Clues of ancient incomplete lineage sorting during bivalve evolution undermine support for Heterodonta

A long-standing challenge in phylogenomics has been the resolution of relationships originated from ancient radiations. In these cases, phenomena such as incomplete lineage sorting can increase the support for conflicting resolutions. Most of the diversity in the Class Bivalvia originated during an Ordovician radiation; indeed, several deep relationships among Bivalvia have not been fully resolved yet. Traditionally, Heterodonta clusters the Subclasses Archiheterodonta and Euheterodonta; however, recent analyses supported Archiheterodonta as sister to the other Subclass Palaeoheterodonta (A + P). Until now, Archiheterodonta was the last major Bivalvia clade lacking a genome assembly: we sequenced the genome of Cardita leana (Archiheterodonta, Carditidae) and inferred the phylogeny from a supermatrix including 64 bivalve species. Although different methods supported Heterodonta, many genes (27% of the dataset) favoured Archiheterodonta + Palaeoheterodonta (A + P). This discordance could not be ascribed to any systematic phylogenetic biases. However, divergence times obtained from the respective supporting genes datasets placed the origin of Heterodonta significantly deeper than the origin of A + P, appearing inconsistent with the fossil record. This suggests that genes supporting Heterodonta reflect ancestral polymorphisms that persisted in Archiheterodonta and Heterodonta lineages through incomplete lineage sorting. Overall, we suggested a phylogenomic framework to study deep radiations and showed that A + P represents a plausible hypothesis.