The R script and input files needed to run code for generating species urban tolerance estimates, statistical analyses, and plots. A Readme file describing input file content is also included. These data are associated with the manuscript, "Estimates of species-level tolerance of urban habitat in North American birds". Fanelli R.E., P.R. Martin, O.J. Robinson, F. Bonier. 2022. Ecology.

This dataset has been requested for 'the Horizon e4Warning project on mapping and modelling West Nile Virus Disease and its Hosts' then been downloaded from ebird.org and it includes weekly abundance geospatial tifs for for 2021 and 2022 for 23 species:

1. weekly presence
2. weekly species richness
3. week abundance sum

Data obtained from Ebird https://science.ebird.org/en/status-and-trends/species/

Species Names:

File Names:

Population size is a key metric for management and policy decisions, yet wildlife monitoring programs are often limited by the spatial and temporal scope of surveys. In these cases, citizen science data may provide complementary information at higher resolution and greater extent. We present a case study demonstrating how data from the eBird citizen science program can be combined with regional monitoring efforts by the U.S. Fish and Wildlife Service to produce high-resolution estimates of golden eagle abundance. We developed a model that uses aerial survey data from the western United States to calibrate high-resolution annual estimates of relative abundance from eBird. Using this model, we compared regional population size estimates based on the calibrated eBird information to those based on aerial survey data alone. Population size estimates based on the calibrated eBird information had strong correspondence to estimates from aerial survey data in two out of four regions, and popula..., , , # Leveraging the strengths of citizen science and structured surveys to achieve scalable inference on population size

https://doi.org/10.5061/dryad.dfn2z357x

Description of the data and file structure

This file contains information and explanation for the data and code that accompany the following project: Stillman, A.N., P.E. Howell, G.S. Zimmerman, E.R. Bjerre, B.A. Millsap, O.J. Robinson, D. Fink, E.F. Stuber, and V. Ruiz-Gutierrez. 2023. Leveraging the strengths of citizen science and structured surveys to achieve scalable inference on population size. Journal of Applied Ecology.

This .README file accompanies the archived data for this project. Two files marked with the word "Script:" provide R code for two Bayesian models described in the main text. Two files marked with the word "Dataset:" provide the necessary data to run the models. Data from the eBird Status and Trends program are freely available online from the Cornell Lab of...

Wildfires are a common natural disturbance, forging and reshaping ecosystems around the world. With 7.2 million acres of land burned annually in the United States, most research on the impacts of wildfires on birds and other wildlife has focused on how animals respond to the loss and transformation of habitat. However, direct impacts of wildfires extend far beyond the burn perimeter. Smoke from wildfires can be transported hundreds of miles, exposing birds to toxic air across a large geographic area. Yet, research on the impacts of wildfire smoke on wild birds is extremely limited. Quantifying the relationship between wildfire smoke and bird detection is a critical first step in assessing the broader ecological impacts of smoke disturbance. In this study, we assess how fine particulate matter (PM2.5), a well-established marker of wildfire smoke and important pollutant, influences the probability of observing birds in New York, USA, during the 2021–2023 wildfire seasons. We used generalized linear mixed models to model bird observations from 98,960 eBird checklists to local measurements using daily mean concentration of PM2.5. After accounting for habitat, time of day, weather, seasonality, and survey effort, we found that PM2.5 affected the probability of observing 70% (55 of 84) study species. Of the total 84 study species, 18% (15 species) had a positive interaction with increased PM2.5 concentration, while 48% (40 species) had a negative interaction with PM2.5 concentration. Our findings demonstrate that wildfire smoke influences the probability of observing birds, likely due to species-specific behavioral responses to smoke pollution. Furthermore, our results support previous research suggesting that wildfire smoke (and air pollution in general) is an important and underexplored component of the detection process; failing to account for the effect air quality may bias models of species distributions and abundance. As climate change continues to escalate global wildfire activity, it is critical to understand how birds will be impacted by more frequent and intense smoke pollution. Our study provides insights into which species may be most vulnerable to acute smoke exposure and guide conservation action in the Pyrocene.

