Radiation without phylogenetic signal

According to the genic view of species and speciation, species are formed and 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 endemic to the Greater Caribbean that differ most notably in terms of color pattern and are reproductively isolated to a large extent 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 phylogenetically 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 an outstanding topology that relates to species diversification. These results show that phenotypic diversification and prezygotic reproductive isolation—two major attributes of species—may unfold in the near-absence of phylogenetic signal at both the genome-wide and gene-tree levels.