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 a..., 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 s..., 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, # 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, formatte...尽管繁殖成功率是适合度的核心组成部分，但个体间的繁殖成功率差异显著，且此类差异的成因在各生物类群中仍未得到充分阐释。在作为模式鸣禽的斑胸草雀中，精子形态与游动速度的几乎全部变异均由Z染色体（Z chromosome）上的大型多态性倒位（通常称为超基因（supergene））所维持。该多态性与繁殖成功率之间的关联尚未完全阐明，尤其在雌性个体中。本研究以圈养斑胸草雀种群为对象，探讨雌性单倍型以及雌雄基因型组合对多项核心繁殖性状的影响。尽管已知该倒位多态性对精子性状具有显著影响，但我们并未发现证据表明倒位单倍型会影响雌性的产卵量或胚胎至孵化阶段的存活率。不过，本研究结果确实支持了现有证据，即该倒位多态性由杂合子维持[原文截断]。 本数据集主要整理自本研究2019年与2022年采集的单核苷酸多态性（SNP, single nucleotide polymorphism）基因分型数据，另有部分SNP数据来自另一项研究（详见Kim et al., 2017）。繁殖数据源自谢菲尔德大学1985年至2016年间维持的驯化斑胸草雀种群的繁殖数据库。 该种群的个体以单对饲养，不接触其他个体，且不允许自然择偶，每一枚卵的父本均已明确。采集的数据包括亲本标识（脚环编号）、亲本年龄、每对个体的繁殖尝试次数、每次繁殖尝试的产卵数（窝卵数）、孵化3天时通过照蛋法检测的卵的受精/发育状态、每枚卵的最终结局（孵化成功率）以及后代性别。 基因分型数据涵盖雌雄个体的Z染色体超基因（supergene）SNP基因型，通过LGC SNPLine平台的KASP基因分型技术（KASP-genotyping）完成测定[原文截断]。本研究代码基于R语言（v4.2.1）编写。 所有数据文件均采用.csv格式。所需R包包括：brms、Matrix、tidyverse、dplyr、tidybayes、bayestestR、bayesplot、posterior、ggpubr、cowplot、gghalves、modelr。# 关联代码与数据集：《性连锁超基因对精子性状影响显著，但对雌性斑胸草雀繁殖性状影响微弱》 ## 数据集结构 本数据集包含5个独立数据表，对应5项核心分析：1）产卵量分析、2）卵受精与早期胚胎发育分析、3）发育卵的孵化成功率分析、4）后代性别比例分析、5）后代基因型分析。另有第6个数据表，用于提供诊断性SNP信息与聚类分析原始输出结果。 ### 数据集详情 **1) "EggProductionBCBoth":** 用于产卵量分析的数据集，以窝为单位整理（每一行代表一个独立的产卵窝）。 **2) "DevelopedBoth":** 用于卵受精与早期发育分析的数据集，以繁殖对为单位整理（每一行代表一个独立的繁殖对）。 **3) "HatchedBoth":** 用于发育卵孵化成功率分析的数据集，以繁殖对为单位整理（每一行代表一个独立的繁殖对）。 **4) "Sex_data":** 用于后代性别比例分析的数据集[原文截断]。