DOI: 10.5281/zenodo.16755599
title: Data from: Interspecific variation in gut microbiome diversity across the Etosha National Park herbivore community

description: 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

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

Herbivore_points.csv – Latitude and longitude GPS points of each herbivore sample used for calculating geographic distance for Mantel tests

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

Phyla_tests.R – Identifying core phyla in each herbivore species; ANOVA tests analyzing significant core phylum (Verrucomicrobiota) abundance by zone; generating Figs. 2, 3a, S1_Table

Genera_tests.R – Identifying core genera in each herbivore species; ANOVA and t-tests analyzing significant core genera (Christensenellaceae_R-7 group, P-251-05, Monoglobus, RF39, and Alistipes) by sex, gut morphology, waterhole site, and zone; generating Figs. 3b, 3c, 3d, 4, 5, and S1_Table

Alpha_tests.R – Analyzing significant alpha diversity metrics (richness and Bulla evenness) by sex and host species, generating Fig. 6

Beta_tests.R – PERMANOVA tests analyzing beta diversity metrics (weighted and unweighted UniFrac) by each of the six intrinsic and extrinsic variables; Mantel tests; generating Fig. 7

FDR_phyla.csv – Raw p-values from significance tests of Verrucomicrobiota abundance by zone for FDR adjustment 

FDR_genera.csv – Raw p-values from significance tests of core genera abundance by sex, zone, waterhole site, and gut morphology for FDR adjustment

FDR_alpha.csv – Raw p-values from significance tests of richness and evenness by host species, gut morphology, and sex for FDR adjustment