DOI: 10.5061/dryad.ht76hdrnd
title: The impact of helping experience on helper life-history and fitness in a cooperatively breeding bird

description: The data and accompanying .R scripts were used to test whether having
 experience as a helper affected a number of different breeding and fitness
 related parameters in the Seychelles warbler (Acrocephalus sechellensis)
 in the paper "The impact of helping experience on helper life-history
 and fitness in a cooperatively breeding bird." 
 DatasetsstatusInfo.xlsx: data collected over a focal individual's
 lifetime. natalInfo.xlsx: data pertaining to the natal environment of the
 focal bird. lastSeen.xlsx: data used to calculate when the bird was last
 seen alive. summerIndex.xlsx: data used to determine whether a particular
 field period was during a summer or winter season.territoryQuality.xlsx:
 data used to determine the territory quality of each territory during a
 particular field period. Statistical analyses experiencePrep.R:
 the script used to prepare the data and calculate the necessary model
 variables prior to running the analyses. experienceAnalyses.R: the script
 used to run the analyses and generate the related graphs.  More
 detailed information regarding the contents of each dataset can be found
 in the READ.ME From this, we found that helping experience had no
 significant association with any of the metrics considered, except that
 individuals with helping experience had an older age at first dominance,
 and dominant females with helping experience had longer lifespans than
 those that had never helped. In addition, we found that females with
 co-breeding experience produced more adult offspring (≥1 year old) after
 acquiring dominance, and had a higher lifetime reproductive success than
 females that had never co-bred.
description: # The impact of helping experience on helper life-history and fitness in a
 cooperatively breeding bird
 [https://doi.org/10.5061/dryad.](https://doi.org/10.5061/dryad.ht76hdrnd):
 ## Description of the data and file structure The data and accompanying .R
 scripts were used to test whether having experience as a helper affected a
 number of different breeding and fitness related parameters in the
 Seychelles warbler (*Acrocephalus sechellensis*) in the paper "The
 impact of helping experience on helper life-history and fitness in a
 cooperatively breeding bird." Specifically, they were used to test
 whether helping experience had an effect on: * Whether or not an
 individual acquired a dominant breeding position (binary response
 variable: yes/no) * The age at which an individual acquired a dominant
 breeding position (if ever; continuous response variable) * The length of
 an individual's dominant breeding tenure (if dominance was acquired;
 continuous response variable) * The number of genetic offspring produced
 after an individual first acquired dominance (i.e., the "skills"
 hypothesis; continuous response variable) * An individual's lifetime
 reproductive success (continuous response variable) * An individual's
 lifespan (ad-hoc analysis; continuous response variable) From this, it was
 found that helping experience alone has no effect on any of the breeding
 or fitness-related parameters above, except that individuals with helping
 experience started breeding at an older age and dominant females with
 prior helping experience had longer lifespans than individuals that did
 not have helping experience. In addition, females with co-breeding
 experience produced more offspring after acquiring a dominant breeding
 position and had a higher lifetime reproductive success than females
 without co-breeding experience. For all datasets, empty cells correspond
 to an N/A value. #### **natalInfo.xlsx** Data collected during the natal
 field period of the focal bird, providing information on their natal
 environment. These data were used to determine variables such as whether
 or not the focal bird had a helper, the identity of their social father,
 variables relating to their genetic mother and social father (e.g., age
 when the focal individual hatched). Genetic parents with a p-value of
 &lt;0.8 were also removed from the dataset during data preparation in
 experiencePrep.R. Information about the natal territory was also collected
 so that it could be combined with data from an additional dataset
 (territoryQuality.xlsx) to determine the natal territory quality.
