DOI: 10.5061/dryad.cz8w9gj7w
title: Code and datasets associated with: A sex-linked supergene with large effects on sperm traits has little impact on reproductive traits in female zebra finches

description: Despite constituting an essential component of fitness, reproductive
 success can vary remarkably between individuals and the causes of such
 variation are not well understood across taxa. In the zebra finch – a
 model songbird, almost all the variation in sperm morphology and swimming
 speed is maintained by a large polymorphic inversion (commonly known as a
 supergene) on the Z chromosome. The relationship between this polymorphism
 and reproductive success is not fully understood, particularly for
 females. Here, we explore the effects of female haplotype, and the
 combination of male and female genotype, on several primary reproductive
 traits in a captive population of zebra finches. Despite the inversion
 polymorphism’s known effects on sperm traits, we find no evidence that
 inversion haplotype influences egg production by females or survival of
 embryos through to hatching. However, our findings do reinforce existing
 evidence that the inversion polymorphism is maintained by a heterozygote
 advantage for male fitness. This work provides an important step in
 understanding the causes of variation in reproductive success in this
 model species. 
description: The dataset has been curated primarily from SNP genotyping data
 collected as part of this study in 2019 and 2022, with some additional SNP
 data obtained from a separate study (see Kim et al., 2017). Breeding data
 originates from a breeding database for a population of domesticated zebra
 finches maintained at The University of Sheffield between 1985 and
 2016. Birds from this population were bred in single
 pairs without access to other individuals, where no natural mate choice
 was permitted, and where the paternity was conclusively known for every
 egg. Data was collected on parental identity (ring number), parental age,
 number of breeding attempts per pair, number of eggs laid per breeding
 attempt (clutch), the fertility/development status of the eggs at 3 days
 of incubation (by candling), the outcome of every egg (hatching success),
 and offspring sex. Genotyping data included the SNP Z
 chromosome supergene genotypes for males and females, determined by
 KASP-genotyping on an LGC SNPLine system using tissue samples from frozen
 stored birds.
description: Code created in R (v 4.2.1). Data files are
 all in .csv format. Packages required: brms, Matrix,
 tidyverse, dplyr, tidybayes, bayestestR, bayesplot, posterior, ggpubr,
 cowplot, gghalves, modelr
description: # Code and datasets associated with: A sex-linked supergene with large
 effects on sperm traits has little impact on reproductive traits in female
 zebra finches ## Dataset structure Five separate sheets of data are
 provided corresponding to the five primary analyses: 1) Egg Production, 2)
 Egg fertility and early embryo development, 3) Hatching success of
 developing eggs, 4) Offspring sex ratio and 5) Offspring genotype. An
 additional data sheet (6) is provided for the diagnostic SNP information,
 and raw cluster analysis output. ### Datasets **1) EggProductionBCBoth:**
 Dataset for the egg production analysis, formatted by clutch (each row is
 a separate clutch). **2) DevelopedBoth:** Dataset for the fertility/early
 development analysis, formatted by pair (each row is a separate pair).
 **3) HatchedBoth:** Dataset for the hatching success of developed eggs
 analysis, formatted by pair (each row is a separate pair). **4)
 Sex_data:** Dataset for the offspring sex ratio analysis, formatted by
 clutch (each row is a separate clutch) **5) OffspringGenotypes:** Dataset
 for the offspring genotype analysis (each row is a separate
 individual/offspring) **6) GenotypeCalling.SNPInfo:** Diagnostic SNP info,
 used for calling genotypes, and the raw output from the cluster analysis
 (for the data collected in the current study, excluding the additional Kim
 et al. (2017) data). ### Variables common to all datasets: **NewPairNo** A
 unique pair ID **MotherRing** Unique ID for the female of the pair
 **FatherRing** Unique ID for the male of the pair **AllelesShared** Number
 of supergene haplotypes shared between the male and female in a pair
 **Combination** The combination of male and female Z chromosome supergene
 genotypes **FatherGenotype** Z chromosome supergene genotype for the
 father **MotherGenotype** Z chromosome supergene genotype for the mother
 **FatherAgeFirstLay** Father age (in years) at the first egg laid for that
 pair **MotherAgeFirstLay** Mother age (in years) at the first egg laid for
 that pair **FatherAgeAtLay_Z** Father age at the first egg laid for that
 pair, Z-scored (scaled and mean centered) **MotherAgeAtLay_Z** Mother age
 at the first egg laid for that pair (scaled and mean centered)
 **MBirthYear** Year the mother was born **NA** No data available. In
 GenotypeCalling.SNPInfo, NA's are due to ambiguous genotype calling
 during cluster analysis for that SNP. ### Variables specific to
 'EggProductionBCBoth': **TotalEggs** The total number of eggs
 laid per pair across all clutches **TotalClutches** The total number of
 clutches/attempts per pair **ClutchNumber** Which clutch in the series the
 row corresponds to **Eggs** The number of eggs laid within a clutch
 **EggsP** The number of eggs laid within a clutch plus 1 (to remove
 0's for statistical analysis) ### Variables specific to
 'DevelopedBoth': **Developed** The number of eggs laid by that
 pair that had a visible embryo at day 3 of incubation **Undeveloped** The
 number of eggs laid by that pair that did not have a visible embryo at day
 3 of incubation **Hatched** The number of eggs laid by that pair that
 successfully hatched **NoClutches** Number of clutches laid by pair ###
 Variables specific to 'HatchedBoth': **NoClutches** The number
 of clutches laid by pair **Hatched** The number of developed eggs (eggs
 with a visible embryo at 3 days of development) that also hatched
 **Failed** The number of developed eggs (eggs with a visible embryo at 3
 days of development) that failed to hatch ### Variables specific to
 'Sex\_data': **AttemptNo** Which clutch in series the row
 corresponds to **Eggs** The number of eggs laid in the clutch
 **FemaleOffspring** The number of eggs in that clutch that were female
 **MaleOffspring** The number of eggs in that clutch that were male ###
 Variables specific to 'OffspringGenotype': **HatchDate**
 Offspring hatch date **Ring** Unique offspring ID **OffspringGenotype**
 Offspring genotype