Deep-sea lineages are generally thought to arise from shallow-water ancestors, but this hypothesis is based on a relatively small number of taxonomic groups. Anthozoans, which include corals and sea anemones, are significant contributors to the faunal diversity of the deep sea, but the timing and mechanisms of their invasion into this biome remain elusive. Here, we reconstruct a fully resolved, time-calibrated phylogeny of 83 species in the order Antipatharia (black coral) to investigate their bathymetric evolutionary history. Our reconstruction indicates that extant black coral lineages first diversified in continental slope depths (~250–3,000 m) during the early Silurian (~437 Ma) and subsequently radiated into, and diversified within, both continental shelf (<250 m) and abyssal (>3,000 m) habitats. Ancestral state reconstruction analysis suggests that the appearance of morphological features that enhanced the ability of black corals to acquire nutrients coincided with their invasion of novel depths. Our findings have important conservation implications for anthozoan lineages, as the loss of “source” slope lineages could threaten millions of years of evolutionary history and confound future invasion events, thereby warranting protection.

DNA was extracted using a Qiagen Puregene Tissue Kit using the DNA Purification from Tissue protocol. PCR inhibitors were removed from DNA using a Qiagen DNeasy PowerClean Clean Up Kit. A Qubit 2.0 fluorometer was used to measure the initial concentration of each extracted DNA sample and then the DNA was precipitated out, dried down and sent to Arbor Biosciences (Ann Arbor, MI) for library preparation, hybrid enrichment and sequencing, following details in Quattrini et al. The targeted enrichment of UCE and exonic loci was carried out using the hexacoral-v2 probe design, which includes 25,514 baits targeting 2,499 loci. Bioinformatic post-sequencing analyses were conducted following the Phyluce online documentation (https://phyluce.readthedocs.io/en/latest/tutorial-one.html), including raw read trim and matching of loci to UCE and exon probes. SPAdes v3.12.0 was used outside of the phyluce pipeline to assemble trimmed raw reads using the main executable script spades.py and a coverage cutoff of 2. Individually aligned UCE/exon loci were filtered to include only those that were present in at least 50% of the samples. All code used in this study is detailed in Dataset S1.

Phyluce and SPAdes v3.12.0.