Data from: Ranked tree shapes, non-random extinctions and the loss of phylogenetic diversity

Phylogenetic diversity (PD) is a measure of the evolutionary legacy of a group of species, which can be used to define conservation priorities. It has been shown that an important loss of species diversity can sometimes lead to a much less important loss of PD, depending on the topology of the species tree and on the distribution of its branch lengths. However, the rate of decrease of PD strongly depends on the relative depths of the nodes in the tree and on the order in which species become extinct.
We introduce a new, sampling-consistent, three-parameter model generating random trees with covarying topology, clades relative depths and clades relative extinction risks. This model can be seen as an extension to Aldous' one parameter splitting model (β, which controls for tree balance) with two additional parameters: a new parameter α quantifying the relation between age and richness of subclades, and a parameter η quantifying the relation between relative abundance and richness of subclades, taken herein as a proxy for overall extinction risk. We show on simulated phylogenies that loss of PD depends on the combined effect of all three parameters, β, α and η.
In particular, PD may decrease as fast as species diversity when high extinction risks are clustered within small, old clades, corresponding to a parameter range that we term the `danger zone' (β<-1 or α<0; η>1). Besides, when high extinction risks are clustered within large clades, the loss of PD can be higher in trees that are more balanced (β>0), in contrast to the predictions of earlier studies based on simpler models. We propose a Monte-Carlo algorithm, tested on simulated data, to infer all three parameters. Applying it to a real dataset comprising 120 bird clades (class Aves) with known range sizes, we show that parameter estimates precisely fall close to a danger zone: the combination of their ranking tree shape and non-random extinctions risks makes them prone to a sudden collapse of PD.

系统发育多样性（Phylogenetic Diversity，PD）是衡量一组物种演化遗留特征的指标，可用于界定保护优先级。已有研究表明，物种多样性的显著丧失有时仅会导致系统发育多样性的小幅降低，这一结果取决于物种树的拓扑结构及其分支长度的分布。然而，系统发育多样性的下降速率强烈依赖于物种树中节点的相对深度以及物种灭绝的先后顺序。
我们提出一种全新的、采样一致性的三参数模型，可生成具备共变拓扑结构、支系相对深度与支系相对灭绝风险的随机树。该模型可视为对奥尔达斯（Aldous）单参数分裂模型的扩展：原模型仅通过参数β控制树的平衡性，新增的两个参数分别为：用于量化亚支系年龄与丰富度之间关系的参数α，以及被用作整体灭绝风险代理变量、用于量化亚支系相对多度与丰富度之间关系的参数η。基于模拟系统发育树的分析结果表明，系统发育多样性的丧失取决于β、α、η三个参数的共同作用。
具体而言，当高灭绝风险聚集于小型古老支系时，系统发育多样性的下降速率可与物种多样性的下降速率相当，该参数区间被我们定义为“危险区”（β<-1 或 α<0；η>1）。此外，当高灭绝风险聚集于大型支系时，在平衡性更强的物种树（β>0）中，系统发育多样性的丧失程度会更高，这与基于简化模型的早期研究结论相悖。我们提出一种经模拟数据验证的蒙特卡洛（Monte-Carlo）算法，用于推断上述三个参数。将该算法应用于包含120个已知分布范围的鸟纲（Aves）支系的真实数据集后发现，参数估计值恰好落在危险区附近：鸟类支系的分级树形状与非随机灭绝风险的共同作用，使其极易出现系统发育多样性的突发性崩塌。