DOI: 10.5061/dryad.qf731
title: Data from: Hierarchical social networks shape gut microbial composition in wild Verreaux's sifaka

description: In wild primates, social behaviour influences exposure to environmentally
 acquired and directly transmitted microorganisms. Prior studies indicate
 that gut microbiota reflect pairwise social interactions among chimpanzee
 and baboon hosts. Here, we demonstrate that higher-order social network
 structure—beyond just pairwise interactions—drives gut bacterial
 composition in wild lemurs, which live in smaller and more cohesive groups
 than previously studied anthropoid species. Using 16S rRNA gene sequencing
 and social network analysis of grooming contacts, we estimate the relative
 impacts of hierarchical (i.e. multilevel) social structure, individual
 demographic traits, diet, scent-marking, and habitat overlap on bacteria
 acquisition in a wild population of Verreaux's sifaka (Propithecus
 verreauxi) consisting of seven social groups. We show that social group
 membership is clearly reflected in the microbiomes of individual sifaka,
 and that social groups with denser grooming networks have more homogeneous
 gut microbial compositions. Within social groups, adults, more gregarious
 individuals, and individuals that scent-mark frequently harbour the
 greatest microbial diversity. Thus, the community structure of wild lemurs
 governs symbiotic relationships by constraining transmission between hosts
 and partitioning environmental exposure to microorganisms. This social
 cultivation of mutualistic gut flora may be an evolutionary benefit of
 tight-knit group living.
description: sifaka_GLMM_covariates_duration Place in "data" folder before running analyses. For use in pairwise_dissimilarity_predictors.R script beta_groom_same_12mo Place in "data" folder before running analyses. For use in beta_div_glmms.R script. Animal_DOB_sex Place in "data" folder before running analyses. Perofsky_mapping_file_sifaka QIIME mapping file. Place in "data" folder before running analyses. sifaka_relatedness Matrix of genetic relatedness values among sifaka. Place in "data" folder before running analyses. For use in mantel_tests_relatedness_vs_microbiome.R script. social_group_matrix_2012 Place in "data" folder before running analyses. For use in mantel_tests_relatedness_vs_microbiome.R script. sifaka_unifrac_weighted_marked_openref Matrix of weighted Unifrac distances among microbiome samples. Place in "data" folder before running analyses. sifaka_trimmed_phyloseq_raw_openref Phyloseq object containing raw OTU counts (but with infrequent OTUs taken out). Place in "data" folder before running analyses. census_data Place in "data" folder before running analyses. focal_data Place in "data" folder before running analyses. scan_data Place in "data" folder before running analyses. full_table_for_poisson_glmm Place in "data" folder before running analyses. For use in poisson_glmms.R script. sifaka_plant_spp_rel_abund Relative abundances of plant species consumed by individual sifaka. For use in diet_analyses.R script. Place in "data" folder before running analyses. sifaka_plant_parts_rel_abund Relative abundances of plant parts consumed by individual sifaka. For use in diet_analyses.R script. Place in "data" folder before running analyses. sifaka_trimmed_phyloseq_markedonly_normalized_openref Phyloseq object containing normalized OTU counts for sifaka of known identity only. Place in "data" folder before running analyses. mantel_tests_social_distance_vs_microbiome R script that tests for correlations between social distance and microbiome dissimilarity. samseq_differential_abundance_across_groups R script that tests for differential abundance of bacterial phyla, families, and genera among sifaka social groups. alpha_diversity R script that rarefies the raw OTU table 100 times to calculate microbiome diversity for individual samples. social_data R script that loads in census, focal, and scan data. diet_analyses R script that tests between-group and between-individual differences in diet. beta_div_glmms R script that uses generalized linear mixed models (GLMMs) to estimate the effects of pairwise predictors (social distance, relatedness, group membership) on microbiome dissimilarity. mantel_tests_relatedness_vs_microbiome R script that tests for correlations between genetic relatedness and microbiome dissimilarity. pairwise_dissimilarity_predictors R script testing the effects of habitat overlap, dispersal history, and vertical inheritance on microbiome dissimilarity among samples. network_duration_function_dyad R script that creates a social network using census, focal, and scan data. poisson_glmms R script that uses generalized linear mixed models (GLMMs) to estimate the effects of age, network centrality, diet, and scent-marking rate on within-host microbiome richness. beta_diversity_adonis R script for PERMANOVA analyses. diet_diversity_table_for_poisson_glmm Place in "data" folder before running analyses. For use in poisson_glmms.R script. sifaka_trimmed_phyloseq_normalized_openref Phyloseq object containing normalized OTU counts for all individuals. Place in "data" folder before running analyses. sifaka_braycurtis_marked_openref Matrix of Bray Curtis dissimilarities among microbiome samples. Place in "data" folder before running analyses. diet_diversity_df Table of individual dietary richness values. Place in "data" folder before running analyses. For use in diet_analyses.R script. sifaka_allotus_phyloseq_openref Phyloseq object containing raw OTU counts (but singletons are removed). Place in "data" folder before running analyses.