Comparing cal3 and other a posteriori time-scaling approaches in a case study with the pterocephaliid trilobites
Comparing cal3 and other a posteriori time-scaling approaches in a case study with the pterocephaliid trilobites
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DOI：
10.1017/pab.2016.34
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发表时间：
2017-12-01
期刊：
影响因子：
2.7
通讯作者：
Hopkins, Melanie J.
中科院分区：
文献类型：
--
作者：
Bapst, David W.;Hopkins, Melanie J.
重建生命之树不仅需要识别血统之间的关系，还需要准确估计血统何时分化。古生物学家通常通过直接参考地层记录中第一次出现的分类群来调整分支图以进行后验时间。一些方法使用分支，灭绝和采样过程的概率模型来确定树木样本的日期，例如最近开发的cal3方法，该方法在给定这些过程的一组速率的情况下随机绘制分歧日期。然而，这些模型需要估计这些过程的速率，这可能很难获得，特别是对于采样。在这里，我们对比使用cal3和其他后验时间尺度的方法，通过检查以前的研究，记录了在pterocephalid三叶虫形态进化的减速率。尽管数据集的某些方面使得分支、灭绝和采样率的估计变得困难，但我们使用多方面的方法来计算和评估应用Cal 3所需的速率估计。与以前的模拟研究一致，我们发现系统发育年代测定方法的选择影响下游宏观进化的结论。我们还发现矛盾的祖先后代对比分析（基于祖先性状重建方法）和最大似然参数估计之间的进化推论。祖先的分类推断在cal3证实了以前假设的祖先后代序列，但cal3建议更大的支持萌芽的分支比进化。本案例研究证明了cal3方法的潜力和广泛的适用性，以及选择cal3而不是简单的后验时间尺度方法所带来的好处。
Reconstructing the tree of life involves more than identifying relationships among lineages; it also entails accurately estimating when lineages diverged. Paleontologists typically scale cladograms to time a posteriori by direct reference to first appearances of taxa in the stratigraphic record. Some approaches use probabilistic models of branching, extinction, and sampling processes to date samples of trees, such as the recently developed cal3 method, which stochastically draws divergence dates given a set of rates for those processes. However, these models require estimates of the rates of those processes, which may be hard to obtain, particularly for sampling. Here, we contrast the use of cal3 and other a posteriori time-scaling approaches by examining a previous study that documented a decelerating rate of morphological evolution in pterocephaliid trilobites. Although aspects of the data set make estimation of branching, extinction, and sampling rates difficult, we use a multifaceted approach to calculate and evaluate the rate estimates needed for applying cal3. In agreement with previous simulation studies, we find that the choice of phylogenetic dating method impacts downstream macroevolutionary conclusions. We also find contradictory evolutionary inferences between analyses on ancestor-descendant contrasts (based on ancestor trait reconstruction methods) and maximum-likelihood parameter estimates. Ancestral taxon inference in cal3 corroborates previously hypothesized ancestor-descendant sequences, but cal3 suggests greater support for budding cladogenesis than anagenesis. This case study demonstrates the potential and wide applicability of the cal3 method and the benefits afforded by choosing cal3 over simpler a posteriori time-scaling approaches.