Data from: ultimate drivers of forced extra-pair copulations in birds lacking penises: jackdaws as a case-study

# Data from: ultimate drivers of forced extra-pair copulations in birds lacking penises: jackdaws as a case-study Author: "Beki Hooper" Date: '2024-01-07' GENERAL INFORMATION 1. Title of Dataset: Ultimate drivers of forced extra-pair copulations in birds lacking penises: jackdaws as a case-study 2. Author Information A. Principal Investigator Contact Information Name: Alex Thornton Institution: University of Exeter Email: B. Associate or Co-investigator Contact Information Name: Beki Hooper Institution: NA Email: 3. Date of data collection (single date, range, approximate date): 2014 – 2019 4. Geographic location of data collection: Cornwall, UK 5. Information about funding sources that supported the collection of the data: Natural Environment Research Council GW4 Studentship (NERC 107672G), NERC biomolecular analysis facility (NBAF1152), British Ornithologists’ Union (BOU), BBSRC David Phillips Fellowship (BB/H021817/2), Leverhulme Grant (RGP-2020-170), Wellcome Trust (Multi-User Equipment Grant award number 218247/Z/19/Z). SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain 2. Links to publications that cite or use the data: NA 3. Links to other publicly accessible locations of the data: None 4. Links/relationships to ancillary data sets: None 5. Was data derived from another source? No, except in "Supplementary Data.xlsx" in which all sources are reported A. If yes, list source(s): NA 6. Recommended citation for this dataset: Hooper, R.C., Maher, K., Moore, K., McIvor, G.M., Hosken, D. & Thornton, A. (2023). Data from: Ultimate drivers of forced extra-pair copulations in birds lacking penises: jackdaws as a case-study. Dryad Digital Repository: DATA & FILE OVERVIEW 1. File List: A) fine_scale-behav.csv B) time_tog_total.csv C) birthyear_sequoia.csv D) site_sequoia.csv E) ped_sequoia.csv F) SNPs_site_X.PED G) SNPs_site_YZ.PED H) Forced-Extrapair-Copulations-in-Jackdaws.rmd I) sequoia_script.R J) Supplementary Video 1 (Y09-220414-0827-E1) K) Supplementary Video 2 (Y17-100418-0701-B) L) Supplementary Video 3 (Y20-160414-1054-E1) M) Supplementary Data.xlsx N) .fastq files 2. Relationship between files, if important: Forced-Extrapair-Copulations-in-Jackdaws.rmd, an R script) input files: time together (time_tog_total.csv), fine scale behaviour (fine_scale_behav.csv) Pedigree reconstruction script (sequoia_script.R, an R script) input files: SNP data for site X (SNPs_site_X.ped), SNP data for site YZ (SNPs_site_YZ.ped), Site data for each individual (site_sequoia.csv), Birth/year data for each individual (birthyear_sequoia.csv), Social pedigree for each individual (ped_sequoia.csv) 3. Additional related data collected that was not included in the current data package: None 4. Are there multiple versions of the dataset? A. If yes, name of file(s) that was updated: i. Why was the file updated? ii. When was the file updated? \######################################################################### DATA-SPECIFIC INFORMATION FOR: fine_scale-behav.csv This file contains the fine-scale behavioural data for each pair. It is the concatenated video code data, where each new row is a new behaviour that has been recorded within a video. 1. Number of variables: 44 2. Number of rows: 11241 3. Variable List: male.ID ID of the male fem.ID ID of the female BOX_YEAR Nestbox in which the video was filmed and the year it was collected (e.g. X2514 = nestbox X25, 2014) METHOD Method of video coding (BORIS or manual, where manual was coding via Microsoft Excel) CODER Initials of the person who coded the video UNIQUE_ID Concatenation of method, date of video recording and nestbox, to give each video a unique identifier YEAR Year of video recording STAGE Stage of the breeding season the video was filmed. E = incubation. INDIVIDUAL The individual engaging in the recorded behaviour (M = male, F = female, Unknown 1 = unknown if male or female, No focal subject = extrapair individual) BEHAVIOUR The behaviour that the ‘individual’ is engaged in. See the Ethogram in the Supplementary Material. TIME_START The time into the video that the behaviour starts (seconds) TIME_END The time into the video that the behaviour ends (seconds) TREATMENT If the video was collected during the consolation experiment (see manuscript) then this column says which treatment the video was from (B = before stressor, A = after stressor). If the video collected captured a natural intrusion event, it says “INTRUSION”. In two videos, there were two intrusions. The first it INTRUSION 1, the second is INTRUSION 2, and the time between in BETWEEN. For all videos without an intrusion or simulated intrusion event, NA. FEPC_IN_VIDEO Is there an FEPC in this video: Yes or No UNIQUE_TR_ID Same as UNIQUE_ID but with Treatment included as an identifier. VIDEO_STARTS_DEC The time of day the video started but converted to decimal. BEHAVIOUR_DURATION The duration of the behaviour (n seconds). OBSERVATION_MINUS_LATENCY The length of the video in seconds MALE_VISIT_N The number of the resident male’s visit to the nestbox. E.g. on his first visit of the video it is 1; on the second visit of the video it is 2. UNIQUE_TR_ID_M_VISIT Same as UNIQUE_TR_ID but with MALE_VISIT_N concatenated COPULATION_VISIT Whether the male copulated with the female during the visit (Y = Yes, N = No) COPULATION_VIDEO Whether the male copulated with the female during the video (Y = Yes, N = No) FEPC_in_pairyear Whether there was an FEPC event for the female during the breeding season (Y = Yes, N = No) Site The site in which the pair were filmed lay.date The date of that the female laid her first egg cl.size The number of eggs in the clutch hatch.date The date of the first egg hatching n.hatch The number of eggs that hatched fledge.date The date of fledging n.fledge The number of chicks that fledge mass.fledge The cumulative mass of the fledged chicks in grams pair.ID The male ID and the female ID, concatenated