Data from: Phylogenomics of marine angelfishes: diagnosing sources of systematic discordance for an iconic reef fish family (F: Pomacanthidae)
Data files
Apr 02, 2025 version files 88.68 MB
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PMC_aln_e95.nexus
84.31 MB
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PMC_beast.tre
63.30 KB
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PMC_iqtree_e95.tree
6.71 KB
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PMC_raxml_gene_trees.tre
842.46 KB
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PMC_TOP50_PIS.nexus
3.06 MB
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README.md
1.57 KB
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Supplementary_material_TablesS3_S9.xlsx
398.62 KB
Apr 02, 2025 version files 88.68 MB
-
PMC_aln_e95.nexus
84.31 MB
-
PMC_beast.tre
63.30 KB
-
PMC_iqtree_e95.tree
6.71 KB
-
PMC_raxml_gene_trees.tre
842.46 KB
-
PMC_TOP50_PIS.nexus
3.06 MB
-
README.md
1.56 KB
-
Supplementary_material_TablesS3_S9.xlsx
398.62 KB
Abstract
Genome-scale datasets are resolving challenging nodes across the tree of life. These datasets, however, characterized by inherent heterogeneity, often push traditional phylogenetic reconstruction methods to their limits. By integrating multiple phylogenomic approaches, we can identify the causes of topological discordance within genomic partitions while accounting for various sources of heterogeneity and systematic errors. Here we conduct the first in-depth analysis of discordance for the reef family Pomacanthidae (marine angelfishes) using target enrichment data of ~1,000 ultraconserved elements from 45 pomacanthid species. Our combined phylogenomic approach resolved the systematics of the family at the base of the pomacanthid tree. Despite this resolution, our analyses also highlight discordance in ancestral nodes associated with the paraphyletic Centropyge genus and monotypic Pygoplites lineage, and the impact of incomplete lineage sorting in the evolutionary history of pomacanthids. Species network searches and model selection supported a reticulated evolutionary history, suggesting three ancient gene flow events between ghost (or unsampled) lineages at the root of the Pomacanthidae tree and ancestors of Genicanthus, Centropyge, Chaetodontoplus, and Pomacanthus lineages. This study advances our understanding of diagnosing topological discordance in genome-scale phylogenies and provide an analytical pathway for limiting systematic errors. In the process of diagnosing discordance, we identify key evolutionary processes involved in the complex evolution of marine angelfishes. While often inconvenient in phylogenetic analyses, patterns of discordance can shed light on underlying biological and evolutionary processes that shape the evolution of biodiversity.
https://doi.org/10.5061/dryad.r4xgxd2n4
Data available in this Dryad repository includes supplementary materials text file, input UCE alignments and gene trees, and output tree files from phylogenomics analyses for associated study.
Data and File Overview
Supplementary_Material.docx (found on Zenodo): includes supplementary figures, alignment summaries and fossil calibration details for associated study.
Supplementary_material_TableS3_S9.xlsx: includes metadata associated with genomic analyses and results from concordance factor, influential gene, and introgression analyses
PMC_aln_e95.nexus: final 95% complete edge-trimmed concatenated alignment (880 UCE alignments)
PMC_TOP50_PIS.nexus: concatenated alignment containing 50 alignments for most parsimony informative UCE loci
PMC_raxml_gene_trees.tre: 969 gene trees generated with RAxML v.8.2.12 for species network searches in PhyloNet v.3.8.2
PMC_iqtree_e95.tree: output tree file generated with IQTree v.2.2.2 using alignment matrix PMC_aln_e95
PMC_beast.tre: combined output tree file from three independent MCMC runs conducted with BEAST v.1.6.7 using concatenated alignment PMC_TOP50_PIS.nexus
Data access
SRA BioProject accession number: PRJNA1101094
SRA contains raw reads from target enrichment of UCEs from 45 pomacanthid species and 18 outgroup species.
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