Radiation with reproductive isolation in the near-absence of phylogenetic signal

According to the genic view, species are characterized by the genes that underlie functional divergence. Here, we take a phylogenomic approach to assess this view at the scale of a whole radiation. The hamlets ( Hypoplectrus spp.) represent a recent radiation of reef fishes from the Greater Caribbean that are reproductively isolated through assortative mating. A total of 335 genomes from 15 locations revealed a single well-supported phylogenetic split among species, with a large share of the radiation unresolved. The polytomic nature of the hamlet radiation is extreme compared to other recent radiations such as Lake Victoria cichlids. At the gene-tree level, we identified just one genomic region, centered around the casz1 transcription factor, with a topology that reflects species differences. These results show that phenotypic diversification and reproductive isolation—two major attributes of species—may unfold in the near-absence of phylogenetic signal, both genome-wide and at the gene-tree level.