Data from: A likelihood-based approach for assessment of extra-pair paternity and conspecific brood parasitism in natural populations

Genotypes are frequently used to assess alternative reproductive strategies such as extra-pair paternity and conspecific brood parasitism in wild populations. However, such analyses are vulnerable to genotyping error or molecular artefacts that can bias results. For example, when using multilocus microsatellite data, a mismatch at a single locus, suggesting the offspring was not directly related to its putative parents, can occur quite commonly even when the offspring is truly related. Some recent studies have advocated an ad-hoc rule that offspring must differ at more than one locus in order to conclude that they are not directly related. While this reduces the frequency with which true offspring are identified as not directly related young, it also introduces bias in the opposite direction, wherein not directly related young are categorized as true offspring. More importantly, it ignores the additional information on allele frequencies which would reduce overall bias. In this study, we present a novel technique for assessing extra-pair paternity and conspecific brood parasitism using a likelihood-based approach in a new version of program cervus. We test the suitability of the technique by applying it to a simulated data set and then present an example to demonstrate its influence on the estimation of alternative reproductive strategies.基因型（Genotypes）常被用于评估野生种群中的替代繁殖策略，例如婚外父权（extra-pair paternity）与同种巢寄生（conspecific brood parasitism）。然而此类分析易受基因分型误差（genotyping error）与分子伪迹（molecular artefacts）的干扰，进而导致结果出现偏差。例如，在使用多位点微卫星数据时，即便后代与疑似亲本（putative parents）确实存在直接亲缘关系，单一位点的基因分型错配——即提示后代与疑似亲本无直接亲缘关系的情况——也可能频繁发生。近期部分研究提出了一项特设规则（ad-hoc rule）：若要判定后代与亲本无直接亲缘关系，需确保二者在至少两个位点上存在基因型差异。尽管该规则可降低将真实亲缘后代误判为非直接亲缘个体的概率，但同时也会引入反向偏差，即将非直接亲缘个体归类为真实亲缘后代。更为关键的是，该规则忽略了等位基因频率（allele frequencies）这一可降低整体偏差的额外信息。本研究基于新版Cervus程序（program cervus）中的基于似然的方法（likelihood-based approach），提出了一种用于评估婚外父权与同种巢寄生的全新技术。我们通过将该技术应用于模拟数据集以验证其适用性，并通过实例展示其对替代繁殖策略估算的影响。