Phylogenetic inference using discrete characters: performance of ordered and unordered parsimony and of three-item statements

The cladistic literature does not always specify the kind of multistate character treatment that is applied for an analysis. Characters can be treated either as unordered transformation series or as rooted [three-item analysis (3ia)] or unrooted state trees (ordered characters). We aimed to measure the impact of these character treatments on phylogenetic inference. Discrete characters can be represented either as rows or columns in matrices (e.g. for parsimony) or as hierarchies for 3ia. In the present study, we use simulated and empirical examples to assess the relative merits of each method considering both the character treatment and representation. We measure two parameters (resolving power and artefactual resolution) using a new tree comparison metric, ITRI (inter-tree retention index). Our results suggest that the hierarchical character representation not only results (with our simulation settings) in the greatest resolving power, but also in the highest artefactual resolution. Ou...

分支系统学（cladistic）文献往往未明确说明分析中所采用的多态性状处理（multistate character treatment）方式。性状可被处理为无序变换序列（unordered transformation series），或是有根[三分类元分析（three-item analysis, 3ia）]或无根性状树（即有序性状（ordered characters））。本研究旨在量化此类性状处理方式对系统发育推断（phylogenetic inference）的影响。离散性状（discrete characters）既可在矩阵中以行或列的形式呈现（例如用于简约法（parsimony）分析），也可作为三分类元分析的层级结构（hierarchies）进行表征。在本研究中，我们采用模拟与实证案例（simulated and empirical examples），综合考量性状处理方式与表征形式，评估各方法的相对优劣。我们借助一项全新的树结构比较指标——树间保留指数（inter-tree retention index, ITRI），对两项参数（分辨能力（resolving power）与人工伪分辨率（artefactual resolution））进行量化。研究结果表明，在本研究设置的模拟条件下，层级化性状表征不仅可实现最高的分辨能力，同时也可获得最高的人工伪分辨率。Ou...