Bamboozled! Systematic studies of the Keratoisididae (Octocorallia: Scleralcyonacea)
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Deep-sea corals are globally distributed and form a three-dimensional habitat on the benthos which hosts a diverse invertebrate community. Despite this importance, a global lack of taxonomic expertise and low resolution single-gene barcodes has meant they are rarely identified to species level. Bamboo corals, specifically referring to those in the family Keratoisididae, are an exclusively deep-sea group of octocorals that are particularly taxonomically challenging due to the historic use of labile traits as diagnostic characters for genera. This has led to polyphyly within the family, and large amounts of undescribed biodiversity. Chapter 2 uses an integrative taxonomic approach to provide an upper and lower estimate to the number of species of calcaxonian octocorals present along the Irish margin. I found between 14 – 27 species of Keratoisididae, 6 – 7 species of Primnoidae, and 4 – 5 species of Chrysogorgiidae. The phylogenetic relationships among the different groups within Keratoisididae were unresolved despite using a ~3000 bp portion of the mitogenome. Chapter 3 further interrogates the phylogenomic relationships of Keratoisididae. Using hundreds of nuclear markers, generated using target-capture techniques, deep evolutionary nodes within the phylogeny of keratoisidids were resolved. The phylogeny found a deep split in the family forming two distinct clades. Furthermore, there is evidence that some keratoisidid groups are polyphyletic. This phylogeny is the first to use such high genomic resolution and is incongruent with previous phylogenies created using multiple gene regions from the mitogenome. Chapter 4 further compares phylogenies generated from full mitochondrial genomes with that from hundreds of nuclear markers and discovers mitonuclear discordance within the keratoisidids. Furthermore, by investigating the characteristics and genomic diversity within the keratoisidid mitogenome, three unknown Open Reading Frames were discovered in the space between cob and nad6.