Yearly trend When averaged across all points with trends, upland forest bird abundance increased by 0.98% per year from 2012-2022. Species used were cerulean warbler, Louisiana waterthrush, wood thrush, and worm-eating warbler. These species are Regional Species of Greatest Conservation Need for states in the Southeast, primarily occur in this ecosystem, and have sufficient data for trend analysis in eBird Status and Trends. Trends varied across the Southeast, with the biggest declines occurring in the Central Hardwoods, Appalachians, and northeast part of the Southeast Coastal Plain Bird Conservation Regions. For two widespread species, points were mostly increasing: wood thrush (91% increasing) and Louisiana waterthrush (64% increasing). For two species with smaller ranges in the Southeast, points were mostly declining: cerulean warbler (78% declining) and worm-eating warbler (78% declining). Breeding Bird Survey trends, which cover more coarse areas, also show similar patterns. On track to meet SECAS goal Yes. The increase of about 3.92% every 4 years is greater than the SECAS goal of a 1% increase every 4 years. Data source eBird Status and Trends Confidence in trend Low. Less than half of the points that were increasing (38%) were statistically significant. Interpretation This is an indicator of both local and landscape conditions across the upland forest ecosystem. Upland hardwood birds benefit from conversion of historic grassland and savanna ecosystems into closed canopy forest. In areas with increases, that may mean increases in closed canopy forest overall are offsetting the negative impacts of land use changes like greater forest fragmentation. Some areas of upland forest bird decline, like Southeast Missouri, could actually be positive signs of conservation overall as these areas are restored to the more open forest types that historically occurred there.

Species-specific trends also highlight how more widespread generalist species (Louisiana waterthrush, wood thrush) seem to be poised to take advantage of changing landscape conditions. More specialist and range-limited species (cerulean warbler, worm-eating warbler) seem to be less able to take advantage of these changes. Based on range-wide trends for these species, it doesn’t appear that climate change is a major driver of trends during this time period. It’s also important to note that all these species are neotropical migrants. Threats to survival during migration (e.g., communication towers) and on their wintering grounds (e.g., habitat loss) are likely also impacting population trends. Other information available A table of state-level summaries for each species, a map by Bird Conservation Region (BCR), and tabular data associated with the chart above are available in Appendix I of the pdf report: https://secassoutheast.org/pdf/SECAS-goal-report-2024.pdf.

Data related to the manuscript: Continental-scale biomass redistribution by migratory birds in response to seasonal variation in productivity, accepted for publication in Global Ecology and Biogeography. DOI of article to be provided later.Data included:- Biomass and abundance estimates from the interpolation models, fitted using the 2016 eBird Reference Dataset (Fink et al., 2017).- Species richness estimates, based on the eBird Status and Trends occurrence maps (eBird S&T; Fink et al., 2020b).- EVI estimates, extracted from those used in La Sorte & Graham (2021).- Estimates of bioclimatic variables, extracted from the WorldClim database (WorldClim version 2.1; Fick & Hijmans, 2017).All data are in the RData format. See "readme.txt" for details.

Abstract

A series of weekly bird abundance distribution datasets is now available from EBIRD (https://science.ebird.org/en/status-and-trends). ERGO has processed these data in several tranches to provide weekly species richness and weekly aggregated abundance indices at 3km resolution. Data for thirty species have now been processed. These species have been selected as being West Nile Virus hosts, using literature search, inference from mosquito WNV vector blood meals and from bird serology reports. The two tranches are a) all 30 selected species and b) the top 15 E4Warning priority species . Details are provided in the accompanying Excel Spreadsheet (e4ebird readmeJune24.xls).

Description

This dataset has been requested for 'the Horizon e4Warning project on mapping and modelling West Nile Virus Disease and its Hosts' then been downloaded from ebird.org and it includes weekly abundance geospatial tifs for 30 species:

weekly presence

weekly species richness

week abundance sum

Data obtained from Ebird https://science.ebird.org/en/status-and-trends/species/

Species Names:

