Reconstruction of phylogenetic trees and estimation of divergence times under nonconstant rates of evolution.
Reconstruction of phylogenetic trees and estimation of divergence times under nonconstant rates of evolution.
复制标题
系统发育树的重建和非恒定进化速率下分歧时间的估计。
DOI：
10.1101/sqb.1987.052.01.092
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发表时间：
1987
期刊：
影响因子：
--
通讯作者：
Sharp,PM
中科院分区：
文献类型：
--
作者：
Li,WH;Wolfe,KH;Sourdis,J;Sharp,PM
速率恒定性或”分子钟”假说经常被用作重建生物体或基因之间的系统发育关系以及确定进化事件的年代的基础（参见Dayhoff 1972; Wilson et al. 1977）。然而，现在有强有力的证据表明，利率恒定性假设往往被严重违反（见，例如，Britten 1986）。例如，在不同的哺乳动物目中，核苷酸取代的速率可能相差2或3倍，在灵长类动物中，有充分的证据表明，在通往人类的谱系中，核苷酸取代的速率有所减缓（Wu和Li，1985年; Britten，1986年; Koop等人，1986年; Li和Tanimura，1987年）。因此，重要的是要考虑到不平等的可能性率之间的谱系重建系统发育树时，定年分歧事件。当不同谱系的进化速度差异很大，并且所研究的分类群或DNA序列是远亲时，系统发育重建是极其困难的。我们已经研究了这个问题的简单情况下，只有四个分类群（DNA序列）。我们使用计算机模拟来比较几种方法的性能，看看哪种方法对不平等的进化速率最有效（参见Saitou和Nei 1987）。通常认为，当一个或多个外群可用时，系统发育重建变得更加简单（Saitou和Nei 1986）。然而，外群的有用性取决于它与所研究的分类群的距离。因此，我们研究了外群参考的可靠性随着距离的增加而下降的速度。我们还研究了添加第二个外群体的有用性。这些方法已通过计算机模拟进行了检查。当谱系之间发生率存在巨大差异时，如何确定分歧事件的日期是一个具有挑战性的问题。我们（Li和Tanimura 1987）最近提出了一种近似方法。该方法是启发式的，因此需要仔细研究，使用分析和模拟的方法。最后，我们考虑了人类，黑猩猩，大猩猩和猩猩之间的分支顺序和分歧时间，使用大量的DNA序列数据从四个物种。
The rate-constancy or" molecular clock" hypothesis has often been taken as a basis for reconstructing phylogenetic relationships among organisms or genes and for dating evolutionary events (see, eg, Dayhoff 1972; Wilson et al. 1977). However, there is now strong evidence that the rate-constancy assumption is often seriously violated (see, eg, Britten 1986). For example, among different mammalian orders, the rate of nucleotide substitution may vary by a factor of two or three, and within primates, there is a well-documented slowdown in the lineage leading to man (Wu and Li 1985; Britten 1986; Koop et al. 1986; Li and Tanimura 1987). It is therefore important to take into consideration the possibility of unequal rates among lineages when reconstructing phylogenetic trees and when dating divergence events. Phylogenetic reconstruction is extremely difficult when the rates of evolution differ greatly among lineages and when the taxa or DNA sequences under study are distantly related. We have studied this problem for the simple case of only four taxa (DNA sequences). We used computer simulation to compare the performance of several methods to see which are most effective against unequal rates of evolution (see also Saitou and Nei 1987).It is commonly thought that phylogenetic reconstruction becomes much simpler when one or more outgroups are available (Saitou and Nei 1986). However, the usefulness of an outgroup depends on its distance from the taxa under study. We therefore studied how quickly the reliability of an outgroup reference decreases with that distance. We also studied the usefulness of adding a second outgroup. These approaches have been examined by computer simulation. How to date divergence events is a challenging problem when large differences in rates occur among lineages. We (Li and Tanimura 1987) have recently proposed an approximation method. The method is heuristic and so needs to be examined carefully, using both analytic and simulation approaches. Finally, we consider the branching order and divergence times among human, chimpanzee, gorilla, and orangutan, using a large amount of DNA sequence data from the four species.