Dataset DOI: 10.5061/dryad.9cnp5hqwb

Description of the data and file structure

Data is sourced from a long-term study of superb fairy-wrens from approx 1988-2020, which includes social & genetic data to establish parentage, and regular censusing to establish survival. This allows estimation of both inbreeding (pedigree and genomic), and fitness measures (nestling condition, juvenile survival, adult lifespan and adult fitness). 

Blood and DNA samples were sent to Diversity Arrays Technology (DArT Pty Ltd, Canberra, ACT, Australia) for reduced-representation sequencing.

Below, we have provided:

1. The original DArTseq data (allele counts Malurus_cyaneus_DArTseq_counts.RDS and standard DArT format Malurus_cyaneus_DArTseq_DArTcalls.RDS) and our methods for applying genotype calling to the original DArTseq data (SFW_ID_gencallscript.R).
2. the script for analysing inbreeding depression in various fitness traits (SFW_ID_modelscript.R) using a number of datasets and additive genetic relatedness matrices. 
3. our methods for analysing immigrant genetic contributions (SFW_ID_immcontscript.R)

Files and variables

SCRIPT: SFW_ID_gencallscript.R

DATA: 

• Malurus_cyaneus_DArTseq_counts.RDS
  A table containing the allele count data from DArT in raw format. The table includes metadata for alleles (columns 1:30) and individuals (rows 1:7). A detailed breakdown of metadata variable naming conventions are provided below. Values represent the sequencing count of alleles for that individual and allele/loci. Loci (being two alleles) occur over two rows. 
• Malurus_cyaneus_DArTseq_DArTcalls.RDS
  A genlight object containing default genotype calls for loci and individuals. Created by reading standard DArT data using gl.read.dart() from the package dartR.
  Genlight objects are designed to store tabular genetic data and associated metadata. When in matrix format, row names represent a unique individual ID (e.g. ID_001) and columns names represent a unique loci name (e.g. 68193903-25-C/G). Values represent genotype call for that individual and loci, where 0/2 = Homozygous, 1 = Heterozygous and NA = genotype missing. 

PARAMETERS FOR LOCI METADATA: 

• AlleleID and CloneID: the unique ID of that loci (e.g. 68193903-25-C/G) and clone (e.g. 68193903)
• AlleleSequence and TrimmedSequence: the genetic sequence for that allele and a trimmed version of the genetic sequence
• Chrom_Malurus_cyaneus_v2, ChromPosTag_Malurus_cyaneus_v2, ChromPosSnp_Malurus_cyaneus_v2, AlnCnt_Malurus_cyaneus_v2, AlnEvalue_Malurus_cyaneus_v2 and Strand_Malurus_cyaneus_v2: parameters associated with the mapping of the locus to the Malurus cyaneus genome, including the chromosome, tag position, SNP position, number of locations the locus was mapped against, mapping e-value, and DNA strand for that allele.
• Chrom_Yellow_robin_HiC_v2, ChromPosTag_Yellow_robin_HiC_v2, ChromPosSnp_Yellow_robin_HiC_v2, AlnCnt_Yellow_robin_HiC_v2, AlnEvalue_Yellow_robin_HiC_v2 V16 and Strand_Yellow_robin_HiC_v2: parameters associated with the mapping of the locus to the Yellow Robin genome, including the chromosome, tag position, SNP position, number of locations the locus was mapped against, mapping e-value, and DNA strand for that allele.
• Chrom_Zebra_finch_v1p, ChromPosTag_Zebra_finch_v1p, ChromPosSnp_Zebra_finch_v1p, AlnCnt_Zebra_finch_v1p, AlnEvalue_Zebra_finch_v1p and Strand_Zebra_finch_v1p: parameters associated with the mapping of the locus to the Zebra Finch genome, including the chromosome, tag position, SNP position, number of locations the locus was mapped against, mapping e-value, and DNA strand for that allele.
• SNP and SnpPosition indicate the position within the genetic sequence where the single nucleotide polymorphism is located (e.g SnpPosition = 25), and for the variant allele, the character of that polymorphism (e.g. SNP = 25:C>G) 
• A number of standard parameters auto-calculated by DArT are also included, including CallRate, OneRatioRef, OneRatioSnp, FreqHomRef, FreqHomSnp, FreqHets, PICRef, PICSnp, AvgPIC, AvgCountRef, AvgCountSnp and RepAvg. Please refer to DArT and dartR documentation for further information on these parameters.

