Analysis of gut microbiome 16S data from a threespine stickleback fish common garden experiment

This archive contains data, metadata, code, summary files, and plots that support the findings reported in the paper "Host genomic variation shapes gut microbiome diversity in threespine stickleback fish." The analyses and visualizations captured in the archive include ASV (from 16S amplicon sequencing) data formatting, normalization, differential abundance, and various multivariate statistical approaches to understanding how microbiome diversity is related to host (stickleback fish) genetic diversity. Each main directory in the archive includes a readme file with relevant information. "Stickleback_CGmicro_v2" includes added analyses. The first is a post hoc analysis of potential contaminant ASVs. The second is a reworking of genome-wide partial Mantel tests (testing for positive relationships between local genetic and microbiome dissimilarity) to account for overall, genome-wide genetic dissimilarity