Jin Lu, Liu Jia-Jia, Xiao Tian-Wen, Li Qiao-Ming, Lin Lu-Xiang, Shao Xiao-Na, Ma Chen-Xin, Li Bu-Hang, Mi Xiang-Cheng, Ren Hai-Bao, Qiao Xiu-Juan, Lian Ju-Yu, Hao Gang, Ge Xue-Jun
College of Life Sciences, South China Agricultural University, Guangzhou, China.
Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
Mol Ecol Resour. 2022 Jan;22(1):319-333. doi: 10.1111/1755-0998.13462. Epub 2021 Jul 18.
Phylogenetic trees have been extensively used in community ecology. However, how the phylogeny construction affects ecological inferences is poorly understood. In this study, we constructed three different types of phylogenetic trees (a synthetic-tree generated using V.PhyloMaker, a barcode-tree generated using rbcL+matK+trnH-psbA, and a plastome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six forest dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the plastome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith's PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the plastome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and plastome-tree detected phylogenetic signal in maximum height, but only the plastome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the improvement of plastome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.
系统发育树已在群落生态学中得到广泛应用。然而，系统发育构建如何影响生态推断却鲜为人知。在本研究中，我们构建了三种不同类型的系统发育树（一种使用V.PhyloMaker生成的综合树、一种使用rbcL+matK+trnH-psbA生成的条形码树，以及一种由质体基因组生成的质体基因组树），这些树代表了来自中国亚热带常绿阔叶林六个森林动态样地的580种木本植物物种中系统发育分辨率不断提高的水平。然后，我们评估了每种系统发育在群落系统发育结构估计、周转率和功能性状系统发育信号方面的表现。正如预期的那样，质体基因组树在物种间关系上的分辨率最高且支持度最强。对于局部系统发育结构，这三种树在Faith's PD和MPD方面显示出一致的结果；然而，只有综合树在某些样地使用MNTD产生了显著的聚类模式。对于系统发育周转率，分子树和综合树之间的对比结果仅在最近邻距离上出现差异。在系统发育结构和周转率方面，条形码树与质体基因组树的一致性高于综合树。对于功能性状，条形码树和质体基因组树都检测到了最大高度的系统发育信号，但只有质体基因组树检测到了叶宽的信号。这是第一项在大规模群落系统发育学中使用质体基因组的研究。我们的结果突出了质体基因组树相对于条形码树和综合树在本研究分析中的优势。我们的结果还指出，在使用综合树估计系统发育结构和周转率以及检测系统发育信号时可能存在I型和II型错误。
