DOI: 10.5061/dryad.fttdz08xr
title: Evidence for maintenance of key components of vocal learning in aging budgerigars despite diminished affiliative social interaction

description: In some species, the ability to acquire new vocalizations persists into
 adulthood and may be an important mediator of social interactions. While
 it is generally assumed that vocal learning persists undiminished
 throughout the lifespan of these open-ended learners, the stability of
 this trait remains largely unexplored. We hypothesize that vocal learning
 exhibits senescence, as is typical of complex cognitive traits, and that
 this decline may relate to age-dependent changes in sociality. The
 budgerigar (Melopsittacus undulatus), an open-ended learner which develops
 new contact call types that are shared with social associates upon joining
 new flocks, provides a robust assay for measuring the effects of aging on
 vocal learning ability. We formed captive flocks of 4 previously
 unfamiliar adult males of the same age class, either “young adults” (6
 mo.-1 yr.) or “older adults” (≥ 3 yr.), and concurrently tracked changes
 in contact call structure and social interactions over time. Older adults
 exhibited decreased vocal diversity, which may be related to the sparser
 and weaker affiliative bonds observed in older adults. Older adults,
 however, displayed equivalent levels of vocal plasticity and vocal
 convergence compared to young adults, suggesting vocal learning ability is
 largely maintained into later adulthood in an open-ended learner.
description: This dataset contains dataframes (.csv & .xlsx) of both
 vocal and social raw data and the corresponding code used in analyzing
 this data in the form of R scripts (.R & .Rmd). A description of
 the contents of each data or script file can be found in the README file
 provided. The dataset also contains example video recordings of the types
 of budgerigar affiliative and agonistic social interactions measured in
 the study.
description: # Title of Dataset: Evidence for persistent vocal learning in aging
 budgerigars (Melopsittacus undulatus) despite diminished social
 connectedness --- This dataset contains vocal and social data from an
 experiment investigating the effect of aging on vocal production learning
 and social integration in flocks of male budgerigars (Melopsittacus
 undulatus). This open-ended learner develops new contact call types that
 are shared with social associates upon joining new social groups. We
 formed captive flocks of 4 previously unfamiliar adult male birds
 belonging to the same age class, either “young adults” (6 mo-1 yr) or
 “older adults” (≥ 3 yr), and concurrently tracked changes in contact call
 structure and affiliative, agonistic, and proximity-based social
 interactions over time. Contact calls were isolated from audio recordings
 using an automated selection procedure and they were characterized in
 two-dimensional 'acoustic space' based on various extracted
 spectrographic features to measure vocal output, change in vocal
 diversity, vocal plasticity, and vocal convergence. Video recordings of
 flock social behavior were coded for inter-individual proximity, and
 dyadic affiliative & agonistic interactions to build social networks
 and measure flock connectedness and strength of social ties.This dataset
 contains dataframes (.csv & .xlsx) of both vocal and social raw data
 and the corresponding code used to analyze this data in the form of R
 scripts(.R & .Rmd). A description of each individual file can be found
 below. ## Description of the Data and file structure # Vocal Analysis
 Files: ``` Raw Data: - sp_selections_analysis.csv: Contact call selection
 tables including spectrographic measurements. - selec: number of the sound
 selection in the sequence of automatically detected sounds from each audio
 filemthat was visual confirmed to be a budgerigar contact call. -
 duration: length of call in seconds. - meanfreq: mean of frequency
 spectrum in kHz. - sd: standard deviation of frequency in kHz. -
 freq.median: median frequency in kHz. - freq.IQR: interquartile frequency
 range in kHz. - time.IQR: interquartile time range in seconds. - skew:
 skewness. - kurt: kurtosis. - sp.ent: spectral entropy (Pure tone is ~ 0;
 noisy is ~ 1). - time.ent: time entropy (Pure tone is ~ 0; noisy is ~ 1).
 - entropy: spectrographic entropy (product of time and spectral entropy).
 - meandom: average of dominant frequency in kHz. - mindom: minimum of
 dominant frequency in kHz. - maxdom: maximum of dominant frequency in kHz.
 - dfrange: range of dominant frequency in kHz. - modindx: modulation
 index, computed as the cumulative absolute difference between adjacent
 measurements of dominant frequencies divided by dominant frequency range
 where a value of 1 indicates no modulation. - meanpeakf: mean peak
 frequency in kHz. - ID: bird individual ID, where the number indicates the
 experimental flock the bird was assigned to and the letter indicates the
 source population. - date: date of audio recording. -
 sp_selections_analysis_metadata.csv: Contact call selection tables
 including acoustic measurements and metadata. - see previous file
 description for definitions of each acoustic variable. - treatment: adult
 age class (either Young or Old). - round: experimental round (1, 2, or 3).
