Erickson David L, Jones Frank A, Swenson Nathan G, Pei Nancai, Bourg Norman A, Chen Wenna, Davies Stuart J, Ge Xue-Jun, Hao Zhanqing, Howe Robert W, Huang Chun-Lin, Larson Andrew J, Lum Shawn K Y, Lutz James A, Ma Keping, Meegaskumbura Madhava, Mi Xiangcheng, Parker John D, Fang-Sun I, Wright S Joseph, Wolf Amy T, Ye W, Xing Dingliang, Zimmerman Jess K, Kress W John
Department of Botany, Museum Routing Code-166, National Museum of Natural History, Smithsonian Institution Washington, DC, USA.
Department of Botany and Plant Pathology, Oregon State University Corvallis, OR, USA ; Smithsonian Tropical Research Institute, Panamá Panamá
Front Genet. 2014 Nov 5;5:358. doi: 10.3389/fgene.2014.00358. eCollection 2014.
Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of phylogenetic diversity in the mega-phylogeny were more consistent, thereby removing a potential source of bias at the plot-level, and demonstrating the value of assessing phylogenetic relationships simultaneously within a mega-phylogeny. An unexpected result of the comparisons among plots based on the mega-phylogeny was that the communities in the ForestGEO plots in general appear to be assemblages of more closely related species than expected by chance, and that differentiation among communities is very low, suggesting deep floristic connections among communities and new avenues for future analyses in community ecology.
森林动态监测样地如今遍布全球的经度、纬度和栖息地类型，为深入了解决定物种如何组合成群落的生态和进化过程提供了无与伦比的视角。了解群落中物种间的系统发育关系已成为评估群落构建过程的重要组成部分。然而，进化信息在群落生态学问题中的应用在很大程度上受到群落中单个物种系统发育关系缺乏准确估计的限制，在群落间比较时尤为受限。因此，精简并最大化这些群落系统发育的信息含量成为当务之急。为了测试多群落系统发育的可行性和优势，我们利用DNA条形码序列数据（rbcL、matK和psbA-trnH）构建了一个包含森林全球生态监测网络中15个森林动态监测样地的1347种树的多样地大型系统发育树，并比较了每个单独样地的群落系统发育在拓扑结构和分支长度支持方面的情况，这些会影响群落过程的进化推断。通过量化整个系统发育中解析节点的频率来检查系统发育上的分类分化水平。此外，为每个样地估计了三种常用于推断群落构建过程的系统发育距离（PD）指标[PD、平均系统发育距离（MPD）和平均最近分类单元距离（MNTD）]。最后，我们通过量化群落间的MPD和MNTD来研究群落样地间系统发育多样性的分配。总体而言，基于DNA条形码的大型系统发育树中进化关系得到了高度解析，并且当在大型系统发育树的背景下进行估计时，每个群落样地的系统发育分辨率得到了提高。同样，与单个样地的系统发育树相比，大型系统发育树中系统发育多样性的估计更一致，从而消除了样地水平上潜在的偏差来源，并证明了在大型系统发育树中同时评估系统发育关系的价值。基于大型系统发育树的样地间比较得出的一个意外结果是，森林全球生态监测样地中的群落总体上似乎是比随机预期的更密切相关物种的集合，并且群落间的分化非常低，这表明群落间存在深刻的植物区系联系以及群落生态学未来分析的新途径。
