Data from: Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: a case-study in Carex sect. Racemosae

PREMISE OF THE STUDY: Relationships among closely related and recently diverged taxa can be especially difficult to resolve. Here we use both Sanger sequencing and next-generation RADseq data sets to estimate phylogenetic relationships among species of Carex section Racemosae (Cyperaceae), a clade largely restricted to high latitudes and elevations. Interest in relationships among these taxa derives from questions about the species’ biogeographic histories and possible links between diversification and Pleistocene glaciations. METHODS: A combination of approaches and molecular markers were used to estimate relationships among Carex species within sect. Racemosae and taxa from closely related sections. Nuclear and chloroplast loci generated by Sanger sequencing were analyzed with *BEAST, and SNP data from RADseq loci were analyzed as a concatenated data set using maximum likelihood and as independent loci using SVDquartets. KEY RESULTS: Sanger sequencing data sets resolved relationships among taxa at intermediate phylogenetic depths (albeit with low levels of support). Only the RADseq data resolved relationships with strong support at all phylogenetic depths. Moreover, different methods and data partitions of the RADseq data resulted in nearly identical topologies. Carex sect. Racemosae is a strongly supported clade, although a handful of species were found to group with closely related sections. Herbarium specimens up to 35 yr old successfully produced informative RADseq data. CONCLUSIONS: Despite the short read lengths of RADseq data, they nevertheless resolved relationships that Sanger sequencing data did not. Resolution of the phylogenetic relationships among recently and rapidly diversifying taxa within sect. Racemosae clades suggest a role for the Pleistocene glaciations in clade diversification.

### 研究背景
近缘且近期分化的类群之间的系统发育关系往往极难解析。本研究同时采用Sanger测序（Sanger sequencing）与新一代RADseq（RADseq）数据集，对主要分布于高纬度与高海拔区域的薹草属（Carex）总状薹草组（Carex section Racemosae，莎草科Cyperaceae）内各物种的系统发育关系进行推断。针对该类群系统发育关系的研究兴趣，源于对其生物地理历史的探讨，以及物种分化与更新世冰期（Pleistocene glaciations）之间潜在关联的疑问。

### 研究方法
本研究结合多种实验手段与分子标记，对总状薹草组内的薹草物种及其近缘组类群的系统发育关系进行推断。通过Sanger测序获得的核基因座与叶绿体基因座数据，采用*BEAST软件进行分析；由RADseq位点得到的SNP数据则以最大似然法（maximum likelihood）构建串联数据集，并采用SVDquartets方法将其作为独立基因座进行分析。

### 主要研究结果
Sanger测序数据集仅能解析中等系统发育深度下的类群间关系（尽管支持度较低）。唯有RADseq数据集可在所有系统发育深度下以高支持度解析类群间的系统发育关系，且针对RADseq数据采用不同分析方法与数据分区策略得到的系统发育拓扑结构几乎完全一致。总状薹草组为支持度极高的单系分支，仅少数物种被聚类至近缘组类群中。馆藏时长可达35年的蜡叶标本，亦可成功获取具备信息价值的RADseq数据。

### 研究结论
尽管RADseq数据的读长较短，但其仍可解析Sanger测序数据无法解决的系统发育关系。总状薹草组内近期快速分化类群的系统发育关系解析结果表明，更新世冰期在该分支的物种分化过程中发挥了重要作用。