README: Observed declines in body size have differential effects on survival and recruitment, but no effect on population growth in tropical birds

https://doi.org/10.5061/dryad.nzs7h4508

Rebecca C. Wilcox, Thomas J. Benson, Jeffrey D. Brawn, Corey E. Tarwater

Summary: These are the data and code used in the manuscript, Observed declines in body size have differential effects on survival and recruitment, but no effect on population growth in tropical birds. This project includes the data and code used to produce the results and figures in the manuscript. Code was run in R version 4.3.3.

File name: Panama_BodySize_data.csv

Description: This dataset contains morphological measurements of (body size, wing length) of birds captured using mist-nets as part of a long-term demographic study. An in-depth description of the methods used for collecting the capture data can be found in Pollock et al. 2022 (PNAS; doi: 10.1073/pnas.2108731119). We use a subset of that dataset, from 1993-2020. Temperature and precipitation data come from Smithsonian Tropical Research Institute (STRI) Physical Monitoring Program’s Barro Colorado Island weather station (Paton 2020, STRI). Annual dry and wet season start and end dates were determined by the Panama Canal Authority (1954-2019, Meteorological and Hydrological Branch of the Panama Canal Authority).

Location: Parque Nacional Soberanía located in Central Panama (9°9'35"N, 79°44'36"W)

Number of variables: 18
Number of rows: 7755
Variable list:

• Scientific.name: species
• General.Diet: ecological foraging guild
• Family: family of the species
• birdID: unique identifier for specific individuals
• year: year in which the capture occurred
• week: week in which the capture occurred
• season: if the capture occurred in the wet or dry season.
• mass: mass of the bird at capture (g)
• s.mass: scaled mass of the bird at capture
• wing: wing length of bird at capture (mm)
• s.wing: scaled wing length of the bird at capture
• s.bodycondition: the residual body mass for the capture
• mean.temp: mean temperature from the preceding two season before capture (°C)
• dry.season.length: dry season length from the preceding dry season (days)
• dry.rain.precip: precipitation from the preceding dry season (mm)
• dry.rain.anomalies: precipitation anomalies from the preceding dry season (days)
• wet.rain.precip: precipitation from the preceding wet season (mm)
• wet.rain.anomalies: precipitation anomalies from the preceding wet season (days)

File name: SpThroughTime_randomEffects.csv

Description: List of species and appropriate random effects used in the analyses to assess species level changes in body size metrics through time (Step 1_Species through time analysis.R), the same as Table S4 in the manuscript supplemental material.

Number of variables: 4
Number of rows: 51
Variable list:

• Scientific.name: species name
• Wing.RE: notes which random effects were included in the model assessing the change in wing length through time
• resid.RE.scaled: notes which random effects were included in the model assessing the change in body condition through time
• mass.RE: notes which random effects were included in the model assessing the change in body mass through time
• Abbreviations used:
• Both: indicates both individual ID (birdID) and year were included as random effects
• Year: just year was included as a random effect
• Bird: only individual ID was included as a random effect

File name: Demgraphy_betaEstimates.csv

Description: Results from the MARK analysis used to assess the impact of body size on demographic parameters: population growth rate, apparent annual survival, and per capita recruitment. The table includes parameter beta estimates for each of the body size metrics (body condition, wing length, and body mass).

Number of variables: 10
Number of rows: 270
Variable list:

• bodySizeMetric: the body size metric, resid mass (body condition), wing (length), and mass.
• dem.var: the demographic variable, population growth rate (lam:cov), apparent annual survival (phi:cov), and per capita recruitment (f:cov)
• fam.tax: family of the species
• General.Diet: ecological foraging guild
• Scientific.name: species
• Estimate: parameter’s beta estimate
• SE: standard error associated with the estimate
• LCI: lower 95% confidence interval
• UCL: upper 95% confidence interval
• wng.len: mean wing length for the species (mm)

Code

Step 1_Species through time analysis.R: Species level analysis to determine if body condition and wing length are changing across the study period. Includes code to create Figures 1e and 1f.

Step 2_Guild temporal variation: Guild level analysis to assess if body condition and wing length change though time, if changes are nonlinear, and if guilds are changing differently. Includes code to create Figures 1g-n.

Step 3_Guild weather metrics analysis.R: Guild level analysis assessing the effect of weather metrics on changes in body condition and wing length. Includes code to create Figure 2.

Step 4_Demography MCMCglmm analysis.R: Analysis assessing if guilds differ in how body size metrics influence demographic parameters. Includes code to create Figure 3.