DISTANCE METHODS FOR INFERRING PHYLOGENIES - A JUSTIFICATION
DISTANCE METHODS FOR INFERRING PHYLOGENIES - A JUSTIFICATION
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DOI：
10.1111/j.1558-5646.1984.tb00255.x
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发表时间：
1984-01-01
期刊：
影响因子：
3.3
通讯作者：
FELSENSTEIN, J
中科院分区：
文献类型：
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作者：
FELSENSTEIN, J
从物种间的表型距离的措施推断遗传学的逻辑检查，并构建一个统计模型。法里斯（Farris，1981）对从距离推断同源性的方法提出的批评依赖于对被推断实体的一种特定解释。如果树上的分支长度是期望距离而不是路径长度，那么对这些方法的主要批评就失去了意义。在期望距离观下，没有理由仅仅因为距离测度不满足三角不等式就放弃距离测度。预期的距离解释自然符合统计推断框架，用于推断相似性。这反过来又为树和观测距离之间的拟合优度的一些最广泛使用的标准提供了理由。统计框架强调的弱点，距离的方法，如果加性的距离之间的树和独立的测量误差的距离不满足的假设。可加性和独立性的可能失败似乎是使用距离方法的最严重的问题。这些假设对于许多经常用距离方法分析的数据是可疑的。分子钟的假设影响了计算的细节，但可以毫无困难地适应统计框架。考虑到可加性和独立性假设的有效性，可以对时钟进行统计检验。
The logic of inferring phylogenies from measures of the phenotypic distance between species is examined, and a statistical model constructed. Criticisms which have been leveled by Farris (1981) against methods of inferring phylogenies from distances are dependent on one particular interpretation of the entity being inferred. If the branch lengths on the tree are expected distances rather than path lengths, the major criticisms of these methods lose their force. Under the expected distance view, there is no reason to abandon distance measures solely because they fail to satisfy the triangle inequality. The expected distance interpretation fits naturally into a statistical inference framework for inferring phylogenies. This in turn provides justification for some of the most widely-used criteria of goodness of fit between a tree and the observed distances. The statistical framework does emphasize the weakness of distance methods if the assumptions of additivity of distances among the tree and of independence of the measurement errors of the distances are not met. The possible failure of additivity and of independence seem to be the most serious problems with using distance methods. These assumptions are dubious for many kinds of data often analyzed by distance methods. The assumption of a molecular clock affects the details of the computations, but can be fit into the statistical framework without difficulty. Given the validity of the additivity and independence assumptions, a statistical test of the clock could be performed.