Novel approaches for phylogenetic inference from morphological data and total-evidence dating in squamate reptiles (lizards, snakes, and amphisbaenians)

Here, I combine previously underutilized models and priors to perform more biologically-realistic phylogenetic inference from morphological data, with an example from squamate reptiles. When coding morphological characters, it is often possible to denote ordered states with explicit reference to observed or hypothetical ancestral conditions. Using this logic, we can integrate across character-state labels and estimate meaningful rates of forward and backwards transitions from plesiomorphy to apomorphy. I refer to this approach as MkA, for 'asymmetric.' The MkA model incorporates the biological reality of limited reversal for many phylogenetically informative characters, and significantly increases likelihoods in the empirical datasets. Despite this, the phylogeny of Squamata remains contentious. Total-evidence analyses using combined morphological and molecular data and the MkA approach tend towards recent consensus estimates supporting a nested Iguania. However, support for this topology is not unambiguous across datasets or analyses, and no mechanism has been proposed to explain the widespread incongruence between partitions, or the hidden support for various topologies in those partitions. Furthermore, different morphological datasets produced by different authors contain both different characters and different states for the same or similar characters, resulting in drastically different placements for many important fossil lineages. Effort is needed to standardize ontology for morphology, resolve incongruence, and estimate a robust phylogeny. The MkA approach provides a preliminary avenue for investigating morphological evolution while accounting for temporal evidence and asymmetry in character-state changes.

本研究结合此前未被充分利用的模型与先验信息，基于形态学数据开展更贴合生物学真实场景的系统发育推断（phylogenetic inference），并以有鳞目爬行动物（squamate reptiles）为例进行说明。在编码形态学性状（morphological characters）时，通常可通过明确参照观测所得或假想的祖先状态，对有序性状状态进行标注。基于该逻辑，我们可整合不同性状状态标签，并估算从祖征（plesiomorphy）到衍征（apomorphy）的正向与逆向转换有效速率。本研究将该方法命名为MkA，即‘非对称（asymmetric）’模型。MkA模型贴合多数具备系统发育信息价值的性状存在有限逆转这一生物学真实情况，且可显著提升经验数据集的似然值。尽管如此，有鳞目（Squamata）的系统发育关系仍存在较大争议。结合形态学与分子数据并采用MkA方法的总证据分析，逐渐趋近于近期的共识性估计，即支持鬣蜥亚目（Iguania）为嵌套类群。不过，不同数据集或分析中对该拓扑结构的支持度并不明确，目前尚无相关机制可解释分区间普遍存在的拓扑冲突，亦无法阐明这些分区内对不同拓扑结构的隐性支持。此外，不同研究者构建的形态学数据集，不仅所包含的性状存在差异，同一或相似性状的状态定义也各不相同，这导致诸多重要化石支系的系统发育位置出现显著分歧。当前亟需推进形态学本体论的标准化工作，以解决拓扑冲突问题并构建可靠的系统发育关系。MkA方法为形态演化研究提供了初步路径，可同时兼顾时间证据与性状状态转换的非对称性。