Data from: The utility of cranial ontogeny for phylogenetic inference: a case study in crocodylians using geometric morphometrics

The degree to which the ontogeny of organisms could facilitate our understanding of phylogenetic relationships has long been a subject of contention in evolutionary biology. The famed notion that ‘ontogeny recapitulates phylogeny’ has been largely discredited, but there remains an expectation that closely related organisms undergo similar morphological transformations throughout ontogeny. To test this assumption, we used three-dimensional geometric morphometric methods to characterize the cranial morphology of 10 extant crocodylian species and construct allometric trajectories that model the post-natal ontogenetic shape changes. Using time-calibrated molecular and morphological trees, we employed a suite of comparative phylogenetic methods to assess the extent of phylogenetic signal in these trajectories. All analyses largely demonstrated a lack of significant phylogenetic signal, indicating that ontogenetic shape changes contain little phylogenetic information. Notably, some Mantel tests yielded marginally significant results when analysed with the morphological tree, which suggest that the underlying signal in these trajectories is correlated with similarities in the adult cranial morphology. However, despite these instances, all other analyses, including more powerful tests for phylogenetic signal, recovered statistical and visual evidence against the assumption that similarities in ontogenetic shape changes are commensurate with phylogenetic relatedness and thus bring into question the efficacy of using allometric trajectories for phylogenetic inference.

生物体个体发育（ontogeny）对我们理解系统发育关系（phylogenetic relationships）的助力程度，长期以来都是进化生物学（evolutionary biology）中颇具争议的议题。著名的‘个体发育重演系统发育（ontogeny recapitulates phylogeny）’假说已在很大程度上被证伪，但学界仍普遍认为亲缘关系相近的生物体在个体发育过程中会经历相似的形态学转变（morphological transformations）。为验证这一假设，我们采用三维几何形态测量法（three-dimensional geometric morphometric methods）对10种现存鳄类的颅骨形态（cranial morphology）进行了表征，并构建了异速生长轨迹（allometric trajectories）以模拟产后个体发育的形状变化。我们借助时间校准的分子和形态学树（time-calibrated molecular and morphological trees），运用一系列比较系统发育学方法（comparative phylogenetic methods）评估了这些轨迹中的系统发育信号（phylogenetic signal）强度。所有分析均未检测到显著的系统发育信号，表明个体发育的形状变化几乎不含系统发育信息。值得注意的是，部分曼特尔检验（Mantel tests）在基于形态学树分析时呈现出边际显著性结果，这提示这些轨迹背后的信号与成年颅骨形态的相似性存在关联。然而，尽管存在上述案例，其余所有分析——包括效力更强的系统发育信号检验——均通过统计与可视化证据，不支持‘个体发育形状变化的相似性与系统发育亲缘关系相匹配’这一假设，从而对使用异速生长轨迹进行系统发育推断（phylogenetic inference）的有效性提出了质疑。