Sensitivity analysis of different methods of coding taxonomic polymorphism: an example from higher‐level bat phylogeny
Sensitivity analysis of different methods of coding taxonomic polymorphism: an example from higher‐level bat phylogeny
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编码分类多态性的不同方法的敏感性分析：来自高级蝙蝠系统发育的例子
DOI：
10.1111/j.1096-0031.2002.tb00293.x
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发表时间：
2002
期刊：
影响因子：
3.6
通讯作者：
J. Geisler
中科院分区：
文献类型：
--
作者：
N. Simmons;J. Geisler
关于编码分类多态性的不同方法的优点和缺点的新信息表明，以前的一些研究结果可能无意中因所采用的方法而产生偏差。在这项研究中，我们证明了一种形式的敏感性分析可用于评估不同的分类多态性编码方法对系统发育分析结果的影响。我们早期对蝙蝠（哺乳动物：翼手目）高级关系的分析采用超特异性分类群作为终端，并使用歧义编码对分类多态性进行评分。对相同数据应用处理多态性的其他方法（排除可变字符、推断祖先状态、多数编码）产生的系统发育结果与最初报告的基于歧义编码的结果有些不同。所有分析都支持一些进化枝的单系性（例如，微翅目、犀牛总科和纳塔洛总科），而在原始研究中发现的其他类群（例如，新热带纳塔洛总科）在使用其他方法编码分类多态性时似乎未解决或非单系。一些分析支持了在最初的研究中明显被驳斥的几个分组（例如夜光亚科，包括Mystacinidae），减少了我们早期分析中的树木（主要基于形态学）与基于分子数据的其他树木之间的一些明显不一致。在某些情况下，所采用的方法会显着影响对各种分组（分支支持、引导值）的感知支持。这些结果表明，敏感性分析为评估处理超特异末端类群中分类多态性的不同方法的效果提供了有用的工具。使用不同方法获得的结果的差异表明，当较高级别的分类单元表现出分类多态性时，总是优选在物种水平上进行采样，从而避免在数据分析过程中与处理分类多态性的不同方法相关的方法偏差。
New information concerning strengths and weaknesses of different methods of coding taxonomic polymorphisms suggests that results of some previous studies may have been unintentionally biased by the methods employed. In this study, we demonstrate that a form of sensitivity analysis can be used to evaluate the effects of different methods of coding taxonomic polymorphisms on the outcome of phylogenetic analyses. Our earlier analysis of higher‐level relationships of bats (Mammalia: Chiroptera) employed superspecific taxa as terminals and scored taxonomic polymorphisms using ambiguity coding. Application of other methods of dealing with polymorphisms (excluding variable characters, inferring ancestral states, majority coding) to the same data yields phylogenetic results that differ somewhat from those originally reported based on ambiguity coding. Monophyly of some clades was supported in all analyses (e.g., Microchiroptera, Rhinopomatoidea, and Nataloidea), while other groups found to be monophyletic in the original study (e.g., neotropical Nataloidea) appeared unresolved or nonmonophyletic when other methods were used to code taxonomic polymorphisms. Several groupings that were apparently refuted in the initial study (e.g., Noctilionoidea including Mystacinidae) were supported in some analyses, reducing some of the apparent incongruence between the trees in our earlier analysis (which were based principally on morphology) and other trees based on molecular data. Perceived support for various groupings (branch support, bootstrap values) were in some cases significantly affected by the methods employed. These results indicate that sensitivity analysis provides a useful tool for evaluating effects of different methods of dealing with taxonomic polymorphism in superspecific terminal taxa. Variation in results obtained with different methods suggests that it is always preferable to sample at the species level when higher‐level taxa exhibit taxonomic polymorphism, thus avoiding methodological biases associated with different methods of dealing with taxonomic polymorphisms during data analysis.