Puritz Jonathan B, Matz Mikhail V, Toonen Robert J, Weber Jesse N, Bolnick Daniel I, Bird Christopher E
Marine Genomics Laboratory, Harte Research Institute, Texas A&M University-Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX, 78412-5869, USA.
Mol Ecol. 2014 Dec;23(24):5937-42. doi: 10.1111/mec.12965.
We are writing in response to the population and phylogenomics meeting review by Andrews & Luikart (2014) entitled 'Recent novel approaches for population genomics data analysis'. Restriction-site-associated DNA (RAD) sequencing has become a powerful and useful approach in molecular ecology, with several different published methods now available to molecular ecologists, none of which can be considered the best option in all situations. A&L report that the original RAD protocol of Miller et al. (2007) and Baird et al. (2008) is superior to all other RAD variants because putative PCR duplicates can be identified (see Baxter et al. 2011), thereby reducing the impact of PCR artefacts on allele frequency estimates (Andrews & Luikart 2014). In response, we (i) challenge the assertion that the original RAD protocol minimizes the impact of PCR artefacts relative to that of other RAD protocols, (ii) present additional biases in RADseq that are at least as important as PCR artefacts in selecting a RAD protocol and (iii) highlight the strengths and weaknesses of four different approaches to RADseq which are a representative sample of all RAD variants: the original RAD protocol (mbRAD, Miller et al. 2007; Baird et al. 2008), double digest RAD (ddRAD, Peterson et al. 2012), ezRAD (Toonen et al. 2013) and 2bRAD (Wang et al. 2012). With an understanding of the strengths and weaknesses of different RAD protocols, researchers can make a more informed decision when selecting a RAD protocol.
我们撰写此信是为了回应安德鲁斯和路易卡特（2014年）题为《群体基因组学数据分析的最新新方法》的群体与系统发育基因组学会议综述。限制性位点关联DNA（RAD）测序已成为分子生态学中一种强大且有用的方法，目前分子生态学家可以使用几种不同的已发表方法，在所有情况下都没有一种方法可被视为最佳选择。A&L报告称，米勒等人（2007年）和贝尔德等人（2008年）的原始RAD方案优于所有其他RAD变体，因为可以识别推定的PCR重复序列（见巴克斯特等人，2011年），从而减少PCR假象对等位基因频率估计的影响（安德鲁斯和路易卡特，2014年）。作为回应，我们（i）质疑原始RAD方案相对于其他RAD方案能将PCR假象的影响降至最低这一说法，（ii）指出RADseq中存在的其他偏差，这些偏差在选择RAD方案时至少与PCR假象一样重要，（iii）强调四种不同的RADseq方法的优缺点，这四种方法是所有RAD变体的代表性样本：原始RAD方案（mbRAD，米勒等人，2007年；贝尔德等人，2008年）、双酶切RAD（ddRAD，彼得森等人，2012年）、ezRAD（图嫩等人，2013年）和2bRAD（王等人，2012年）。了解不同RAD方案的优缺点后，研究人员在选择RAD方案时可以做出更明智的决定。
