Data from: Photoperiod and rainfall are associated with seasonal shifts in social structure in a songbird
Data files
Nov 30, 2022 version files 43.84 MB
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Input_files.zip
6.36 MB
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Output_files.zip
37.46 MB
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README.md
25.31 KB
Nov 30, 2022 version files 43.84 MB
-
Input_files.zip
6.36 MB
-
Output_files.zip
37.46 MB
-
README.md
25.39 KB
Abstract
Seasonally breeding animals often exhibit different social structures during non-breeding and breeding periods that coincide with seasonal environmental variation. Therefore, ongoing climate change may play an important role in determining the future structure of animal societies, especially if climate determines when seasonal shifts in social structure occur. However, we know little about the environmental cues that determine the timing of seasonal shifts in social structure, a lack of knowledge that contrasts with our well-defined knowledge of the environmental cues that trigger a shift to breeding physiology in seasonally breeding species. Here we tested whether the environmental cues that drive seasonal shifts in social structure are similar to those that determine timing of breeding in the red-backed fairywren (Malurus melanocephalus), an Australian songbird. Social network analyses revealed that social groups, which are highly territorial during the breeding season, interact in social “communities” on larger ranges during the non-breeding season. Interactions among non-breeding groups were related to rainfall, with more rainfall leading to reductions in home range size and fewer interactions among non-breeding social groups. Similarly, onset of breeding was also determined by rainfall during the non-breeding season, with greater rainfall leading to earlier breeding. These findings reveal that for some species, the cues that determine the timing of shifts in social structure across seasonal boundaries can be similar to those that determine timing of breeding. This study increases our understanding of how social structure and the selection pressures that result from different social structures might respond to changing climates.
Publication: Behavioral Ecology
File preparation date: 5 November 2022
Authors: Joseph F. Welklin, Samantha M. Lantz, Sarah Khalil, Nicole M. Moody, Jordan Karubian, Michael S. Webster
Contact Joseph Welklin at jwelklin@gmail.com with questions
Summary of data and code
This paper included tests of many different questions and many of our datasets used to answer these questions did not
overlap. Therefore, we typically used different R scripts to answer each question or set of questions.
The data for these scripts are included in two folders. The Input files folder contains mostly raw data from a database
and data collected in the field. The Output files folder contains processed data files created using the attached
scripts and the raw data files. These output files were used in further analyses. Scripts can be run by first loading
the R-project file in RStudio, then opening each of the script files. Scripts should run without setting a working
directory if all files are left in their current folders thanks to the here package in R. See below for descriptions
of each script and each data file.
List of R scripts
Script: Networks_Dedrograms_Groups_Communities 2_pub.R
Summary: Use this script to identify social groups and social communities within the network data for
all four years where we have social network data.
Script: Robustness and Randomizations_pub.R
Summary: Use this script to test whether the observed group and community structure is more structured
than expected by random chance.
Script: Relatedness in Non-breeding Networks_pub.R
Summary: Use this script to test whether genetic relatedness within groups and communities is different from chance
Script: Assortment of groups across seasons 4_pub.R
Summary: Use this script to test whether past breeding group members and upcoming breeding group members are
also assorted (strongly connected) during the non-breeding season. Also can see which social relationships
from breeding (Father-son, breeding pair, etc) explain non-breeding season group membership.
Script: Home Ranges 3 (AKDE)_pub.R
Summary: Use this script to measure changes in home range size over the non-breeding season
Script: Groups per Observation dataframe v2_pub.R
Summary: Use this script to build the groups-by-observation dataframe that is used to model climate effects
on interactions among social groups. This script builds from Networks_Dedrograms_Groups_Communities 2_pub.R
Script: Climwin and Models 7_pub.R
Summary: Use this script to test whether climate factors influence the number of groups per observation
Script: Climwin Breeding Start 2_pub.R
Summary: Use this script to test whether climate factors influence timing of initiation of breeding across years
Script: Rainfall predict NDVI script_pub.R
Summary: Use this script to test whether rainfall predicts NDVI at our field site
Scripts in 'Cluster Scripts folder' - described below
Summary: These scripts were used to conduct randomization tests for the sliding window analyses and home range analyses
included in the paper. These scripts were run on machines with multiple cores at the Cornell BioHPC computing cluster
to greatly decrease run time. The scripts and data files were placed in the same folder so setting the working directory
was not necessary. Scripts were run from linux coding on computing cluster machines.
