Phylogenetic Distance Metrics for Studies of Focal Species in Communities: Quantiles and Cumulative Curves
Phylogenetic Distance Metrics for Studies of Focal Species in Communities: Quantiles and Cumulative Curves
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DOI：
10.3390/d14070521
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发表时间：
2022-07-01
期刊：
影响因子：
2.4
通讯作者：
Parker, Ingrid M.
中科院分区：
文献类型：
--
作者：
Gilbert, Gregory S.;Parker, Ingrid M.
物种之间的系统发育距离往往预示着生态重要特征的差异。生物群落的系统发育多样性和结构可以让我们了解塑造这些群落的过程，并且有一个比较群落系统发育结构的成熟框架。然而，特别是在研究从一个焦点物种到其集合中其他成员的系统发育距离（一对多框架）时，由于大多数生物群落中成对系统发育距离的左偏分布，全群落研究的标准指标遇到了显着的局限性。社区。对于需要估计一个焦点分类单元的系统发育隔离程度的研究，平均系统发育距离（MPD）通常不能提供区分分类单元的能力，因为它被许多方式所加权，以远距离相关，而最近的分类单元距离（NTD）是高度特异性的，忽略了多个近亲可能同样强烈地影响焦点种的情况。在这里，我们强调的价值，研究系统发育距离的累积分布，采取焦点种的方法。我们描述并讨论了两个新指标的好处。系统发育距离的综合度量（AUPhyDC）使用来自整个累积分布的信息，而第十分位数（PD10）是一个非常简单的度量，通过捕获多个近亲对生态相互作用的影响来改进NTD。最近的几个例子发现，PD10在揭示生态模式方面比NTD或MPD做得更好。我们提供了R代码，以促进这些方法的使用，并主张将PD10沿着NTD和MPD纳入系统发育生态学的统计软件包。
The phylogenetic distance between species often predicts differences in ecologically important traits. The phylogenetic diversity and structure of biological communities can inform our understanding of the processes that shape those communities, and there is a well-developed framework for comparing phylogenetic structures of communities. However, particularly in studies of phylogenetic distances from one focal species to other members of its assemblage (a one-to-many framework), the standard metrics of community-wide studies encounter significant limitations due to the left-skewed distribution of pairwise phylogenetic distances in most biological communities. For studies that require estimating the degree of phylogenetic isolation of a focal taxon, the mean phylogenetic distance (MPD) usually provides little power to distinguish among taxa because it is heavily weighted by the many ways to be distantly related, whereas the nearest taxon distance (NTD) is highly idiosyncratic and ignores cases where multiple close relatives may contribute equally strongly to influence the focal species. Here we highlight the value of examining the cumulative distribution of phylogenetic distances in studies that take a focal-species approach. We describe and discuss the benefits of two new metrics. An integrated metric of phylogenetic distances (AUPhyDC) uses information from the whole cumulative distribution, whereas the tenth quantile (PD10) is an extremely simple metric that improves on NTD by capturing the influence of multiple close relatives on ecological interactions. Several recent examples found that PD10 did a better job of revealing ecological patterns than NTD or MPD. We provide R code to facilitate the use of these approaches and advocate for the inclusion of PD10 along with NTD and MPD in statistical packages for phylogenetic ecology.