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.本研究基于两项前期研究成果：(1)蔡斯等（Chase et al.）于1993年发表于《密苏里植物园纪事》（Ann. Missouri Bot. Gard.）第80卷528-580页的、基于质体rbcL基因序列的大型种子植物分子系统发育研究，以及(2)索利斯等（Soltis et al.）于1997年发表于同刊第84卷1-49页的被子植物（angiosperms）18S核基因系统发育研究，针对357个类群开展了被子植物的系统发育分析，所用分子标记为第二个质体基因atpB，分别对其单独进行系统发育分析，或将其与rbcL序列联合分析。尽管存在部分不一致之处，但基于atpB基因构建的系统发育树与基于rbcL和18S rDNA分析得到的系统发育树高度一致；联合atpB与rbcL DNA序列（总长约3000个碱基对）得到的分析结果，为多个主要类群提供了更高的自展支持率（bootstrap support）。被子植物可划分为两大核心类群：一类为具有单萌发孔或无萌发孔花粉的非真双子叶植物（noneudicots）类群，包含单子叶植物（monocots）以及樟目、木兰目、胡椒目、金鱼藻目，还有无油樟科（Amborellaceae）、睡莲科（Nymphaeaceae）与八角茴香科（Illiciaceae）；另一类为具有三萌发孔花粉的真双子叶植物（eudicots）类群，其中尤以菊类（asterids）与蔷薇类（rosids）为代表类群。基于单独的rbcL序列以及atpB与rbcL的联合序列分析，非真双子叶植物类群（排除金鱼藻属（Ceratophyllum））为单系类群；而在仅基于atpB的系统发育树中，该类群则呈现为级群（grade）。在单独使用rbcL序列，以及联合atpB与rbcL的分析中，金鱼藻属为其余被子植物的姊妹群；但仅使用atpB序列时，无油樟科、睡莲科以及八角茴香科/五味子科（Schisandraceae）则构成被子植物基部的级群。我们对每个密码子位点的系统发育信息，以及不同类型的碱基替换（系统发育树中观察到的转换（transition）与颠换（transversion），相较于成对序列比对的结果）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位点与碱基转换是本项系统发育重建中最具效用的特征。本研究进一步证明了大型矩阵系统发育分析的可行性。