Bell Charles D, Soltis Douglas E, Soltis Pamela S
Florida Museum of Natural History, Dickinson Hall, University of Florida, Gainesville, Florida 32611, USA.
Evolution. 2005 Jun;59(6):1245-58.
The age of the angiosperms has long been of interest to botanists and evolutionary biologists. Many early efforts to date the age of the angiosperms and evolutionary divergences within the angiosperm clade using a molecular clock have yielded age estimates that are grossly inconsistent with the fossil record. We investigated the age of angiosperms using Bayesian relaxed clock (BRC) and penalized likelihood (PL) approaches. Both of these methods allow the incorporation of multiple fossil constraints into the optimization procedure. The BRC method allows a range of values for among-lineage rate of substitution, from a nearly clocklike behavior to a condition in which each branch is allowed an optimal substitution rate, and also accounts for variation in molecular evolution across multiple genes. A topology derived from an analysis of genes from all three plant genomes for 71 taxa was used as a backbone. The effects on age estimates of different genes, single-gene versus concatenated datasets, and the inclusion and assumptions of fossils as age constraints were examined. In addition, the influence of prior distributions on estimates of divergence times was also explored. These results indicate that widely divergent age estimates can result from the different methods (198-139 million years ago), different sources of data (275-122 million years ago), and the inclusion of temporal constraints to topologies. Most dates, however, are between 180-140 million years ago, suggesting a Middle Jurassic-Early Cretaceous origin of flowering plants, predating the oldest unequivocal fossil angiosperms by about 45-5 million years. Nonetheless, these dates are consistent with other recent studies that have used methods that relax the assumption of a strict molecular clock and also agree with the hypothesis that the angiosperms may be somewhat older than the fossil record indicates.
被子植物的起源时间长期以来一直是植物学家和进化生物学家感兴趣的问题。许多早期利用分子钟来确定被子植物的起源时间以及被子植物分支内进化分歧时间的尝试，所得到的时间估计与化石记录严重不符。我们使用贝叶斯松弛时钟（BRC）和惩罚似然（PL）方法来研究被子植物的起源时间。这两种方法都允许在优化过程中纳入多个化石约束条件。BRC方法允许谱系间替换率有一系列值，从近乎时钟般的行为到每个分支都有最优替换率的情况，并且还考虑了多个基因间分子进化的差异。一个基于对71个分类群的所有三个植物基因组的基因分析得出的拓扑结构被用作主干。我们研究了不同基因、单基因数据集与串联数据集以及将化石作为时间约束条件的纳入和假设对时间估计的影响。此外，还探讨了先验分布对分歧时间估计的影响。这些结果表明，不同的方法（1.98亿至1.39亿年前）、不同的数据来源（2.75亿至1.22亿年前）以及对拓扑结构纳入时间约束，都可能导致差异很大的时间估计。然而，大多数时间估计在1.8亿至1.4亿年前之间，这表明开花植物起源于中侏罗世 - 早白垩世，比最古老的确切被子植物化石早约4500万至500万年。尽管如此，这些时间估计与其他最近使用放宽严格分子钟假设方法的研究结果一致，也与被子植物可能比化石记录显示的年龄稍大这一假设相符。
