The role of holobiont composition and environmental history in thermotolerance of Tropical Eastern Pacific corals
This GitHub repository contains the code and part of the data to recreate the analyses of:
Glynn, V.M., Marangoni, L.F., Guglielmetti, M., Tapia, E.R., Ali, V., Quintero, H., Guerra, E.C.R., Yuval, M., Kline, D.I., Leray, M., Connolly, S.R., Barrett, R.D.H. (2025) The role of holobiont composition and environmental history in thermotolerance of Tropical Eastern Pacific corals. Current Biology in press.
This repository contains six folders:
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"Population genetics" : R scripts for downstream population genetic analyses, and associated sample metadata and input files (e.g., vcf files)
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"ITS2" : R scripts for ITS2 marker-gene alpha and beta diversity analyses using SymPortal's taxonomic assignment on the basis of intragenomic variants (DIVs)
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"16S" : R scripts to generate amplicon sequence variants (ASVs) from our 16S marker-gene data using DADA2 (Callahan et al., 2016), the resulting RDS file from DADA2, and beta diversity analyses of this data
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"Physiology" : R scripts for host protein and chlorophyll a models, alongside the associated data
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"Oxidative metabolism" : R scripts for lipid peroxidation (LPO) and non-enzymatic total antioxidant capacity (TAC) models, alongside the associated data
If you have questions about the scripts please contact Dr. Victoria Marie Glynn (victoria.glynn@mail.mcgill.ca).
