Vocal development and patterns of vocal variation inform conservation of a critically endangered macaw
Data files
Apr 23, 2026 version files 497.76 MB
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2024_GGM_adult_recording_analysis_final_revised.R
17.04 KB
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3-4_weeks_binary_matrix_groups.xlsx
19.19 KB
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5-6_weeks_binary_matrix_groups.xlsx
11.64 KB
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Adult_binary_matrix_groups.xlsx
10.90 KB
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Age_binary_matrix_groups.xlsx
26.91 KB
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All_adult_GGM_selections.zip
27.69 KB
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All_nestling_GGM_selections.zip
208.20 KB
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ext_st_adults.RDS
19.77 MB
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ext_st_combined_nestlings_1.4kHz_highpass.RDS
172.37 MB
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ext_st_combined_nestlings_200Hz_highpass.RDS
172.38 MB
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GGM_chick_development_analysis_final_revised.R
35.64 KB
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GGM_chick_development_analysis_with_200_Hz_bandpass.R
31.36 KB
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Less_than_or_equal_to_2_weeks_binary_matrix_groups.xlsx
38.43 KB
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mds_data_final_200Hz_highpass.xlsx
175.23 KB
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mds_data_final_adults.xlsx
24.78 KB
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mds_data_final_nestlings_1.4kHz_highpass.xlsx
174.09 KB
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pca_data_final_200Hz_highpass.xlsx
186.15 KB
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pca_data_final_adults.xlsx
27.47 KB
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pca_data_final_nestlings_1.4kHz_highpass.xlsx
185.41 KB
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README.md
17.19 KB
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SPCC_output_adults.RDS
603.17 KB
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SPCC_output_nestlings_1.4kHz_highpass.RDS
65.29 MB
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SPCC_output_nestlings_200Hz_highpass.RDS
65.32 MB
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spectro_analysis_output_adults.RDS
48.07 KB
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spectro_analysis_output_nestlings_1.4kHz_highpass.RDS
381.01 KB
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spectro_analysis_output_nestlings_200Hz_highpass.RDS
383.24 KB
Abstract
Reintroductions are increasingly used as a tool to bolster declining populations of birds, but the potential for communication barriers arising from learned vocal variation between introduced and wild populations has rarely been considered. The critically endangered great green macaw, Ara ambiguus, is one such declining species, but it is currently unknown whether there is vocal variation in adult contact calls among geographically isolated populations. Furthermore, variation in nestling calls among populations has never been investigated and could offer insight into how the nestling social environment shapes the formation of dialects. We investigated whether adult and nestling great green macaws show among-population variation in the acoustic structure of their calls by recording vocalizations in one wild, one captive, and one reintroduced population in Costa Rica. We assessed acoustic similarity among the three populations by measuring 26 parameters from the spectrogram of each call and performing spectrographic cross-correlation. We tested for population differences in the acoustic structure of adult and nestling calls using linear mixed models and Mantel tests. Only minimal variation was detected among adult contact calls from the three populations. During mid-development, nestling calls showed variation among populations that may be explained by individual morphological differences and overproduction of call types. Minimal variation later in development may be explained by selective attrition of the vocal repertoire as well as vocal convergence driven by the pressure to form and maintain flocks during adulthood. Investigating adult and nestling calls across isolated populations of threatened parrot species can give insight into how vocal variation develops among populations and when conservation managers should consider vocal differences between released and wild birds during the reintroduction process.
Dataset DOI: 10.5061/dryad.z8w9ghxrb
Description of the data and file structure
We made audio recordings of adult and nestling Great Green Macaws in Costa Rica, in 2023 and 2024. We recorded adults using a handheld recording rig and we recorded nestlings using autonomous recording units (ARUs). Audio data (adult and nestling calls) were used to test for vocal variation among three geographically isolated populations in Costa Rica. We also characterized vocal development for nestlings.
Files and variables
File: All_adult_GGM_selections.zip
Description: This zip folder contains text files for all the adult calls selected in RavenPro software. Each text file is a different track and includes the exact selection time and frequency dimensions. Text files are inputs for the "2024_GGM_adult_recording_analysis_final_revised" R script.
File: All_nestling_GGM_selections.zip
Description: This zip folder contains text files for all the nestling calls selected in RavenPro software. Each text file is a different track and includes the exact selection time and frequency dimensions. Text files are inputs for the "GGM_chick_development_analysis_with_200_Hz_bandpass" and "GGM_chick_development_analysis_final_revised" R scripts.
