Data from: Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

1. The amount and patterns of phylodiversity in a community are often used to draw inferences about the local and historical factors affecting community assembly and can be used to prioritize communities and locations for conservation. Because measures of phylodiversity are based on the topology and branch lengths of phylogenetic trees, which are affected by the number and diversity of taxa in the tree, these analyses may be sensitive to changes in taxon sampling and tree reconstruction methods. 2. To investigate the effects of taxon sampling and tree reconstruction methods on measures of phylodiversity, we investigated the community phylogenetics of the Ordway-Swisher Biological Station (Florida), which is home to over 600 species of vascular plants. We studied the effects of 1) the number of taxa included in the regional phylogeny; 2) random vs. targeted sampling of species to assemble the regional species pool; 3) including only species from specific clades rather than broad sampling; 4) using trees reconstructed directly for the taxa under study compared to trees pruned from a larger reconstructed tree; and 5) using phylograms compared to chronograms. 3. We found that including more taxa in a study increases the likelihood of observing significantly non-random phylogenetic patterns. However, there were no consistent trends in the phylodiversity patterns based on random taxon sampling compared to targeted sampling, or within individual clades compared to the complete dataset. Using pruned and reconstructed phylogenies resulted in similar patterns of phylodiversity, while chronograms in some cases led to significantly different results from phylograms. 4. The methods commonly used in community phylogenetic studies can significantly impact the results, potentially influencing both inferences of community assembly and conservation decisions. We highlight the need for both careful selection of methods in community phylogenetic studies and appropriate interpretation of results, depending on the specific questions to be addressed.

1. 群落中的系统发育多样性（phylodiversity）水平与分布模式，常被用于推演影响群落构建的局域与历史因子，同时可用于确定优先保护的群落与区域。由于系统发育多样性的测度指标基于系统发育树的拓扑结构与分支长度，而后者受树内类群的数量与多样性影响，因此这类分析对类群采样方案与树重建方法的变化较为敏感。
2. 为探究类群采样与树重建方法对系统发育多样性测度的影响，我们以佛罗里达州奥德韦-斯威舍生物站的群落系统发育为研究对象，该区域分布有超过600种维管植物。本研究考察了5类因素的效应：1）区域系统发育树所包含的类群数量；2）用于构建区域物种库的物种随机采样与针对性采样方案；3）仅纳入特定支系而非全面采样的情形；4）直接为研究类群构建的系统发育树，与从已构建的大型系统发育树修剪得到的系统发育树的对比；5）带分支长度的系统发育树（phylograms）与时间校准系统发育树（chronograms）的对比。
3. 研究结果显示，研究中纳入的类群越多，观测到显著非随机系统发育模式的概率越高。不过，相较于针对性采样，随机类群采样得到的系统发育多样性模式并无一致趋势；相较于完整数据集，单个支系的分析结果也未呈现一致差异。使用修剪得到与直接构建的系统发育树，所得的系统发育多样性模式相近；而时间校准系统发育树在部分情形下，会得到与带分支长度的系统发育树显著不同的结果。
4. 群落系统发育研究中常用的分析方法可对研究结果产生显著影响，甚至可能同时干扰群落构建的推演与保护决策的制定。我们强调，需根据具体研究问题，谨慎选择群落系统发育研究的分析方法，并对所得结果进行合理阐释。