Cluster Script: Cluster_akde_randXX.R
Summary: XX stands in for the year 2016-2019. Use these scripts to run the randomizations for the home range size permutations
comparing whether home range size varied over the non-breeding season.
Cluster Script: Cluster_CLIMATE_WINDOW_rand_custom.R
Summary: One script for each climate variable looked at in the sliding window analysis testing whether associations among
non-breeding groups were associated with climate variation within years. These are the randomizations used to
test whether the observed climate windows were false positives.
Cluster Script: Cluster_breeding_CLIMATE_WINDOW_rand_lin_k.R
Summary: One script for each climate variable looked at in the sliding window analysis testing whether initiation of
breeding across years was associated with climate variables. These are the randomizations used to
test whether the observed climate windows were false positives.
Input files folder - descriptions of data files:
NOTE all year numbers in file names and in data files refer to the field season year which is the year the breeding season
ended in. Breeding seasons ended in January/February so most data collection during the 2015 field season occurred in 2014.
Dates in files refer to exact dates. RBFW = Red-backed Fairywren. NA values represent missing data that was not able to be collected.
Data file: agesexstatusxx.csv
Summary: Ages and sexes of RBFWs during the 2016, 2017, 2018, 2019 field seasons. All files are in a similar structure.
Column descriptions:
Bird Color bands on birds this ID can change across years if color bands break/need replaced.
Sex Male (M) or Female (F)
Current.Age Age in years of bird in field season year (in file name).
Age.Exact. Is the exact age known? min=exact age not known, at least this age but may be older. exact=exact age known.
FWNo Numeric ID unique to each individual Red-backed Fairywren. This number never changes.
Year.variable - Not important, left over from database structure.
PrevBreedingYear - Previous field season.
Status.variable - Not important, left over from database structure.
PrevBreedingStatus - Individual's breeding status in previous breeding season. BF = breeding female, BM = breeding male,
AHELP = helper, UNK = unknown, HY = hatch year
class - Previous breeding class based on PrevBreedingStatus
Data file: All Non-breeding GPS YEAR.csv
Summary: GPS waypoints from 2016 - 2019 non-breeding seasons
Column descriptions:
Waypoint - GPS waypoint ID
lat - latitude
lon - longitude
Data file: birdXX.csv
Summary: Raw data for network observations for 2016 - 2019 non-breeding seasons in an individuals list format.
Used to create group-by-individual matrices. XX stands in for year 16-19 ID.
Column descriptons:
Sighting - Unique sampling point ID number. Sampling points were collected approximately every 5 minutes and
each bird present was recorded.
Observation - Unique observation ID number. Observations are groups of sampling points, usually ranging from
15 to 60 minutes in length with sampling points collected every 5 minutes.
Initials - Observer ID
Date - Collection date - actual date
Time - Collection time
Number - Number of birds present at sighting/sampling point, estimated by observer, may be larger than number of
individual IDs recorded.
WP - waypoint associated with where the sampling point was collected.
Bird - Bird's color bands.
Kerfuffle - did the association in the sighting/sampling point occur within 8 minutes of a courtship or aggressive
event involving some of the birds in the sampling point? Y = yes, N = no.
Data file: birdsXX_banded_unks.csv
Summary: Further information on number of birds and number of unknown individuals in each sampling point in birdXX.csv files.
XX stands in for year 16-19 ID.
Column descriptions:
Sighting - Unique sampling point ID number. Sampling points were collected approximately every 5 minutes and
each bird present was recorded.
Observation - Unique observation ID number. Observations are groups of sampling points, usually ranging from
15 to 60 minutes in length with sampling points collected every 5 minutes.
Banded - number of banded birds in the sighting/sampling point.
