bbsBayes: An R Package for Hierarchical Bayesian Analysis of North American Breeding Bird Survey Data

Edwards, Brandon P.M.; Smith, Adam C.

doi:10.1101/2020.05.27.118901

Cited by 6 publications

(12 citation statements)

References 16 publications

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“…Population trends and trajectories were estimated using a Bayesian hierarchical Generalized Additive Model with Year Effects (GAMYE) 32 in R 51 . The survey-wide analyses were run during the annual analysis of the BBS data conducted by the Canadian Wildlife Service 52 , and additional summaries and maps were created with the R-package bbsBayes 53 . Data were stratified both by geopolitical regions (states and provinces), as well as internationally ratified Bird Conservation Regions (BCRs) 54 .…”

Section: Methodsmentioning

confidence: 99%

Current contrasting population trends among North American hummingbirds

English

Bishop

Wilson

et al. 2021

Sci Rep

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As pollinators, hummingbirds play a critical role for both the function of ecological communities and in providing ecosystem services for people. To examine the conservation status of North American hummingbirds, we analyzed Breeding Bird Survey data for 8 species and 3 genera from 1970 to 2019 (long-term) and from 2009 to 2019 (short-term, approximately three generations). Among the Selasphorus genus, Allen’s, rufous, and broad-tailed hummingbirds have declined since 1970, and the rate of decline increased from 2009 to 2019. Contrasting the trends from the past half-century, ruby-throated hummingbirds of Eastern North America have declined since approximately 2004 throughout most of the species’ breeding range. In contrast, Anna’s hummingbird populations have increased dramatically since 1970 in their range in western North America. We also tested whether apparent declines might be due to a growing mismatch between the timing of breeding and the timing of BBS surveys. We found no evidence for such an effect, thus supporting the hypothesis that trends reflect true demographic change. Our analyses and geographic modelling highlight the urgent need of regulatory action to conserve hummingbirds uniquely capable of filling their niche in North America.

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Section: Methodsmentioning

confidence: 99%

Current contrasting population trends among North American hummingbirds

English

Bishop

Wilson

et al. 2021

Sci Rep

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“…We used a general additive model with a random year effect, the current model used by the Canadian Wildlife Service (Edwards and Smith 2021). Otherwise, we used the default model parameters (e.g., burn‐in = 10,000, chains = 3, iterations = 20,000, thinning = 10) with a heavy‐tailed t‐distribution for the extra‐Poisson error distribution, as suggested by Edwards and Smith (2021). Only black duck conservation regions where enough survey routes were available could be modeled (i.e., ≥3 routes with black duck observations; ≥3 years with non‐zero observations on ≥1 route).…”

Section: Methodsmentioning

confidence: 99%

“…We determined regional indices of black duck abundance using the North American BBS data (1966–2019; Pardieck et al 2020) analyzed using hierarchical Bayesian analysis within the bbsBayes package (version 2.3.8.2020; Edwards and Smith 2021). We used a general additive model with a random year effect, the current model used by the Canadian Wildlife Service (Edwards and Smith 2021).…”

Section: Methodsmentioning

confidence: 99%

Origins of harvested American black ducks: stable isotopes support the flyover hypothesis

et al. 2022

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Waterfowl management is more effective when based on detailed information on population connectivity between breeding, wintering, and stopover sites. For the American black duck (Anas rubripes), a species of conservation concern, estimates for the fall age ratio at harvest differed depending on whether harvest data were derived from Canada or the United States, suggesting regional differences. Within Canada, hunters in Atlantic Canada were more likely to harvest black ducks from nearby breeding locations compared to hunters in southern Ontario and Quebec, Canada, who were more likely to harvest individuals from the Boreal Softwood and Taiga Shield of eastern Canada. Black ducks harvested in the United States are thought to originate predominantly from northern portions of the breeding range, leading to the flyover hypothesis, which postulates that black ducks produced in the Boreal Softwood and Taiga Shield region are less susceptible to harvest by hunters in Atlantic Canada and northeastern United States. To test the flyover hypothesis, we examined regional and temporal differences in the origins of harvested black ducks using feathers from wings (n = 664) submitted by hunters to the species composition and parts collection surveys across 3 hunting seasons (2017-2018, 2018-2019, 2019-2020). We used a likelihood-based assignment method that relied on feather stable-hydrogen isotopes (δ 2 H) and stable-carbon isotopes (δ 13 C) to determine the natal or molt origin of individuals harvested within eastern Canada and the United States. We also used a spatial clustering

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“…We aggregated route‐level count data into population indices within 2° latitude x 2° longitude grid cells (mean area 36,267 km 2 · cell −1 , range 29,192−43,596 km 2 ) with a Bayesian hierarchical model (heavy‐tailed GAMYE) (Edwards & Smith 2020). The model, which accounts for observer effects among other sources of bias, has the following structure:

\log false(λ_{s, j, t} false) = θ_{s} + ω_{j} + η I [j, t] + ε_{s, j, t} + {normalΔ}_{s} (t)

where (λ s,j,t ) is the mean count per grid cell ( s ), observer‐route combination ( j ), and year ( t ); θ s is a grid‐cell‐specific intercept; ω j is an observer‐route effect; ηI [ j,t ] is a first‐time observer effect; ε s,j,t is a random effect to account for overdispersion; and Δ s ( t ) is a generalized additive model based on year (for details see Smith & Edwards [2020]).…”

Section: Methodsmentioning

confidence: 99%

Mapping shifts in spatial synchrony in grassland birds to inform conservation planning

Allen

Lockwood

2021

Conservation Biology

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Spatial synchrony, defined as the correlated fluctuations in abundance of spatially separated populations, can be caused by regional fluctuations in natural and anthropogenic environmental population drivers. Investigations into the geography of synchrony can provide useful insight to inform conservation planning efforts by revealing regions of common population drivers and metapopulation extinction vulnerability. We examined the geography of spatial synchrony and decadal changes in these patterns for grassland birds in the United States and Canada, which are experiencing widespread and persistent population declines. We used Bayesian hierarchical models and over 50 years of abundance data from the North American Breeding Bird Survey to generate population indices within a 2°latitude by 2°longitude grid. We computed and mapped mean local spatial synchrony for each cell (mean detrended correlation of the index among neighboring cells), along with associated uncertainty, for 19 species in 2, 26-year periods, 1968-1993 and 1994-2019. Grassland birds were predicted to increase in spatial synchrony where agricultural intensification, climate change, or interactions between the 2 increased. We found no evidence of an overall increase in synchrony among grassland bird species. However, based on the geography of these changes, there was considerable spatial heterogeneity within species. Averaging across species, we identified clusters of increasing spatial synchrony in the Prairie Pothole and Shortgrass Prairie regions and a region of decreasing spatial synchrony in the eastern United States. Our approach has the potential to inform continental-scale conservation planning by adding an additional layer of relevant information to species status assessments and spatial prioritization of policy and management actions. Our work adds to a growing literature suggesting that global change may result in shifting patterns of spatial synchrony in population dynamics across taxa with broad implications for biodiversity conservation.

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bbsBayes: An R Package for Hierarchical Bayesian Analysis of North American Breeding Bird Survey Data

Cited by 6 publications

References 16 publications

Current contrasting population trends among North American hummingbirds

Current contrasting population trends among North American hummingbirds

Origins of harvested American black ducks: stable isotopes support the flyover hypothesis

Mapping shifts in spatial synchrony in grassland birds to inform conservation planning

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