FEM_FERTILE Whether the female was in her fertile period (N = No, Y = Yes) DAYS_SINCE_FERTILE Number of days since the females fertile period ended incubation_duration The duration (in days) of the female’s incubation period fem_wing Length of the female’s wing in cm fem_tarsus Length of the female’s tarsus in cm fem_exact_age 0 = not exact, 1 = exact male_wing Length of the male’s wing in cm male_tarsus Length of the male’s tarsus in cm male_exact_age 0 = not exact, 1 = exact min_age_male Minimum age of the male min_age_female Minium age of the female years_together_min Minimum number of years the pair have been together 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: None \######################################################################### DATA-SPECIFIC INFORMATION FOR: time_tog_total.csv This file contains the amount of time (in seconds) that a pair spend together in a single video 1. Number of variables: 2 2. Number of rows: 133 3. Variable List: UNIQUE_TR_ID As above – unique identifier per video. TIME_TOG_TOTAL Time spent together in the nestbox in seconds. 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: None \######################################################################### DATA-SPECIFIC INFORMATION FOR: birthyear_sequoia.csv This file contains birth year and sex data on each individual used in the genomic analysis. 1. Number of variables: 5 2. Number of rows: 193 3. Variable List: ID ID of the jackdaw Sex Sex of the individual (1 is female, 2 is male) Birthyear Year of birth (NA = unknown) Minbirthyear If year of birth unknown, the minimum possible birth year Maxbirthyear If year of birth unknown, the maximum possible birth year 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: None \######################################################################### DATA-SPECIFIC INFORMATION FOR: site_sequoia.csv This file contains the site in which each individual was born. 1. Number of variables: 2 2. Number of rows: 4153 3. Variable List: ID ID of the jackdaw LOCATION Site where the jackdaw was born 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: None \######################################################################### DATA-SPECIFIC INFORMATION FOR: ped_sequoia.csv This file contains the dam and sire of each sampled individual 1. Number of variables: 3 2. Number of rows: 193 3. Variable List: id ID of the jackdaw dam mother of the individual. NA if unknown. sire father of the individual. NA if unknown. 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: None \######################################################################### DATA-SPECIFIC INFORMATION FOR: SNPS_site_X.ped This file contains the SNP data of each sequenced individual. Each individual is a row and columns G – ACV are sites. Please read .PED file documentation for more information on how to read this file. This file is for individuals from site X only. \######################################################################### DATA-SPECIFIC INFORMATION FOR: SNPS_site_YZ.ped This file contains the SNP data of each sequenced individual. Each individual is a row and columns G – AHW are sites. Please read .PED file documentation for more information on how to read this file. This file is for individuals from site Y and site Z only (merged due to gene flow between sites). \######################################################################### Forced-Extrapair-Copulations-in-Jackdaws.rmd Running this script, with the input data as stated above, will give you all the results for our behavioural analysis. \######################################################################### sequoia_script.R Running this script, with the input data, will give you all the results for our pedigree analysis. Sequoia help files clearly explain the data structure of each input file. Note you will need to download the version of Sequoia used in the script (described within). \######################################################################### Supplementary Videos 1 – 3 Example footage of internal nestbox footage. 1 and 2 are examples of attempted FEPC. 3 is an example of a within-pair copulation. Note the copulation call made by the male in each. In Video S2, the second individual to enter the nestbox is the resident male. \######################################################################### Supplementary Data.xlsx This file contains information on bird species without penises in which FEPCs have been observed. 1. Number of variables: 13 2. Number of rows: 49 3. Variable List: species (common) The common name of the species species (latin) The latin name of the species family The Family order The Order mating system* The mating system (U = unknown) colonial breeder* Whether the species is a colonial breeder or not (Y = yes, Y (sometimes) = sometimes, N = No) intruding male identityᶧ (PN:paired neighbouring male, N:neighbouring male, P:paired male, UP:unpaired male, U:no info; WPG:within-group male; EPG:extra-group male) Self-explanatory unforced extrapair copulations reportedᶧᶧ (Y: reported, N: not reported) in previous review whether the fact that this species engages in FEPC is in a previous review paper, and the review paper is reported. NA = Not reported in a previous review. ᶧprimary source of FEPC observation(s) Self-explanatory *Birds of the World citation Self-explanatory ᶧᶧsource of unforced extra-pair copulation observation(s) Self-explanatory Notes Any associated notes 4\. Missing data codes: NA/U 5\. Specialized formats or other abbreviations used: None \######################################################################### .Fastq files All raw samples that were successfully sequenced are shared (n = 190 individuals, n = 380 samples consisting of two reads per individual – R1 and R2). Please see the manuscript methods and Supplementary methods for full details on how these files were generated * Files are zipped in DRYAD (fq.gz) * All filtering steps are described in our methods (manuscript and supplementary materials)