Unknowns - number of unknown birds in the sighting/sampling point - means they were probably banded but the
observer was not able to identify their color bands to get an ID.
Data file: RelatednessEstimates_8xdenovo80_14to19.csv
Summary: Genetic relatedness data for each possible pair of birds active from the 2014-2019 seasons.
Column descriptions:
Pair - Unique ID number for each pair comparison.
ind1 - individual 1 in the comparison
ind2 - individual 2 in the comparison
wang - Wang 2002 estimator of genetic relatedness - typically ranges from 0 (not related at all) to 1 (same individual)
Siblings should be around 0.5, half-sibs around 0.25. Relatedness estimates are slightly lower than expected
becuase few individuals were able to genotyped at every single SNP loci. See supplemental methods for a validation
of this method using known mother-offspring pairs.
Data file: RemovalorControl 2017.csv
Summary: Record of whether each bird belonged to a removal or control community in the 2017 non-breeding season.
See supplemental methods for more information on this experiment.
Column descriptions:
Bird - Color bands of each bird active in 2017
Community - "Neighborhood" bird was present in. Not defined via social network analysis. For individuals with a value of
"X" in this column, it means they were not part of any of these communities.
TreatmentGroup - Whether the neighborhood was a control or removal treatment. For individuals with a value of
"X" in this column, it means they were not part of any of these treatment groups.
Data file: Upcoming_statusXX.csv
Summary: Breeding statuses for each bird in the upcoming breeding season - breeding season following each non-breeding season.
XX stands in for year 16-19 ID.
Column descriptions:
Year - Non-breeding season and breeding season year. 2016 non-breeding season (Feb-July/Aug) leads into Aug-Jan breeding
season.
Date.Created - date the breeding group was created - used each individual's first breeding group in a year.
Group.Number - unique breeding group ID
Bird - bird's color bands
Status - bird's first breeding status in a breeding season.
Output files folder - list of which scripts that created each data file in the Output Files folder:
#NOTE: Refer to script and input files that created it for descriptions of each column in the data.
Some of these files like the climate files were created in scripts not included on Dryad. Their
creation scripts just filtered for relevant dates or combined data from different measurement sites.
NA values represent missing data that was not able to be collected.
Data file: akde_randXX.csv
Summary: Randomization results for home range analyses. XX stands in for year 16-19 ID.
Script where created: Cluster_akde_randXX.R XX stands in for year 16-19 ID.
Column descriptions:
X1.2 - Difference in home rage size between period 1 and period 2 from randomizations
X1.3 - Difference in home range size between period 1 and period 3 from randomizations
X2.3 - Difference in home range size between period 2 and period 3 from randomizations
Data file: AverageSilhouetteWidths.csv
Summary: Saved average silhouette widths for each season's network.
Script where created: Networks_Dedrograms_Groups_Communities 2_pub.R
Column descriptions:
year - Year of study
avg.s - Average silhoutte width
Data file: birdlistXXnoKsub.csv
Summary: List of birds in each year's network. XX stands in for year 16-19 ID.
Script where created: Networks_Dedrograms_Groups_Communities 2_pub.R
Column descriptions:
Bird - Bird ID
SightFreq - Number of times the bird was seen
degXXnoK - Network degree
Data file: birdlistXXnoKsubc.csv
Summary: List of birds in each year's network that were also assigned to social communities. XX stands in for year 16-19 ID.
Script where created: Networks_Dedrograms_Groups_Communities 2_pub.R
Column descriptions:
Bird - Bird ID
Social.Group - Bird's social group defined via dendrograms
SightFreq - Number of times the bird was seen
degxxnoK - Network degree
Community - Network community
Sex - Bird's sex (male/female)
Current.Age - Bird's age in that season
Age.Exact - Is the exact age known? min=exact age not known, at least this age but may be older. exact=exact age known.
FWnumber - Numeric ID unique to each individual Red-backed Fairywren. This number never changes.
Year.variable - Leftover from database
PrevBreedingYear - Previous breeding season ID
Status.variable - Leftover from database
PrevBreedingStatus - Bird's breeding status in previous breeding season
class - Bird's non-breeding social class
Data file: birdlistXXnoKsubcb.csv
Summary: List of birds in each year's network that were also assigned to social communities with previous and upcoming
breeding group info. XX stands in for year 16-19 ID.
