Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA,
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA, Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA, and.
Syst Biol. 2016 Sep;65(5):910-24. doi: 10.1093/sysbio/syw036. Epub 2016 Jun 10.
Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two genomic enrichment strategies for applying next-generation sequencing technologies to systematics studies. At shallow timescales, such as within species, RAD-Seq has been widely adopted among researchers, although there has been little discussion of the potential limitations and benefits of RAD-Seq and sequence capture. We discuss a series of issues that may impact the utility of sequence capture and RAD-Seq data for shallow systematics in non-model species. We review prior studies that used both methods, and investigate differences between the methods by re-analyzing existing RAD-Seq and sequence capture data sets from a Neotropical bird (Xenops minutus). We suggest that the strengths of RAD-Seq data sets for shallow systematics are the wide dispersion of markers across the genome, the relative ease and cost of laboratory work, the deep coverage and read overlap at recovered loci, and the high overall information that results. Sequence capture's benefits include flexibility and repeatability in the genomic regions targeted, success using low-quality samples, more straightforward read orthology assessment, and higher per-locus information content. The utility of a method in systematics, however, rests not only on its performance within a study, but on the comparability of data sets and inferences with those of prior work. In RAD-Seq data sets, comparability is compromised by low overlap of orthologous markers across species and the sensitivity of genetic diversity in a data set to an interaction between the level of natural heterozygosity in the samples examined and the parameters used for orthology assessment. In contrast, sequence capture of conserved genomic regions permits interrogation of the same loci across divergent species, which is preferable for maintaining comparability among data sets and studies for the purpose of drawing general conclusions about the impact of historical processes across biotas. We argue that sequence capture should be given greater attention as a method of obtaining data for studies in shallow systematics and comparative phylogeography.
序列捕获和限制位点相关 DNA 测序 (RAD-Seq) 是两种基因组富集策略，可将下一代测序技术应用于系统发育研究。在较短的时间尺度内，例如在物种内，RAD-Seq 已被研究人员广泛采用，尽管对于 RAD-Seq 和序列捕获的潜在局限性和优势还很少有讨论。我们讨论了一系列可能影响非模式物种浅系统发育中序列捕获和 RAD-Seq 数据实用性的问题。我们回顾了使用这两种方法的先前研究，并通过重新分析来自新热带鸟类 (Xenops minutus) 的现有 RAD-Seq 和序列捕获数据集来研究两种方法之间的差异。我们建议，RAD-Seq 数据集在浅系统发育中的优势在于标记在基因组中的广泛分布、实验室工作的相对容易和成本、回收基因座的深度覆盖和读取重叠，以及产生的高总体信息量。序列捕获的优势包括靶向基因组区域的灵活性和可重复性、使用低质量样本的成功、更直接的读取同源性评估以及更高的每个基因座信息量。然而，一种方法在系统发育学中的实用性不仅取决于其在研究中的表现，还取决于数据集和推断与先前工作的可比性。在 RAD-Seq 数据集中，跨物种同源标记的低重叠和数据集中遗传多样性对所研究样本的自然杂合度水平与同源性评估使用的参数之间相互作用的敏感性会影响可比性。相比之下，保守基因组区域的序列捕获允许在不同物种中检测相同的基因座，这对于保持数据集和研究之间的可比性以及为在生物群中绘制历史过程影响的一般结论提供了更好的方法。我们认为，序列捕获作为获取浅系统发育和比较系统地理学研究数据的方法应该得到更多关注。
