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.

个体间的遗传关系信息，对诸多野生生物的行为与生态学研究而言至关重要。基于大量单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点的亲权鉴定与亲缘关系分析，相较于传统用于此类研究的微卫星标记，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；该流程经优化后，可从大量个体（单次运行最多可处理240个）中获取一组统计效力强劲的SNP标记，经严格过滤后通常为150~600个。我们针对具有复杂社会系统的杂色细尾鹩莺（Malurus lamberti）开展一系列实验，以此探究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该流程的有效性。通过与基于一套稳健高变异微卫星标记组合的平行数据集进行直接对比，我们证实该ddRAD-seq方法可显著提升潜在亲缘关系的鉴别效力，并能更为精准地估算亲缘系数。该流程设计为可通用适配所有鸟类，稍加修改即可适用于多数其他生物类群；兼具成本与时间效益，且可在独立运行间实现重复，从而支持随野外样本的积累，将不同研究时期获得的基因型数据进行合并分析。