Species English Name filname code

Alcedo atthis Common Kingfisher comkin1

Anas platyrhynchos Mallard mallar3

Anser anser Graylag Gose gragoo

Athene noctua Little Owl litowl1

Bulbulcus ibis Cattle Egret categr

Buteo buteo Common Buzzard combuz1

Columba palumbus Commin Wood Piegon cowpig

Corvus cornix Hooded Crow hoocro1

Corvus corone cornix Carrion Crow carcro1

Corvus monedula Eurasian Jackdaw eurjac

Cyanistes caeruleus Blue Tit blutit

Egretta garzetta (Little Egret) litegr

Eremophila alpestris Horned Lark horlar

Falco tinnunculus Eurasian Kestrel eurkes

Garrulus glandarius Eurasian Jay eurjay1

Hirundo rustica Barn Swallow barswa

Larus argentatus Herring Gull hergul

Lulua arborea Woodlark woolar1

Luscinia Luscinia Thrush Nightinglae thrnig1

Luscinia megarhynchos Common nightingale comnig1

Passer domesticus (including Passer italiae and Passer hispaniolensis) House Sparrow houspa

Pica pica Eurasian Magpie eurmag1

Streptopelia decaocto Eurasian Collared Dove eucdov

Turdus merula Eurasian Blackbird eurbla

Ciconia ciconia White Stork whisto1

Sturnus vulgaris European Starling eursta

Sylvia atricapilla Eurasian Bl;ackcap blackc1

Acrocephalus scirpaceus Common Reed Warbler eurwar1

Fulica atra Eurasian Coot eurcoo

Columba livia Rock Pigeon rocpig

Gallus gallus Domestic chicken

File Names:

a) e4ebirdabundanceall30weeklyJune24 All weekly abundance datasets for 30 availablke spp at 3km resolution, June 24

b) e4ebirdPAall30weeklyJune24 Presence absence with missing recoded to 0 for all 30 species available in June 24. This recoding is based of ad hoc checks of weekly datasets against the birdlife species ranges, which suggest that the maximum extents of combined weekly abundance distributions match the rage boundares fairly well

c) e4ebirdspprichnessall23SUMMEANweeklyFeb24 Summed and mean weekly presence absence for 23 available species calc Feb24. If a species in missing a weekly dataset, missing weeks are filled with last valid presence week up to halfway through the gap in availability, then with the first available distribution after the gap

d) e4ebirdspprichnesse415SUMMEANweeklyJun24 Summed and mean weekly presence absence for e4 15 priority species calc June 24. If a species in missing a weekly dataset, missing weeks are filled with last valid presence week up to halfway through the gap in availability, then with the first available distribution after the gap

e) e4ebirdspprichnessall30SUMMEANweeklyJun24 Summed and mean weekly presence absence for 30 available species calc June 24. If a species in missing a weekly dataset, missing weeks are filled with last valid presence week up to halfway through the gap in availability, then with the first available distribution after the gap

f) e4ebirdabundanceall30summeanweekJun24 Summed and mean weekly median abundance for 30 available species calc June 24. If a species in missing a weekly dataset, missing weeks are filled with last valid presence week up to halfway through the gap in availability, then with the first available distribution after the gap

g) e4ebirdeabundance415summeanweekJun24 Summed and mean weekly median abundance for e4 15 priority species calc June 24. If a species in missing a weekly dataset, missing weeks are filled with last valid presence week up to halfway through the gap in availability, then with the first available distribution after the gap

Yearly trendWhen averaged across all points with trends, forest wetland bird abundance increased by 2.85% per year from 2012-2022. Species used were prothonotary warbler, Swainson's warbler, swallow-tailed kite, and yellow-throated warbler. These species are Regional Species of Greatest Conservation Need for states in the Southeast, primarily occur in this ecosystem, and have sufficient data for trend analysis in eBird Status and Trends. Most points across the SECAS region were increasing. Declines were mostly in areas experiencing major impacts from sea-level rise. Individual species trends also followed this pattern. Breeding Bird Survey trends, which cover more coarse areas, also show similar patterns.On track to meet SECAS goalYes. The increase of about 11.4% every 4 years is greater than the SECAS goal of a 1% increase every 4 years.Data sourceeBird Status and TrendsConfidence in trendMedium. Most of the points (57%) that were on track for the goal were statistically significant.InterpretationThis is an indicator of both local and landscape conditions across the forested wetland ecosystem. While there are some declines, especially in areas impacted by sea-level rise, overall, forested wetland birds appear to be on track to meet the SECAS goal. This may be due to the extensive conservation investments in forested wetlands, policies restricting wetland development, and growing interest from urban communities in protecting water supply and reducing flood risks.Other information availableA table of state-level summaries for each species, a map by Bird Conservation Region (BCR), and tabular data associated with the chart above are available in Appendix I of the pdf report: https://secassoutheast.org/pdf/SECAS-goal-report-2024.pdf.

