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 s..., , # Radiation with reproductive isolation in the near-absence of phylogenetic signal

**DOI:** 10.5061/dryad.gxd2547z7

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## Overview

This data package contains large sequencing datasets associated with the above study. For smaller datasets and code, please see the accompanying GitHub repository [(https://github.com/mhelmkampf/hamlet_phylogeny)](https://github.com/mhelmkampf/hamlet_phylogeny]).

* Files prefixed with `phyps` are based on hamlet (genus *Hypoplectrus*) genotypes only
* Files prefixed with `phylo` include *Hypoplectrus* and *Serranus* (outgroup) data
* The suffix `-all` refers to datasets containing (nearly) continuous sequences, including invariant sites
* The suffix `-snp` indicates datasets filtered to contain only bi-allelic SNPs with a minor allele count (MAC) ≥ 2 (see Materials and Methods for full filtering criteria)

Additional file-specific filters are noted below:

```
phylo-all_ftol.tar.gz # Gene alignments used for the FToL phylogeny
phylo-all_mtg.vc...,