Data from: Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences

Following (1) the large scale molecular phylogeny of seed plants based on plastid rbcL gene sequences (published in 1993 by Chase et al., Ann. Missouri Bot. Gard. 80: 528-580) and (2) the 18S nuclear phylogeny of flowering plants (published in 1997 by Soltis et al., Ann. Missouri Bot. Gard. 84: 1-49), we present a phylogenetic analysis of flowering plants based upon a second plastid gene, atpB, analyzed separately and in combination with rbcL sequences for 357 taxa. Despite some discrepancies, the atpB-based phylogenetic trees were highly congruent with those derived from the analysis of rbcL and 18S rDNA, and the combination of atpB and rbcL DNA sequences (comprising ca. 3000 base pairs) produced increased bootstrap support for many major sets of taxa. The angiosperms are divided into two major groups: noneudicots with inaperturate or uniaperturate pollen (monocots plus Laurales, Magnoliales, Piperales, Ceratophyllales, and Amborellaceae-Nymphaeaceae-Illiciaceae) and the eudicots with triaperturate pollen (particularly asterids and rosids). Based on rbcL alone and atpB/rbcL combined, the noneudicots (excluding Ceratophyllum) are monophyletic, whereas they form a grade in the atpB trees. Ceratophyllum is sister to the rest of angiosperms whith rbcL alone and in the combined atpB/rbcL analysis, whereas with atpB alone, Amborellaceae, Nymphaeaceae, and Illiciaceae/Schisandraceae form a grade at the base of the angiosperms. The phylogenetic information at each codon position and the different types of substitutions (observed transitions and transversions in the trees versus pairwise comparisons) were examined; taking into account their respective consistency and retention indices, we demonstrate that third codon positions and transitions are the most useful characters in these phylogenetic reconstructions. This study further demonstrates that phylogenetic analysis of large matrices is feasible.

本研究以蔡斯（Chase）等人1993年发表于《密苏里植物园年报》（Ann. Missouri Bot. Gard.）第80卷第528-580页、基于质体rbcL基因 (plastid rbcL gene) 序列的大型种子植物分子系统发育研究，以及索尔特蒂斯（Soltis）等人1997年发表于同刊第84卷第1-49页的被子植物18S核基因 (18S nuclear gene) 系统发育研究为基础，针对357个类群 (taxa) 的第二个质体基因atpB (atpB gene)，分别单独分析并与rbcL序列联合后，开展被子植物的系统发育分析。尽管存在部分拓扑差异，但基于atpB基因的系统发育树与rbcL和18S rDNA分析得到的系统发育树高度一致；联合atpB与rbcL序列（总长约3000个碱基对）后，多个主要类群的自展支持率 (bootstrap support) 得到显著提升。被子植物可分为两大支系：具无萌发孔或单萌发孔花粉的非真双子叶植物类群（包含单子叶植物、樟目、木兰目、胡椒目、金鱼藻目以及互叶梅科-睡莲科-八角茴香科），和具三萌发孔花粉的真双子叶植物类群（尤以菊亚纲和蔷薇亚纲为代表）。基于单独的rbcL序列以及atpB/rbcL联合序列分析，非真双子叶植物类群（不含金鱼藻属）为单系类群 (monophyletic group)；但在仅采用atpB序列的系统发育树中，该类群构成级群 (grade)。仅采用rbcL序列以及atpB/rbcL联合分析时，金鱼藻属 (Ceratophyllum) 为其余被子植物的姊妹群 (sister group)；而仅采用atpB序列分析时，互叶梅科、睡莲科以及八角茴香科/五味子科构成被子植物基部的级群 (grade)。本研究对每个密码子位点 (codon position) 的系统发育信息以及不同类型的碱基替换（包括树中观察到的碱基转换 (transitions) 与碱基颠换 (transversions)，相较于两两序列比对结果）进行了考察；结合各自的一致性指数 (consistency index) 与保留指数 (retention index)，我们证实密码子第三位与碱基转换是本次系统发育重建 (phylogenetic reconstruction) 中最具效用的特征。本研究进一步证实，针对大型序列矩阵 (large matrix) 开展系统发育分析是完全可行的。