A framework phylogeny of the American oak clade based on sequenced RAD data

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 equ...此前针对栎属（*Quercus*, 壳斗科Fagaceae）的系统发育研究均未能获得高支持度的属内主干拓扑结构解析结果。本研究利用限制性位点关联DNA（restriction-site associated DNA, RAD-Seq）的二代测序技术，对以美洲类群为主的栎属演化支构建框架系统发育树，该演化支的冠群年龄估算为2300万至3300万年。本研究借助新近开发的RAD-Seq系统发育分析流程，构建了包含1.40×10^6个比对后核苷酸位点的串联矩阵，共涵盖27727个序列簇。不同测序批次的RAD-Seq数据可便捷合并，技术重复样本的系统发育定位结果无差异，二者的位点覆盖度重叠率仅为43%至64%。本研究分析的位点中有17%（4715个）可被高置信度比对至NCBI GenBank中的一个或多个表达序列标签（expressed sequence tags, EST）。针对至少能比对至一条EST序列的位点构建的串联矩阵，其可变位点或简约信息位点的数量约为完整矩阵的一半……