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.

本存储库包含了对题为《珊瑚礁上的初级生产者：从多样性到功能》的论文进行分析所使用的支持数据集和脚本。该论文系香港大学生物科学学院生态与生物多样性领域博士学位申请的部分要求，并由David M. Baker博士为主要指导老师，Shelby McSharry McIlroy博士共同指导完成。第二章（挑战城市生物同质化假说：通过18S DNA代谢条形码表征的海洋真核生物群落）和第三章（在香港特别行政区城市化海景中调查藻类生物多样性：寻找潜在的代谢条形码生物指标）分别基于同一套DNA扩增子序列和相应的环境数据进行了独立分析。这两个章节的内容合并存放在一个名为Ch2Ch3_MarineGeo18S的目录中，其中包含原始数据文件夹和生物信息学脚本文件夹。第四章（利用双重同位素标记追踪Acropora Holobiont中营养物质的流动）和第五章（通过碳和氮的化合物特异性稳定同位素分析比较Acropora Holobiont中的自养和异养氨基酸代谢）各自拥有独立的文件夹，其中包含数据和脚本目录。关于每个文件夹内容的更详细信息，请参阅README文件。