Phylogenomics of marine angelfishes: diagnosing sources of systematic discordance for an iconic reef fish family (F: Pomacanthidae)

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...., , , # Data from: Phylogenomics of marine angelfishes: diagnosing sources of systematic discordance for an iconic reef fish family (F: Pomacanthidae).

[https://doi.org/10.5061/dryad.r4xgxd2n4](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

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