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

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. 

Methods
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.