Symbiodiniaceae diversity varies by host and environment across thermally distinct reefs

Analysis for Coral population ecology predicts Symbiodiniaceae diversity across thermally distinct reefs
Authors: Magena R. Marzonie, Matthew R. Nitschke, Line K. Bay, David G. Bourne, Hugo B. Harrison

1_Analysis.Rmd contains all scripts required to run analyses within the manuscript. Analysis are structured as follows within the Rmd: (use Outline tab in Rmd for easy navigating)

1. Library statistics for ITS2 type profiles/DIVs <br
2. UPGMA trees for ITS2 type profiles/DIVs
3. Marker alignment tanglegram psba-ITS2
4. PCoAs with UniFrac distance
5. distance-based RDAs
6. Procrustes rotation analysis
7. distance-based RDA subset models with host genetic data

2_R2Analyses.Rmd

1. Scripts to run host NJ (neighbour-joining trees)
2. Run final distance based RDA models (host and environmental conditional models)

Other files needed to run scripts>

O_SymPortal folder contains post-med sequence analysis of symbiont DIVs and Type Profiles which are required to run 1_Analysis

Metadata.csv contains environmental and host species data associated with each sample. Note that 'Vial' refers to each coral individual sample collected

Metadata_mtorf.csv contains environmental and host species data associated with each sample, with updated mtORF alignment. Both metadata files are required for 1_Analysis. Note that 'Vial' refers to each coral individual sample collected

psba txt files are required to run the marker alignment

PverDart_CSS/ PmeaDart_CSS/ AcroDart_AlCluster_CSS contains the scripts required to run host filtering These files are not needed to directly run 1_Analysis.Rmd scripts, but show the pre-filtering steps prior to importing host genetic data.