Data from: Apparent annual survival of adult Vermivora chrysoptera (Golden-winged Warbler) does not differ by sex or region
Data files
Nov 10, 2025 version files 322.11 KB
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All_App_v2.csv
48.90 KB
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All_GL_v4.csv
64.36 KB
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App_Simulation_Model.R
18.23 KB
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Figure3_Site_Estimates.R
11.26 KB
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Figure4_Sex_Estimates.R
2.78 KB
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Figure5_Simulations.R
43.43 KB
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FigureA1_Temporal_GreatLakes.R
21.63 KB
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FigureA2_Temporal_Appalachians.R
18.26 KB
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FigureA3_Recap_Probability.R
7.01 KB
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FigureA4_Sex_Effect.R
13.04 KB
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FigureA5_App_Simulation.R
7.93 KB
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GWWA_Appalachian_Annual_Survival.R
23.35 KB
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GWWA_GreatLakes_Annual_Survival.R
27.80 KB
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README.md
14.11 KB
Abstract
Understanding range-wide demographic, spatial, and temporal variation in annual survival is essential for managing species of conservation concern. Multi-population models are useful tools for integrating diverse datasets, reducing biases, and deriving survival estimates across differing spatial scales. We conducted a range-wide, multi-population apparent annual survival analysis for a declining songbird, Vermivora chrysoptera (Golden-winged Warbler), using data from 18 sites across its breeding and nonbreeding grounds. This Nearctic-Neotropical migrant breeds in 2 disjunct regional populations, the Great Lakes and Appalachian Mountains, which are experiencing different rates of decline. We aimed to quantify regional-, site-, and sex-specific apparent annual survival estimates to identify geographic patterns or demographic factors influencing population declines. We used simulations to assess the precision of our estimates. Our models did not reveal a substantial difference in apparent annual survival between the Great Lakes (0.41, 95% credible interval (CrI):0.31–0.50) and the Appalachian regions (0.49, 95% CrI: 0.36–0.60), as CrIs overlapped. Site-specific estimates also showed no clear differences in apparent annual survival among sites representing both regional populations. Male apparent annual survival tended to be greater than female apparent annual survival in both regions, though CrI’s overlapped. Our study suggests demographic factors other than adult annual survival likely play a larger role in recent regional and range-wide population declines, such as productivity, juvenile/immature survival, or recruitment. Simulations indicate that improving recapture probability and study duration of datasets could lead to more precise apparent annual survival estimates. However, our model produced CrI ranges comparable to the most ideal data collection scenario, suggesting the lack of trends we found was not due to variability in our estimates. We stress the importance of addressing inherent biases in survival datasets and the need for standardized collaborative efforts to inform species conservation on a range-wide scale.
Dataset DOI: 10.5061/dryad.v41ns1s9f
Description of the data and file structure
Script used to run a range-wide, multi-population, apparent annual survival analysis (CJS) for Golden-winged Warbler, a declining songbird. Data was sourced from 18 sites across their range (8 sites represent the Appalachian population and 10 sites represent the Great Lakes population). Capture-mark-recapture data were collected by collaborators during field seasons ranging from 2000-2022. Data was used if capture histories could be generated for unique individuals with at least three years of presence/absence information. The purpose of these models is to provide informed regional-, site-, and sex-specific apparent annual survival estimates to identify particular spatial or demographic populations that might be driving species decline.
Description of the data and file structure
Files and variables
File: All_App_v2.csv
Description: Cumulative presence/absence dataset for the Appalachian population.
Variables
- 2000 - 2021: Years where presence/absence was recorded. 1 indicates presence, 0 indicates absence. Blank cells represent data not collected during that year for respective sites.
- Site: Unique sites corresponding to specific monitoring locations where individuals were captured and resighted.
- Sex.Letter: Coded letter representing the sex of each individual (M = male, F = female).
- Sex: Numeric label for the individual’s sex (Male = 1, Female = 0).
- Age: Age class of the individual at the time of initial capture (AHY = after hatch year, ASY = after second year, SY = second year, U = unknown).
File: All_GL_v4.csv
Description: Cumulative presence/absence dataset for the Great Lakes population.
Variables
- 2001 - 2022: Years where presence/absence was recorded. 1 indicates presence, 0 indicates absence. Blank cells represent data not collected during that year for respective sites.
- Site: Unique sites corresponding to specific monitoring locations where individuals were captured and resighted.
- Sex.Letter: Coded letter representing the sex of each individual (M = male, F = female).
- Sex: Numeric label for the individual’s sex (Male = 1, Female = 0).
- Age: Age class of the individual at the time of initial capture (AHY = after hatch year, ASY = after second year, SY = second year, U = unknown).
Model Code
File: GWWA_GreatLakes_Annual_Survival.R
Description: Script to run a hierarchical multi-population apparent annual survival CJS model for the Great Lakes population of Golden-winged Warbler. Ten CMR historical datasets ranging from 2001-2022 were collected and compiled. We selected vague prior distributions for all parameters to reflect a lack of prior knowledge on range-wide annual survival for this declining species. Year is treated as a random effect to account for unknown and variable search effort throughout individual study periods. This model aims to produce informed regional-, site-, and sex-specific apparent annual survival estimates to identify particular spatial or demographic populations that might be driving declines of these populations. Sex effect was only assessed for sites that had at least 1% female representation in the dataset.
