Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens.
Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens.
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DOI：
10.1002/ece3.3065
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发表时间：
2017-07
影响因子：
2.6
通讯作者：
Dumbacher JP
中科院分区：
文献类型：
--
作者：
Linck EB;Hanna ZR;Sellas A;Dumbacher JP
高通量测序的实验室技术增强了我们从分子时代之前收集的数百万自然历史标本中生成DNA序列数据的能力，但在较浅的进化时间尺度上仍然缺乏测试。利用限制性内切位点相关DNA探针（hyRAD）进行杂交捕获是最近发展起来的一种博物馆标本群体基因组学方法。hyRAD方法采用限制性内切位点相关的双重消化产生的片段作为捕获感兴趣样品中同源位点的探针的基础。虽然它不需要参考基因组，但hyRAD尚未在独立实验室的研究系统中应用。在这里，我们提供了一个独立的评估hyRAD对新鲜鸟类组织和博物馆标本的干燥组织的有效性，并研究了不同数量的输入DNA如何影响测序、组装和群体遗传推断。我们提出了一个改进的台架协议和生物信息学管道，包括三个步骤检测和去除微生物和线粒体DNA污染物。我们证实hyRAD是一种有效的工具，可以从历史博物馆标本中取样数以千计的同源snp来描述系统地理模式。我们发现，在测序过程中，现代DNA的表现明显好于历史DNA，但装配性能在很大程度上是相同的。我们还发现，输入DNA的数量可以预测组装的连续序列的GC含量，这表明PCR存在偏差。我们对包括现代和历史样本的分类或地理自相关的抽样方案提出了警告。
Laboratory techniques for high‐throughput sequencing have enhanced our ability to generate DNA sequence data from millions of natural history specimens collected prior to the molecular era, but remain poorly tested at shallower evolutionary time scales. Hybridization capture using restriction site‐associated DNA probes (hyRAD) is a recently developed method for population genomics with museum specimens. The hyRAD method employs fragments produced in a restriction site‐associated double digestion as the basis for probes that capture orthologous loci in samples of interest. While promising in that it does not require a reference genome, hyRAD has yet to be applied across study systems in independent laboratories. Here, we provide an independent assessment of the effectiveness of hyRAD on both fresh avian tissue and dried tissue from museum specimens up to 140 years old and investigate how variable quantities of input DNA affect sequencing, assembly, and population genetic inference. We present a modified bench protocol and bioinformatics pipeline, including three steps for detection and removal of microbial and mitochondrial DNA contaminants. We confirm that hyRAD is an effective tool for sampling thousands of orthologous SNPs from historic museum specimens to describe phylogeographic patterns. We find that modern DNA performs significantly better than historical DNA better during sequencing but that assembly performance is largely equivalent. We also find that the quantity of input DNA predicts %GC content of assembled contiguous sequences, suggesting PCR bias. We caution against sampling schemes that include taxonomic or geographic autocorrelation across modern and historic samples.