 Description of variable, data-type, and descriptions for the abbreviations
 of categorical data are provided. * **BirdID:** The unique ID of the focal
 bird (numerical). * **HelpingLRS\_07\_SexEstimate:** The sex of the focal
 bird, determined using molecular sexing techniques (numerical; 0: female;
 1: male; converted to categorical in experiencePrep.R). * **BirthDate:**
 Hatch dates are estimated from nest watches based on observed lay dates,
 hatch dates, or fledge dates. If this information is not available, hatch
 date may also be estimated by considering the physiological features of
 the focal bird e.g., eye colour (date). * **MumID:** The unique ID of the
 genetic mother of the focal bird, determined using the genetic pedigree
 (numerical). * **MumBirthDate:** The estimated hatch date of the genetic
 mother of the focal bird (date). * **DadID:** The unique ID of the genetic
 father of the focal bird, determined using the genetic pedigree
 (numerical). * **DadBirthDate:** The esimated hatch date of the genetic
 father of the focal bird (date). * **p:** The p value indicating the
 confidence of the relationship between the focal bird and the assigned
 genetic mother and father (continuous). * **FieldPeriodID:** The unique ID
 of the field period in which the focal bird hatched (numerical). *
 **NatalTerritoryNumber:** The unique territory number in which the focal
 bird hatched (numerical). * **TerritoryID:** The unique territory ID in
 which the focal bird hatched (numerical). * **BreedGroupID:** The specific
 group of birds that reside within the breeding group during the field
 period in which the focal bird hatched (numerical). * **GroupMembers:**
 The unique IDs of all birds existing within the breeding group when the
 focal bird hatched (numerical). * **sys\_SexEstimates\_SexEstimate:** The
 estimated sex of each group member within the breeding group in which the
 focal bird hatched (numerical; 0: female; 1: male; converted to
 categorical in experiencePrep.R). * **GroupMembersStatus:** The breeding
 status of each group member within a breeding group during the field
 period in which the focal bird hatched. (categorical; EGG: egg; CH: chick;
 FL: fledgling; OFL: old fledgling; H: helper; AB: additional bird
 (non-helper); ABX: not enough information to determine helper status; B:
 budder (taking over another territory); NSA: not seen within that
 particular field period, but seen in a subsequent field period; BrF:
 dominant, breeding female; BrM: dominant, breeding male; TBRF: breeding
 female that was translocated to a different island; TBRM: breeding male
 that was translocated to a different island; SBR: subordinate breeder
 (however, co-breeding females were recalculated within the
 experiencePrep.R dataset); U: unknown status). *
 **GroupMembersBirthDate:** The estimated hatch date of each group member
 within the breeding group in which the focal bird hatched (date). ####
 **statusInfo.xlsx** The following data were collected over a focal
 individual’s lifetime, to gain insight into the breeding statuses that
 they held within different territories at different points in time. These
 data were used, primarily, to determine whether they been a helper (males
 and females) or co-breeder (females only) before acquiring dominance or at
 any point throughout their lifetime. Description of variable, data-type,
 and descriptions for the abbreviations of categorical data are provided. *
 **BirdID**: The unique ID of the focal bird (numerical). * **BirthDate:**
 Hatch dates are estimated from nest watches based on observed lay dates,
 hatch dates, or fledge dates. If this information is not available, hatch
 date may also be estimated by considering physiological features of birds
 when they are first caught e.g., eye colour (date). * **BreedGroupID:**
 Corresponds to the specific group of birds that resided within a territory
 during a specific field period in which the focal bird was alive
 (numerical). * **TerritoryID:** The unique territory number in which the
 focal bird was assigned a breeding status (numerical). * **Status:** The
 breeding status that the focal bird held within each unique breeding group
 (categorical; EGG: egg; CH: chick; FL: fledgling; OFL: old fledgling; H:
 helper; AB: additional, sexually mature bird (non-helper); ABX: not enough
 information to determine helper status of additional bird; B: budder
 (individual taking over another territory); NS: not seen in this field
 period; NSA: not seen within this particular field period, but seen in a
 subsequent field period so known to be alive; BrF: dominant breeding
 female; BrM: dominant breeding male; TBRF: breeding female that was
 translocated to a different island; TBRM: breeding male that was
 translocated to a different island; SBR: subordinate breeder (however,
 co-breeding females were recalculated within the experiencePrep.R
 dataset); U: unknown status; SEEN1: seen once within this territory;
 SEEN2: seen twice within this territory: FLOAT: non-territorial individual
 with no permanent breeding status within the territory). *
 **FieldPeriodID**: The field period in which the focal individual held a
 breeding status within the particular breeding group (numerical). *
 **PeriodStart**: The date at which the field period started (date). *
 **PeriodEnd**: The date at which the field period ended (date). ####
 **lastSeen.xlsx** These data were used to determine the lifespan of each
 focal bird (supplementary model 2), as well as exclude birds that were
 believed to be alive at at the end of the sampling period in 2018 (as
 their fitness metrics have the capacity to still change). To determine
 lifespan, the last date for each of these variables was taken (or the
 midpoint of last field period in which they had a breeding status
 assigned, if catch/seen data are not available). Description of variable,
 data-type, and descriptions for the abbreviations of categorical data are
 provided. * **BirdID:** The unique ID of the focal bird (numerical). *
 **LastCaught:** The date when the focal bird was last caught in the
 mist-net (date). * **LastSeen:** The date when the focal bird was last
 observed in the field (date). * **ChickCollection:** The date when the
 focal bird was captured in the nest as a chick (if ever; date). *
 **EggCollection:** The date when the focal bird was captured in the nest
 as an egg (if ever; date). #### **summerIndex.xlsx** These data were used
 to estimate territory quality when datapoints were missing for particular
 field seasons. The summer index was used to determine whether the field
 period was in the summer or winter, and then then the mean of the previous
 and following field period of the same season-type were used to estimate
 territory quality for the field period with the missing datapoint. Field
 periods with a summerIndex of ≥0.5 were classed as summer seasons, whereas
 field periods with a summer index of &lt;0.5 were considered winter
 seasons. Description of variable, data-type, and descriptions for the
 abbreviations of categorical data are provided. * **TerritoryID:** Each
 unique territory ID present within a particular field period (numerical).
