The Biodiversity of Calcaxonian Octocorals from the Irish Continental Slope Inferred from Multilocus Mitochondrial Barcoding

Abstract

Deep-sea corals are important benthic inhabitants that support the biodiversity and function of the wider faunal community; however, their taxonomy is underdeveloped and their accurate identification is often difficult. In our study, we investigated the utility of a superextended (>3000 bp) barcode and explored the effectiveness of various molecular species delimitation techniques with an aim to put upper and lower bounds on the estimated number of calcaxonian species in Irish waters. We collected 112 calcaxonians (70 Keratoisididae, 22 Primnoidae, 20 Chrysogorgiidae) and one chelidonisid from the Irish continental slope and sequenced a 3390 bp DNA barcode comprising four mitochondrial regions (mtMutS, COI + igr1, 16S rRNA-ND2, and igr4), recovering 38 haplotypes. Individuals that shared a haplotype were often morphologically distinct, and we thus undertook detailed morphological work, including SEM of sclerites, on one representative of each morphotype within each haplotype. GMYC, bGMYC, and mPTP returned incongruent estimates of species numbers. In total, there are between 25 and 40 species, although no definitive number could be assigned, primarily due to poorly defined keratoisidid species boundaries. As expected, the superextended barcode provided greater discrimination power than single markers; bGMYC appeared to be the most effective delimiter. Among the identified species were Chelidonisis aurantiaca, collected deeper than previously known at 1507 m, and Calyptrophora clinata, recorded for the second time from the Northeast Atlantic. A full understanding of the diversity and distribution of calcaxonians requires substantial taxonomic work, but we highlight the Irish continental slope as harbouring significant diversity.

Bamboozled! Resolving Deep Evolutionary Nodes within the Phylogeny of Bamboo Corals (Octocorallia: Scleralcyonacea: Keratoisididae)

“…These 121 individuals span 11 of 12 previously defined groups, with only G1 absent from our analyses. Previous phylogenies (mtMutS-5′, mtMutS-3′, and 18S in Watling et al, 2022; mtMutS-5′, 16S, and igr4 in Dueñas et al, 2014; and mtMutS-5′,CO1 + igr1, 16S-nad2, and igr4 in Morrissey et al, 2022), including the single gene mtMutS presented herein, did not resolve deep nodes within the family. In contrast, there was congruence at all deep nodes in the 75% and 50% conserved element phylogenomic treeswhich were all highly supportedwith only the relationship among M1 specimens and the relationship of group D1 to D2 incongruent between trees.…”

“…Eknomisis was described in 2011 and, like Keratoisis which was described in 1869, it branches from the internodes . Previous molecular phylogenies, and our mtMutS phylogeny, have recovered Eknomisis nested within the larger Keratoisis D2 group (Dueñas et al, 2014;Morrissey et al, 2022;Watling et al, 2022). In both our 50% and 75% conserved elements phylogenomic inferences, all individuals tentatively identified as Eknomisis from Morrissey et al (2022) and USNM1516861 (identified as Eknomisis due to similarity in polyp morphology and sclerite arrangement to Eknomisis sp., figure S6 in Morrissey et al (2022)) form a distinct clade that is sister to the wider D1&D2 (including H1 representative NIWA106530) group.…”

“…Previous molecular phylogenies, and our mtMutS phylogeny, have recovered Eknomisis nested within the larger Keratoisis D2 group (Dueñas et al, 2014;Morrissey et al, 2022;Watling et al, 2022). In both our 50% and 75% conserved elements phylogenomic inferences, all individuals tentatively identified as Eknomisis from Morrissey et al (2022) and USNM1516861 (identified as Eknomisis due to similarity in polyp morphology and sclerite arrangement to Eknomisis sp., figure S6 in Morrissey et al (2022)) form a distinct clade that is sister to the wider D1&D2 (including H1 representative NIWA106530) group. Eknomisis is distinct from Keratoisis due to its oblique arrangement of sclerites along the polyp body and some individuals having distinct volcano-shaped polyps (which may be absent if the polyps were not fully contracted or fully formed) when preserved .…”

Analysis of mitogenomes from the family Keratoisididae reveals mitonuclear discordance and the presence of unknown open reading frames

“…Both phylogenies recovered a deep divergence in keratoisidids, referred to as Clade I and Clade II. This divergence has been reported previously in other conserved element based phylogenomic reconstruction (Morrissey et al 2023a), but was not found in previous phylogenies that used a handful of exclusively mitochondrial markers (mtMuts-5', cox1 + igr1, 16s-nad2, and igr4, (Morrissey et al 2022) or a combination of nuclear and mitochondrial gene regions (mtMuts-5' and 3' and partial 18s, Watling et al 2022) probably due to a lack of phylogenetic signal. The topology of the conserved element phylogeny presented in this study is identical to Morrissey et al's (2023a) conserved element phylogenomic tree, despite the reduced taxon sampling herein (to match the mitochondrial genome sampling).…”

Unfolding the secrets of microbiome (Symbiodiniaceae and bacteria) in cold-water coral

“…All corals were identified based on morphology observation and molecular analysis of the mitochondrial COI gene ( 49 ) ( Fig. 1 ; Additional file 5: sequences of COI gene).…”