This dataset was analysed in : Quilodrán CS, Sandvig EM, Aguirre F, Rivero de Aguilar J, Barroso O, Vásquez RA, and R Rozzi. 2022. Effects of the extreme rainfall gradient in the Cape Horn Biosphere Reserve on forest bird richness. <em>Biodiversity and Conservation</em>. </p> <p> </p> <p><strong>Acknowledgments </strong></p> <p>This study was funded by grants for Technological Centers of Excellence with Basal Financing of the National Agency for Research and Development (ANID-Chile), granted to the Cape Horn International Center (CHIC- FB210018) and the Institute of Ecology and Biodiversity (IEB-AFB170008). CSQ acknowledges support from the Swiss National Science Foundation (N°P5R5PB_203169). </p>
A dataset of bird assemblages in different successional pathways– a comparative study in hemiboreal mixed forests
<p><strong>Abstract:</strong></p> <p><strong>Context </strong>The most productive forest lands have naturally the richest bird assemblages but tend to be also most intensively managed. Sustainable solutions to this conflict are unclear.</p> <p><strong>Aim </strong>To assess bird assemblages and their successional dynamics in planted Norway spruce (<em>Picea abies </em>L.) stands compared to naturally developing stands.</p> <p><strong>Methods </strong>We mapped breeding bird assemblages in forty 5-ha plots on highly productive soils in Estonia. The plots included sets of naturally regenerated and planted stands, and (as successional endpoints) clear-cuts and old stands.</p> <p><strong>Results </strong>Planted stands had fewer bird species and pairs than naturally regenerated stands; the latter having a species composition resembling late-successional deciduous-dominated stands. Importantly, the species composition in mature spruce plantations converged toward the composition observed in late-successional conifer-dominated stands. Downed dead wood, stand age, deciduous trees, and stock density were the most significant stand characteristics shaping bird assemblages.</p> <p><strong>Conclusion</strong> The habitat value of established spruce plantations can be primarily improved by allowing for some deciduous trees and gaps with deciduous undergrowth. At the landscape scale, the bird diversity of even-aged systems would be enhanced by multi-scale applications of retention forestry – from retention trees to old-growth set-asides.</p> <p> </p> <p> </p> <p>The given dataset includes observations of breeding pairs on all 40 study plots with different management types. Variables explained in supplementary txt file. </p> <p> </p>
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
Data for "Vegetation complexity and pool size predict species richness of forest birds"
<p>This xlsx file contains data needed to replicate analyses in our article on species richness of Australian passerine birds.</p> <p>AUTHOR of data files: Vladimir Remes<br> CONTACT: vlad.remes/at/gmail,com<br> AUTHORS of the MS: V. Remes, L. Harmacková, B. Matysiokova, L. Rubacova, E. Remesova<br> DATE CREATED: 8 June 2022</p> <p>The file was saved in MS Excel for Mac 16.42.</p> <p>The file is named "data_SR_AU_passerines.xlsx" and has two sheets:<br> "data": contains the data<br> "legend": contains explanations of data columns</p> <p>The related article is:</p> <p>Remeš V, Harmáčková L, Matysioková B, Rubáčová L and Remešová E (2022) Vegetation complexity and pool size predict species richness of forest birds. Front. Ecol. Evol. 10:964180. doi: 10.3389/fevo.2022.964180</p>
Data from: Active restoration accelerates recovery of tropical forest bird assemblages over two decades
<p>Choosing effective methods to restore habitat for the diverse faunal assemblages of tropical forests is hampered by lack of long-term data comparing multiple restoration treatments. We conducted area counts of bird assemblages over 12 years (~5-17 years since restoration) in a blocked experiment with two active planted treatments (tree plantations and applied nucleation) and a passive restoration treatment (natural regeneration) replicated at 11 sites in Costa Rica. We also surveyed six pastures and five remnant forest sites to assess recovery of avian species richness, composition, forest specialists, and range-restricted species in restoration plots relative to degraded and reference systems. Restoration treatments showed increased resemblance of avian assemblages to remnant forest over time. Applied nucleation proved equally effective as plantation, despite a reduced planted area, whereas natural regeneration recovered more slowly. Assemblage-level trends in avian species richness and compositional similarity to reference forest are underpinned by reductions in use by pasture birds and by gradual increases in richness of forest-affiliated species. Because forest-affiliated species tend to have narrower distributions than the open-country species they replace, forest restoration can reduce biotic homogenization at the local scale. Restoration practitioners should consider applied nucleation as an alternative to standard plantations if seeking rapid recovery of bird assemblages. However, the ecological return on investment from natural regeneration increases over a couple of decades. Managers should monitor trends in forest-affiliated and range-restricted species to track the recovery of the full avian assemblages, since coarse metrics like species richness and overall compositional similarity may plateau relatively quickly.</p>
Figure 1 in Composition and spatio-temporal dynamics of aquatic bird community in humid areas of Alto Parana Atlantic Forest
Figure 1. Map of the RPPN Foz do Rio Aguapeí and location of the six studied areas in the RPPN Foz do Rio Aguapeí. Legend: (1) Lagoa São Gabriel; (2) Lagoa das Piranhas; (3) Lagoa dos Porcos; (4) Constructed wetland; (5) Aguapei river –; and (6) Lagoa da sede. Sources: CESP (2013) and Google Earth (2021).