 - source.room: source room in which the individual bird was housed prior
 to novel flock formation (A, B, C, or D); each experimental flock is
 composed from 1 bird from each of the four separate source rooms. -
 record.group: experimental flock (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or
 12). - record.block: recording block corresponding to the date of audio
 recording. There were 5 audio-recording blocks (block 1 contains
 recordings of birds' baseline repertoire and blocks 2-5 contain
 recordings of birds' while in their novel flocks). Blocks were 4 days
 long and separated by a break day. Scripts: - optimized_auto_detec_BM.R: R
 code for autodetection of contact calls from collected audio files.
 Autodetection was run in batched on audio files grouped by experimental
 flock for computing efficiency. Autodetected calls were then visually
 confirmed in Raven Pro before spectrographic measurements. -
 spectrogram_analysis_prep_BM.R: R code for spectrographic measurements of
 final contact calls. - Spectrogram_analysis_BM.Rmd: R markdown code for
 visualizing spectrographic measurements of contact calls &
 corresponding statistical analysis. - Call_analysis_BM_VSCODE.Rmd: R
 markdown code for projecting contact calls in 'acoustic space'
 and computing vocal learning measurements. - CallAnalysis_STATS.r: R code
 for statistics of vocal learning measurements. ``` # Social Analysis
 Files: ``` Raw Data: - Social_Interaction_Video_Examples.mp4 : Annotated
 video of examples of the types of budgerigar affiliative and agonistic
 social interactions measured in the study. -
 BehaviorCodingRawData_EarlyMorning.csv : Raw data file for social
 interaction coding from collected videos used to generate affiliative and
 agonistic social networks and metrics. - Treatment: adult age class
 (either Young or Old). - Group: experimental flock (1, 2, 3, 4, 5, 6, 7,
 8, 9, 10, 11, or 12). - Video date: date of video-recording
 (month/day/year). - Time of day: time of day at which video-recording took
 place. This data set only contains recordings taken during "Early
 Morning" defined as 0700-0900 since birds were most active at this
 time. - Actor: individual bird that initiated the social interaction. -
 Recipient: individual bird that the interaction was directed towards. -
 Behavior: specific social interaction that was observed. - KS: kiss
 (affiliative) - HB: head bob (affiliative) - AF: allofeed (affiliative) -
 AP: allopreen (affiliative) - BT: bill thrust (agonistic) - KI: kick
 (agonistic) - KS-RJ: rejected kiss (agonistic) - HB-RJ: rehected head bob
 (agonistic) - AF-RJ: rejected allofeed (agonistic) - AP-RJ: rejected
 allopreen (agonistic) - Start time: time in the video recording at which
 the social interaction began. - End time: time in the video recording at
 which the social interaction ended. - Duration: duration of the social
 interaction in h:mm:ss (for allofeeding and allopreening interactions
 only). - BehaviorCodingRawData_EarlyMorning_ForTotals.csv : Raw data file
 identical to as above but including individual social interactions
 categorized as affiliative or agonistic and including recording block
 metadata. - see previous file description for definitions of other
 variables. - Category: AFF for affiliative or AGO for agonistic. - Block:
 recording block corresponding to the date of video recording. There were 4
 video-recording blocks. Blocks were 4 days long and separated by a break
 day. - Half: recordings classified as being taken during the first or
 second half of the experimental round. Half 1 contains recordings from
 blocks 1 and 2 and half 2 contains recordings from blocks 3 and 4. -
 Proximity Raw Data_R.csv: Raw data file for proximity coding from
 collected videos used to generate proximity social networks and metrics. -
 Treatment: adult age class (either Young or Old). - Group: experimental
 flock (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12). - Video_date: date of
 video-recording (day-month-year). - Snapshot_#: snapshot number; snapshots
 were taken at 4-minute intervals starting from 30 minutes after the
 experimenter left the room and for a duration of 40 minutes, yielding 11
 snapshots per flock for each daily video recording. - Neighbor_1 and
 Neighbor_2: the two individual birds between which the inter-individual
 distance has been measured in cm; distance was measured using an in-frame
 ruler as a scale and the line tool in Image J. - block: recording block
 corresponding to the date of video recording. There were 4 video-recording
