Data from: 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具生物学真实性的系统发育推断（phylogenetic inference），并以有鳞目爬行动物（squamate reptiles）为例展开说明。在进行形态学性状编码时，通常可通过明确参照观测到的或假想的祖先状态（ancestral conditions）来标记有序性状状态。基于该逻辑，我们可以整合所有性状状态标签，并估算从祖征（plesiomorphy）到衍征（apomorphy）的正向与反向转换的具有生物学意义的速率。本研究将该方法命名为MkA，取“不对称（asymmetric）”之意。MkA模型纳入了“多数系统发育信息性状的逆转存在局限”这一生物学现实，并显著提升了经验数据集的似然值。尽管如此，有鳞目的系统发育关系仍存在争议。采用形态学与分子数据联合分析（combined morphological and molecular data）结合MkA方法的总证据分析（total-evidence analyses），结果倾向于支持近期的共识性推断，即鬣蜥亚目（Iguania）为嵌套类群。但不同数据集或分析方法对该拓扑结构（topology）的支持度并不明确，且目前尚无相关机制可解释分区间普遍存在的拓扑不一致性，以及这些分区中对不同拓扑结构的隐藏支持信号。此外，不同学者构建的形态学数据集不仅性状存在差异，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谱系（fossil lineages）的系统发育位置出现极大分歧。未来亟需开展形态学本体论（ontology）标准化工作，以解决拓扑不一致性问题并构建稳健的系统发育树（robust phylogeny）。MkA方法为研究形态演化提供了初步路径，可同时兼顾时间证据与性状状态变化的不对称性。