File: ext_st_adults.RDS
Description: An R object that combines all adult call selections with the corresponding sound files via a function in the warbleR package. This is an output from the "2024_GGM_adult_recording_analysis_final_revised" R script.
Variables
- selec: a byproduct of creating selection tables, not important for interpretation of this file
- Channel: a byproduct of creating selection tables, not important for interpretation of this file
- start: the beginning of a selection, in seconds, standardized to 0.1 s
- end: the end of a selection, in seconds, from the standardized start of 0.1 s
- bottom.freq: the lowest frequency that appears in a selection, in kHz
- top.freq: the highest frequency that appears in a selection, in kHz
- sound.files: the name of each track and selection
- tailored: denotes whether a selection's time and frequency bounds have been tailored using the warbleR package ("y" for yes and "n" for no)
File: ext_st_combined_nestlings_1.4kHz_highpass.RDS
Description: An R object that combines all nestling call selections with the corresponding sound files via a function in the warbleR package. A 1.4 kHz highpass filter is used in this file. This is an output from the "GGM_chick_development_analysis_final_revised" R script.
Variables
- selec: a byproduct of creating selection tables, not important for interpretation of this file
- Channel: a byproduct of creating selection tables, not important for interpretation of this file
- start: the beginning of a selection, in seconds, standardized to 0.1 s
- end: the end of a selection, in seconds, from the standardized start of 0.1 s
- bottom.freq: the lowest frequency that appears in a selection, in kHz
- top.freq: the highest frequency that appears in a selection, in kHz
- sound.files: the name of each track and selection
- tailored: denotes whether a selection's time and frequency bounds have been tailored using the warbleR package ("y" for yes and "n" for no)
File: spectro_analysis_output_adults.RDS
Description: An R object that is the result of measuring 26 acoustic parameters from each selected adult call included in the extended selection table. This is an output from the "2024_GGM_adult_recording_analysis_final_revised" R script. For variable definitions, please see the warbleR package manual at: https://cran.r-project.org/web/packages/warbleR/warbleR.pdf.
File: SPCC_output_adults.RDS
Description: An R object that is the result of running spectrographic cross-correlation (SPCC) on all adult calls in the extended selection table, generating a square pairwise similarity matrix. Each row and column is a selected vocalization, with similarity of each pair of selections given on a scale from 0 (completely dissimilar) to 1 (completely similar). This is an output from the "2024_GGM_adult_recording_analysis_final_revised" R script.
File: spectro_analysis_output_nestlings_1.4kHz_highpass.RDS
Description: An R object that is the result of measuring 26 acoustic parameters from each selected nestling call included in the extended selection table. A 1.4 kHz highpass filter is used in this file. For variable definitions, please see the warbleR package manual at: https://cran.r-project.org/web/packages/warbleR/warbleR.pdf. This is an output from the "GGM_chick_development_analysis_final_revised" R script.
File: SPCC_output_nestlings_1.4kHz_highpass.RDS
Description: An R object that is the result of running spectrographic cross-correlation (SPCC) on all nestling calls in the extended selection table, generating a square pairwise similarity matrix. Each row and column is a selected vocalization, with similarity of each pair of selections given on a scale from 0 (completely dissimilar) to 1 (completely similar). A 1.4 kHz highpass filter is used in this file. This is an output from the "GGM_chick_development_analysis_final_revised" R script.
File: mds_data_final_adults.xlsx
Description: A spreadsheet that includes data from a multi-dimensional scaling (MDS) analysis on SPCC results from adult calls. This is an output from the "2024_GGM_adult_recording_analysis_final_revised" R script.
Variables
- sound.files: the name of each track and selection
- x: the x-coordinate of the MDS analysis
- y: the y-coordinate of the MDS analysis
- Population: denotes which population each track/selection comes from
- Group: denotes which nest, aviary, or random location within each population each track/selection comes from
File: pca_data_final_adults.xlsx
Description: A spreadsheet that includes data from a principal components analysis (PCA) on all parameter measurements from adult calls. This is an output from the "2024_GGM_adult_recording_analysis_final_revised" R script.
