A nonparametric approach to estimating divergence times in the absence of rate constancy
A nonparametric approach to estimating divergence times in the absence of rate constancy
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DOI：
10.1093/oxfordjournals.molbev.a025731
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发表时间：
1997-12-01
影响因子：
10.7
通讯作者：
Sanderson, MJ
中科院分区：
文献类型：
--
作者：
Sanderson, MJ
提出了一种新的方法估计分歧时间时，进化率是可变的跨谱系。该方法，称为非参数率平滑（NPRS），依赖于最小化的祖先-后代的本地速率变化，是由进化速率在时间上自相关的可能性的动机。化石信息有关的最小和/或最大年龄的节点在一个遗传算法被纳入约束优化技术的算法。NPRS的准确性进行了检查，比较基于时钟的最大似然法在计算机模拟。当（1）序列长度足够长，（2）速率真正非时钟样，（3）速率在时间上中度到高度自相关时，NPRS提供了更准确的发散时间估计。该算法被应用于估计分歧时间在种子植物的叶绿体rbcL基因的数据的基础上。约束和无约束的NPRS方法往往产生分歧的时间估计更符合古植物学证据比时钟为基础的估计。
A new method for estimating divergence times when evolutionary rates are variable across lineages is proposed. The method, called nonparametric rate smoothing (NPRS), relies on minimization of ancestor-descendant local rate changes and is motivated by the likelihood that evolutionary rates are autocorrelated in time. Fossil information pertaining to minimum and/or maximum ages of nodes in a phylogeny is incorporated into the algorithms by constrained optimization techniques. The accuracy of NPRS was examined by comparison to a clock-based maximum-likelihood method in computer simulations. NPRS provides more accurate estimates of divergence times when (1) sequence lengths are sufficiently long, (2) rates are truly nonclocklike, and (3) rates are moderately to highly autocorrelated in time. The algorithms were applied to estimate divergence times in seed plants based on data from the chloroplast rbcL gene. Both constrained and unconstrained NPRS methods tended to produce divergence time estimates more consistent with paleobotanical evidence than did clock-based estimates.