Phylogenetic Reconstruction of Cephalaspidea Using Multiple Datasets and Inference Frameworks

ABSTRACT Cephalaspidea is a key group within the Heterobranchia characterized by high species diversity and broad ecological disparity, and it is widely studied in marine ecology and systematics. Previous studies have proposed a preliminary phylogenetic framework for Cephalaspidea using few sanger sequenced phylogenetic markers and transcriptome‐scale datasets. However, relationships among several lineages remain contentious, which may partly reflect sparse sampling of key taxa and differences in topological signal among markers, datasets and analytical assumptions. To clarify the phylogenetic backbone of Cephalaspidea, newly generated shallow‐genome data from 13 species are integrated with published mitochondrial genomes and transcriptomes. Relationships within Cephalaspidea are reconstructed and compared across multiple inference frameworks. Both mitochondrial gene matrices and phylogenomic multilocus matrices are analysed. Across datasets and analytical strategies, strong support for Cephalaspidea monophyly is consistently recovered. Several major backbone relationships are also recovered consistently. Newnesioidea is placed at the base of the Cephalaspidea tree. Philinoidea is recovered as sister to the clade comprising all Bulloidea, Cylichnoidea and Haminoeoidea. However, within the Bulloidea–Cylichnoidea–Haminoeoidea clade, topological differences are observed across data types and inference frameworks. Bullidae and Tornatinidae are not recovered as sister lineages in any analysis, leaving the monophyly of the traditional Bulloidea unsupported under the current taxon sampling. Tornatinidae is placed near Cylichnidae in phylogenomic analyses, suggesting a relationship that warrants further testing. By contrast, Mnestiidae does not cluster with Cylichnidae but is instead recovered closer to Haminoeoidea, which warrants further scrutiny of the circumscription of Cylichnoidea. Overall, a broadly consistent backbone topology is recovered through expanded taxon sampling of key lineages. New molecular evidence and analytical frameworks are provided to further test unresolved phylogenetic relationships, thereby refining our understanding of Cephalaspidea phylogeny.