A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes
Target enrichment of conserved nuclear loci has helped reconstruct evolutionary relationships among a wide variety of species. While there are preexisting bait sets to enrich a few hundred loci across all fishes or a thousand loci from acanthomorph fishes, no bait set exists to enrich large numbers (>1,000 loci) of ultraconserved nuclear loci from ostariophysans, the second largest actinopterygian superorder. In this study, we describe how we designed a bait set to enrich 2,708 ultraconserved nuclear loci from ostariophysan fishes by combining an existing genome assembly with low coverage sequence data collected from two ostariophysan lineages. We perform a series of enrichment experiments using this bait set across the ostariophysan tree of life, from the deepest splits among the major groups (>150 Ma) to more recent divergence events that have occurred during the last 50 million years. Our results demonstrate that the bait set we designed is useful for addressing phylogenetic questions from the origin of crown ostariophysans to more recent divergence events, and our in silico results suggest that this bait set may be useful for addressing evolutionary questions in closely related groups of fishes, like Clupeiformes.
Relationships among the major otocephalan subclades and their taxonomic names. See Data Accessibility for tree file.
Maximum likelihood phylogenetic hypothesis of relationships among taxa comprising the gymnotiform dataset with family names in color. Danio rerio is the outgroup taxon, and bootstrap support is indicated at each node. An asterisk by any taxon name indicates that these data were harvested, in silico, from existing genome assemblies, and the numbers in parentheses to the right of each taxon denote the count of loci enriched/harvested from that organism. See Data Accessibility for tree file.
Maximum likelihood phylogenetic hypothesis of relationships among taxa comprising the anostomoid dataset with family names in color. Parodon hilarii is the outgroup taxon, and bootstrap support is indicated at each node. The numbers in parentheses to the right of each taxon denote the count of loci enriched from that organism. See Data Accessibility for tree file.
Maximum likelihood phylogenetic hypothesis of relationships among taxa comprising the loricarioid dataset with family names in color. Ictalurus punctatus is the outgroup taxon, and bootstrap support is indicated at each node. An asterisk by any taxon name indicates that these data were harvested, in silico, from existing genome assemblies, and the numbers in parentheses to the right of each taxon denote the count of loci enriched/harvested from that organism. See Data Accessibility for tree file.
Maximum likelihood phylogenetic hypothesis of relationships among taxa comprising the characiform dataset with family names in color. Ictalurus punctatus is the outgroup taxon, and bootstrap support is indicated at each node. An asterisk by any taxon name indicates that these data were harvested, in silico, from existing genome assemblies, and the numbers in parentheses to the right of each taxon denote the count of loci enriched/harvested from that organism. See Data Accessibility for tree file.
Maximum likelihood phylogenetic hypothesis of relationships among taxa comprising the otocephalan dataset with family names in color. Lepisosteus oculatus is the outgroup taxon, and bootstrap support is indicated at each node. An asterisk by any taxon name indicates that these data were harvested, in silico, from existing genome assemblies, and the numbers in parentheses to the right of each taxon denote the count of loci enriched/harvested from that organism. See Data Accessibility for tree file.
Venn diagram indicating the number of ultraconserved element (UCE) loci detected in four genome-enabled taxa for each of three existing UCE bait sets designed for fishes (Faircloth et al., 2013; Alfaro et al., 2018; this study).
Contributor Notes
Associate Editor: W. L. Smith.