Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland.
Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland.
Syst Biol. 2018 May 1;67(3):458-474. doi: 10.1093/sysbio/syx082.
The estimation of diversification rates is one of the most vividly debated topics in modern systematics, with considerable controversy surrounding the power of phylogenetic and fossil-based approaches in estimating extinction. Van Valen's seminal work from 1973 proposed the "Law of constant extinction," which states that the probability of extinction of taxa is not dependent on their age. This assumption of age-independent extinction has prevailed for decades with its assessment based on survivorship curves, which, however, do not directly account for the incompleteness of the fossil record, and have rarely been applied at the species level. Here, we present a Bayesian framework to estimate extinction rates from the fossil record accounting for age-dependent extinction (ADE). Our approach, unlike previous implementations, explicitly models unobserved species and accounts for the effects of fossil preservation on the observed longevity of sampled lineages. We assess the performance and robustness of our method through extensive simulations and apply it to a fossil data set of terrestrial Carnivora spanning the past 40 myr. We find strong evidence of ADE, as we detect the extinction rate to be highest in young species and declining with increasing species age. For comparison, we apply a recently developed analogous ADE model to a dated phylogeny of extant Carnivora. Although the phylogeny-based analysis also infers ADE, it indicates that the extinction rate, instead, increases with increasing taxon age. The estimated mean species longevity also differs substantially, with the fossil-based analyses estimating 2.0 myr, in contrast to 9.8 myr derived from the phylogeny-based inference. Scrutinizing these discrepancies, we find that both fossil and phylogeny-based ADE models are prone to high error rates when speciation and extinction rates increase or decrease through time. However, analyses of simulated and empirical data show that fossil-based inferences are more robust. This study shows that an accurate estimation of ADE from incomplete fossil data is possible when the effects of preservation are jointly modeled, thus allowing for a reassessment of Van Valen's model as a general rule in macroevolution.
多样性速率的估计是现代系统学中最具争议的话题之一，围绕着系统发育和化石方法在估计灭绝方面的能力存在着相当大的争议。范瓦伦（Van Valen）1973 年的开创性工作提出了“恒灭定律”（Law of constant extinction），该定律指出灭绝的概率与灭绝物种的年龄无关。这种年龄独立灭绝的假设已经流行了几十年，其评估是基于生存曲线，然而，这些曲线并没有直接考虑化石记录的不完整性，而且很少在物种水平上应用。在这里，我们提出了一种贝叶斯框架，从化石记录中估计考虑年龄相关灭绝（Age-Dependent Extinction，ADE）的灭绝速率。我们的方法与以前的实现不同，它明确地对未观察到的物种进行建模，并考虑了化石保存对所采样谱系观察到的寿命的影响。我们通过广泛的模拟来评估我们方法的性能和稳健性，并将其应用于过去 4000 万年的陆生 Carnivora 化石数据集。我们发现了强烈的 ADE 证据，因为我们发现灭绝速率在年轻物种中最高，随着物种年龄的增加而下降。相比之下，我们将最近开发的类似 ADE 模型应用于现生 Carnivora 的有时间的系统发育树上。尽管基于系统发育的分析也推断出了 ADE，但它表明灭绝速率反而随着分类单元年龄的增加而增加。估计的平均物种寿命也有很大差异，基于化石的分析估计为 200 万年，而基于系统发育的推断则为 980 万年。仔细研究这些差异，我们发现化石和基于系统发育的 ADE 模型在物种形成和灭绝速率随时间增加或减少时都容易出现高错误率。然而，模拟和实证数据分析表明，基于化石的推断更为稳健。这项研究表明，当共同建模保存效应时，可以从不完整的化石数据中准确估计 ADE，从而重新评估范瓦伦（Van Valen）的模型作为宏观进化的一般规律。
