Supporting Data for "Primary Producers on Coral Reefs: From Diversity to Function"

This repository contains the supporting datasets and scripts for analyses of the thesis titled "Primary Producers on Coral Reefs: From Diversity to Function", submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at The University of Hong Kong, School of Biological Sciences, Area of Ecology and Biodiversity.

This thesis was completed under the primary supervision of Dr. David M. Baker, and co-supervision of Dr. Shelby McSharry McIlroy.

Chapter 2 (Challenging the Urban Biotic Homogenization Hypothesis: Marine Eukaryote Communities Characterized through 18S DNA Metabarcoding) and Chapter 3 (Surveying Algal Biodiversity Across the Urbanized Seascape of the Hong Kong SAR: A Search for Potential Metabarcoding Bioindicators) present separate anlyses based on the same set of DNA amplicon sequences and accompanying environmental data. These two chapters are combined in one directory (Ch2Ch3_MarineGeo18S), within which there is a folder for the raw data and another folder for bioinformatics scripts. Chapters 4 (Tracing the Flow of Nutrients through an Acropora Holobiont Using Dual-Isotope Labelling) and 5 (Comparing Autotrophic and Heterotrophic Amino Acid Metabolism in an Acropora Holobiont through Compound-Specific Stable Isotope Analyses of Carbon and Nitrogen) each have their own folder, within which there are separate directories for the data and scripts.

Further details regarding the contents of each folder can be found in the README file.