类群取样与系统发育分析精确度之探索

Appropriate and extensive taxon sampling is one of the most important determinants of accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary processes obtained from phylogenetic analyses is improved significantly by thorough taxon sampling efforts. Many recent efforts to improve phylogenetic estimates have focused instead on increasing sequence length or the number of overall characters in the analysis, and this often does have a beneficial effect on the accuracy of phylogenetic analyses. However, phylogenetic analyses of few taxa (but each represented by many characters) can be subject to strong systematic biases, which in turn produce high measures of repeatability (such as bootstrap proportions) in support of incorrect or misleading phylogenetic results. Thus, it is important for phylogeneticists to consider both the sampling of taxa, as well as the sampling of characters, in designing phylogenetic studies. Taxon sampling also improves estimates of evolutionary parameters derived from phylogenetic trees, and is thus important for improved applications of phylogenetic analyses. Analysis of sensitivity to taxon inclusion, the possible effects of long-branch attraction, and sensitivity of parameter estimation for model-based methods should be a part of any careful and thorough phylogenetic analysis. Furthermore, recent improvements in phylogenetic algorithms and in computational power have removed many constraints on analyzing large, thoroughly sampled data sets. Thorough taxon sampling is thus one of the most practical ways to improve the accuracy of phylogenetic estimates, as well as the accuracy of biological inferences that are based on these phylogenetic trees.     

Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

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太白山森林样地系统发育多样性格局及其影响因素 系统发育多样性指数常被用作区分植物群落构建过程中生态和演化过程的相对作用。系统发育多样性格局的推断方法(如系统树的构建和不同的系统发育多样性指数)、演化历史(如生活型)以及环境梯度都可能影响系统发育多样性格局的估计值,进而可能影响我们对植物群落构建过程的认知。因此,有必要区分这些因素如何作用于系统发育多样性格局的估计值,但其相对重要性及其交互作用仍不清楚。本研究利用位于太白山北坡沿海拔分布的20个森林样地(整体高差2800 m左右)的野外调查数据,包括274种木本植物和581种草本植物。对于上述样地内所有植物,我们构建了当前广泛采用的合成树和分子树以比较系统树的构建,特别是合成树末端的多歧分支结构,及其对系统发育多样性格局估计值的可能影响。同时,我们计算了每个样地的3种不同的系统发育多样性指数,包括Faith’s PD, 平均成对距离(MPD)和平均最近类群距离(MNTD),并分别对木本和草本植物进行计算。多模型比较分析系统发育多样性格局的估计值与系统树重建方法、多样性指数、生活型、海拔及其交互作用的最简约关系。研究结果表明,基于合成树和分子树所得到的系统发育多样性格局之间没有显著差异。海拔和多样性指数与生活型在解释系统发育多样性格局方面存在强烈的交互作用,并且能够解释44%以上的变异。系统发育多样性格局的估计值总体随海拔升高而降低,但草本植物相比木本植物变化更平缓。对于木本植物,3种系统发育多样性指数表现出一致的海拔分布格局(即系统发育聚集),而草本植物的平均成对距离指数则表现为随机的海拔分布格局。因此,分析沿环境梯度的系统发育多样性格局需要考虑系统发育格局的推断方法和演化历史的影响,以帮助我们更好地理解植物群落的构建过程。     

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Comprehensive understanding of the patterns and drivers of microbial diversity at a landscape scale is in its infancy, despite the recent ease by which soil communities can be characterized using massively parallel amplicon sequencing. Here we report on a comprehensive analysis of the drivers of diversity distribution and composition of the ecologically and economically important Phytophthora genus from 414 soil samples collected across Australia. We assessed 22 environmental and seven categorical variables as potential predictors of Phytophthora species richness, α and β diversity, including both phylogenetically and non‐phylogenically explicit methods. In addition, we classified each species as putatively native or introduced and examined the distribution with respect to putative origin. The two most widespread species, P. multivora and P. cinnamomi, are introduced, though five of the ten most widely distributed species are putatively native. Introduced taxa comprised over 54% of Australia's Phytophthora diversity and these species are known pathogens of annual and perennial crop habitats as well as urban landscapes and forestry. Patterns of composition were most strongly predicted by bioregion (R² = 0.29) and ecoregion (R² = 0.26) identity; mean precipitation of warmest quarter, mean temperature of the wettest quarter and latitude were also highly significant and described approximately 21, 14 and 13% of variation in NMDS composition, respectively. We also found statistically significant evidence for phylogenetic over‐dispersion with respect to key climate variables.This study provides a strong baseline for understanding biogeographical patterns in this important genus as well the impact of key plant pathogens and invasive Phytophthora species in natural ecosystems.     

Plastome-based phylogeny improves community phylogenetics of subtropical forests in China

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.     

A taxonomic and phylogenetic perspective on plant community assembly along an elevational gradient in subtropical forests

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Global patterns of amphibian phylogenetic diversity

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