Script where created: Networks_Dedrograms_Groups_Communities 2_pub.R
Column descriptions:
Bird - Bird ID
Social.Group - Bird's social group defined via dendrograms
SightFreq - Number of times the bird was seen
degxxnoK - Network degree
Community - Network community
Sex - Bird's sex (male/female)
Current.Age - Bird's age in that season
Age.Exact - Is the exact age known? min=exact age not known, at least this age but may be older. exact=exact age known.
FWnumber - Numeric ID unique to each individual Red-backed Fairywren. This number never changes.
Year.variable - Leftover from database
PrevBreedingYear - Previous breeding season ID
Status.variable - Leftover from database
PrevBreedingStatus - Bird's breeding status in previous breeding season
class - Bird's non-breeding social class
PrevBrGrp - Bird's previous breeding group ID
UpcomingBrGrp - Bird's upcoming season breeding group ID
Data file: communitiesXX.csv
Summary: Community membership of non-breeding groups in each season. XX stands in for year 16-19 ID.
Script where created: Networks_Dedrograms_Groups_Communities 2_pub.R
Column descriptions:
Group - Social Group ID
Community - Social community ID
Data file: firstegg_final.csv
Summary: First egg date data used in initiation of breeding analyses
Column descriptions:
GroupId - Breeding group ID
Year - Field season year
Nest - Nest ID
Date.found - Date nest was found
First.egg.date - Date of first egg
First.egg.date.known - whether first egg date was "Known" (seen as 1 egg) or "Estimated" (backdated)
Clutch.comp.date - date clutch completed (last egg laid)
Clutch.comp.date.known - whether clutch completion date was known or estimated
Female.fwno - Female ID, unlike color bands this cannot change across years
Male.fwno - Male ID, unlike color bands this cannot change across years
Female.Age - Female's age
First.egg.jdate - Julian date of first egg (day of year)
Paired.prev - Whether the pair was paired in the previous year
Helpers - Number of helpers in the breeding group
Data file: gbiXX.csv
Summary: Group by individual matrix for non-breeding season network. XX stands in for year 16-19 ID.
Script where created: Networks_Dedrograms_Groups_Communities 2_pub.R
Column descriptions:
-Each column is an individual bird and each row represents a sampling point showing whether a bird was recorded
in that sampling point (1) or not (0)
Data file: gbiXXnoK.csv
Summary: Group by individual matrix for non-breeding season network with kerfuffle interactions not included.
XX stands in for year 16-19 ID.
Script where created: Networks_Dedrograms_Groups_Communities 2_pub.R
Column descriptions:
-Each column is an individual bird and each row represents a sampling point showing whether a bird was recorded
in that sampling point (1) or not (0)
Data file: gbssubmaxall.csv
Summary: Groups by observation data file used to test whether climate was associated with interactions among
non-breeding groups.
Script where created: Groups per Observation dataframe v2_pub.R
Column descriptions:
-Sighting - Unique sampling point ID
-Observation - Observation ID
-Number - Number of birds
-Date - Collection date
-Social.Groups.Total - Number of social groups present
-Focal.Sightings - Number of sampling points the focal social group was seen in during the observation
-Social.Group.Size - Size of the focal social group (number of birds)
-Groups.in.Community - Number of groups in the focal social group's community
-WP - GPS waypoint ID
-Year - Study season
-Focal.Group.Year - Combination of focal group ID and Year variable
-Community.Year - Combination of focal group community ID and Year variable
-jdate - Julian date - day of year
Data file: groupXX.csv
Summary: List of what social group each bird was in. XX stands in for year 16-19 ID.
Script where created: Networks_Dedrograms_Groups_Communities 2_pub.R
Column descriptions:
Bird - Bird ID
Social.Group - Social group ID for that bird
Data file: Landsat 8 NDVI yearly polygons noclouds.csv
Summary: Landsat 8 NDVI scores for the area of our fieldsite covered by RBFW territories.
