A framework phylogeny of the American oak clade based on sequenced RAD data.
A framework phylogeny of the American oak clade based on sequenced RAD data.
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DOI：
10.1371/journal.pone.0093975
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Manos PS
中科院分区：
文献类型：
--
作者：
Hipp AL;Eaton DA;Cavender-Bares J;Fitzek E;Nipper R;Manos PS
以往的系统发育研究橡树（栎属，壳斗科）未能解决的骨干拓扑结构的有力支持。在这里，我们利用限制性位点相关DNA（RAD-Seq）的下一代测序来解决一个主要是美国橡树的分支，其冠龄估计为23-33万年的框架遗传。使用最近开发的用于RAD-Seq测序遗传学的分析管道，我们创建了1.40 E06比对核苷酸的级联矩阵，构成27，727个序列簇。RAD-Seq数据很容易跨运行组合，技术重复之间的系统发育位置没有差异，其在基因座覆盖率上仅重叠43-64%。我们分析的17%（4，715）的基因座可以以高置信度定位到NCBI Genbank中的一个或多个表达序列标签。BLAST到至少一个EST序列的基因座的级联矩阵提供了与来自非EST基因座的相等大小的数据集大约一半的可变或简约信息字符。EST相关的矩阵是更完整的（更少的缺失位点），并具有较低的同源性比非EST子采样矩阵相同的大小，但没有显着差异的系统发育支持或相对归因的碱基替换内部与终端分支的同源性。我们介绍了分区RAD可视化方法（在R包RADami实现; http：//cran.r-project.org/web/packages/RADami）调查的可能性，次优拓扑支持大量的loci，由于，例如，网状进化或谱系排序被掩盖的全局最优树。我们在研究中没有发现强有力的替代拓扑结构的证据，这表明我们恢复的系统发育是对美国橡树进化枝中大规模系统发育模式的可靠估计。我们的研究是第一个证明RAD-Seq数据在2300 - 3300万年的进化枝中推断进化的实用性的研究之一。
Previous phylogenetic studies in oaks (Quercus, Fagaceae) have failed to resolve the backbone topology of the genus with strong support. Here, we utilize next-generation sequencing of restriction-site associated DNA (RAD-Seq) to resolve a framework phylogeny of a predominantly American clade of oaks whose crown age is estimated at 23–33 million years old. Using a recently developed analytical pipeline for RAD-Seq phylogenetics, we created a concatenated matrix of 1.40 E06 aligned nucleotides, constituting 27,727 sequence clusters. RAD-Seq data were readily combined across runs, with no difference in phylogenetic placement between technical replicates, which overlapped by only 43–64% in locus coverage. 17% (4,715) of the loci we analyzed could be mapped with high confidence to one or more expressed sequence tags in NCBI Genbank. A concatenated matrix of the loci that BLAST to at least one EST sequence provides approximately half as many variable or parsimony-informative characters as equal-sized datasets from the non-EST loci. The EST-associated matrix is more complete (fewer missing loci) and has slightly lower homoplasy than non-EST subsampled matrices of the same size, but there is no difference in phylogenetic support or relative attribution of base substitutions to internal versus terminal branches of the phylogeny. We introduce a partitioned RAD visualization method (implemented in the R package RADami; http://cran.r-project.org/web/packages/RADami) to investigate the possibility that suboptimal topologies supported by large numbers of loci—due, for example, to reticulate evolution or lineage sorting—are masked by the globally optimal tree. We find no evidence for strongly-supported alternative topologies in our study, suggesting that the phylogeny we recover is a robust estimate of large-scale phylogenetic patterns in the American oak clade. Our study is one of the first to demonstrate the utility of RAD-Seq data for inferring phylogeny in a 23–33 million year-old clade.
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