Bathymetric evolution of black corals through deep time

Abstract

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 (∼250–3000 m) during the early Silurian (∼437 millions of years ago (Ma)) and subsequently radiated into, and diversified within, both continental shelf (less than 250 m) and abyssal (greater than 3000 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.

Skimming genomes for systematics and DNA barcodes of corals

“…The black coral phylogeny is mostly congruent with previous reconstructions (Horowitz, et al., 2022 ; Horowitz, Quattrini et al., 2023 ); however, this study includes three genera ( Distichopathes Opresko, 2004, Plumapathes Opresko, 2001, and Tanacetipathes Opresko, 2001) that have been sequenced for the first time with high‐throughput genomic techniques, providing new insights into phylogenomic relationships within the order. Distichopathes Opresko, 2004 was recovered sister to Elatopathes Opresko, 2004.…”

“…In all cases, the numbers of UCE loci obtained from the skimmed samples were slightly higher (by ~200 loci) than the same target‐captured samples, and five pairs of skimmed/target‐captured samples included in the phylogeny were recovered as sister taxa. Second, more UCE/exon loci were recovered in genome skimmed samples compared to target‐captured samples from prior studies (Horowitz, Quattrini et al., 2023 ; McFadden et al., 2022 ) and on average these loci obtained from skimming were longer (Table 1 ). The recovery of longer loci is perhaps due to the inclusion of more “off‐target” reads (i.e., reads not matched by baits) that are adjacent to or overlap with the target regions, resulting in longer assembled contigs.…”

“…To assess whether this method can yield results similar to those obtained through target‐capture enrichment, we compared our results with previously published, target‐capture data (Horowitz, Quattrini et al., 2023 ; McFadden et al., 2022 ). First, nine octocorals that were genome skimmed in this study were also target‐captured in prior work (McFadden et al., 2022 ).…”

“… a Octocorals: McFadden et al., 2022 , OCT Samples only, Hexacorals: Horowitz, Quattrini et al., 2023 . …”

“…Before aligning with MAFFT v7.130b (Katoh & Standley, 2013 ), we combined the data from 208 octocoral samples and the zoanthid Umimayanthus with previously published target‐capture data obtained from 187 octocorals and 11 outgroups (Quattrini et al., 2018 , 2020 , Untiedt et al., 2021 , Erickson et al., 2021 , McFadden et al., 2022 ). We combined the data from 30 black coral samples and the stony coral Javania with previously published (Horowitz et al., 2022 ; Horowitz, Opresko et al., 2023 ; Horowitz, Quattrini et al., 2023 ; Quattrini et al., 2018 , 2020 ) target‐capture data from 106 black corals and four outgroups. After alignment, phyluce was used to create a 60% taxon‐occupancy matrix of all loci to maximize locus number while keeping a majority of taxa present per locus.…”