Community structure of coral-associated fauna of reefs in the Chagos Archipelago
Keywords: Barcoding
coral reefs
Cryptofauna
community phylogenetics
Chagos Archipelago
biodiversity

The aim of this study is to assess the biodiversity of the reef cryptofauna (with a focus on the decapods, Crustacea) on dead coral microhabitats, and to begin to understand the processes underpinning their community structure in the Chagos Archipelago. The majority of reef biodiversity is comprised of the cryptofauna, defined as small, often cryptic, mainly invertebrates, which inhabit the reef structure. Despite this the cryptofauna are severely understudied relative to the fish and coral faunal components. An estimated 168,000 species of reef invertebrates have been described on coral reefs, and approximately 20% of reef invertebrates are crustaceans, making them one of the most speciose taxa on coral reefs.
The Chagos Archipelago represents one of the most resilient reefs globally, partly because of its remote location, away from the majority of human pressures. Consequently, it serves as an unaffected reference site for biodiversity and ecosystem function studies. The decapod species richness estimate for Chagos (at least 217 species) exceeds that of any other location globally. A high proportion (32%) were observed to be rare species (singletons), this may be an artefact of incomplete sampling, however if this observation represents true rarity it would suggest this component of biodiversity could be more vulnerable to biodiversity loss than previously thought. Furthermore, any biodiversity loss could also have implications for ecosystem function if rare species contribute disproportionately more to vulnerable ecosystem processes than dominant species. Data presented on determining the most accurate species delimitation method for estimating decapod species richness utilising DNA barcoding. Performance of species delimitation methods was taxon-specific within the decapods, and delimitation of singletons was challenging for all methods. However, the Poisson tree processes (PTP) approach was generally the most accurate at delimiting decapod putative species.
Whilst assessing decapod diversity a high prevalence of obligate coral-dwellers on dead coral microhabitats were discovered. Obligate coral-dwellers are almost universally found on live coral, inferring they have a strong reliance on live coral for food, habitat and/or recruitment. The prevalence of obligate coral-dwellers on dead coral suggests that these decapods are not simply persisting on coral hosts that have died but may be explicitly recruiting to or moving to dead coral hosts at certain stages in their life cycle.
Finally, the processes influencing community assembly and maintenance of a family of decapods, the Palaemonidae, on dead coral colonies was investigated. There was spatial hierarchy in trait and phylogenetic diversity, with environmental filtering acting only at the local level (within atolls and between coral colonies). Whilst phylogenetic signal at the metacommunity level (the archipelago) was inconclusive, trait convergence and lability of trait evolution were key processes determining species distribution at the local level.
This thesis represents the first biodiversity estimation of the cryptofauna in Chagos on any microhabitat and subsequently provides a baseline against which to compare this component of biodiversity in other areas experiencing higher levels of anthropogenic stressors, at least in the Indian Ocean. I also produce a rare empirical evaluation of species delimitation methods, which will provide guidance for future decapod molecular studies. The prevalence of obligate coral-dwellers on dead corals demonstrates the complexity of these organisms' habitat associations and highlights the need for further investigation to establish their vulnerability to habitat degradation on coral reefs. Furthermore the identification of some of the deterministic processes driving community structure of the Palaemonidae contributes to understanding of ecosystem function.