Radiation with reproductive isolation in the near-absence of phylogenetic signal
Data files
May 16, 2025 version files 28.48 GB
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phylo-all_ftol.tar.gz
43.18 KB
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phylo-all_mtg.vcf.gz
9.77 MB
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phylo-all_windows2k.tar.gz
99.44 MB
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phylo-snp_5kb.vcf.gz
188.27 MB
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phylo-snp_phased.vcf.gz
1.31 GB
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phyps-snp_LDfilt.vcf.gz
2.33 GB
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phyps-snp.vcf.gz
24.54 GB
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README.md
1.77 KB
Abstract
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.
DOI: 10.5061/dryad.gxd2547z7
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).
- Files prefixed with
phypsare based on hamlet (genus Hypoplectrus) genotypes only - Files prefixed with
phyloinclude Hypoplectrus and Serranus (outgroup) data - The suffix
-allrefers to datasets containing (nearly) continuous sequences, including invariant sites - The suffix
-snpindicates 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.vcf.gz # Full mitochondrial genomes in VCF format
phylo-all_windows2k.tar.gz # Alignments of 2000 randomly selected genomic windows
phylo-snp_5kb.vcf.gz # SNPs filtered by a minimum physical distance of 5000 bp
phylo-snp_phased.vcf.gz # Phased SNPs
phyps-snp_LDfilt.vcf.gz # SNPs filtered by linkage disequilibrium, no missing data
phyps-snp.vcf.gz # SNPs with basic filters only (bi-allelic, MAC ≥ 2)
Notes
- All
.vcf.gzfiles are compressed VCF files compatible with standard bioinformatics tools (e.g., VCFtools and BCFtools) - Archive files (
.tar.gz) contain multi-FASTA alignments in standard format - For detailed methods and downstream usage, see the manuscript and supplementary materials