DOI: 10.5061/dryad.r4xgxd2n4
title: Data from: Phylogenomics of marine angelfishes: diagnosing sources of systematic discordance for an iconic reef fish family (F: Pomacanthidae)

description: 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.
description: # 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 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.  ##