File: GWWA_Appalachian_Annual_Survival.R
Description: Script to run a hierarchical multi-population apparent annual survival CJS model for the Appalachian Mountain population of Golden-winged Warbler. Eight CMR historical datasets ranging from 2001-2021 were collected and compiled. We selected vague prior distributions for all parameters to reflect a lack of prior knowledge on range-wide annual survival for this declining species. Year is treated as a random effect to account for unknown and variable search effort throughout individual study periods. This model aims to produce informed regional-, site-, and sex-specific apparent annual survival estimates to identify particular spatial or demographic populations that might be driving declines of these populations. Sex effect was only assessed for sites that had at least 1% female representation in the dataset.
File: App_Simulation_Model.R
Description: R code to run a series of simulations to see under which scenarios we could expect to increase precision in our parameters. Different scenarios included running survival models that involved different occasion lengths (3, 6, and 9 years), different levels of female representation in the datasets (30% and 50%), different sample sizes of initial capture at each occasion (10, 30, and 50), and different recapture probabilities (30%, 60%, and 90%).
Figures Code
File: Figure3_Site_Estimates.R
Description: R code to create figure for site-specific apparent annual survival estimates for both populations of V. chrysoptera. The horizontal red dashed line separates sites representing the Great Lakes population (above) and the Appalachian population (below). Gray numerical values on the right denote the sample size used for each respective site analysis. Vertical dashed blue lines represent the regional mean respective to each regional population for reference. Points represent the posterior means, and lines represent 95% CrIs.
File: Figure4_Sex_Estimates.R
Description: R code to create figure for sex-specific apparent annual survival estimates for the Great Lakes and Appalachian populations. Boxes represent the interquartile range (IQR) between 1st and 3rd quantiles. Horizontal lines inside boxes indicate respective medians. Whiskers represent 1.5 times the respective IQR. Dots beyond whiskers indicate outliers.
File: Figure5_Simulations.R
Description: R code to create figure for sex-specific apparent annual survival and 95% quantile estimates for the Appalachian population taken from mean posterior estimates of 30 simulations for 3 selected scenarios. Each plotted scenario represents a particular number of occasions (o), female sex representation (sr), number of new individuals banded per year (n), and recapture probability (p). Male estimates are depicted in gray, and female estimates are depicted in black.
File: FigureA1_Temporal_GreatLakes.R
Description: R code to create figure for temporal site-specific Great Lakes apparent annual survival estimates. Boxes represent interquartile range (IQR) between 1st and 3rd quantiles. Horizontal lines inside boxes indicate respective medians. Whiskers represent 1.5 times respective IQR. Dots beyond whiskers indicate outliers.
File: FigureA2_Temporal_Appalachians.R
Description: R code to create figure for temporal site-specific Appalachians apparent annual survival estimates. Boxes represent interquartile range (IQR) between 1st and 3rd quantiles. Horizontal lines inside boxes indicate respective medians. Whiskers represent 1.5 times respective IQR. Dots beyond whiskers indicate outliers.
File: FigureA3_Recap_Probability.R
Description: R code to create figure for site-specific recapture probability estimates for both sexes of Golden-winged Warblers. The horizontal red dashed line separates sites representing the Great Lakes population (above) and Appalachian population (below). Vertical dashed blue line represents the regional mean respective to each regional population for reference. Gray numbers indicate percentage of female representation for each site. Points represent the posterior means and lines represent 95% CrI’s.
File: FigureA4_Sex_Effect.R
Description: R code to create figure for delta estimates comparing male and female apparent annual survival at each respective site. Males are depicted as a reference point, with positive estimates indicating higher male survival and negative estimates indicating higher female survival. Delta estimates further from zero (both positive and negative) indicate a larger difference in male and female survival. Points represent posterior delta estimates and lines represent 95% CrI’s. Sites with CrI’s not overlapping zero signify a statistical difference between male and female survival. Gray values to the right depict female representation for each respective site.
File: FigureA5_App_Simulation.R
Description: R code to create figure for mean overall apparent survival and 95% quantile estimates for the Appalachian region taken from mean posterior estimates of 30 simulations for each respective scenario (n=56). Numbers on the left signify CrI range. Numbers on the right signify each scenario, with various number of occasions (o), female sex representations (sr), number of new individuals banded per year (n), and recapture probabilities (p).
Code/software
R Environment for Statistical Computing
R 4.1.0
- cowplot
- dplyr
- ggplot2
- ggpubr
- IPMbook
- jagsUI
- lme4
- MCMCvis
- performance
- reshape2
- scales
- sjPlot
- stringr
- tidyr
- tidyverse
- truncnorm
Access information
Datasets were associated with the following publications, if applicable. Additional datasets were unpublished data.
