Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny

Juniper (Juniperus) is an ecologically important conifer genus of the Northern Hemisphere, the members of which are often foundational tree species of arid regions. The serrate leaf margin clade is native to topologically variable regions in North America, where hybridization has likely played a prominent role in their diversification. Here we use a reduced-representation sequencing approach (ddRADseq) to generate a phylogenomic data set for 68 accessions representing all 22 species in the serrate leaf margin clade, as well as a number of close and distant relatives, to improve understanding of diversification in this group. Phylogenetic analyses using three methods (SVDquartets, maximum likelihood, and Bayesian) yielded highly congruent and well-resolved topologies. These phylogenies provided improved resolution relative to past analyses based on Sanger sequencing of nuclear and chloroplast DNA, and were largely consistent with taxonomic expectations based on geography and morphology. ...圆柏属（Juniperus）是北半球一类具有重要生态意义的针叶树属，其成员常为干旱地区的建群树种。具锯齿叶边的演化支原产于北美地形复杂多变的区域，杂交事件很可能在该类群的物种分化过程中发挥了关键作用。本研究采用简化基因组测序（reduced-representation sequencing, ddRADseq）技术，为涵盖该锯齿叶边演化支全部22个物种以及诸多近缘、远缘类群的68份种质材料构建了系统发育基因组数据集，以深化对该类群物种分化机制的认知。通过SVDquartets、最大似然法与贝叶斯法三种分析方法开展的系统发育分析，得到了高度一致且分辨率优异的拓扑结构。相较于以往基于核DNA与叶绿体DNA桑格测序（Sanger sequencing）的研究，这些系统发育树的分辨率得到了显著提升，且大体上与基于地理分布与形态学特征的分类学预期相符。...