Data from: Phylogenomic analyses of Sabal (Arecaceae) species relationships using targeted sequence capture

With the increasing availability of high-throughput sequencing, phylogenetic analyses are no longer constrained by the limited availability of a few loci. Here, we describe a sequence capture methodology, which we used to collect data for analyses of diversification within Sabal (Arecaceae), a palm genus native to the south-eastern USA, Caribbean, Bermuda and Central America. RNA probes were developed and used to enrich DNA samples for putatively low copy nuclear genes and the plastomes for all Sabal species and two outgroup species. Sequence data were generated on an Illumina MiSeq sequencer and target sequences were assembled using custom workflows. Both coalescence and supermatrix analyses of 133 nuclear genes were used to estimate species trees relationships. Plastid genomes were also analysed, yielding generally poor resolution with regard to species relationships. Species relationships described in both nuclear gene and plastome sequences largely reflect the biogeography of the group and, to a lesser extent, previous morphology-based hypotheses. Beyond the biological implications, this research validates a high-throughput methodology for generating a large number of genes for coalescence-based phylogenetic analyses in plant lineages.随着高通量测序（high-throughput sequencing）技术的可及性持续提升，系统发育分析（phylogenetic analyses）不再受限于少数基因座（loci）的数量匮乏。本研究介绍一种序列捕获技术（sequence capture methodology），我们依托该方法采集数据，用以解析菜棕属（Sabal，棕榈科Arecaceae）的物种多样化进程；该属为原生分布于美国东南部、加勒比海地区、百慕大及中美洲的棕榈类群。我们开发了RNA探针（RNA probes），用于富集所有菜棕属物种及2个外类群物种的DNA样本，靶向获取推测为低拷贝的核基因与质体基因组（plastomes）序列。序列数据通过Illumina MiSeq测序仪（Illumina MiSeq sequencer）生成，并通过自定义分析流程组装目标序列。我们采用溯祖分析（coalescence）与超级矩阵分析（supermatrix analyses）两种方法，基于133个核基因估算物种树（species trees）的亲缘关系。同时对质体基因组开展分析，但所得物种亲缘关系分辨率普遍较低。核基因与质体基因组所揭示的物种亲缘关系，整体上与该类群的生物地理学（biogeography）分布特征高度契合，且在一定程度上呼应此前基于形态学提出的分类假说。除却本研究的生物学意义外，该工作还验证了一种高通量研究方法，可用于获取植物支系中开展基于溯祖分析的系统发育研究所需的大量基因序列。