Data from: Hierarchical social networks shape gut microbial composition in wild Verreaux's sifaka

Perofsky AC, Lewis RJ, Abondano LA, Di Fiore A, Meyers LA

Date Published: November 15, 2017

DOI: https://doi.org/10.5061/dryad.qf731

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Title sifaka_GLMM_covariates_duration
Downloaded 11 times
Description Place in "data" folder before running analyses. For use in pairwise_dissimilarity_predictors.R script
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Title beta_groom_same_12mo
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Description Place in "data" folder before running analyses. For use in beta_div_glmms.R script.
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Title Animal_DOB_sex
Downloaded 6 times
Description Place in "data" folder before running analyses.
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Title Perofsky_mapping_file_sifaka
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Description QIIME mapping file. Place in "data" folder before running analyses.
Download Perofsky_mapping_file_sifaka.txt (9.928 Kb)
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Title sifaka_relatedness
Downloaded 5 times
Description Matrix of genetic relatedness values among sifaka. Place in "data" folder before running analyses. For use in mantel_tests_relatedness_vs_microbiome.R script.
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Title social_group_matrix_2012
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Description Place in "data" folder before running analyses. For use in mantel_tests_relatedness_vs_microbiome.R script.
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Title sifaka_unifrac_weighted_marked_openref
Downloaded 3 times
Description Matrix of weighted Unifrac distances among microbiome samples. Place in "data" folder before running analyses.
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Title sifaka_trimmed_phyloseq_raw_openref
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Description Phyloseq object containing raw OTU counts (but with infrequent OTUs taken out). Place in "data" folder before running analyses.
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Title census_data
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Description Place in "data" folder before running analyses.
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Title focal_data
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Description Place in "data" folder before running analyses.
Download focal_data.txt (387.9 Kb)
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Title scan_data
Downloaded 3 times
Description Place in "data" folder before running analyses.
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Title full_table_for_poisson_glmm
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Description Place in "data" folder before running analyses. For use in poisson_glmms.R script.
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Title sifaka_plant_spp_rel_abund
Downloaded 2 times
Description Relative abundances of plant species consumed by individual sifaka. For use in diet_analyses.R script. Place in "data" folder before running analyses.
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Title sifaka_plant_parts_rel_abund
Downloaded 2 times
Description Relative abundances of plant parts consumed by individual sifaka. For use in diet_analyses.R script. Place in "data" folder before running analyses.
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Title sifaka_trimmed_phyloseq_markedonly_normalized_openref
Downloaded 2 times
Description Phyloseq object containing normalized OTU counts for sifaka of known identity only. Place in "data" folder before running analyses.
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Title mantel_tests_social_distance_vs_microbiome
Downloaded 6 times
Description R script that tests for correlations between social distance and microbiome dissimilarity.
Download mantel_tests_social_distance_vs_microbiome.R (7.066 Kb)
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Title samseq_differential_abundance_across_groups
Downloaded 2 times
Description R script that tests for differential abundance of bacterial phyla, families, and genera among sifaka social groups.
Download samseq_differential_abundance_across_groups.R (6.708 Kb)
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Title alpha_diversity
Downloaded 4 times
Description R script that rarefies the raw OTU table 100 times to calculate microbiome diversity for individual samples.
Download alpha_diversity.R (9.248 Kb)
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Title social_data
Downloaded 2 times
Description R script that loads in census, focal, and scan data.
Download social_data.R (2.295 Kb)
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Title diet_analyses
Downloaded 2 times
Description R script that tests between-group and between-individual differences in diet.
Download diet_analyses.R (15.09 Kb)
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Title beta_div_glmms
Downloaded 4 times
Description R script that uses generalized linear mixed models (GLMMs) to estimate the effects of pairwise predictors (social distance, relatedness, group membership) on microbiome dissimilarity.
Download beta_div_glmms.R (6.319 Kb)
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Title mantel_tests_relatedness_vs_microbiome
Downloaded 2 times
Description R script that tests for correlations between genetic relatedness and microbiome dissimilarity.
Download mantel_tests_relatedness_vs_microbiome.R (2.305 Kb)
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Title pairwise_dissimilarity_predictors
Downloaded 3 times
Description R script testing the effects of habitat overlap, dispersal history, and vertical inheritance on microbiome dissimilarity among samples.
Download pairwise_dissimilarity_predictors.R (3.055 Kb)
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Title network_duration_function_dyad
Downloaded 2 times
Description R script that creates a social network using census, focal, and scan data.
Download network_duration_function_dyad.R (11.44 Kb)
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Title poisson_glmms
Downloaded 5 times
Description 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.
Download poisson_glmms.R (2.641 Kb)
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Title beta_diversity_adonis
Downloaded 3 times
Description R script for PERMANOVA analyses.
Download beta_diversity_adonis.R (6.122 Kb)
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Title diet_diversity_table_for_poisson_glmm
Downloaded 2 times
Description Place in "data" folder before running analyses. For use in poisson_glmms.R script.
Download diet_diversity_table_for_poisson_glmm.RData (2.331 Kb)
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Title sifaka_trimmed_phyloseq_normalized_openref
Downloaded 2 times
Description Phyloseq object containing normalized OTU counts for all individuals. Place in "data" folder before running analyses.
Download sifaka_trimmed_phyloseq_normalized_openref.RData (2.896 Mb)
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Title sifaka_braycurtis_marked_openref
Downloaded 2 times
Description Matrix of Bray Curtis dissimilarities among microbiome samples. Place in "data" folder before running analyses.
Download sifaka_braycurtis_marked_openref.RData (6.302 Kb)
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Title diet_diversity_df
Downloaded 1 time
Description Table of individual dietary richness values. Place in "data" folder before running analyses. For use in diet_analyses.R script.
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Title sifaka_allotus_phyloseq_openref
Downloaded 1 time
Description Phyloseq object containing raw OTU counts (but singletons are removed). Place in "data" folder before running analyses.
Download sifaka_allotus_phyloseq_openref.RData (3.913 Mb)
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When using this data, please cite the original publication:

Perofsky AC, Lewis RJ, Abondano LA, Di Fiore A, Meyers LA (2017) Hierarchical social networks shape gut microbial composition in wild Verreaux's sifaka. Proceedings of the Royal Society B 284(1868): 20172274. https://doi.org/10.1098/rspb.2017.2274

Additionally, please cite the Dryad data package:

Perofsky AC, Lewis RJ, Abondano LA, Di Fiore A, Meyers LA (2017) Data from: Hierarchical social networks shape gut microbial composition in wild Verreaux's sifaka. Dryad Digital Repository. https://doi.org/10.5061/dryad.qf731
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