A hidden Markov Model approach to variation among sites in rate of evolution
A hidden Markov Model approach to variation among sites in rate of evolution
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DOI：
10.1093/oxfordjournals.molbev.a025575
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发表时间：
1996-01-01
影响因子：
10.7
通讯作者：
Churchill, GA
中科院分区：
文献类型：
--
作者：
Felsenstein, J;Churchill, GA
隐马尔可夫模型的方法被用来考虑分子序列中不同位点的不相等和未知的进化速率。假设不同地点的进化速率是从一组可能的速率中得出的，这些可能的速率是有限的。系统发育的总体可能性是用一组项的总和来计算的，每一项都是给定特定的速率分配给位点的数据的概率，乘以该特定速率组合的先验概率。不同速率组合的概率由固定马尔可夫链指定，该链将速率类别分配给站点。虽然将费率分配给站点的可能方法非常多，但一个简单的递归算法允许在与单个站点的不同费率数量成比例的时间内，将所有可能的费率组合对可能性的贡献相加。因此，对于三种汇率，所涉及的工作量不超过单一汇率的三倍。这种“隐马尔可夫模型”方法允许不同站点之间的速率差异以及相邻站点之间的速率相关性。通过对所有可能性求和，我们不需要知道个别地点的速率。然而，它不允许非相邻站点的费率相互关联，也不允许站点间费率的连续分布。展示了如何使用牛顿-拉夫森方法来估计系统发育的分支长度，并从系统发育中推断出什么分配速率到站点具有最大的后验概率。给出了在8种哺乳动物中使用β -血红蛋白DNA序列的例子；推断出高进化率和低进化率的区域，以及相似进化率斑块的平均长度。
The method of Hidden Markov Models is used to allow for unequal and unknown evolutionary rates at different sites in molecular sequences. Rates of evolution at different sites are assumed to be drawn from a set of possible rates, with a finite number of possibilities. The overall likelihood of phylogeny is calculated as a sum of terms, each term being the probability of the data given a particular assignment of rates to sites, times the prior probability of that particular combination of rates. The probabilities of different rate combinations are specified by a stationary Markov chain that assigns rate categories to sites. While there will be a very large number of possible ways of assigning rates to sites, a simple recursive algorithm allows the contributions to the likelihood from all possible combinations of rates to be summed, in a time proportional to the number of different rates at a single site. Thus with three rates, the effort involved is no greater than three times that for a single rate. This ''Hidden Markov Model'' method allows for rates to differ between sites and for correlations between the rates of neighboring sites. By summing over all possibilities it does not require us to know the rates at individual sites. However, it does not allow for correlation of rates at nonadjacent sites, nor does it allow for a continuous distribution of rates over sites. It is shown how to use the Newton-Raphson method to estimate branch lengths of a phylogeny and to infer from a phylogeny what assignment of rates to sites has the largest posterior probability. An example is given using beta-hemoglobin DNA sequences in eight mammal species; the regions of high and low evolutionary rates are inferred and also the average length of patches of similar rates.