Column descriptions:
Date - NDVI collection date
NDVI - Normalized difference vegetation index score
Year - Field season year
Data file: Landsat7_all_years.csv
Summary: Landsat 7 NDVI scores for the area of our fieldsite covered by RBFW territories.
Column descriptions:
Date.n - Date as numeric in R.
NDVI - Normalized difference vegetation index score
Date - Collection date
Data file: maxtemp_1994-2020.csv
Summary: Maximum temperature data from the Brisbane airport
Column descriptions:
Date - Collection date
maxtemp - Maximum temperature in Celsius
jdate - Julian date of Date (day of year)
Year - Field season year
Data file: maxtempallyears.csv
Summary: Maximum temperature data from the Brisbane airport
Column descriptions:
Date - Collection date
Max.Temp - Maximum temperature in Celsius
jDate - Julian date of Date (day of year)
Year - Field season year
Data file: mintemp_1994-2020.csv
Summary: Minimum temperature data from the Brisbane Airport
Column descriptions:
Date - Collection date
mintemp - Maximum temperature in Celsius
jdate - Julian date of Date (day of year)
Year - Field season year
Data file: mintempallyears.csv
Summary: Minimum temperature data from the Brisbane airport
Column descriptions:
Date - Collection date
Min.Temp - Maximum temperature in Celsius
jDate - Julian date of Date (day of year)
Year - Field season year
Data file: modularity_scores.csv
Summary: Average modularity scores of social communities for each field season.
Script where created: Networks_Dedrograms_Groups_Communities 2_pub.R
Column descriptions:
year - Study year
modularity - Average modularity score for that year
Data file: rain_2004-2018.csv
Summary: Rainfall data from three sites near our field site.
Column descriptions:
Date - Collection date
Rainfall.amount..millimetres..x - Rainfall in mm for the first site
Rainfall.amount..millimetres..y - Rainfall in mm for the second site
Rainfall.amount..millimetres. - Rainfall in mm for the third site
amount - Average amount of all three sites
jDate - Julian Date of collection date (day of year)
cumulative - Cumulative rainfall for each year
Year - Field season year
amountcm - "amount" column in cm
Data file: rainallyears.csv
Summary: Rainfall data from three sites near our field site.
Column descriptions:
Date - Collection date
Rainfall.amount..millimetres..x - Rainfall in mm for the first site
Rainfall.amount..millimetres..y - Rainfall in mm for the second site
Rainfall.amount..millimetres. - Rainfall in mm for the third site
amount - Average amount of all three sites
jDate - Julian Date of collection date (day of year)
cumulative - Cumulative rainfall for each year
Year - Field season year
amountcm - "amount" column in cm
Data file: rnetXX.csv
Summary: Reduced network for each year - network of social groups
Script where created: Networks_Dedrograms_Groups_Communities 2_pub.R
Column descriptions:
Network matrix of reduced network. Each row and column ID represents a social group.
Data file: windallyears.csv
Summary: Wind data for our field site
Column descriptions:
Date - Collection date
Windspeed - Average daily windspeed in m/s for our field site.
Data files in 'Climwin model outputs' folder - described below
Summary: Outputs from Sliding window analyses
Data file: EncM_mean_CLIMATE_WINDOW.rds
Summary: Outputs from social group association sliding window climate models
Script where created: Climwin and Models 7_pub.R
Data file: FE_CLIMATE_WINDOW.rds
Summary: Outputs from first egg date (breeding initiation) sliding window climate models.
Script where created: Climwin Breeding Start 2_pub.R
Data file: rain_predicts_NDVI_season.rds
Summary: Output from sliding window analysis testing if rainfall predicts NDVI
Script where created: Rainfall predict NDVI script_pub.R
Data files in 'Climwin randomizations' folder
Summary: Outputs from sliding window randomization analyses
Data file: Breeding_CLIMATE_WINDOW_randomizations.csv
Summary: Outputs from breeding initiation randomization analyses run on cluster.
