Symbionts in a mussel hybrid zone

The purpose of this repository is to illustrate the analyses performed in our study about sulphur-oxidising (SOX) symbionts of hybrid and parental Bathymodiolus mussels in Broken Spur. The scripts should help interested readers to better understand the methods used. Please be aware that they are not tools intended for further usage.

Analysis of average nucleotide identity of Bathymodiolus SOX symbionts from Broken Spur

Visualise ANI values of SOX symbionts at Broken Spur and test for correlation with host genetics and sampling year
Script: Heatmap+Mantel_ANI_SOX_BS.R
Data needed: Average_nucleotide_identity_SOX_symbionts_Broken_Spur.csv, Pairwise_distances_host_SNPs_ANI.txt

Analysis of F_ST values of Bathymodiolus SOX symbionts from Broken Spur

Visualise F_ST values of SOX symbionts at Broken Spur and test for correlation with host genetics and sampling year
Script: Heatmap+Mantel_FST_SOX_BS.R
Data needed: Pairwise_mean_FST_SOX_symbionts_Broken_Spur.csv, Pairwise_distances_host_SNPs_FST.txt

Analysis of Bathymodiolus SOX symbiont gene counts from Broken Spur

Test for difference in gene abundances between symbionts of hybrids and parental mussels with ALDEx2
Script: ALDEx2_Gene_counts_SOX_BS_Bhyb_vs_Bput.R
Data needed: Gene_counts_kallisto_SOX_symbionts_Broken_Spur.matrix

Analysis of Bathymodiolus SOX symbiont F_ST vs. geography at the NMAR (addition to phylogenomic analysis)

Plot and test for correlation between symbiont F_ST and geographic distances
Script: Mantel+Plot_FST_vs_geographic_distances_SOX_symbionts_NMAR.Rmd
Data needed: Phylogenomics_NMAR.fasta, Groups_NMAR.csv, Pop_NMAR.csv, Geographic_distances_NMAR.csv

Redundancy analysis of Bathymodiolus SOX symbiont allele frequencies at the NMAR

Analyse the variation in symbiont allele frequencies that can be explained by either spatial information, host species, rock type or depth
Script: Redundancy_analysis_allele_frequencies.Rmd
Data needed: Allele_frequencies_SOX_symbionts_NMAR.csv, Metadata_for_RDA.csv

Analysis of Bathymodiolus SOX symbiont per gene F_ST values

Find genes that are more differentiated between symbionts of hybrids and parental mussels than within either of the groups
Script: Per_gene_FST_analysis.Rmd
Data needed: Per_gene_FST_SOX_symbionts_Broken_Spur.zip