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.
Dryad_Sanders_etal_MolEcol_2013
DIRECTORY: ./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.zip
figures
DIRECTORY: ./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_data
DIRECTORY: ./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_analysis
DIRECTORY: ./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_analysis
DIRECTORY: ./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).