Data from: Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: a proof of concept in a highly promiscuous bird

Information on genetic relationships among individuals is essential to many studies of the behavior and ecology of wild organisms. Parentage and relatedness assays based on large numbers of SNP loci hold substantial advantages over the microsatellite markers traditionally used for these purposes. We present a double-digest restriction site-associated DNA sequencing (ddRAD-seq) analysis pipeline that, as such, simultaneously achieves the SNP discovery and genotyping steps and which is optimized to return a statistically powerful set of SNP markers (typically 150-600 after stringent filtering) from large numbers of individuals (up to 240 per run). We explore the tradeoffs inherent in this approach through a set of experiments in a species with a complex social system, the variegated fairy-wren (Malurus lamberti), and further validate it in a phylogenetically broad set of other bird species. Through direct comparisons with a parallel dataset from a robust panel of highly variable microsatellite markers, we show that this ddRAD-seq approach results in substantially improved power to discriminate among potential relatives and considerably more precise estimates of relatedness coefficients. The pipeline is designed to be universally applicable to all bird species (and with minor modifications to many other taxa), to be cost- and time-efficient, and to be replicable across independent runs such that genotype data from different study periods can be combined and analyzed as field samples are accumulated.个体间遗传关系信息，对诸多野生生物行为与生态学研究至关重要。相较于传统用于此类研究的微卫星标记，基于大量单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点的亲权与亲缘关系鉴定分析，具备显著优势。本研究提出一套双酶切限制性位点相关DNA测序（double-digest restriction site-associated DNA sequencing, ddRAD-seq）分析流程，可同步完成SNP发现与基因分型步骤，且经优化后能够从大量个体（单次运行最多可处理240个样本）中获取一套统计学效力优异的SNP标记集（经严格过滤后通常可保留150~600个标记）。我们以具有复杂社会系统的杂色细尾鹩莺（Malurus lamberti）为实验对象，通过一系列实验探究了该方法固有的权衡取舍，并在系统发育覆盖范围广泛的其他鸟类类群中进一步验证了该流程的有效性。通过与一组经过验证的高变异微卫星标记的平行数据集进行直接对比，我们证实：该ddRAD-seq方法可大幅提升鉴别各类潜在亲缘个体的能力，并显著提升亲缘系数的估算精度。该分析流程设计为可广泛适配所有鸟类（经小幅修改后亦可应用于多数其他生物类群），兼具成本效益与时间效率，且可在独立实验中重复实施，因此能够随着野外样本的累积，整合不同研究周期获得的基因型数据并开展联合分析。