DOI: 10.5061/dryad.v41ns1s9f
title: Data from: Apparent annual survival of adult <em>Vermivora chrysoptera</em> (Golden-winged Warbler) does not differ by sex or region

description: 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.
description: # Data from: Apparent annual survival of adult *Vermivora chrysoptera*
 (Golden-winged Warbler) does not differ by sex or region Dataset DOI:
 [10.5061/dryad.v41ns1s9f](https://doi.org/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
 1^st^ and 3^rd^ 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 1^st^ and
 3^rd^ 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 ###### ***Language and
 Environment*** R Environment for Statistical Computing ######
 ***Version*** R 4.1.0 ###### ***Dependencies*** * 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.