A genetic approach to the biodiversity of shallow water alcyonacea in South Africa.
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The cnidarian order Alcyonacea (Octocorallia) represents a diverse group of marine invertebrates that are dominant taxa on shallow and deep reefs. These organisms constitute sensitive indicators of climate change and have bioprospecting potential. In South Africa, alcyonacean soft corals form the dominant faunal component of the high latitude marginal reefs on the east coast, an understudied region of interest that forms some of the southernmost distribution limits for key taxa in this order. Globally, soft corals are understudied whereby systematic, ecological, and biochemical studies are challenged by inconclusive taxonomy. This is in contrast to the growing understanding of the necessity for genetics in the systematics of Scleractinia, where large scale reclassification has been successful in reconstructing more accurate phylogenies of the order. The knowledge deficit in the systematics and evolution of Alcyonacea is paralleled in South African taxa. An integrative assessment using morphological classification in combination with phylogenetics of Alcyonacea is the most promising approach to assess their biodiversity in South Africa. Accordingly, the aims of these studies were to advance the taxonomic knowledge of soft corals in South Africa; assess species richness and provide a national checklist; and investigate evolutionary relationships between taxa. In so doing, this thesis also aimed to support the global taxonomy of Alcyonacea. Particular attention was given to Alcyonacea that dominate the reef biota in the UNESCO world heritage site, the iSimangaliso Wetland Park (iSWP). Three genetic markers, cytochrome c oxidase I (COI), bacterial MutS homolog (MutS) and nuclear 28S ribosomal RNA (28S rRNA) were used to determine genus and species boundaries in the closely related Alcyoniidae genera; Cladiella, Aldersladum and Klyxum. The use of these genes corroborated taxonomic analyses and demonstrated that morphologically aberrant members of the genus Cladiella should be reassigned to another as yet undescribed genus. The undescribed genus, Beta6, is characterised by an absence of platelet sclerites in the polyp region, features that demonstrate major distinctions from the genera Cladiella, Aldersladum and Klyxum. The species richness of 67 Sinularia specimens in the iSWP was estimated 6 Beta was selected as a placeholder name until the full taxonomic descriptions of this new genus and any of its associated species are published. using DNA barcoding (MutS and concatenated MutS+28S respectively). Phylogenetics and species delimitation methods were used to infer identifications for 63% of the specimens in the study, including a new record for Sinularia grandilobata. In addition, 16 putative species of Sinularia were discovered that are considered potentially undescribed or new records that require further taxonomic investigation by an octocoral expert. Furthermore, S. brassica exhibited two distinct morphotypes that were genetically differentiated and indicative of two distinct species. Taxonomic boundaries were investigated using integrative taxonomic approaches for 239 specimens of Alcyonacea from the iSWP. Specimens were assigned to ~61 putative species that were inferred from phylogenies, divergence estimates, colony photographs and sclerite characters for taxa in this study. Molecular evidence supported the reassignment of non-S. brassica congeners of Sinularia to an undescribed genus due to significant large scale polyphyly. Furthermore, this study reported new records for three genera; Scleronephthya, Paraplexaura, and Chironephthya and an undescribed species of Lobophytum. The results of this study, in conjunction with previously published records, contributed towards revised species estimates for the iSWP that increased from 37 to 81 species (with 12% endemism), 11 to 47 genera and 4 to 17 families. An updated checklist of the Alcyonacea across South Africa was compiled using records from chapters 2 to 4 in this thesis and published records. Two hundred and twenty-six different species from among 89 genera and within 25 families of Alcyonacea were reported. Seventy-five of these species are endemic to South Africa (33%). This represents a substantial increase from the last published estimates in South Africa of 130 species of Alcyonacea. This body of research represents a significant advancement in the knowledge of the biodiversity of an important group of marine invertebrates in South Africa. It provides resolution within some problematic identification assignations (Cladiella, Sinularia brassica). Sinularia, Beta and the Lobophytum-Sarcophyton complex require further taxonomic work for a better perspective on the diversity of this complex, marginal and neglected aspect of South Africa’s marine heritage.