Nonparametric phylogenetic inference from restriction cleavage sites.
Nonparametric phylogenetic inference from restriction cleavage sites.
复制标题
从限制性酶切位点进行非参数系统发育推断。
DOI：
10.1093/oxfordjournals.molbev.a040440
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发表时间：
1987
影响因子：
10.7
通讯作者：
Templeton,AR
中科院分区：
文献类型：
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作者：
Templeton,AR
Nei和Tajima（1985）最近批评了我的算法（Templeton 1983 a，19833），这些算法从限制位点图中进行系统发育推断。这封信的目的是解决他们的批评，并检查我们对我的算法的有效性范围的意见分歧的原因。这些观点也将通过一个夏威夷果蝇的例子来说明。Nei和Tajima（1985）认为，如果数据中包含某些限制性位点的重复计数，那么我对两种灵长类动物遗传学的区分（Templeton 19833）可能存在统计学缺陷。重叠可能是由于具有多个识别序列的酶而产生的，这些识别序列包括单个切割物的识别序列。然而，在生成用于检验这些假设的分数时（Templeton 19833的表2），我只使用了多个切割器揭示的新的信息模式。没有部位被计数两次。因此，内和田岛提出的关注并不适用。内和田岛的主要批评关注的范围内的有效性的算法。我已经得出结论（Templeton 19838），如果平均替换率（1）乘以发散时间（t）为-~ 0.05，则算法有效。Nei和Tajima（1985）认为，0.01这个小得多的值是必要的。他们根据两个理论论证来证明这个较小的ht值。第一个问题是，在缺乏外群数据的情况下，难以区分限制性位点的单一收敛性整合与双重缺失。(fig. 3 Nei和Tajima [19851和相关艾德文本）。然而，受到批评的算法被明确地限制在具有外群的数据上（Templeton 1983 b）。因此，这一理论上的反对是在我（Templeton，1983 b）划定的推理范围之外的，因此与0.05 ht标准的有效性完全无关。
Nei and Tajima (1985) recently have criticized my algorithms (Templeton 1983a, 19833) that make phylogenetic inference from restriction-site maps. The purpose of this letter is to address their criticisms and to examine the reasons for our difference of opinion concerning the range of validity of my algorithms. These points will also be illustrated by a worked example using Hawaiian Drosophila. Nei and Tajima (1985) have suggested that my discrimination between two primate phylogenies (Templeton 19833) might be statistically flawed if the data included a double counting of some restriction sites. Overlap could arise owing to enzymes with multiple recognition sequences that include the recognition sequences of single cutters. However, in generating the scores used to test these hypotheses (table 2 of Templeton 19833), I used only the novel informative patterns revealed by the mutiple cutters. No site was counted twice. Hence, the concern raised by Nei and Tajima does not apply.The primary criticism of Nei and Tajima concerns the range of validity of the algorithms. I have concluded (Templeton 19838) that the algorithms are valid if the average substitution rate (1) times the time of divergence (t) is-~ 0.05. Nei and Tajima (1985) argue that the much smaller value of 0.01 is necessary. They justi fy this smaller ht value on the basis of two theoretical arguments. The first concerns the difficulty, in the absence of outgroup data, of distinguishing a single convergent ga in of restriction sites from a double loss.(fig. 3 of Nei and Tajima [19851 and associat ed text). However, the criticized algorithms were explicitly limited to data with an outgro up (Templeton 1983b). Hence, this theoretical objection lies outside the inference domai n delimited by me (Templeton 1983b) and is therefore completely irrelevant to the validity of the 0.05 ht criterion.