Data from: Detecting macroevolutionary self-destruction from phylogenies

Phylogenetic analyses have lent support to the concept of lineage selection: that biological lineages can have heritable traits that influence their capacity to persist and diversify, and thereby affect their representation in biodiversity. While many discussions have focussed on “positive” lineage selection, where stably heritable properties of lineages enhance their diversification rate, there are also intriguing examples that seem to represent “negative” lineage selection, where traits reduce the likelihood that a lineage will persist or speciate. In this paper, we test whether a particular pattern of negative lineage selection is detectable from the distributions of the trait on a phylogeny. “Self-destructive” traits are those that arise often but then disappear again because they confer either a raised extinction rate or they are prone to a high rate of trait loss. For such a trait, the reconstructed origins will tend to be dispersed across the tips of the phylogeny, rather than defining large clades of related lineages that all share the trait. We examine the utility of four possible measures of “tippiness” as potential indicators of macroevolutionary self-destruction, applying them to phylogenies on which trait evolution has been simulated under different combinations of parameters for speciation, extinction, trait gain and trait loss. We use an efficient simulation approach that starts with the required number of tips with and without the trait and uses a model to work “backwards” to construct different possible trees that result in that set of tips. We then apply these methods to a number of case studies: salt tolerance in grasses, colour polymorphism in birds of prey, and selfing in nightshades. We find that the relative age of species, measured from tip length, can indicate a reduced speciation rate but does not identify traits that increase the extinction rate or the trait loss rate. We show that it is possible to detect cases of macroevolutionary self-destruction by considering the number of tips with the trait that arise from each inferred origin, and the degree to which the trait is scattered across the phylogeny. These metrics, and the methods we present, may be useful for testing macroevolutionary hypotheses from phylogenetic patterns.

系统发育分析（phylogenetic analyses）为谱系选择（lineage selection）这一概念提供了实证支撑：即生物谱系可携带可遗传性状，这些性状会影响其存续与分化的能力，进而改变其在生物多样性中的占比。尽管诸多讨论多聚焦于“正向”谱系选择——即谱系的稳定可遗传性状可提升其分化速率——但也有不少引人关注的案例似乎属于“负向”谱系选择：这类案例中的性状会降低谱系存续或形成新物种的可能性。
本研究旨在检验，能否通过某一性状在系统发育树（phylogeny）上的分布模式，检测出特定类型的负向谱系选择。“自毁性状（self-destructive traits）”指的是虽频繁出现但会迅速消失的性状：这类性状要么会提升物种灭绝速率，要么极易发生性状丢失。对于这类性状而言，其重建的起源位点往往会分散在系统发育树的类群末梢（tips），而非形成包含所有携带该性状的相关谱系的大型演化支（clade）。
本研究评估了四种可用于衡量“末梢分布性”的指标，将其作为宏观演化（macroevolutionary）自毁现象的潜在检测标志，并将这些指标应用于多组系统发育树——这些树的性状演化过程，是在不同物种形成、灭绝、性状获得与性状丢失参数组合下模拟得到的。我们采用了一种高效的模拟方法：先确定携带与不携带该性状的类群末梢的所需数量，再通过模型反向推演，构建出能产生该类群末梢集合的多种可能系统发育树。
随后，我们将这些方法应用于多个案例研究：禾本科植物的耐盐性、猛禽的体色多态现象，以及茄科植物的自交繁殖特性。研究结果表明，基于类群末梢长度计算得到的物种相对年龄，可用于反映物种形成速率的降低，但无法识别出会提升灭绝速率或性状丢失速率的性状。我们证实，通过统计每个推断起源所对应的携带该性状的类群末梢数量，以及该性状在系统发育树上的分散程度，即可检测宏观演化自毁现象的案例。这些指标与本文提出的方法，或可用于基于系统发育模式验证宏观演化假说。