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

Raw sequencing reads from Argonne National Laboratory: 
- Undetermined_S0_L001_I1_001.fastq (barcodes)
- Undetermined_S0_L001_R1_001.fastq (forward)
- Undetermined_S0_L001_R2_001.fastq (reverse)

HerbivoreMeta2.tsv – Metadata file with each row representing individual samples and columns representing sample ID (SampleID), host species (sample_Species), sex (Sex), geographic zone each sample was collected from in Etosha National Park (Zone), feeding strategy of host species (FeedStrat), gut morphology of host species (GutMorph), waterhole site sample was collected from (Waterhole), and host 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

Beta_tests.R – Analyzing beta diversity metrics by herbivore family; PERMANOVA tests analyzing weighted and unweighted UniFrac distances by herbivore family; Mantel tests correlating host divergence times and UniFrac distances; Simper analysis identifying taxa driving differences between host families; generating Fig. 2, Fig. 3, Fig. 4, Additional Fig. 1, Additional Table 1, Additional Table 2, and Additional Table 3