quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage
quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage
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DOI：
10.1111/mec.14077
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发表时间：
2017-05-01
影响因子：
4.9
通讯作者：
Meyer, Axel
中科院分区：
文献类型：
--
作者：
Franchini, Paolo;Parera, Daniel Monne;Meyer, Axel
识别基因组中数以千计的变异并对其进行准确的基因分型对于估计解决一系列分子、生态和进化问题所需的遗传参数至关重要。随着大规模并行高通量测序技术的快速发展，最近已经开发出几种方法来访问关于种群变异的全基因组数据。最成功和最广泛使用的技术之一依赖于限制性内切酶和合成测序的结合：限制位点相关DNA测序(RADSeq)。我们开发了一种新的、更具时间和成本效益的双消化RAD配对端协议(QuaddRAD)，它简化和加快了PCR副本的识别，并允许大规模多路复用。在一个技术数据集上评估了它的性能，我们还应用了QuaddRAD方法在一个新热带慈鱼种群样本上评估了它的遗传结构和人口历史。虽然我们确定了异地湖间遗传差异，很可能是由漂移驱动的，但没有检测到共面差异的特征。这不同于在Midas cichlids分支中观察到的情况，该分支生活在相同的湖泊中，有着相似的人口学历史，但通过同域物种形成进化成了小规模的适应性辐射。我们证明了QuaddRAD是一种稳健而有效的方法，可以高精度地对大量和广泛重叠的基因座进行基因分型。此外，关于中央尖吻吸虫的研究结果开辟了新的研究途径，为研究基因组水平的机制提供了一个理想的系统，这些机制可能会改变不同但密切相关的慈鱼谱系的物种形成潜力。
The identification of thousands of variants across the genomes and their accurate genotyping are crucial for estimating the genetic parameters needed to address a host of molecular ecological and evolutionary questions. With rapid advances of massively parallel high-throughput sequencing technologies, several methods have recently been developed to access genomewide data on population variation. One of the most successful and widely used techniques relies on the combination of restriction enzymes and sequencing-by-synthesis: restriction-site-associated DNA sequencing (RADSeq). We developed a new, more time- and cost-efficient double-digest RAD paired-end protocol (quaddRAD) that simplifies and speeds up the identification of PCR duplicates and permits large-scale multiplexing. Assessing its performance on a technical data set, we also applied the quaddRAD method on population samples of a Neotropical cichlid fish lineage (Archocentrus centrarchus) to assess its genetic structure and demographic history. While we identified allopatric interlake genetic divergence, most likely driven by drift, no signature of sympatric divergence was detected. This differs from what has been observed in the clade of Midas cichlids (Amphilophus citrinellus spp.), another cichlid lineage that inhabits the same lakes and shares a similar demographic history, but has evolved into small-scale adaptive radiations via sympatric speciation. We demonstrate that quaddRAD is a robust and efficient method for genotyping a massive number and widely overlapping set of loci with high accuracy. Furthermore, the results on A.centrarchus open new research avenues providing an ideal system to investigate genome-level mechanisms that could alter the speciation potential of different but closely related cichlid lineages.