Dataset DOI: 10.5061/dryad.zkh1893qg

Description of the data and file structure

Data is sourced from a long-term study of purple-crowned fairy-wrens from approx 2005-2022, which includes social & genetic data to establish parentage, and regular censusing to establish survival & age. This allows estimation of both inbreeding (pedigree and genomic), and fitness measures including telomere length. 

Blood and DNA samples were sent to Diversity Arrays Technology (DArT Pty Ltd, Canberra, ACT, Australia) for reduced-representation sequencing. To estimate nestling telomere length, we used a relative qPCR method based on Criscuolo et al. (2009) which has been validated for use in purple-crowned fairy-wrens (Eastwood et al., 2018). For details see Eastwood et al. (2022).

Below, we have provided:

1. the original DArTseq data (allele counts Malurus_coronatus_DArTseq_counts.RDS and standard DArT format Malurus_coronatus_DArTseq_DArTcalls.RDS) our methods for applying genotype calling to the original DArTseq data (PCFW_gencall_script.R)
2. the script for analysing inbreeding depression in telomere length (Mcoro_telomere_SCRIPT.R) in using the dataset (modelT_data.RDS) and additive genetic relatedness matrix (modelT_Amat.RDS).

Files and variables

File: Mcoro_telomere_DRYAD.zip

Description: 

SCRIPT: PCFW_gencall_script.R

DATA: 

• Malurus_coronatus_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_coronatus_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.
• 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: Mcoro_telomere_SCRIPT.R

DATA:

•  modelT_data.RDS
  A dataframe with individuals (ID), telomere length measured from nestling blood samples, F_GRM, and other variables. A detailed breakdown of variable naming conventions are provided below and in comments in the script. 
• modelT_Amat.RDS
  A matrix demonstrating the additive genetic relatedness between individuals (ID) 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. Table values represent the additive genetic relatedness between the two individuals of the relevant column and row.

PARAMETERS:

• ID: unique individual ID number (note this is deidentified)
• NestlingTelomere: relative telomere length measured from nestling blood samples
• FGRM: genomic inbreeding (Fhat3) measure
• Age: age of nestling (days) when sampled
• Sex: factor male/female
• BroodSize: number of chicks in brood
• HatchSeason: factor dry/wet describing season in which chick hatched
• NumberHelpers: factor (0, 1, 2+) describing the number of helpers associated with that brood of chicks
• NatalTerritoryQuality: variable describing quality of natal territory on which chick hatched
• NestlingAvgTmax: variable describing mean maximum temperature during nestling phase from hatching to 7 days
• Water_available: factor high/low describing a combination of rainfall in nestling period and hatch season
• NestID: factor accounting for nest (i.e. for each brood)
• Cohort: factor accounting for year individual hatched in (e.g. 2006 cohort being birds hatched July 2006 through June 2007)
• Mother: mother of individual (often genetically validated, alongside social data - deidentified ID)
• Father: father of individual (often genetically validated, alongside social data - deidentified ID)
• Maternal.FGRM: genomic inbreeding of mother
• Paternal.FGRM: genomic inbreeding of father
• Maternal.age: age of mother at conceptions (days)
• Paternal.age: age of father at conception (days)

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
• ggplot2 v 3.5.1
• ggpubr v 0.6.0

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