EVOLUTIONARY TREES FROM NUCLEIC-ACID AND PROTEIN SEQUENCES
EVOLUTIONARY TREES FROM NUCLEIC-ACID AND PROTEIN SEQUENCES
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DOI：
10.1098/rspb.1985.0096
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发表时间：
1985-01-01
期刊：
影响因子：
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通讯作者：
FRIDAY, AE
中科院分区：
文献类型：
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作者：
BISHOP, MJ;FRIDAY, AE
这个问题是通过对活生物体的核酸或蛋白质序列的比较研究来估计进化关系。在这篇文章中最重要的一点是，对进化关系的估计应该基于明确定义的模型，这些模型的假设是可以检验的。这些模型应尽可能符合有关生物体的进化变化过程的已知情况。流行的方法，在这里被归类为分歧模型，下面以这样一种方式陈述，很明显，它们涉及关于进化变化本质的不切实际的假设。重点放在进化变化的概率模型的使用上。这些模型的历史发展是与更常用的“简约”方法并行进行的。假设遗传传递途径符合树状结构，可以简化系统发育重建问题。树形模型是合理的，因为这样的途径可以在谱系中追踪，然而，树形模型忽略了杂交和遗传物质的水平传递。另一个重要组成部分是遗传变化过程的概率公式。考虑到遗传可靠性（将突变视为不能正确复制信息的观点）导致了这样的概率描述。提出了几种对DNA中碱基取代相对频率进行数值评估的方案。接下来，我们将研究基于概率模型的系统发育树估计方法。对散度时间的两两估计迅速导致进化关系的假设，但强调的是，联合估计程序，同时考虑到所有的数据，导致更完整的关系估计。所述的各种方法用于分析来自哺乳动物线粒体基因组的核酸序列数据。最后，我们讨论了当前随机模型的弱点，并指出了积累实验信息可能导致其改进或反驳的方法。
The problem addressed is that of estimating evolutionary relationship by the comarative study of the nucleic acid or protein sequences of living organisms. The most important point made in this acocunt is that estimation of evolutionary relationship should be based on clearly defined models the assumptions of which are open to test. The models should as far as possible conform to what is known about the processes of evolutionary change in the organisms concerned. Prevailing approaches, grouped here as divergence models, are stated below in such a way that it is clear that they involve unrealistic assumptions about the the nature of evolutionary change. Emphasis is placed on the use of probabilistic models of evolutionary change. The historical development of these models has proceeded in parall with the more commonly used ''parsimony'' methods. The problem of reconstructing phylogenies is simplified by assuming that the pathways of genetic transmission conform to a tree structure. The tree model is justified on the grounds that such pathways may be traced in a genealogy, however, the tree model ignores hybridization and horizontal transmission of the genetic material. The other essential component is a probabilistic formulation of the processes of genetic change. Consideration of genetic reliability (a view of mutation as failure correctly to copy information) leads to such a probabilistic description. Several proposed schemes which make numerical assessment of the relative frequencies of base substitution in DNA are considered. We next examine methods for the estimation of phylogenetic trees on the basis of probabilistic models. Pairwise estimates of divergence times lead rapidly to hypotheses of evolutionary relationship, but it is stressed that joint estimation procedures, which simultaneously take account of all the data, lead to more complete estimates of relationship. The various methods are illustrated as applied to the analysis of nucleic acid sequence data from the mammalian mitochondrial genome. Finally, we discuss weaknesses of the current stochastic models and point out ways in which accumulating experimental information may lead to their refinement or refutation.