 * **FieldPeriodID:** The unique field period ID corresponding to to the
 data in PeriodStart/PeriodEnd/SummerIndex (numerical). * **PeriodStart:**
 The date at which the field period started (date). * **PeriodEnd:** The
 date at which the field period ended (date). * **SummerIndex:** The summer
 index corresponding to the field period, with ≥0.5 indicating a summer
 field period (numerical). #### **territoryQuality.xlsx** These data were
 used to allow territory quality to be used as a variable in the necessary
 models. From this, the natal territory quality could be calculated for
 each focal bird, as well as the mean territory qualities for the field
 periods prior to dominance, during their dominance tenures, and over their
 lifetimes. These data were also used in conjunction with the data from the
 summerIndex datasheet, which allowed for missing territory quality data to
 be estimated. Description of variable, data-type, and descriptions for the
 abbreviations of categorical data are provided. * **Island:** The island
 where the data was collected, used to subset data to only include data
 from Cousin Island. Description of variable, data-type, and descriptions
 for the abbreviations of categorical data are provided (categorical; CN:
 Cousin; CE: Cousine; DN: Denis; FR: Fregate). * **Year:** The year that
 the territory quality data was collected (continuous). * **TerritoryID:**
 The unique territory number corresponding to the value in TQcorrected
 (numerical). * **FieldPeriodID:** The unique field period ID (numerical).
 * **TQcorrected:** The territory quality data for the corresponding
 territory within the given field period. TQcorrected is determined by
 considering the arthropod abundance within the particular territory
 (continuous). <br> ## Code/Software All statistical analyses were
 performed in RStudio (4.2.1) using the datasets described above. ####
 **experiencePrep.R** Within this script, all of the datasets above were
 imported and used to calculate the variables used in the models within
 experienceAnalyses.R. The variables used within the models (and the type
 of data i.e., factor, continuous) include: * Whether the focal individual
 helped at any point prior to dominance, or during their lifetime (factor:
 yes/no). * Whether the focal individual co-bred at any point prior to
 dominance, or during their lifetime (females only; factor: yes/no). * The
 age of their genetic mother when the focal individual was born (both as
 linear and quadratic variables; continuous). * The natal territory quality
 of the focal individual (continuous). * The mean territory quality of all
 of the territories that the focal individual inhabited prior to acquiring
 dominance (continuous). * The mean territory quality of all of the
 territories in which the focal individual was a dominant breeder
 (continuous). * The mean territory quality of all of the territories that
 the focal individual inhabited over the course of their lifetime
 (continuous). * Whether or not the focal individual had a helper
 themselves when they were a nestling/fledgling (factor: yes/no). * The
 proportion of breeding seasons that the focal individual had helpers
 during their dominant breeding tenure (continuous). * The ID of the focal
 individual's genetic mother (factor). * The ID of the focal
 individual's social father (factor). * The cohort (year of birth) of
 the focal individual (continuous). <br> ####
 **experienceAnalyses.R** This script was used to run the analyses detailed
 in 'Description of the data and file structure', as well as
 generate the corresponding graphs for models with the relevant significant
 results.