Data from: The colour of paternity: extra-pair paternity in the wild Gouldian finch does not appear to be driven by genetic incompatibility between morphs

In socially monogamous species, individuals can use extra-pair paternity and offspring sex allocation as adaptive strategies to ameliorate costs of genetic incompatibility with their partner. Previous studies on domesticated Gouldian finches (Erythrura gouldiae) demonstrated a genetic incompatibility between head colour morphs, the effects of which are more severe in female offspring. Domesticated females use differential sex allocation, and extra-pair paternity with males of compatible head colour, to reduce fitness costs associated with incompatibility in mixed-morph pairings. However, laboratory studies are an oversimplification of the complex ecological factors experienced in the wild, and may only reflect the biology of a domesticated species. This study aimed to examine the patterns of parentage and sex-ratio bias with respect to colour pairing combinations in a wild population of the Gouldian finch. We utilized a novel PCR assay that allowed us to genotype the morph of offspring before the morph phenotype develops, and to explore bias in morph paternity and selection at the nest. Contrary to previous findings in the laboratory, we found no effect of pairing combinations on patterns of extra-pair paternity, offspring sex ratio, or selection on morphs in nestlings. In the wild, the effect of morph incompatibility is likely much smaller, or absent, than was observed in the domesticated birds. Furthermore, the previously studied domesticated population is genetically differentiated from the wild population, consistent with the effects of domestication. It is possible that the domestication process fostered the emergence (or enhancement) of incompatibility between colour morphs previously demonstrated in the laboratory.

Usage Notes
2009 GenotypesGenotypes for individuals caught in 2009 for CERVUS analysis. In CERVUS format. Age classes & sexes in the Readme.2009_genotypes.csv2008 GenotypesGenotypes for individuals used in CERVUS analysis caught in 2008. Readme includes the age and sex of individuals used.2008_genotypes.csvAdultsDetails for each Adult caught over 2008-2009.ChicksDetails of all offspring in this study including results from parentage analysis.Nest data for Spatial EPP analysisAll breeding observations in nestboxes and hollows (without genetic samples) at Wyndham in 2008-2009, including anonymised co-ordinates for nest locations, where inter nest differences are preserved but do not reflect the real position on the globe. README file also includes the code used to calculate the number of synchronous nests and how far away they are.Nests.csvGenotypes of Wild and Captive birdsGenotypes of the wild and captive birds in Arlequin format. Readme file includes the key that will allow the ID numbers to be broken down into which morph they are.WvC.arp

在社会单配制物种（socially monogamous species）中，个体可借助婚外父权（extra-pair paternity）与后代性别分配（offspring sex allocation）作为适应性策略，以缓解与配偶间遗传不相容性（genetic incompatibility）带来的适应性代价。此前针对驯养Gouldian雀（Gouldian finch，学名*Erythrura gouldiae*）的研究已证实其头部色型（head colour morphs）间存在遗传不相容性，且该效应在雌性后代中更为显著。驯养的雌性个体通过差异化性别分配，以及与头部色型匹配的雄性进行婚外父权交配，来降低混合色型配对中不相容性带来的适合度成本。然而，实验室研究对野外环境中复杂的生态因子存在过度简化，仅能反映驯养物种的生物学特性。本研究旨在探究Gouldian雀野生种群中，亲权模式与性别比例偏差相对于色型配对组合的分布规律。我们采用了一种新型聚合酶链式反应（PCR）检测法，可在色型表型（morph phenotype）显现前对后代的色型进行基因分型（genotype），并探索巢内父权的色型偏差与选择模式。与此前实验室研究结果相悖，本研究未发现配对组合对婚外父权模式、后代性别比例或雏鸟（nestlings）的色型选择存在显著影响。在野外环境中，色型不相容性的效应可能远小于驯养种群中观察到的结果，甚至不存在该效应。此外，此前研究所用的驯养种群与野生种群存在遗传分化（genetically differentiated），这与驯养过程（domestication）带来的效应相符。推测驯养过程可能催生（或强化）了实验室中已证实的色型间不相容性。

### 使用说明
2009年基因型数据：2009年捕获个体用于CERVUS分析（CERVUS analysis）的基因型文件，格式为CERVUS格式，年龄分组与性别信息详见Readme文件，文件名为2009_genotypes.csv。
2008年基因型数据：2008年捕获个体用于CERVUS分析的基因型文件，Readme文件包含所用个体的年龄与性别信息，文件名为2008_genotypes.csv。
成鸟信息：2008-2009年捕获的所有成鸟的详细记录。
雏鸟信息：本研究中所有后代的详细信息，包括亲权分析（parentage analysis）结果。
空间婚外父权分析巢数据：2008-2009年Wyndham地区巢箱与树洞中的所有繁殖观测记录（无遗传样本），包含巢位的匿名化坐标——保留了巢间差异，但不反映全球真实地理位置。README文件还包含用于计算同步巢数量及其间距的代码，文件名为Nests.csv。
野生与圈养鸟类基因型数据：以Arlequin格式（Arlequin format）存储的野生与圈养鸟类基因型数据。Readme文件包含可将ID编号拆解为对应色型的分类键值表，文件名为WvC.arp。