Smith Andrew B, Pisani Davide, Mackenzie-Dodds Jacqueline A, Stockley Bruce, Webster Bonnie L, Littlewood D Timothy J
Department of Palaeontology, The Natural History Museum, London, United Kingdom.
Mol Biol Evol. 2006 Oct;23(10):1832-51. doi: 10.1093/molbev/msl039. Epub 2006 Jun 15.
The phylogenetic relationships of 46 echinoids, with representatives from 13 of the 14 ordinal-level clades and about 70% of extant families commonly recognized, have been established from 3 genes (3,226 alignable bases) and 119 morphological characters. Morphological and molecular estimates are similar enough to be considered suboptimal estimates of one another, and the combined data provide a tree that, when calibrated against the fossil record, provides paleontological estimates of divergence times and completeness of their fossil record. The order of branching on the cladogram largely agrees with the stratigraphic order of first occurrences and implies that their fossil record is more than 85% complete at family level and at a resolution of 5-Myr time intervals. Molecular estimates of divergence times derived from applying both molecular clock and relaxed molecular clock models are concordant with estimates based on the fossil record in up to 70% of cases, with most concordant results obtained using Sanderson's semiparametric penalized likelihood method and a logarithmic-penalty function. There are 3 regions of the tree where molecular and fossil estimates of divergence time consistently disagree. Comparison with results obtained when molecular divergence dates are estimated from the combined (morphology + gene) tree suggests that errors in phylogenetic reconstruction explain only one of these. In another region the error most likely lies with the paleontological estimates because taxa in this region are demonstrated to have a very poor fossil record. In the third case, morphological and paleontological evidence is much stronger, and the topology for this part of the molecular tree differs from that derived from the combined data. Here the cause of the mismatch is unclear but could be methodological, arising from marked inequality of molecular rates. Overall, the level of agreement reached between these different data and methodological approaches leads us to believe that careful application of likelihood and Bayesian methods to molecular data provides realistic divergence time estimates in the majority of cases (almost 80% in this specific example), thus providing a remarkably well-calibrated phylogeny of a character-rich clade of ubiquitous marine benthic invertebrates.
已根据3个基因（3226个可比对碱基）和119个形态特征，建立了46种海胆类动物的系统发育关系，这些海胆类动物代表了14个目级分支中的13个，以及约70%的现存公认科。形态学和分子估计结果足够相似，可被视为彼此的次优估计，并且综合数据提供了一棵树，当根据化石记录进行校准时，可提供分歧时间和其化石记录完整性的古生物学估计。分支图上的分支顺序在很大程度上与首次出现的地层顺序一致，这意味着它们在科级水平以及500万年时间间隔的分辨率下，化石记录的完整性超过85%。应用分子钟和宽松分子钟模型得出的分歧时间分子估计，在多达70%的情况下与基于化石记录的估计一致，使用桑德森的半参数惩罚似然方法和对数惩罚函数可获得最一致的结果。在树的3个区域中，分歧时间的分子估计和化石估计始终不一致。将这些结果与从（形态学 + 基因）组合树估计分子分歧日期时获得的结果进行比较表明，系统发育重建中的错误仅解释了其中之一。在另一个区域，错误很可能在于古生物学估计，因为该区域的类群化石记录非常差。在第三种情况下，形态学和古生物学证据要强得多，分子树这一部分的拓扑结构与从综合数据得出的拓扑结构不同。此处不匹配的原因尚不清楚，但可能是方法学上的，源于分子速率的显著不平等。总体而言，这些不同数据和方法学方法之间达成的一致程度使我们相信，在大多数情况下（在此特定示例中几乎为80%），将似然法和贝叶斯方法谨慎应用于分子数据可提供现实的分歧时间估计，从而为一个特征丰富的普遍存在的海洋底栖无脊椎动物类群提供了一个校准良好的系统发育树。
