The use of DNA barcodes to estimate phylogenetic diversity in forest communities of southern China
The use of DNA barcodes to estimate phylogenetic diversity in forest communities of southern China
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利用DNA条形码估算中国南方森林群落的系统发育多样性
DOI：
10.1002/ece3.5128
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发表时间：
2019-04
影响因子：
2.6
通讯作者：
Burgess Kevin S
中科院分区：
文献类型：
--
作者：
Liu Jiajia;Liu Juan;Shan You Xia;Ge Xue Jun;Burgess Kevin S
摘要为了阐明与植物群落组装相关的潜在生态和进化过程，现在广泛使用基于各种DNA条形码区域和系统发育构建方法的系统发育多样性估计。然而，相对较少的研究考虑了系统发育多样性的估计如何受到纳入序列矩阵（保守区与高变区）的单个DNA条形码以及使用骨干家族水平同源性的影响。在这里，我们使用一般的线性混合效应模型来研究核心DNA条形码（rbcL，matK，ITS和ITS2）的不同组合和系统发育构建方法对中国南方广东两个亚热带森林样地的一系列群落系统发育多样性估计的影响。我们问：（a）单DNA条形码对估计系统发育多样性指标的相对影响是什么？和（B）使用主干家族水平的系统发育来估计基于拓扑的系统发育多样性度量的效果是什么？多于一个条形码的组合（即，rbcL + matK + ITS）和使用骨干家族水平的同源性提供了最简约的解释，在估计系统发育多样性的变化。与基于分支长度的系统发育多样性指标相比，使用主干家族水平的系统发育对基于树形拓扑的系统发育多样性指标的影响更大。此外，由顶级模型解释的系统发育多样性估计值的变化范围为0.1%至31%，并且取决于系统发育群落结构度量的类型。我们的研究强调了结合多位点DNA条形码和使用骨干家族水平同源性来推断系统发育多样性的重要性，其中所采用的DNA条形码类型和所使用的系统发育构建方法可以作为系统发育群落结构估计的重要变异来源。
Abstract To elucidate potential ecological and evolutionary processes associated with the assembly of plant communities, there is now widespread use of estimates of phylogenetic diversity that are based on a variety of DNA barcode regions and phylogenetic construction methods. However, relatively few studies consider how estimates of phylogenetic diversity may be influenced by single DNA barcodes incorporated into a sequence matrix (conservative regions vs. hypervariable regions) and the use of a backbone family‐level phylogeny. Here, we use general linear mixed‐effects models to examine the influence of different combinations of core DNA barcodes (rbcL, matK, ITS, and ITS2) and phylogeny construction methods on a series of estimates of community phylogenetic diversity for two subtropical forest plots in Guangdong, southern China. We ask: (a) What are the relative influences of single DNA barcodes on estimates phylogenetic diversity metrics? and (b) What is the effect of using a backbone family‐level phylogeny to estimate topology‐based phylogenetic diversity metrics? The combination of more than one barcode (i.e., rbcL + matK + ITS) and the use of a backbone family‐level phylogeny provided the most parsimonious explanation of variation in estimates of phylogenetic diversity. The use of a backbone family‐level phylogeny showed a stronger effect on phylogenetic diversity metrics that are based on tree topology compared to those that are based on branch lengths. In addition, the variation in the estimates of phylogenetic diversity that was explained by the top‐rank models ranged from 0.1% to 31% and was dependent on the type of phylogenetic community structure metric. Our study underscores the importance of incorporating a multilocus DNA barcode and the use of a backbone family‐level phylogeny to infer phylogenetic diversity, where the type of DNA barcode employed and the phylogenetic construction method used can serve as a significant source of variation in estimates of phylogenetic community structure.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
3.7
作者：
Swenson NG
通讯作者：
Swenson NG
影响因子：
56.9
作者：
A. J. Webster;R. Payne;M. Pagel
通讯作者：
A. J. Webster;R. Payne;M. Pagel
社区系统发育学：评估树木重建方法和DNA条形码的效用。
影响因子：
3.7
作者：
Boyle EE;Adamowicz SJ
通讯作者：
Adamowicz SJ
DOI：
10.1073/pnas.0909820106
发表时间：
2009-11-03
影响因子：
11.1
作者：
Kress, W. John;Erickson, David L.;Bermingham, Eldredge
通讯作者：
Bermingham, Eldredge