Phillips Matthew J
Centre for Macroevolution and Macroecology, School of Botany and Zoology, Australian National University, Gould Building, Canberra ACT 0200, Australia.
Gene. 2009 Jul 15;441(1-2):132-40. doi: 10.1016/j.gene.2008.08.017. Epub 2008 Sep 6.
Despite recent methodological advances in inferring the time-scale of biological evolution from molecular data, the fundamental question of whether our substitution models are sufficiently well specified to accurately estimate branch-lengths has received little attention. I examine this implicit assumption of all molecular dating methods, on a vertebrate mitochondrial protein-coding dataset. Comparison with analyses in which the data are RY-coded (AG --> R; CT --> Y) suggests that even rates-across-sites maximum likelihood greatly under-compensates for multiple substitutions among the standard (ACGT) NT-coded data, which has been subject to greater phylogenetic signal erosion. Accordingly, the fossil record indicates that branch-lengths inferred from the NT-coded data translate into divergence time overestimates when calibrated from deeper in the tree. Intriguingly, RY-coding led to the opposite result. The underlying NT and RY substitution model misspecifications likely relate respectively to "hidden" rate heterogeneity and changes in substitution processes across the tree, for which I provide simulated examples. Given the magnitude of the inferred molecular dating errors, branch-length estimation biases may partly explain current conflicts with some palaeontological dating estimates.
尽管最近在从分子数据推断生物进化时间尺度方面取得了方法上的进展，但关于我们的替换模型是否得到充分良好的设定以准确估计分支长度这一基本问题却很少受到关注。我在一个脊椎动物线粒体蛋白质编码数据集上检验了所有分子定年方法的这一隐含假设。与将数据进行RY编码（AG --> R；CT --> Y）的分析相比较表明，即使是位点间速率最大似然法，对于标准（ACGT）核苷酸编码数据中的多次替换也补偿不足，而这些数据遭受了更大的系统发育信号侵蚀。因此，化石记录表明，当从树的更深位置进行校准时，从核苷酸编码数据推断出的分支长度会转化为分歧时间的高估。有趣的是，RY编码却导致了相反的结果。潜在的核苷酸和RY替换模型设定错误可能分别与“隐藏”的速率异质性以及树中替换过程的变化有关，对此我提供了模拟示例。鉴于推断出的分子定年误差的大小，分支长度估计偏差可能部分解释了当前与一些古生物学定年估计的冲突。
