Data_Sheet_1_Phylogenomics of Salvia L. subgenus Calosphace (Lamiaceae).docx

The evolutionary relationships of Salvia have been difficult to estimate. In this study, we used the Next Generation Sequencing method Hyb-Seq to evaluate relationships among 90 Lamiaceae samples, including representatives of Mentheae, Ocimeae, Salvia subgenera Audibertia, Leonia, Salvia, and 69 species of subgenus Calosphace, representing 32 of Epling's sections. A bait set was designed in MarkerMiner using available transcriptome data to enrich 119 variable nuclear loci. Nuclear and chloroplast loci were assembled with hybphylomaker (HPM), followed by coalescent approach analyses for nuclear data (ASTRAL, BEAST) and a concatenated Maximum Likelihood analysis of chloroplast loci. The HPM assembly had an average of 1,314,368 mapped reads for the sample and 527 putative exons. Phylogenetic inferences resolved strongly supported relationships for the deep-level nodes, agreeing with previous hypotheses which assumed that subgenus Audibertia is sister to subgenus Calosphace. Within subgenus Calosphace, we recovered eight monophyletic sections sensu Epling, Cardinalis, Hastatae, Incarnatae, and Uricae in all the analyses (nDNA and cpDNA), Biflorae, Lavanduloideae, and Sigmoideae in nuclear analyses (ASTRAL, BEAST) and Curtiflorae in ASTRAL trees. Network analysis supports deep node relationships, some of the main clades, and recovers reticulation within the core Calosphace. The chloroplast phylogeny resolved deep nodes and four monophyletic Calosphace sections. Placement of S. axillaris is distinct in nuclear evidence and chloroplast, as sister to the rest of the S. subg. Calosphace in chloroplast and a clade with “Hastatae clade” sister to the rest of the subgenus in nuclear evidence. We also tested the monophyly of S. hispanica, S. polystachia, S. purpurea, and S. tiliifolia, including two samples of each, and found that S. hispanica and S. purpurea are monophyletic. Our baits can be used in future studies of Lamiaceae phylogeny to estimate relationships between genera and among species. In this study, we presented a Hyb-Seq phylogeny for complex, recently diverged Salvia, which could be implemented in other Lamiaceae.

鼠尾草属（Salvia）的演化关系迄今仍难以准确推断。本研究采用下一代测序（Next Generation Sequencing）技术中的杂交捕获测序（Hyb-Seq），对90份唇形科（Lamiaceae）样本的亲缘关系进行解析，样本涵盖薄荷族（Mentheae）、罗勒族（Ocimeae）、鼠尾草属的Audibertia亚属、Leonia亚属、鼠尾草亚属，以及代表埃普林划分的32个组的69份Calosphace亚属物种。研究人员借助MarkerMiner工具，利用已公开的转录组数据设计捕获探针组，以富集119个多态性核基因座。本研究利用hybphylomaker（HPM）组装核基因座与叶绿体基因座序列，随后针对核数据采用溯祖分析方法（ASTRAL、BEAST）进行分析，针对叶绿体基因座则采用串联最大似然法开展分析。HPM组装结果显示，每份样本平均可比对到1,314,368条序列读段，共得到527个推定外显子。系统发育推断结果为深层节点提供了极强的支持度，与此前提出的‘Audibertia亚属为Calosphace亚属姊妹群’的假说一致。在Calosphace亚属内，本研究共恢复出埃普林定义的8个单系组：其中Cardinalis组、Hastatae组、Incarnatae组与Uricae组在所有分析（核DNA与叶绿体DNA分析）中均得到支持；Biflorae组、Lavanduloideae组与Sigmoideae组仅在核分析（ASTRAL、BEAST）中被恢复；Curtiflorae组则仅在ASTRAL树中得到支持。网络分析验证了深层节点与部分主要演化支的亲缘关系，并发现核心Calosphace类群内部存在网状进化现象。叶绿体系统发育树解析了深层节点，并恢复出4个Calosphace亚属的单系组。腋生鼠尾草（S. axillaris）的系统位置在核基因与叶绿体证据中存在显著差异：在叶绿体分析中，它为Calosphace亚属其余类群的姊妹群；而在核基因分析中，它与‘Hastatae演化支’构成一支，且该支为亚属其余类群的姊妹群。本研究还针对西班牙鼠尾草（S. hispanica）、多穗鼠尾草（S. polystachia）、紫鼠尾草（S. purpurea）与椴叶鼠尾草（S. tiliifolia）开展单系性检验，每个物种均包含2份样本，结果显示西班牙鼠尾草与紫鼠尾草为单系类群。本研究设计的捕获探针可应用于未来唇形科系统发育研究，以解析属间及物种间的亲缘关系。本研究构建了针对复杂且近期分化的鼠尾草属的Hyb-Seq系统发育框架，该方法亦可推广应用于其他唇形科类群的研究。