Scripts where created: Scripts in 'Cluster scripts' folder
Column descriptions:
deltaAICc - Change in AICc value from null model
Open - Window open day
Close - Window close day
ModelBeta - Coefficient of climate variable from the top model in each randomization
Data file: CLIMATE_WINDOW_randomizations.csv
Summary: Outputs from non-breeding social group associations sliding window climate randomizations.
Scripts where created: Scripts in 'Cluster scripts' folder
Column descriptions:
deltaAICc - Change in AICc value from null model
Open - Window open day
Close - Window close day
Data files in 'Homerange output files' folder
Summary: These are outputs from different parts of the home range analysis process. These analyses took
a long time to run so I saved the data at different intervals to speed up re-analysis.
Data file: akdeXX_list_#.rds
Summary: Auto-correlated-kernel-density estimates for each year. XX stands in for year 16-19 ID. # stands in
for period of the non-breeding season (1-3).
Script where created: Home Ranges 3 (AKDE)_pub.R
Data file: akdeXX.rand.#obs.rds
Summary: Outputs of randomziations used to test whether 5, 7, 10, or 15 observations were required to get a
good estimate of an individual's home range size. XX stands in for year 16-19 ID. # stands in
for the number of observations (5,7,10,15).
Script where created: Home Ranges 3 (AKDE)_pub.R
Data file: birdXX_gps15_list_#L.csv
Summary: List of birds in each period for each season. XX stands in for year 16-19 ID. # stands in
for period of the non-breeding season (1-3).
Script where created: Home Ranges 3 (AKDE)_pub.R
Column descriptions:
individual.local.identifier - Individual ID
n - number of GPS points for that individual
Data file: birdXX_gps15.csv
Summary: Processed GPS data for each season - used in randomization scripts for home range analyses.
XX stands in for year 16-19 ID.
Script where created: Home Ranges 3 (AKDE)_pub.R
Column descriptions:
WP2 - GPS waypoint ID
Sighting - Sampling point ID
Observation - Observation ID
Inititals - Observer's initials
Date - Date
Time - Time sample collected
Number - Number of birds present
WP - Waypoint ID without the initials
inidividual.local.identifier - Individual ID
Kerfuffle - Was the sampling point associated with courtship or aggression?
location.lat - Latitude of gps point
location.long - Longitude of gps point
Time2 - a second time variable
timestamp - full timestamp with date
jdate - julian date (day of year)
Data file: birdlistXXakde15_#.csv
Summary: Summarized home range data for each period for each season. XX stands in for year 16-19 ID.
# stands in for period of the non-breeding season (1-3).
Column descriptions:
Bird - Bird ID
Social.Group - Bird's social group defined via dendrograms
SightFreq - Number of times the bird was seen
degxxnoK - Network degree
Community - Network community
Sex - Bird's sex (male/female)
Current.Age - Bird's age in that season
Age.Exact - Is the exact age known? min=exact age not known, at least this age but may be older. exact=exact age known.
FWnumber - Numeric ID unique to each individual Red-backed Fairywren. This number never changes.
Year.variable - Leftover from database
PrevBreedingYear - Previous breeding season ID
Status.variable - Leftover from database
PrevBreedingStatus - Bird's breeding status in previous breeding season
class - Bird's non-breeding social class
akde - Home range size in hectares
obs - Number of observations the bird was in
WPfreq - number of GPS waypoints the bird was in
akde.period - Home range size in hectares for the analysis period
period - Home range comparison period (1-3)
Sharing/access Information
Links to other publicly accessible locations of the data: Data only on Dryad
Was data derived from another source? No
See README file for descriptions of each dataset and summaries of each R script. See annotated R code for instructions on how to run the analyses. All analyses were conducted in R version 3.5.2 unless otherwise specified.
- Welklin, Joseph F. et al. (2022), Data for: Similar environmental cues guide timing of breeding and seasonal shifts in songbird social structure, , Article, https://doi.org/10.5281/zenodo.7299798
- Welklin, Joseph F; Lantz, Samantha M; Khalil, Sarah et al. (2022). Photoperiod and rainfall are associated with seasonal shifts in social structure in a songbird. Behavioral Ecology. https://doi.org/10.1093/beheco/arac110