Institut de Mathématiques de Luminy, FRE 3529, CNRS, Aix-Marseille Université, Case 907, Campus de Luminy, 13288 MARSEILLE Cedex 9, France.
J Theor Biol. 2012 Dec 21;315:26-37. doi: 10.1016/j.jtbi.2012.08.046. Epub 2012 Sep 13.
Using the fossil record yields more detailed reconstructions of the evolutionary process than what is obtained from contemporary lineages only. In this work, we present a stochastic process modeling not only speciation and extinction, but also fossil finds. Next, we derive an explicit formula for the likelihood of a reconstructed phylogeny with fossils, which can be used to estimate the speciation and extinction rates. Finally, we provide a comparative simulation-based evaluation of the accuracy of estimations of these rates from complete phylogenies (including extinct lineages), from reconstructions with contemporary lineages only and from reconstructions with contemporary lineages and the fossil record. Results show that taking the fossil record into account yields more accurate estimates of speciation and extinction rates than considering only contemporary lineages.
利用化石记录比仅从当代谱系中获得的信息更能详细地重建进化过程。在这项工作中，我们提出了一种随机过程模型，不仅可以模拟物种形成和灭绝，还可以模拟化石的发现。接下来，我们推导出了一个显式公式，用于计算具有化石的重建系统发育的似然性，该公式可用于估计物种形成和灭绝率。最后，我们提供了基于比较模拟的评估，以确定从完整的系统发育（包括灭绝谱系）、仅从当代谱系重建以及从当代谱系和化石记录重建中估算这些速率的准确性。结果表明，与仅考虑当代谱系相比，考虑化石记录可以更准确地估计物种形成和灭绝率。
