Magallón Susana, Sanderson Michael J
Section of Evolution and Ecology, University of California, One Shields Avenue, Davis, California 95616 USA.
Am J Bot. 2002 Dec;89(12):1991-2006. doi: 10.3732/ajb.89.12.1991.
Phylogenetic studies based on different types and treatment of data provide substantially conflicting hypotheses of relationships among seed plants. We conducted phylogenetic analyses of sequences of two highly conserved chloroplast genes, psaA and psbB, for a comprehensive taxonomic sample of seed plants and land plants. Parsimony analyses of two different codon position partitions resulted in well-supported, but significantly conflicting, phylogenetic trees. First and second codon positions place angiosperms and gymnosperms as sister clades and Gnetales as sister to Pinaceae. Third positions place Gnetales as sister to all other seed plants. Maximum likelihood trees for the two partitions are also in conflict. Relationships among the main seed plant clades according to first and second positions are similar to those found in parsimony analysis for the same data, but the third position maximum likelihood tree is substantially different from the corresponding parsimony tree, although it agrees partially with the first and second position trees in placing Gnetales as the sister group of Pinaceae. Our results document high rate heterogeneity among lineages, which, together with the greater average rate of substitution for third positions, may reduce phylogenetic signal due to long-branch attraction in parsimony reconstructions. Whereas resolution of relationships among major seed plant clades remains pending, this study provides increased support for relationships within major seed plant clades.
基于不同类型和处理方式的数据所进行的系统发育研究，对种子植物之间的关系提出了大量相互冲突的假说。我们对种子植物和陆地植物的一个全面分类样本，进行了两个高度保守的叶绿体基因psaA和psbB序列的系统发育分析。对两个不同密码子位置分区的简约分析得出了支持度良好但明显冲突的系统发育树。第一和第二密码子位置将被子植物和裸子植物作为姊妹分支，买麻藤目作为松科的姊妹。第三位置将买麻藤目作为所有其他种子植物的姊妹。两个分区的最大似然树也存在冲突。根据第一和第二位置，主要种子植物分支之间的关系与相同数据简约分析中发现的关系相似，但第三位置最大似然树与相应的简约树有很大不同，尽管在将买麻藤目作为松科的姊妹类群这一点上，它与第一和第二位置的树部分一致。我们研究结果证明了谱系间的高速率异质性，这与第三位置更高的平均替换率一起，可能由于简约重建中的长枝吸引而降低系统发育信号。虽然主要种子植物分支间关系的解析仍未解决，但本研究为主要种子植物分支内的关系提供了更多支持。
