Data from: 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.
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.