Data from: Phylogenetic influence on gut microbiome diversity within an African herbivore community

Data (both phyloseq-R object from imported QIIME2 artifacts, and demultiplexed EMP-paired end sequences from Argonne National laboratory) and R code HerbivoreMeta2.tsv – Metadata file with each row representing individual samples and columns representing sample ID, sample species, sex, geographic zone sample was collected from Etosha National Park (Zone), feeding strategy of host species (FeedStrat), gut morphology of host species (GutMorph), herd composition determined by either mixed or non-mixed groups (HerdComp), waterhole site sample was collected from (Waterhole), and host herbivore taxonomic family (Family) Herbivorerooted-tree-filtered.qza – QIIME2 artifact created after filtering sequences and creating rooted tree for phylogenetic diversity analyses Herbivoretable-clean-unassigned-Unk-Euk.qza – QIIME2 artifact created by filtering out mitochondria, chloroplasts, unassigned taxa, Bacteria-only assigned taxa, and Eukaryota-only assigned taxa from Argonne National Lab sequences Output.nex – Host phylogenetic tree file using mammalian phylogeny subsets (1000 trees) from VertLife Physeq_srs2.rds – Normalized phyloseq object Physeq2.rds – Phyloseq object created with HerbivoreMeta2.tsv, herbivorerooted-tree-filtered.qza, herbivoretable-clean-unassigned-Unk-Euk.qza, and taxonomySILVA.qza and used for downstream analysis in R Pseq.rel2.rds – Normalized phyloseq object with bacterial community composition taxonomySILVA.qza – QIIME2 artifact created from SILVA reference database to assign taxonomy to Argonne National Lab sequences QIIME2 steps.rtf – Step-by-step code used in miniconda3 for joining, quality-filtering, and demultiplexing EMP-paired end sequences from Argonne National Laboratory and creating QIIME2 artifacts for downstream analysis Phyloseq.R – Creates phyloseq object from imported QIIME2 artifacts Alpha_tests.R – Analyzing alpha diversity metrics by herbivore family, generating Fig. 2 Beta_tests.R – Analyzing beta diversity metrics by herbivore family; Mantel tests; Simper analysis; generating Fig. 3, Fig. 4, Fig. 5, Supplemental Fig. 1, and Supplementary Table 1