Aldinger, K. R., and P. B. Wood. 2014. Reproductive success and habitat characteristics of Golden-winged Warblers in high-elevation pasturelands. The Wilson Journal of Ornithology 126:279–287.
Aldinger, K. R., T. M. Terhune, P. B. Wood, D. A. Buehler, M. H. Bakermans, J. L. Confer, D. J. Flaspohler, J. L. Larkin, J. P. Loegering, K. L. Percy, A. M. Roth, and C. G. Smalling. 2015. Variables associated with nest survival of Golden-winged Warblers (Vermivora chrysoptera) among vegetation communities commonly used for nesting. Avian Conservation Ecology 10:6.
Aldinger, K. R. 2018. Ecology and management of Golden-winged Warblers (Vermivora chrysoptera) and associated avian species in the Allegheny mountains of West Virginia. Ph.D. dissertation, West Virginia University, Morgantown, WV, USA.
Buckardt Thomas, A. 2019. Improving conservation of declining young forest birds through adaptive management. M.S. thesis, University of Maine, Orono, ME, USA.
Bulluck, L. P., D. Buehler, R. Vallender, and R. J. Robertson. 2013. Demographic comparison of Golden-winged Warbler (Vermivora chrysoptera) populations in northern and southern extremes of their breeding range. The Wilson Journal of Ornithology 125:479–490.
Chandler, R. B., and D. I. King. 2011. Habitat quality and habitat selection of Golden‐winged Warblers in Costa Rica: An application of hierarchical models for open populations. Journal of Applied Ecology 48:1038–1047.
Confer, J. L., K. W. Barnes, and E. C. Alvey. 2010. Golden- and Blue-winged Warblers: Distribution, nesting success, and genetic differences in two habitats. The Wilson Journal of Ornithology 122:273–278.
Fiss, C. J., D. J. McNeil, A. D. Rodewald, D. Heggenstaller, and J. L. Larkin. 2021. Cross-scale habitat selection reveals within-stand structural requirements for fledgling Golden-winged Warblers. Avian Conservation Ecology 16:16.
Frantz, M. W., K. R. Aldinger, P. B. Wood, J. Duchamp, T. Nuttle, A. Vitz, and J. L. Larkin. 2016. Space and habitat use of breeding Golden-winged Warblers in the central Appalachian Mountains. In Golden-winged Warbler Ecology, Conservation, and Habitat Management (H. M. Streby, D. A. Buehler, and D. E. Andersen, Editors). Studies in Avian Biology 49:81–94.
Jones, J. A., A. C. Tisdale, J. L. Tucker, M. H. Bakermans, J. L. Larkin, C. G. Smalling, and L. Siefferman. 2016. A case of mistaken identity: Understanding the stimulus of agonism between two wood warblers. Animal Behaviour 114:81–91.
Kramer, G. R., H. M. Streby, S. M. Peterson, J. A. Lehman, D. A. Buehler, P. B. Wood, D. J. McNeil, J. L. Larkin, and D. E. Andersen. 2017. Nonbreeding isolation and population-specific migration patterns among three populations of Golden-winged Warblers. The Condor: Ornithological Applications 119:108–121.
Larkin, J. L., D. Raybuck, A. Roth, L. Chavarría‐Duriaux, G. Duriaux, M. Siles, and C. Smalling. 2017. Geolocators reveal migratory connectivity between wintering and breeding areas of Golden‐winged Warblers. Journal of Field Ornithology 88:288–298.
McNeil, D. J., K. R. Aldinger, M. H. Bakermans, J. A. Lehman, A. C. Tisdale, J. A. Jones, P. B. Wood, D. A. Buehler, C. G. Smalling, L. Siefferman, and J. L. Larkin. 2017. An evaluation and comparison of conservation guidelines for an at-risk migratory songbird. Global Ecology and Conservation 9:90–103.
Moulton, L. L., R. Vallender, C. Artuso, and N. Koper. 2017. The final frontier: Early-stage genetic introgression and hybrid habitat use in the northwestern extent of the Golden-winged Warbler breeding range. Conservation Genetics 18:1481–1487.
Percy, K. L. 2012. Effects of prescribed fire and habitat on Golden-winged Warbler (Vermivora chrysoptera) abundance and nest survival in the Cumberland Mountains of Tennessee. M.S. thesis, University of Tennessee, Knoxville, TN, USA.
Ritterson, J. D., D. I. King, and R. B. Chandler. 2021. Habitat‐specific survival of Golden‐winged Warblers (Vermivora chrysoptera) during the non‐breeding season in an agricultural landscape. Journal of Avian Biology 52:e02442.
Roth, A. M., D. J. Flaspohler, and C. R. Webster. 2014. Legacy tree retention in young aspen forest improves nesting habitat quality for Golden-winged Warbler (Vermivora chrysoptera). Forest Ecology and Management 321:61–70.
Vallender, R., V. L. Friesen, and R. J. Robertson. 2007. Paternity and performance of Golden-winged Warblers (Vermivora chrysoptera) and Golden-winged × Blue-winged Warbler (V. pinus) hybrids at the leading edge of a hybrid zone. Behavioral Ecology and Sociobiology 61:1797–1807.