During animal migration, ephemeral communities of taxa at all trophic levels co-occur over space and time. The interactions between predators and prey along migration corridors are ecologically and evolutionarily significant. However, these interactions remain understudied in terrestrial systems and warrant further investigations using novel approaches. We investigated the predator-prey interactions between a migrating avivorous predator and ephemeral avian prey community in the fall migration season. We tested for associations between avian traits and prey selection and hypothesized that prey traits (i.e., relative size, flocking behavior, habitat, migration tendency, and availability) would influence prey selection by a sexually dimorphic raptor on migration. To document prey consumption, we sampled trace prey DNA from beaks and talons of migrating sharp-shinned hawks Accipiter striatus (n=588). We determined prey availability in the ephemeral avian community by extracting weekly abundance indices from eBird Status and Trends data. We used discrete choice models to assess prey selection and visualized frequency of prey in diet and availability on the landscape over the fall migration season. Using eDNA metabarcoding, we detected prey species on 94.1% of the hawks sampled (n=525/588) comprising 1396 prey species detections from 65 prey species. Prey frequency in diet and eBird relative abundance of prey species were correlated over the migration season for top selected prey species, suggesting prey availability is an important component of raptor-songbird interactions during fall. Prey size, flocking behavior, and non-breeding habitat association were prey traits that significantly influenced predator choice. We found differences between female and male hawk prey selection, suggesting that sexual size dimorphism has led to distinct foraging strategies on migration. This research integrated field data collected by a volunteer-powered raptor migration monitoring station and public-generated data from eBird to reveal elusive predator-prey dynamics occurring in an ephemeral raptor-songbird community during fall migration. Understanding dynamic raptor-songbird interactions along migration routes remains a relatively unexplored frontier in animal ecology and is necessary for conservation and management efforts of migratory and resident communities.

Generalized linear model via Bayesian phylogenetic inference to quantify the support for log-linear combination of predictors of D1.1 spread between North American flyways. The predictors include: USDA-confirmed wild bird HPAI cases – originUSDA-confirmed wild bird HPAI cases – destinationSpecies overlap between flyways (eBird data)Bordering flywaysThis file includes data from the eBird Status and Trends Project at the Cornell Lab of Ornithology, eBird.org. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the Cornell Lab of Ornithology.

Yearly trendWhen averaged across all points with trends, grassland and savanna bird abundance declined by 2.2% per year from 2012-2022.Species used were American kestrel, Bachman's sparrow, Eastern meadowlark, grasshopper sparrow, Henslow's sparrow, LeConte's sparrow, loggerhead shrike, Northern Bobwhite, prairie warbler, red-cockaded woodpecker, and scissor-tailed flycatcher. These species are Regional Species of Greatest Conservation Need for states in the Southeast, primarily occur in this ecosystem, and have sufficient data for trend analysis in eBird Status and Trends. Most points across the SECAS region were declining. For most individual species, a majority of points were declining, but there were also a number of points with increases. Two species with most of their range in the longleaf pine ecosystem had a larger number of increasing points than other species: red-cockaded woodpecker (58% increasing) and Bachman’s sparrow (43% increasing). Breeding Bird Survey trends, which cover more coarse areas, also show similar patterns.On track to meet SECAS goalNo. The decline of about 8.8% every 4 years is not enough to meet the SECAS goal of a 1% increase every 4 years.Data sourceeBird Status and TrendsConfidence in trendMedium. Most of the points (65%) that were declining and off track for the goal were statistically significant.InterpretationThis is an indicator of both local and landscape conditions across the grassland and savanna ecosystem. Large declines across most of the region highlight the major problems for this ecosystem and the species that depend on it. Signs of improvement in the longleaf range, South Florida, the Chihuahuan Desert, the West Gulf Coastal Plain, and the Appalachians show that targeted conservation attention can still have an impact. Improvements in specific species like red-cockaded woodpecker and Bachman’s sparrow also show that targeted improvements in habitat quality can make a major difference.Other information availableA table of state-level summaries for each species, a map by Bird Conservation Region (BCR), and tabular data associated with the chart above are available in Appendix I of the pdf report: https://secassoutheast.org/pdf/SECAS-goal-report-2024.pdf.