Data from: Evolutionarily distinct “living fossils” require both lower speciation and lower extinction rates

As a label for a distinct category of life, ‘living fossil’ is controversial. The term has multiple definitions and it is unclear whether the label can be genuinely used to delimit biodiversity. Even taking a purely phylogenetic perspective where a proxy for the living fossil is evolutionary distinctness (ED), an inconsistency arises: does it refer to “dead-end” lineages doomed to extinction or “panchronic” lineages that survive through multiple epochs? Recent tree-growth model studies indicate that speciation rates must have been unequally distributed between species in the past to produce the shape of the tree of life. Although an uneven distribution of speciation rates may create the possibility for a distinct group of living fossil lineages, such a grouping could only be considered genuine if extinction rates also show a consistent pattern, be it indicative of dead-end or panchronic lineages. To determine whether extinction rates also show an unequal distribution, we developed a tree-growth model where the probability of speciation and extinction is a function of a tip’s ED. We simulated 1,000s of trees where the ED function for a tip is randomly and independently determined for speciation and extinction rates. We find that simulations where the most evolutionarily distinct tips have lower rates of speciation and extinction produce phylogenetic trees closest in shape to empirical trees. This implies that a distinct set of lineages with reduced rates of diversification, indicative of a panchronic definition, is required to create the shape of the tree of life.

作为一类独特生命类别的标签，‘活化石(living fossil)’颇具争议。该术语存在多重定义，目前尚不清楚该标签能否真正用于划分生物多样性。即便仅从系统发育(phylogenetic)视角出发，将演化独特性(evolutionary distinctness, ED)作为活化石的代理指标，也会出现矛盾：该术语究竟是指注定走向灭绝的‘死胡同’演化支，还是历经多个地质时代存续至今的‘泛时’演化支？
近期的系统发育树生长模型研究表明，过往物种间的成种速率(speciation rates)分布必然不均，才得以塑造生命之树(tree of life)的形态。尽管成种速率分布不均有可能催生一类独特的活化石演化支，但唯有当灭绝速率(extinction rates)也呈现出一致的模式——无论该模式对应死胡同类群还是泛时类群——时，这类演化支分组才可被认定为真实存在。
为验证灭绝速率是否同样存在不均分布，我们开发了一套系统发育树生长模型，其中成种与灭绝的概率由终端类群(tip)的演化独特性决定。我们模拟了数千棵系统发育树，其中各终端类群的演化独特性函数由成种速率和灭绝速率随机独立确定。研究发现，当演化独特性最高的终端类群拥有更低的成种与灭绝速率时，模拟得到的系统发育树形态最贴近实证系统发育树。
这意味着，若要塑造生命之树的形态，需要存在一类独特的、分化速率降低的演化支——这契合泛时定义的特征。