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，系统发育分类学（phylogenetic systematics）领域内“树”这一术语的使用存在歧义，这一问题持续引发演化关系的解读偏差。核心矛盾在于：尽管诸多具备系统发育或演化关联的树形图表（如分支图（cladograms））均符合图论规范，但系统发育的类树可视化亦可通过其他类型的图形实现，尤以植物学写实树木绘图为甚。因此，此类图表的含义并非始终明确：单幅图表的不同部分可能存在多种解读视角，而两张外观相近的图表实则可能承载着大相径庭的信息。本文作者论证，此类图表并非仅为系统发育的隐喻，而是可被数学定义为一类名为分支剪影图（branching silhouette diagrams）的几何形状，该命名源自其最直观的外观特征。根据构建过程中是否纳入时间维度，以及所描绘的关系为祖先-后裔型还是姊妹群型，此类图表可分为四种基本形式。作者重拾达尔文（Darwin）早年关于活体世界变化可视化的相关观点，提出将兼顾时间维度并展示祖先关系的最常见分支剪影图形式命名为珊瑚（coral）。其余形式在当代实践中较为罕见，且大多仅具备历史价值：这类形式包括仙人掌（cacti，以贝西的一幅图表命名）以及两种橡树（oaks，参照19世纪海克尔（Haeckel）用于描绘系统发育的多个创作母题）。在系统发育分类学中使用上述术语，有助于更清晰地理解科学界对生物多样性组织形式的可视化路径。