PARAMETERS FOR INDIVIDUAL METADATA:

• Row 1 contains information on the individual DArT order in which individuals where submitted (e.g. DMal22-7426)
• Row 2 and 3 contain the unique barcode number for each 96-well plate (e.g. 911122259002), and the unique plate number (e.g. 18)
• Row 4 and 5 contain the row and column of the 96-well plate that the individual sample was placed in (e.g. A and 1)
• Row 6 contains additional information about the sample storage buffer, volume and DNA concentration. 

SCRIPT: SFW_ID_modelscript.R

DATA:

• modelX_data.RDS
  • For each model, a dataframe with at a minimum, individuals (IID) and F_ROH (ROH_totalkb_perc). A detailed breakdown of variable naming conventions are below and in comments in the script. 
• modelX_Amat.RDS
  • For each model, a matrix demonstrating the additive genetic relatedness between individuals (IID) based on the full population pedigree. Column and row names denote the unique individual ID number that corresponds to that column and row. These IDs align with 'ID' parameter described below for each model dataset. Table values represent the additive genetic relatedness between the two individuals of the relevant column and row.

FITNESS PARAMETERS:

• Nestling_weight = Weight (in grams) of nestlings
• Survto41days = Binary did not (0) or did (1) survive from fledging (at 12 days) to independence (41 days old)
• Survto1year = Binary did not (0) or did (1) survive from independence through first overwinter period
• Lifespan = length (days) between hatch date and disappearance from population
• LRS.indep = number of LRS that survive to 41 days
• LRS.WPP.indep = number of LRS sired within-pair that survive to 41 days
• LRS.EPP.indep = number of LRS sired extra-pair that survive to 41 days

OTHER PARAMETERS:

• IID = individual ID (note this is deidentified and randomised across models)
• Sex = M male, F female
• Broodsize = the number of nestlings in a brood
• Helpers.fac = factor (0, 1, 2+) describing the number of helpers associated with that brood of chicks
• Age.if.nestling = age (days) of nestling when banded and weighed
• Age.if.nestling.sq = age (days) of nestling when banded and weighed SQUARED (for quadratic growth expression)
• Nestling_weightProtocol = factor (1992 onwards, Pre 1992) describing which weighing protocol was used
• Nest = factor accounting for nest (i.e. for each brood)
• Mum = mother of individual (usually genetically validated, alongside social data)
• hatch.fortnight = factor 1-14 accounting for intra-annual variation, splitting the breeding season into fortnight intervals from 9 September to 15 March
• Cohort = factor accounting for season individual hatched in (i.e. 2020 cohort includes individuals hatched from September 2020 through March 2021)
• Nestling_weight_mod = modified nestling Nestling_weight variable adjusted based on on age of nestling and weighing protocol (from model 1)
• MeanMax = mean maximum temperature over period 1 April to 1 August
• MeanMin = mean minimum temperature over period 1 April to 1 August
• Breeding.span = number of breeding seasons where individual was alive as a breeder (i.e. adult)
• Social.span = number of breeding seasons where a male held a territory as a dominant male (i.e. social partner)

SCRIPT: SFW_ID_immcontscript.R

DATA: 

• unicorns.txt
  A text file containing information for a pedigree of mythical creatures. 
• VARIABLES:
  • ID: individual identifie
  • MOTHER: genetic mother identifier
  • FATHER: genetic father identifier
  • FIRSTDATE: date hatch / first known in pop
  • LASTDATE: death date / date last seen - if not known, set as a future date
  • STATUS: a factor indicating if individuals are from the core population, or immigrants: "CORE", "IMM"

Code/software

Scripts provided were all written and run in R version 4.2.1, and using packages:

• dartR v 2.9.7
• dplyr v 1.1.2
• brms v 2.19.0
• pedigreemm v 0.3.4
• reshape2 v 1.4.4
• ggplot2 v 3.5.1
• viridis v 0.6.2