 blocks. Blocks were 4 days long and separated by a break day. - half:
 recordings classified as being taken during the first or second half of
 the experimental round. Half 1 contains recordings from blocks 1 and 2 and
 half 2 contains recordings from blocks 3 and 4. - Interobserver
 Assessment.xlsx: Raw data for interobserver assessment of social
 interaction coding. - Sheet 1 (BM Recoding): Recoding by BM of a subset of
 videos coded by observer SO for assessing interobserver reliability. - see
 description of variable definitions for the file
 BehaviorCodingRawData_EarlyMorning.csv. - Sheet 2 (BM Recoded Videos):
 checklist of videos that were recoded. - Sheet 3 (Total Affiliative):
 comparison of affiliative behavior coding between observers SO and BM. -
 SO: total number of affiliative behaviors coded by SO. - BM: total number
 of affiliative behaviors coded by BM. - BM_AP: total number of
 allopreening interactions coded by BM. - SO_AP: total number of
 allopreening interactions coded by SO. - BM_AF: total number of
 allofeeding interactions coded by BM. - SO_AF: total number of allofeeding
 interactions coded by SO. - BM_KS: total number of kiss interactions coded
 by BM. - SO_KS: total number of kiss interactions coded by SO. - BM_HB:
 total number of head bob interactions coded by BM. - SO_HB: total number
 of head bob interactions coded by SO. - Sheet 4 (Total Agonistic):
 comparison of agonistic behavior coding between observers SO and BM. - SO:
 total number of agonistic behaviors coded by SO. - BM: total number of
 agonistic behaviors coded by BM. - BM_BT: total number of bill thrust
 interactions coded by BM. - SO_BT: total number of bill thrust
 interactions coded by SO. - BM_KI: total number of kick interactions coded
 by BM. - SO_KI: total number of kick interactions coded by SO. - BM_KS-RJ:
 total number of rejected kiss interactions coded by BM. - SO_KS-RJ: total
 number of rejected kiss interactions coded by SO. - BM_HB-RJ: total number
 of rejected head bob interactions coded by BM. - SO_HB-RJ: total number of
 rejected head bob interactions coded by SO. - BM_AP-RJ: total number of
 rejected allopreening interactions coded by BM. - SO_AP-RJ: total number
 of rejected allopreening interactions coded by SO. - BM_AF-RJ: total
 number of rejected allofeeding interactions coded by BM. - SO_AF-RJ: total
 number of rejected allofeeding interactions coded by SO. -
 Interobsv_SO_BM_PooledAffiliativeAgonistic.csv: Pooled raw data for
 interobserver assessment of social interaction coding. - Video: Video file
 with a prefix of either AFF for affiliative or AGO for agonistic to
 indicated which category of behavior the totals in the following two
 columns correspond to. - SO: total number of interactions coded by
 observer SO. - BM: total number of interactions coded by observer BM. -
 Edgelists of affiliative interactions with one edgelist per social flock
 per recording block: - These files are named using the following format:
 aff_group#_edgelist_recordingblock#.csv ((File example:
 aff_g1_edgelist_block1.csv)) - the files with the suffix
 "overall" rather than a recording block number, contain all
 affiliative interactions pooled over the four recording blocks - Actor:
 individual ID of bird initiating an observed affiliative interaction -
 Recipient: individual ID of bird receiving an observed affiliative
 interaction - Edgelists of agonistic interactions with one edgelist per
 social group per recording block: - These files are named using the
 following format: ago_group#_edgelist_recordingblock#.csv ((File example:
 ago_g1_edgelist_block1.csv)) - the files with the suffix
 "overall" rather than a recording block number, contain all
 agonistic interactions pooled over the four recording blocks - Actor:
 individual ID of bird initiating an observed agonistic interaction -
 Recipient: individual ID of bird receiving an observed agonistic
 interaction Scripts: - aff_socialnetworkmetrics.R: R code for generating
 affiliative social networks and metrics. - aff_socialnetwork_stats.R : R
 code for statistical analysis of affiliative social metrics. -
 ago_socialnetworkmetrics.R : R code for generating agonistic social
 networks and metrics. - ago_socialnetwork_stats.R: R code for statistical
 analysis of agonistic social metrics. - Interobsv_SO_BM.R: R code for
 performing interobserver reliability assessment of social interaction
 coding between two observers. - Proximity_Proportional.R: R code for
 generating proximity social networks, metrics, and statistics. -
 TotalInteractionSummary.R: R code for summarizing social interaction
 totals. ```