Variables
- sound.files: the name of each track and selection
- selec: a byproduct of creating selection tables, not important for interpretation of this file
- PC1: the first principal component for each track/selection
- PC2: the second principal component for each track/selection
- Population: denotes which population each track/selection comes from
- Group: denotes which nest, aviary, or random location within each population each track/selection comes from
- Group_code: a code for each group
File: mds_data_final_nestlings_1.4kHz_highpass.xlsx
Description: A spreadsheet that includes data from a multi-dimensional scaling (MDS) analysis on SPCC results from nestling calls. A 1.4 kHz highpass filter is used in this file. This is an output from the "GGM_chick_development_analysis_final_revised" R script.
Variables
- sound.files: the name of each track and selection
- x: the x-coordinate of the MDS analysis
- y: the y-coordinate of the MDS analysis
- Population: denotes which population each track/selection comes from
- Nest: denotes which nest each track/selection comes from
- Age_estimate_R: denotes which age group each track/selection falls into
File: pca_data_final_nestlings_1.4kHz_highpass.xlsx
Description: A spreadsheet that includes data from a principal components analysis (PCA) on all parameter measurements from nestling calls. A 1.4 kHz highpass filter is used in this file. This is an output from the "GGM_chick_development_analysis_final_revised" R script.
Variables
- sound.files: the name of each track and selection
- selec: a byproduct of creating selection tables, not important for interpretation of this file
- PC1: the first principal component for each track/selection
- PC2: the second principal component for each track/selection
- Population: denotes which population each track/selection comes from
- Nest: denotes which nest each track/selection comes from
- Age_estimate_R: denotes which age group each track/selection falls into
File: GGM_chick_development_analysis_final_revised.R
Description: An R script file that contains all code used for analysis of nestling calls. A 1.4 kHz highpass filter is used in this script.
File: 2024_GGM_adult_recording_analysis_final_revised.R
Description: An R script file that contains all code used for analysis of adult calls.
File: Adult_binary_matrix_groups.xlsx
Description: A spreadsheet containing a column of population designators that matches the order in which tracks/selections are presented in the SPCC results for adult calls. This column is used in the creation of a binary matrix of population identity for later use in a Mantel test. This is an input for the "2024_GGM_adult_recording_analysis_final_revised" R script.
Variables
- Population: denotes which population should be included in each row and column of the binary matrix
File: 3-4_weeks_binary_matrix_groups.xlsx
Description: A spreadsheet containing a column of population designators that matches the order in which tracks/selections are presented in the SPCC results for nestling calls from the 3-4 weeks age group. This column is used in the creation of a binary matrix of population identity for later use in a Mantel test. This is an input for the "GGM_chick_development_analysis_final_revised" and "GGM_chick_development_analysis_with_200_Hz_bandpass" R scripts.
Variables
- sound.files: the name of each track and selection
- Population: denotes which population should be included in each row and column of the binary matrix
- Age_estimate_R: denotes which age group each track/selection falls into
File: 5-6_weeks_binary_matrix_groups.xlsx
Description: A spreadsheet containing a column of population designators that matches the order in which tracks/selections are presented in the SPCC results for nestling calls from the 5-6 weeks age group. This column is used in the creation of a binary matrix of population identity for later use in a Mantel test. This is an input for the "GGM_chick_development_analysis_final_revised" and "GGM_chick_development_analysis_with_200_Hz_bandpass" R scripts.
Variables
- sound.files: the name of each track and selection
- Population: denotes which population should be included in each row and column of the binary matrix
- Age_estimate_R: denotes which age group each track/selection falls into
File: Age_binary_matrix_groups.xlsx
Description: A spreadsheet containing a column of age group designators that matches the order in which tracks/selections are presented in the SPCC results for nestling calls. This column is used in the creation of a binary matrix of age group identity for later use in a Mantel test. This is an input for the "GGM_chick_development_analysis_final_revised" and "GGM_chick_development_analysis_with_200_Hz_bandpass" R scripts.
Variables
- Age_estimate_R: denotes which age group should be included in each row and column of the binary matrix
File: Less_than_or_equal_to_2_weeks_binary_matrix_groups.xlsx
Description: A spreadsheet containing a column of population designators that matches the order in which tracks/selections are presented in the SPCC results for nestling calls from the less than or equal to 2 weeks age group. This column is used in the creation of a binary matrix of population identity for later use in a Mantel test. This is an input for the "GGM_chick_development_analysis_final_revised" and "GGM_chick_development_analysis_with_200_Hz_bandpass" R scripts.
