Data from: Different from trees, more than metaphors: branching silhouettes—corals, cacti, and the oaks

There has long been ambiguity in the use of the term tree in phylogenetic systematics, which is a continuous source of misinterpretation of evolutionary relationships. The basic problem is that while many trees with phylogenetic or evolutionary relevance, such as cladograms, are consistent with graph theory, tree-like visualization of phylogeny may also be done via other types of graphics, especially botanical (or literal) tree drawings. As a consequence, the meaning of such diagrams is not always clear: a given picture may have multiple interpretations in its different parts and two figures that look similar may actually carry quite different information. I show that these are not merely metaphors of phylogeny and may be defined mathematically as geometric shapes called branching silhouette diagrams, the name referring to their most apparent features. They have four basic forms depending on whether the time factor is considered in their construction and the relationships portrayed are of the ancestor–descendant or sister group type. By revitalizing Darwin’s early suggestions on the illustration of change in the living world, I propose the term coral for the most common forms of branching silhouette which consider time and show ancestry. The others appear rarely in present-day practice and are mostly of historical value—these are cacti (named after one of Bessey’s diagrams) and two types of oaks (with reference to several of Haeckel’s motifs used in depicting phylogeny in the nineteenth century). The use of these terms in phylogenetic systematics facilitates better understanding of how organization of biodiversity has been visualized in science.

长期以来，系统发育系统学（phylogenetic systematics）中“树”这一术语的使用始终存在歧义，这亦是持续引发演化关系误读的核心诱因。核心症结在于，诸多兼具系统发育或演化意义的树形结构（如分支图（cladograms））均符合图论（graph theory）的规范，但系统发育的类树可视化也可通过其他图形类型实现，尤以植物学（或写实风格）树木绘图为典型。由此，这类图表的含义并非始终明确：单幅图像的不同局部可能存在多重解读，而外观相近的两幅图表实则可能承载着迥异的信息。本研究证实，此类图表并非仅仅是系统发育的隐喻，而是可被数学定义为一类名为分支剪影图（branching silhouette diagrams）的几何图形，其名称源于其最直观的形态特征。根据构建过程是否纳入时间因素，以及所描绘的亲缘关系为祖先-后裔（ancestor–descendant）型还是姐妹群（sister group）型，这类图形可分为四种基本形式。通过重拾达尔文（Darwin）早年关于生物界演化变化可视化的见解，作者提出将兼顾时间因素并展示祖先关系的最常见分支剪影图形式命名为珊瑚树（coral）。其余三种形式在当代实践中较为罕见，且大多仅具备历史价值：分别为仙人掌图（cacti，得名自贝西[Bessey]的一幅图表）与两类橡树图（oaks，参考了19世纪海克尔[Haeckel]用于描绘系统发育的多个绘图母题）。在系统发育系统学中使用上述术语，有助于更清晰地理解科学界曾以何种方式对生物多样性的组织架构进行可视化呈现。