Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA.
Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17519-24. doi: 10.1073/pnas.1205818109. Epub 2012 Oct 8.
The angiosperm order Malpighiales includes ~16,000 species and constitutes up to 40% of the understory tree diversity in tropical rain forests. Despite remarkable progress in angiosperm systematics during the last 20 y, relationships within Malpighiales remain poorly resolved, possibly owing to its rapid rise during the mid-Cretaceous. Using phylogenomic approaches, including analyses of 82 plastid genes from 58 species, we identified 12 additional clades in Malpighiales and substantially increased resolution along the backbone. This greatly improved phylogeny revealed a dynamic history of shifts in net diversification rates across Malpighiales, with bursts of diversification noted in the Barbados cherries (Malpighiaceae), cocas (Erythroxylaceae), and passion flowers (Passifloraceae). We found that commonly used a priori approaches for partitioning concatenated data in maximum likelihood analyses, by gene or by codon position, performed poorly relative to the use of partitions identified a posteriori using a Bayesian mixture model. We also found better branch support in trees inferred from a taxon-rich, data-sparse matrix, which deeply sampled only the phylogenetically critical placeholders, than in trees inferred from a taxon-sparse matrix with little missing data. Although this matrix has more missing data, our a posteriori partitioning strategy reduced the possibility of producing multiple distinct but equally optimal topologies and increased phylogenetic decisiveness, compared with the strategy of partitioning by gene. These approaches are likely to help improve phylogenetic resolution in other poorly resolved major clades of angiosperms and to be more broadly useful in studies across the Tree of Life.
被子植物目包括约 16000 种，占热带雨林林下树木多样性的 40%。尽管在过去的 20 年中，被子植物系统学取得了显著进展，但木兰目中的关系仍未得到很好的解决，这可能是由于它在白垩纪中期的快速崛起。我们使用系统基因组学方法，包括对 58 种植物的 82 个质体基因进行分析，在木兰目中确定了另外 12 个分支，并大大提高了主干的分辨率。这一改进后的系统发育史揭示了木兰目中净多样化率变化的动态历史，巴巴多斯樱桃（金虎尾科）、可可（苏木科）和西番莲（西番莲科）的多样化呈爆发式增长。我们发现，常用的先验方法，如通过基因或密码子位置将串联数据分区进行最大似然分析，与使用贝叶斯混合模型后验识别的分区相比效果较差。我们还发现，在从富含分类群、数据稀疏的矩阵中推断出的树中，分支支持更好，而在从分类群稀疏、缺失数据少的矩阵中推断出的树中则较差。尽管这个矩阵有更多的缺失数据，但与基于基因分区的策略相比，我们的后验分区策略减少了产生多个不同但同样最优拓扑的可能性，并提高了系统发育的决断力。这些方法可能有助于提高其他未解决的主要被子植物类群的系统发育分辨率，并在整个生命之树的研究中更广泛地发挥作用。
