Del Cid Carlos Calderón, Hauffe Torsten, Carrillo Juan D, May Michael R, Warnock Rachel C M, Silvestro Daniele
Laboratório de Ecologia Espacial, Instituto de Biologia, Universidade Federal da Bahia, CEP 40170-110, Salvador, Bahia, Brazil.
Department of Biology, University of Fribourg, Switzerland and Swiss Institute of Bioinformatics, Fribourg, Switzerland.
Glob Ecol Biogeogr. 2024 Oct;33(10). doi: 10.1111/geb.13890. Epub 2024 Jul 4.
Species age, the elapsed time since origination, can give insight into how species longevity might influence eco-evolutionary dynamics, which has been hypothesized to influence extinction risk. Traditionally, species' ages have been estimated from fossil records. However, numerous studies have recently used the branch lengths of time-calibrated phylogenies as estimates of the ages of extant species. This approach poses problems because phylogenetic trees only contain direct information about species identity at the tips and not along the branches. Here, we show that incomplete taxon sampling, extinction, and different assumptions about speciation modes can significantly alter the relationship between true species age and phylogenetic branch lengths, leading to high error rates. We found that these biases can lead to erroneous interpretations of eco-evolutionary patterns derived from comparing phylogenetic age and other traits, such as extinction risk.
For bifurcating speciation, the default assumption in most analyses of species age, we propose a probabilistic approach based on the properties of a birth-death process to improve the estimation of species ages. Our approach can reduce the error by one order of magnitude under cases of high extinction and a high percentage of unsampled extant species.
Our results call for caution in interpreting the relationship between phylogenetic ages and eco-evolutionary traits, as this can lead to biased and erroneous conclusions. We show that, under the assumption of bifurcating speciation, we can obtain unbiased approximations of species age by combining information from branch lengths with the expectations of a birth-death process.
物种年龄，即自起源以来所经历的时间，能够让我们深入了解物种寿命如何影响生态进化动态，而这一动态被认为会影响灭绝风险。传统上，物种年龄是通过化石记录来估计的。然而，最近大量研究使用了时间校准系统发育树的分支长度来估计现存物种的年龄。这种方法存在问题，因为系统发育树仅包含末端物种身份的直接信息，而不包含分支上的信息。在此，我们表明不完整的分类单元采样、灭绝以及关于物种形成模式的不同假设会显著改变真实物种年龄与系统发育分支长度之间的关系，导致高错误率。我们发现这些偏差会导致对源自比较系统发育年龄和其他特征（如灭绝风险）的生态进化模式的错误解读。
对于大多数物种年龄分析中的默认假设——二叉分支物种形成，我们基于生死过程的特性提出了一种概率方法，以改进物种年龄的估计。在高灭绝率和高比例未采样现存物种的情况下，我们的方法可以将误差降低一个数量级。
我们的结果呼吁在解释系统发育年龄与生态进化特征之间的关系时要谨慎，因为这可能导致有偏差和错误的结论。我们表明，在二叉分支物种形成的假设下，通过将分支长度信息与生死过程的期望相结合，我们可以获得物种年龄的无偏近似值。
