Department of Botany, National Museum of Natural History Smithsonian Institution, Washington, DC, United States of America.
PLoS One. 2010 Nov 9;5(11):e15409. doi: 10.1371/journal.pone.0015409.
Species number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete) data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny.
METHODOLOGY/PRINCIPAL FINDINGS: Here we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III) regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history.
CONCLUSIONS/SIGNIFICANCE: As first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and evolution.
物种数量、功能特征和系统发育历史都有助于描述植物群落的生物多样性。在物种丰富的热带树木群集中，多样性的系统发育组成部分特别难以量化。通过 Phylomatic 等程序，将以前发表的（通常不完整）物种进化关系数据汇编到一个森林分类群的综合系统发育图中，已被证明有助于构建群落系统发育图，尽管分辨率通常有限。最近，DNA 条形码已被用于使用超级矩阵方法构建巴拿马一个森林动态样地中近 300 个树种的稳健群落系统发育图。在该研究中，来自三个条形码基因座的序列数据用于生成一个分辨率较高的物种水平系统发育图。
方法/主要发现：在这里，我们扩展了早期的研究，并介绍了在波多黎各一个多样化的热带森林动态样地中使用系统发育约束树生成群落系统发育图的结果。这种增强的系统发育重建方法确保了条形码系统发育与广泛接受的开花植物系统发育假说（即 APG III）的一致性，无论采样的分类群数量和分类广度如何。我们还比较了最大简约法和最大似然法估计的群落系统发育关系，并评估了单基因、双基因和三基因条形码在解决群落进化历史方面的有效性。
结论/意义：正如在巴拿马森林动态样地中首次证明的那样，波多黎各样地的结果表明，从 DNA 条形码序列数据得出的高度分辨率系统发育图与基于 APG III 的约束树相结合，特别有助于比较分析系统发育多样性，并将增强社区生态学与进化之间界面的研究。
