Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil.
Department of Ecology and Evolutionary Biology, University of California, 610 Young Drive South, Los Angeles, CA 90095, USA.
Syst Biol. 2019 Jan 1;68(1):47-62. doi: 10.1093/sysbio/syy037.
The fossil record shows that the vast majority of all species that ever existed are extinct and that most lineages go through an expansion and decline in diversity. However, macroevolutionary analyses based upon molecular phylogenies have difficulty inferring extinction dynamics, raising questions about whether the neontological record can contribute to an understanding of the decline phenomenon. Two recently developed diversification methods for molecular phylogenies (RPANDA and BAMM) incorporate models that theoretically have the capacity to capture decline dynamics by allowing extinction to be higher than speciation. However, the performance of these frameworks over a wide range of decline scenarios has not been studied. Here, we investigate the behavior of these methods under decline scenarios caused by decreasing speciation and increasing extinction through time on simulated trees at fixed intervals over diversity trajectories with expansion and decline phases. We also compared method performance over a comprehensive data set of 214 empirical trees. Our results show that both methods perform equally well when varying speciation rates control decline. When decline was only caused by an increase in extinction rates both methods wrongly assign the variation in net diversification to a drop in speciation, even though the positive gamma values of those trees would suggest otherwise. We also found a tendency for RPANDA to favor increasing extinction and BAMM to favor decreasing speciation as the most common cause of decline in empirical trees. Overall our results shed light on the limitations of both methods, encouraging researchers to carefully interpret the results from diversification studies.
化石记录表明，绝大多数曾经存在的物种已经灭绝，而且大多数谱系的多样性都经历了扩张和减少的过程。然而，基于分子系统发育的宏观进化分析很难推断灭绝动态，这引发了一个问题，即新代记录是否可以有助于理解衰退现象。两种最近开发的分子系统发育多样化方法（RPANDA 和 BAMM）纳入了模型，这些模型理论上有能力通过允许灭绝率高于物种形成率来捕捉灭绝动态。然而，这些框架在广泛的衰退情景下的性能尚未得到研究。在这里，我们通过在具有扩张和减少阶段的多样性轨迹上的固定间隔模拟树上的衰退情景，调查了这些方法在由随时间减少的物种形成和增加的灭绝引起的衰退情景下的行为。我们还比较了这两种方法在 214 个经验树的综合数据集上的性能。我们的结果表明，当变化的物种形成率控制衰退时，这两种方法的性能都同样好。当衰退仅由灭绝率的增加引起时，这两种方法都错误地将净多样化的变化归因于物种形成率的下降，尽管这些树的正伽马值表明并非如此。我们还发现，RPANDA 倾向于将增加的灭绝作为衰退的最常见原因，而 BAMM 倾向于将减少的物种形成作为衰退的最常见原因。总体而言，我们的结果揭示了这两种方法的局限性，鼓励研究人员仔细解释多样化研究的结果。
