DOI: 10.5061/dryad.023s6
title: Data from: Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes

description: Correlation between gut microbiota and host phylogeny could reflect
 codiversification over shared evolutionary history or a selective
 environment that is more similar in related hosts. These alternatives
 imply substantial differences in the relationship between host and
 symbiont, but can they be distinguished based on patterns in the community
 data themselves? We explored patterns of phylogenetic correlation in the
 distribution of gut bacteria among species of turtle ants (genus
 Cephalotes), which host a dense gut microbial community. We used 16S rRNA
 pyrosequencing from 25 Cephalotes species to show that their gut community
 is remarkably stable, from the colony to the genus level. Despite this
 overall similarity, the existing differences among species'
 microbiota significantly correlated with host phylogeny. We introduced a
 novel analytical technique to test whether these phylogenetic correlations
 are derived from recent bacterial evolution, as would be expected in the
 case of codiversification, or from broader shifts more likely to reflect
 environmental filters imposed by factors such as diet or habitat. We also
 tested this technique on a published data set of ape microbiota,
 confirming earlier results while revealing previously undescribed patterns
 of phylogenetic correlation. Our results indicated a high degree of
 partner fidelity in the Cephalotes microbiota, suggesting that vertical
 transmission of the entire community could play an important role in the
 evolution and maintenance of the association. As additional comparative
 microbiota data become available, the techniques presented here can be
 used to explore trends in the evolution of host-associated microbial
 communities.
description: Dryad_Sanders_etal_MolEcol_2013DIRECTORY: ./example_scripts These are generalized example scripts that should help you to recreate theses analyses using your own data. They are just guides, and will not run without some (limited) modification. There are four files. 1) ./example_scripts/final_parameters.txt QIIME parameters file 2) ./example_scripts/qiime_script_example.sh bash shell script for Qiime 1.4.0 analysis pipeline 3) ./example_scripts/bdiv_summary_example.sh bash shell script for summarizing jacknifed beta diversity results using the QIIME tree_compare.py script. 4) ./example_scripts/bdiv_rugs.py simple python script for creating SVG images to visualize the results from the beta diversity sensitivity analysis performed in (3) above.example_scripts.zipfiguresDIRECTORY: ./figures This directory contains R code used to generate the alpha rarefaction curves (./figures/alpha), beta diversity box plot comparisons (./figures/box_plots), mantel tests (./figures/mantel), and principle coordinate plots (./figures/PCoA) used in the paper.ochman_original_dataDIRECTORY: ./ochman_original_data ./ochman_original_data contains the original sequence data as supplied by Prof. Howard Ochman (Personal Communication, July 12, 2013). This is in the format of a combined fasta file (primer_trimed.fasta) and a sample mapping file (sample_map.txt). Additionally, the folder contains a simple python script used to convert the sequence file to Qiime post-split_libraries.py format; the result of this script is ./ochman_example_analysis/seqs.fna.ochman_example_analysisDIRECTORY: ./ochman_example_analysis This contains example scripts and analysis similar to the Cephalotes example above. In addition to example output for four OTU widths (./ochman_example_analysis/93, 95, 97, 99), example scripts for analysis at two levels of rarefaction (1000 and 15000 sequences/sample), metadata mapping (./ochman_example_analysis/ochman_split_map.txt), results from the beta diversity sensitivity analysis (./ochman_example_analysis/bdiv_sensitivity_grids), and example host trees (./ochman_example_analysis/ape_phylogram_ILS_relabeled_furcated.tre, ape_cladogram_relabeled_relabeled_furcated.tre), there are several additional files. ape_sample_locations.txt are Lat/Lon values estimated from Figure 1 of Ochman et al 2010, used to estimate geographic distances for the partial Mantel tests.cephalotes_example_analysisDIRECTORY: ./cephalotes_example_analysis This contains the denoised sequence data used in the analysis of Cephalotes ant gut microbiota (./cephalotes_example_analysis/seqs.fna), metadata mapping info (cephalotes_map.txt), host trees with individual samples (ceph_guide_tree.tre) and colonies (ceph_species_tree_SpeciesColony.tre) as leaves, and an example analysis script (cephalotes_script_example). It also contains example output from four different OTU clustering thresholds (./cephalotes_example_analysis/93, 95, 97, and 99), results from the beta diversity sensitivity analysis (./cephalotes_example_analysis/bdiv_sensitivity_grids), and the results of the compute_core_microbiome.py script in Qiime 1.6.0 (./cephalotes_example_analysis/core_otus).