DOI: 10.5061/dryad.cj05t65
title: Data from: Fur seal microbiota are shaped by the social and physical environment, show mother-offspring similarities and are associated with host genetic quality

description: Despite an increasing appreciation of the importance of host-microbe
 interactions in ecological and evolutionary processes, the factors shaping
 microbial communities in wild populations remain poorly understood. We
 therefore exploited a natural experiment provided by two adjacent
 Antarctic fur seal (Arctocephalus gazella) colonies of high and low social
 density and combined 16S rRNA metabarcoding with microsatellite profiling
 of mother-offspring pairs to investigate environmental and genetic
 influences on skin microbial communities. Seal-associated bacterial
 communities differed profoundly between the two colonies, despite the host
 populations themselves being genetically undifferentiated. Consistent with
 the hypothesis that social stress depresses bacterial diversity, we found
 that microbial alpha diversity was significantly lower in the high-density
 colony. Seals from one of the colonies that contained a stream also
 carried a subset of freshwater-associated bacteria, indicative of an
 influence of the physical environment. Furthermore, mothers and their
 offspring shared similar microbial communities, in support of the notion
 that microbes may facilitate mother-offspring recognition. Finally, a
 significant negative association was found between bacterial diversity and
 heterozygosity, a measure of host genetic quality. Our study thus uncovers
 a complex interplay between environmental and host genetic effects, while
 also providing empirical support for the leash model of host control,
 which posits that bacterial communities are driven not only by bottom-up
 species interactions, but also by top-down host regulation. Taken
 together, our findings have broad implications for understanding
 host-microbe interactions as well as prokaryotic diversity in general.
description: AFSmicrobiome_SI_OTUprocessingPipelineScripts_DatasetS1Collection of scripts for the OTU processing pipelineAFSmicrobiome_SI_OTUprocessingPipelineStatistics_DatasetS2Summary statistics for the OTU processing pipelineAFSmicrobiome_SI_Rmarkdown_DatasetS3_htmlR Markdown file in .html format containing all the R code used for the analyses of the Antarctic fur seal microbiomeAFSmicrobiome_SI_Rmarkdown_DatasetS3_Final_revision.htmlAFSmicrobiome_SI_Rmarkdown_DatasetS3_RmdR Markdown file in Rmd format containing all the R code used for the analyses of the Antarctic fur seal microbiomeAFSmicrobiome_SI_Rmarkdown_DatasetS3_Final_revision.RmdAFSmicrobiome_SI_SequencingStatsFile_Rinput_DatasetS4R markdown input file containing sequencing statisticsAFSmicrobiome_SI_MicrosatelliteGenotypes50_P22removed_colnames_Rinput_DatasetS5R markdown input file containing genotypes at 50 microsatellite loci for 95 fur seal individuals (pup P22 was removed due to large number of missing genotypes). Contains table header with loci names.AFSmicrobiome_SI_MicrosatelliteGenotypes50_P22removed_colnames_Rinput_DatasetS5.1R markdown input file containing genotypes at 50 microsatellite loci for 95 fur seal individuals (pup P22 was removed due to large number of missing genotypes). Header line removed.AFSmicrobiome_SI_relatednessWang50Msats_Rinput_DatasetS6R markdown input file containing pairwise relatedness estimatesAFSmicrobiome_SI_otuRDPclassification_Rinput_DatasetS7R markdown input file containing the OTU RDP classifications obtained with the USEARCH sintax commandAFSmicrobiome_SI_otuRDPclassification_phyloseqIn_Rinput_DatasetS8R markdown input file containing the OTU RDP classifications prepared for phyloseq inputAFSmicrobiome_SI_OTUtable_final_trimmed_allSamples_Rinput_DatasetS9R markdown input file containing the trimmed OTU table for all samplesAFSmicrobiome_SI_OTUtable_final_trimmed_raref10000_Rinput_DatasetS10R markdown input file containing the trimmed and rarefied OTU table for 94 samplesAFSmicrobiome_SI_Metadata_allSamples_Rinput_DatasetS11R markdown input file containing metadata for all samplesAFSmicrobiome_SI_alphaDiversity_Rinput_DatasetS12R markdown input file containing alpha diversity estimates (Effective number of species–Jost1) calculated from the non-normalised and rarefied OTU tables in USEARCH for all sampled individualsAFSmicrobiome_SI_alphaDiversity_MainPhyla_Rinput_DatasetS13R markdown input file containing alpha diversity estimates (Effective number of species–Jost1) calculated for OTUs belonging to the main phylaAFSmicrobiome_SI_outgroup_pynastAligned_filtered_Rinput_DatasetS14R markdown input file containing a phylogenetic tree needed for UniFrac distance calculations (created with FastTree in QIIME).AFSmicrobiome_SI_PuppingLocations_Rinput_DatasetS15R markdown input file containing pupping locations at SSBAFSmicrobiome_SI_alphaDiversityMultiRaref_Rinput_DatasetS16R markdown input file containing alpha diversity estimates (Effective number of species–Jost1) calculated for 100 rarefied OTU tables in USEARCH for all sampled individualsAFSmicrobiome_SI_NSTIvalues_filteredTrimmed_rarefied_Rinput_DatasetS17R markdown input file containing NSTI values calculated from PICRUStAFSmicrobiome_SI_Categorize_by_FunctionL3_FilteredTrimmed_rarefied_Rinput_DatasetS18R markdown input file containing read counts for KEGG functional predictions calculated with PICRUSt