Phylogenetic Relationships Within Chrysogorgia (Alcyonacea: Octocorallia), a Morphologically Diverse Genus of Octocoral, Revealed Using a Target Enrichment Approach

Abstract

The octocoral genus Chrysogorgia (Duchassaing and Michelotti, 1864) contains 81 nominal species that are ecologically important components of benthic communities. Taxonomic examination of a large set of samples revealed many provisional new species, exhibiting a wide range of morphological variation. We established nine, distinct morphological groups of Chrysogorgia s.l. that were hypothesized to represent distinct genera. Here, we applied a recently developed universal target enrichment bait method for octocoral exons and ultraconserved elements (UCEs) on 96 specimens varying in morphology, collection ages and DNA quality and quantity to determine whether there was genetic support for these morphologically defined groups. Following Illumina sequencing and SPAdes assembly we recovered 1,682 of 1,700 targeted exon loci and 1,333 of 1,340 targeted UCE loci. Locus recovery per sample was highly variable and significantly correlated with time since specimen collection (2–60 years) and DNA quantity and quality. Phylogenetically informative sites in UCE and exon loci were ∼35% for 50% and 75% taxon-occupancy matrices. Maximum likelihood analyses recovered highly resolved trees with topologies supporting the recognition of 11 candidate genera, corresponding with morphological groups assigned a priori, nine of which are novel. Our results also demonstrate that this target-enrichment approach can be successfully applied to degraded museum specimens of up to 60 years old. This study shows that an integrative approach consisting of molecular and morphological methods will be essential to a proper revision of Chrysogorgia taxonomy and to understand regional diversity of these ecologically important corals.

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

“…Individuals in the genus Chrysogorgia s.l. were assigned, on the basis of morphological characteristics, by coauthor CBU to the established groups of Untiedt et al [18] to better quantify the observed diversity within the genus while it is undergoing a major redescription. We were conservative in our identifications, and only identified individuals to genus and/or species when we were confident that characteristics matched the relevant taxonomic literature [62][63][64][65][66][67][68][69][70].…”

“…The genus Chrysogorgia is another taxonomically confusing group of octocorals. While it is one of the most abundant and diverse groups of octocorals, with 71 currently accepted species [17], recent investigations into the phylogenetic relationships among species within this genus have led to the proposal of 11 candidate genera [18], each of which has been assigned a group number in advance of formal description. There are fewer taxonomic problems within Primnoidae due to the work of dedicated museum taxonomists, unburdened by academic duties that university-based taxonomists face, and perhaps due to the frequent incorporation of genetics into their systematics, which helps test and reinforce the usefulness of certain taxonomic characters (e.g., [19][20][21]).…”

Genetic Divergence and Polyphyly in the Octocoral Genus Swiftia [Cnidaria: Octocorallia], Including a Species Impacted by the DWH Oil Spill

“…A preliminary morphological examination of sclerites from Swiftia exserta phenotypes was conducted using scanning electron microscopy and the results suggested no significant difference in sclerite morphology and composition, spindle size (ANOVA p = 0.97), or capstan size (ANOVA p = 0.61) between the two morphotypes [13,20]. Thus, we proceed with the hypothesis that the impacted species of Swiftia with white polyps in the GoMx is in fact a conspecific of S. exserta, exhibiting phenotypic plasticity, a phenomenon that is very common among octocorals [28,35,[56][57][58]. The red-polyp variant of S. exserta has only been observed at shallower depths (~10-30 m), while the white-polyp variant occurs at mesophotic depths from 50-200 m, and they share a haplotype of mtMutS.…”

Dead man’s fingers point towards new species: A taxonomic revision of Alcyonium aurantiacum with statistical discrimination methods and a survey of integrative taxonomy in Octocorallia

“…Our understanding of genetic species boundaries in octocorals is advancing rapidly, particularly through recent research on restriction site associated DNA (RAD) sequencing (Pante et al 2015a;Herrera and Shank 2016;Quattrini et al 2019) and ultraconserved elements (UCEs) (Quattrini et al 2018;Erickson et al 2020;Untiedt et al 2021). However, these methods are not yet universally employed.…”

“…Perhaps and SNPs by Moore et al 2016). Currently, RAD-sequencing (Pante et al 2015a;Herrera and Shank 2016;Quattrini et al 2019), as well as target-capture enrichment of UCEs and exons (Erickson et al 2020;Quattrini et al 2018Quattrini et al , 2020Untiedt et al 2021) shows promising resolution at all taxonomic levels. Despite the conceptual formalisation of integrative taxonomy in the taxonomic literature over 15 years ago, methodological improvements continue to be necessary, and it is because of this that two of the most enduring problems in octocoral taxonomy have not yet been solved: incongruence between morphological and molecular data, and the nebulous role of interspecific morphological variation in obscuring species boundaries.…”