Variables
- sound.files: the name of each track and selection
- Population: denotes which population should be included in each row and column of the binary matrix
- Age_estimate_R: denotes which age group each track/selection falls into
File: GGM_chick_development_analysis_with_200_Hz_bandpass.R
Description: An R script file that contains all code used for analysis of nestling calls. A 200 Hz highpass filter is used in this script.
File: mds_data_final_200Hz_highpass.xlsx
Description: A spreadsheet that includes data from a multi-dimensional scaling (MDS) analysis on SPCC results from nestling calls. A 200 Hz highpass filter is used in this file. This is an output from the "GGM_chick_development_analysis_with_200_Hz_bandpass" R script.
Variables
- sound.files: the name of each track and selection
- x: the x-coordinate of the MDS analysis
- y: the y-coordinate of the MDS analysis
- Population: denotes which population each track/selection comes from
- Nest: denotes which nest each track/selection comes from
- Age_estimate_R: denotes which age group each track/selection falls into
File: pca_data_final_200Hz_highpass.xlsx
Description: A spreadsheet that includes data from a principal components analysis (PCA) on all parameter measurements from nestling calls. A 200 Hz highpass filter is used in this file. This is an output from the "GGM_chick_development_analysis_with_200_Hz_bandpass" R script.
Variables
- sound.files: the name of each track and selection
- selec: a byproduct of creating selection tables, not important for interpretation of this file
- PC1: the first principal component for each track/selection
- PC2: the second principal component for each track/selection
- Population: denotes which population each track/selection comes from
- Nest: denotes which nest each track/selection comes from
- Age_estimate_R: denotes which age group each track/selection falls into
File: ext_st_combined_nestlings_200Hz_highpass.RDS
Description: An R object that combines all nestling call selections with the corresponding sound files via a function in the warbleR package. A 200 Hz highpass filter is used in this file. This is an output from the "GGM_chick_development_analysis_with_200_Hz_bandpass" R script.
Variables
- selec: a byproduct of creating selection tables, not important for interpretation of this file
- Channel: a byproduct of creating selection tables, not important for interpretation of this file
- start: the beginning of a selection, in seconds, standardized to 0.1 s
- end: the end of a selection, in seconds, from the standardized start of 0.1 s
- bottom.freq: the lowest frequency that appears in a selection, in kHz
- top.freq: the highest frequency that appears in a selection, in kHz
- sound.files: the name of each track and selection
- tailored: denotes whether a selection's time and frequency bounds have been tailored using the warbleR package ("y" for yes and "n" for no)
File: spectro_analysis_output_nestlings_200Hz_highpass.RDS
Description: An R object that is the result of measuring 26 acoustic parameters from each selected nestling call included in the extended selection table. A 200 Hz highpass filter is used in this file. For variable definitions, please see the warbleR package manual at: https://cran.r-project.org/web/packages/warbleR/warbleR.pdf. This is an output from the "GGM_chick_development_analysis_with_200_Hz_bandpass" R script.
File: SPCC_output_nestlings_200Hz_highpass.RDS
Description: An R object that is the result of running spectrographic cross-correlation (SPCC) on all nestling calls in the extended selection table, generating a square pairwise similarity matrix. Each row and column is a selected vocalization, with similarity of each pair of selections given on a scale from 0 (completely dissimilar) to 1 (completely similar). A 200 Hz highpass filter is used in this file. This is an output from the "GGM_chick_development_analysis_with_200_Hz_bandpass" R script.
Code/software
R software is needed to view data and run analyses. R is a free software that can be downloaded on the Internet and run on most computers. R Studio, the graphical user interface, was used for all analyses and is recommended for viewing data. R version 4.4.2 was used for analysis. R packages used include:
remotes
warbleR
Rraven
Sim.DiffProc
phonTools
ggplot2
vegan
stats
readxl
writexl
dplyr
rstatix
MASS
car
EnvStats
extrafont
PhenotypeSpace
tuneR
emmeans
lmerTest
Three R scripts are included for this project, one for analysis of adult calls, and two for analyses of nestling calls with different bandpass filters. Code is annotated and the workflow is described within each script. To run code that relies on sound files, please contact the corresponding author of the associated article to receive the sound files.
Access information
Other publicly accessible locations of the data:
- Data are not available in another publicly accessible location.
Data was derived from the following sources:
- Data were not derived from any other source.
