Bitomský Martin, Mládková Pavla, Pakeman Robin J, Duchoslav Martin
Department of Ecology and Environmental Sciences Palacky University Olomouc Czech Republic.
Department of Ecology Czech University of Life Sciences Prague Czech Republic.
Ecol Evol. 2020 Mar 13;10(8):3747-3757. doi: 10.1002/ece3.6170. eCollection 2020 Apr.
Phylogenetic diversity quantification is based on indices computed from phylogenetic distances among species, which are derived from phylogenetic trees. This approach requires phylogenetic expertise and available molecular data, or a fully sampled synthesis-based phylogeny. Here, we propose and evaluate a simpler alternative approach based on taxonomic coding. We developed metrics, the clade indices, based on information about clade proportions in communities and species richness of a community or a clade, which do not require phylogenies. Using vegetation records from herbaceous plots from Central Europe and simulated vegetation plots based on a megaphylogeny of vascular plants, we examined fit accuracy of our proposed indices for all dimensions of phylogenetic diversity (richness, divergence, and regularity). For real vegetation data, the clade indices fitted phylogeny-based metrics very accurately (explanatory power was usually higher than 80% for phylogenetic richness, almost always higher than 90% for phylogenetic divergence, and often higher than 70% for phylogenetic regularity). For phylogenetic regularity, fit accuracy was habitat and species richness dependent. For phylogenetic richness and divergence, the clade indices performed consistently. In simulated datasets, fit accuracy of all clade indices increased with increasing species richness, suggesting better precision in species-rich habitats and at larger spatial scales. Fit accuracy for phylogenetic divergence and regularity was unreliable at large phylogenetic scales, suggesting inadvisability of our method in habitats including many distantly related lineages. The clade indices are promising alternative measures for all projects with a phylogenetic framework, which can trade-off a little precision for a significant speed-up and simplification, such as macroecological analyses or where phylogenetic data is incomplete.
系统发育多样性量化基于从物种间系统发育距离计算得出的指数，这些距离源自系统发育树。这种方法需要系统发育专业知识和可用的分子数据，或者一个基于充分采样合成的系统发育树。在此，我们提出并评估一种基于分类编码的更简单替代方法。我们基于群落中分支比例以及群落或分支的物种丰富度信息开发了一些指标，即分支指数，这些指标不需要系统发育树。利用中欧草本样地的植被记录以及基于维管植物大型系统发育树模拟的植被样地，我们检验了我们提出的指数对于系统发育多样性所有维度（丰富度、分歧度和规则性）的拟合准确性。对于真实的植被数据，分支指数非常准确地拟合了基于系统发育的指标（对于系统发育丰富度，解释力通常高于80%；对于系统发育分歧度，几乎总是高于90%；对于系统发育规则性，通常高于70%）。对于系统发育规则性，拟合准确性取决于栖息地和物种丰富度。对于系统发育丰富度和分歧度，分支指数表现一致。在模拟数据集中，所有分支指数的拟合准确性随着物种丰富度的增加而提高，这表明在物种丰富的栖息地和更大空间尺度上具有更高的精度。在大的系统发育尺度上，系统发育分歧度和规则性的拟合准确性不可靠，这表明我们的方法在包含许多远缘谱系的栖息地中不可取。对于所有具有系统发育框架的项目，分支指数是很有前景的替代指标，它可以在一定精度上做出权衡，以显著加快速度并简化过程，例如在宏观生态分析或系统发育数据不完整的情况下。