Figure 2 in Composition and spatio-temporal dynamics of aquatic bird community in humid areas of Alto Parana Atlantic Forest
Figure 2. Cumulative curve of the 52 waterfowl bird species in the RPPN Foz do Rio Aguapeí showing stability from sample 27 to 31.
Figure 3 in Composition and spatio-temporal dynamics of aquatic bird community in humid areas of Alto Parana Atlantic Forest
Figure 3. NMDS (stress of 0.097) of the spatial distribution of the aquatic bird community recorded by the transect method in the lagoons of the RPPN Foz do Aguapeí, during the dry (rounded symbols) and rainy seasons (square symbols). Legend: LS = Lagoa da Sede; LSG = Lagoa São Gabriel; LP = Lagoa da Piranha and LPO = Lagoa dos Porcos.
Figure 4 in Composition and spatio-temporal dynamics of aquatic bird community in humid areas of Alto Parana Atlantic Forest
Figure 4. NMDS (stress of 0.001) of the spatial distribution of the aquatic bird community recorded by the transect method in the lotic environments of the RPPN Foz do Aguapeí, during the dry (rounded symbols) and rainy seasons (square symbols). Legend: AR = Aguapeí River and CW = Constructed wetland.
Figure 3 in Birds of Humaitá Forest Reserve, Acre, Brazil: an important forest fragment in south-west Amazonia
Figure 3. Three endemic species from the Inambari center associated with patches of Guadua bamboo recorded in the Humaitá Forest Reserve, Acre, Brazil. (A) Rufous-headed Woodpecker Celeus spectabilis (David P. Guimarães). (B) Rufous Twistwing Cnipodectes superrufus (Tomaz N. de Melo). (C) Acre Tody-Tyrant Hemitriccus cohnhafti (Ricardo Plácido).
Figure 2 in Birds of Humaitá Forest Reserve, Acre, Brazil: an important forest fragment in south-west Amazonia
Figure 2. Examples of migratory species recorded in the Humaitá Forest Reserve, Acre, Brazil. (A) Broad-winged Hawk Buteo platypterus (Diego Pedroza); (B) Yellow-billed Cuckoo Coccyzus americanus (David P. Guimarães); (C) Rufous Casiornis Casiornis rufus (David P. Guimarães). (D) Swainson's Thrush Catharus swainsoni (Diego Pedroza).
Figure 1 in Birds of Humaitá Forest Reserve, Acre, Brazil: an important forest fragment in south-west Amazonia
Figure 1. Location of the Humaitá Forest Reserve (HFR) in the state of Acre, Brazil, near the city of Rio Branco (red star). The area that corresponds to the HFR, administered by the Federal University of Acre, is outlined by the red polygon.
FIGURE 11 in Status of the globally threatened forest birds of northeast Brazil
FIGURE 11: Curaeus forbesi (Sclater, 1886), Forbes Blackbird, Tamandaré, PE, October 2008 (Ciro Albano).
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.