Targeted enrichment of genomic DNA can profoundly increase the phylogenetic resolution of clades and inform taxonomy. Here, we redesign a custom bait set previously developed for the cnidarian class Anthozoa to more efficiently target and capture ultraconserved elements (UCEs) and exonic loci within the subclass Hexacorallia. We test this enhanced bait set (targeting 2,476 loci) on 99 specimens of scleractinian corals spanning both the “complex” (Acroporidae, Agariciidae) and “robust” (Fungiidae) clades.Focused sampling in the staghorn corals (genus Acropora)highlights the ability of sequence capture to inform the taxonomy of a clade previously deficient in molecular resolution. A mean of 1850 (± 298) loci were captured per taxon (955 UCEs, 894 exons), and a 75% complete concatenated alignment of 96 samples included 1792 loci (991 UCE, 801 exons) and ~1.87 million base pairs. Maximum likelihood and Bayesian analyses recovered robust molecular relationships and revealed that species-level relationships within the Acroporaare incongruent with traditional morphological groupings. Both UCE and exon datasets delineated six well-supported clades within Acropora.The enhanced bait set will facilitate investigations of the evolutionary history of many important groups of reef corals, particularly where previous molecular marker development has been unsuccessful.

Cowman_etal_Hexa_v2_PROBE_SETS
Two .fasta files with the designed baits for hexacoral target-capture enrichment. One file contains all Hexacoral specific baits (hexa-v2: 25,514 baits targeting 2,499 loci)  and the other contains a subset of bait for Scleractinian (hexa-v2-scleractinia:16,263 baits targeting 2,497 loci). Baits designed against transcriptomes have “design: hexatrans” in the .fasta headers. Potential Symbiodinium loci have been removed.

Cowman_etal_ALIGNMENTS
.phylip formatted alignment files for 75% and 95% taxon occupancies. Loci are concatenated. There are separate folders and files alignments containing all loci, uce loci only, and exon (trans) loci only for both 75% and 95% matrices. Each alignment also has associated “.charset” indicating loci partitions.

Cowman_etal_TREES
Contains nexus formatted tree files corresponding to RAxML reconstruction with rapid bootstrap for each alignment type and an ExaBayes analysis for the combines UCE/exon 95% occupancy matrix. Tree contain nexus label translation tables.