Three competing ‘methods’ have been endorsed for inferring phylogenetic hypotheses: parsimony, likelihood, and Bayesianism. The latter two have been claimed superior because they take into account rates of sequence substitution. Can rates of substitution be justified on its own accord in inferences of explanatory hypotheses? Answering this question requires addressing four issues: (1) the aim of scientific inquiry, (2) the nature of why-questions, (3) explanatory hypotheses as answers to why-questions, and (4) acknowledging that neither parsimony, likelihood, nor Bayesianism are inferential actions leading to explanatory hypotheses. The aim of scientific inquiry is to acquire causal understanding of effects. Observation statements of organismal characters lead to implicit or explicit why-questions. Those questions, conveyed in data matrices, assume the truth of observation statements, which is contrary to subsequently invoking substitution rates within inferences to phylogenetic hypotheses. Inferences of explanatory hypotheses are abductive in form, such that some version of an evolutionary theory(ies) is/are included or implied. If rates of sequence evolution are to be considered, it must be done prior to, rather than within abduction, which requires renaming those putatively-shared nucleotides subject to substitution rates. There are, however, no epistemic grounds for renaming characters to accommodate rates, calling into question the legitimacy of causally accounting for sequence data.

三种相互竞争的“方法”已被认可用于推断系统发育假设：简约、可能性和贝叶斯主义。后两者被认为是优越的，因为它们考虑了序列替换率。替代率能否在解释性假设的推论中自行证明是合理的？回答这个问题需要解决四个问题：（1）科学探究的目的，（2）为什么问题的性质，（3）作为对为什么问题的答案的解释性假设，以及（4）承认既不简约，可能性，贝叶斯主义也不是导致解释性假设的推理行为。科学探究的目的是获得对影响的因果理解。对有机体特征的观察陈述导致隐含或明确的原因问题。这些问题，在数据矩阵中传达，假设观察陈述的真实性，这与随后在系统发育假设的推论中调用替代率相反。解释性假设的推论在形式上是溯因性的，因此包含或暗示了进化理论的某些版本。如果要考虑序列进化的速率，则必须在诱因之前而不是在诱因内进行，这需要重命名那些受替代率影响的假定共享的核苷酸。然而，重命名字符以适应速率并没有认识论基础，这对因果解释序列数据的合法性提出了质疑。解释性假设的推论在形式上是溯因性的，因此包含或暗示了进化理论的某些版本。如果要考虑序列进化的速率，则必须在诱因之前而不是在诱因内进行，这需要重命名那些受替代率影响的假定共享的核苷酸。然而，重命名字符以适应速率并没有认识论基础，这对因果解释序列数据的合法性提出了质疑。解释性假设的推论在形式上是溯因性的，因此包含或暗示了进化理论的某些版本。如果要考虑序列进化的速率，则必须在诱因之前而不是在诱因内进行，这需要重命名那些受替代率影响的假定共享的核苷酸。然而，重命名字符以适应速率并没有认识论基础，这对因果解释序列数据的合法性提出了质疑。