Department of Biological Sciences, Virginia Polytechnic Institute, State University, 926 West Campus Drive, Blacksburg, VA 24061, USA.
UCI Libraries, University of California, Irvine, Irvine, CA 92623, USA.
Syst Biol. 2022 Oct 12;71(6):1290-1306. doi: 10.1093/sysbio/syac022.
Morphology remains a primary source of phylogenetic information for many groups of organisms, and the only one for most fossil taxa. Organismal anatomy is not a collection of randomly assembled and independent "parts", but instead a set of dependent and hierarchically nested entities resulting from ontogeny and phylogeny. How do we make sense of these dependent and at times redundant characters? One promising approach is using ontologies-structured controlled vocabularies that summarize knowledge about different properties of anatomical entities, including developmental and structural dependencies. Here, we assess whether evolutionary patterns can explain the proximity of ontology-annotated characters within an ontology. To do so, we measure phylogenetic information across characters and evaluate if it matches the hierarchical structure given by ontological knowledge-in much the same way as across-species diversity structure is given by phylogeny. We implement an approach to evaluate the Bayesian phylogenetic information (BPI) content and phylogenetic dissonance among ontology-annotated anatomical data subsets. We applied this to data sets representing two disparate animal groups: bees (Hexapoda: Hymenoptera: Apoidea, 209 chars) and characiform fishes (Actinopterygii: Ostariophysi: Characiformes, 463 chars). For bees, we find that BPI is not substantially explained by anatomy since dissonance is often high among morphologically related anatomical entities. For fishes, we find substantial information for two clusters of anatomical entities instantiating concepts from the jaws and branchial arch bones, but among-subset information decreases and dissonance increases substantially moving to higher-level subsets in the ontology. We further applied our approach to address particular evolutionary hypotheses with an example of morphological evolution in miniature fishes. While we show that phylogenetic information does match ontology structure for some anatomical entities, additional relationships and processes, such as convergence, likely play a substantial role in explaining BPI and dissonance, and merit future investigation. Our work demonstrates how complex morphological data sets can be interrogated with ontologies by allowing one to access how information is spread hierarchically across anatomical concepts, how congruent this information is, and what sorts of processes may play a role in explaining it: phylogeny, development, or convergence. [Apidae; Bayesian phylogenetic information; Ostariophysi; Phenoscape; phylogenetic dissonance; semantic similarity.].
形态学仍然是许多生物群体系统发育信息的主要来源，也是大多数化石分类群的唯一来源。生物体解剖结构不是随机组装和独立的“部分”的集合，而是由个体发生和系统发育产生的一组相互依赖和层次嵌套的实体。我们如何理解这些相互依赖且有时冗余的特征？一种很有前途的方法是使用本体——一种总结解剖实体不同属性知识的结构化受控词汇表，包括发育和结构依赖性。在这里，我们评估进化模式是否可以解释本体注释字符在本体中的接近程度。为此，我们测量字符之间的系统发育信息，并评估它是否与本体知识给出的层次结构相匹配——就像物种多样性结构由系统发育给出一样。我们实现了一种评估本体注释解剖数据子集的贝叶斯系统发育信息 (BPI) 含量和系统发育不和谐的方法。我们将此应用于代表两个截然不同的动物群的数据：蜜蜂（六足动物：膜翅目：Apidae，209 个字符）和鲇形目鱼类（辐鳍鱼：骨鳔总目：鲇形目，463 个字符）。对于蜜蜂，我们发现 BPI 并没有被解剖结构大量解释，因为形态相关的解剖实体之间经常存在很大的不和谐。对于鱼类，我们发现两个解剖实体群的大量信息实例化了来自颌骨和鳃弓骨的概念，但在本体中的子集信息减少，不和谐程度大大增加，向更高层次的子集移动。我们进一步应用我们的方法来解决一个小鲇鱼形态进化的特殊进化假设的问题。虽然我们表明，对于一些解剖实体，系统发育信息确实与本体结构相匹配，但其他关系和过程，如趋同，可能在解释 BPI 和不和谐方面发挥重要作用，值得进一步研究。我们的工作表明，通过允许人们访问信息如何在解剖概念之间层次化传播、信息的一致性如何以及哪些过程可能在解释信息方面发挥作用（系统发育、发育或趋同），可以用本体来研究复杂的形态数据集：蜂科；贝叶斯系统发育信息；骨鳔总目； Phenoscape；系统发育不和谐；语义相似性。
