Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth-death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticised such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study (Louca and Pennell, 2020) has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has led to questioning whether or not diversification rates should be estimated at all. Here we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations we illustrate the characteristics of newly-proposed “pulled rates” and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modelling, but they in no way suggest we should abandon diversification modelling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methods, but by acknowledging them we can better target our joint efforts as a scientific community.

中文翻译：

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拉动多样化率、沿袭时间图和现代宏观进化建模

从现存物种的过时系统发育树（时间树）估计物种形成和灭绝的时间依赖性速率，并确定它们如何以及为什么会发生变化，是理解生态和进化过程如何塑造生物多样性的关键。由于系统发育树的可用性越来越高，在过去十年中，已经开发了越来越多依赖于生死模型的基于过程的方法，以解决宏观进化中的各种问题。然而，这种方法论的进步经常受到批评，以至于人们可能想知道物种形成和灭绝率的估计有多可靠。特别是，最近的一项研究（Louca 和 Pennell，2020 年）使用沿袭时间 (LTT) 图表明，可以生成任何时间树的无限数量的同等可能的多样化情景。这导致人们质疑是否应该估计多样化率。在这里，我们总结、澄清和强调最近关于模型解开多样化历史能力的发现的技术考虑。我们使用模拟来说明新提出的“拉动利率”的特征及其效用。我们认识到，最近的发现是在理解宏观进化建模行为方面向前迈出的一步，但它们绝不意味着我们应该完全放弃多样化建模。相反，使用系统发育树研究宏观进化从未像今天这样令人兴奋和充满希望。在数据可用性和方法方面，我们仍然面临着重要的限制，但通过承认这些限制，我们可以更好地针对我们作为一个科学界的共同努力。