Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Ciudad Universitaria, Coyoacán, México, D.F. C.P. 04510, México.
Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n, Ciudad Universitaria, Coyoacán, México, D.F. C.P. 04510, México.
Syst Biol. 2018 May 1;67(3):543-551. doi: 10.1093/sysbio/syx053.
The conceptualization and coding of characters is a difficult issue in phylogenetic systematics, no matter which inference method is used when reconstructing phylogenetic trees or if the characters are just mapped onto a specific tree. Complex characters are groups of features that can be divided into simpler hierarchical characters (reductive coding), although the implied hierarchical relational information may change depending on the type of coding (composite vs. reductive). Up to now, there is no common agreement to either code characters as complex or simple. Phylogeneticists have discussed which coding method is best but have not incorporated the heuristic process of reciprocal illumination to evaluate the coding. Composite coding allows to test whether 1) several characters were linked resulting in a structure described as a complex character or trait or 2) independently evolving characters resulted in the configuration incorrectly interpreted as a complex character. We propose that complex characters or character states should be decomposed iteratively into simpler characters when the original homology hypothesis is not corroborated by a phylogenetic analysis, and the character or character state is retrieved as homoplastic. We tested this approach using the case of fruit types within subfamily Cinchonoideae (Rubiaceae). The iterative reductive coding of characters associated with drupes allowed us to unthread fruit evolution within Cinchonoideae. Our results show that drupes and berries are not homologous. As a consequence, a more precise ontology for the Cinchonoideae drupes is required.
字符的概念化和编码是系统发育分类学中的一个难题，无论在重建系统发育树时使用哪种推断方法，或者字符是否只是映射到特定的树上，都是如此。复杂字符是可以分为更简单的层次字符的特征组合（简化编码），尽管隐含的层次关系信息可能因编码类型（组合与简化）而异。到目前为止，对于字符是复杂的还是简单的，还没有达成共识。系统发育学家们讨论了哪种编码方法最好，但没有将启发式的相互照亮过程纳入编码评估中。组合编码可以检验以下两种情况：1）几个字符是否相关联，导致被描述为复杂字符或特征的结构；2）独立进化的字符是否导致被错误地解释为复杂字符的构型。当原始同源性假设没有被系统发育分析证实时，我们建议将复杂字符或字符状态迭代地分解为更简单的字符，并且将字符或字符状态视为同形的。我们使用茜草科（茜草科）内亚属中的果实类型的案例来检验这种方法。与核果相关的字符的迭代简化编码使我们能够梳理茜草科内亚属中的果实进化。我们的结果表明，核果和浆果不是同源的。因此，需要为茜草科内亚属的核果建立更精确的本体论。
