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 postnatal ontogenetic shape changes. Using time-calibrated molecular and morphological phylogenies, 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 analyzed 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, recover statistical and visual evidence against the assumption that similarities in ontogenetic shape changes are commensurate with phylogenetic relatedness, and thus, brings 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的助力程度，长期以来都是进化生物学中颇具争议的论题。曾广为人知的‘个体发育重演系统发育’观点已在很大程度上被驳斥，但学界仍存在这样的预期：亲缘关系较近的生物体在个体发育全程中会经历相似的形态学转变。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个现存鳄形类（crocodylian）物种的颅骨形态进行表征，并构建了模拟产后个体发育形状变化的异速生长轨迹。我们借助经时间校准的分子与形态系统发育树，运用一系列比较系统发育学方法评估这些轨迹中系统发育信号（phylogenetic signal）的存在丰度。所有分析均基本未检出显著的系统发育信号，表明个体发育的形状变化几乎不包含系统发育信息。值得注意的是，部分基于形态系统发育树开展的曼特尔检验（Mantel tests）得到了边缘显著的结果，这暗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，尽管存在这类个案，其余所有分析——包括效力更强的系统发育信号检验——均在统计学与可视化层面提供了证据，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符’这一假设，进而对利用异速生长轨迹开展系统发育推断（phylogenetic inference）的有效性提出了质疑。