Euoniticellus_microbiome_dataset

This file contains quality trimmed, demultiplexed sequences without barcodes and primers (seqs.fna) produced from using default parameters in split_libraries_fastq.py script in QIIME 1.8.0; and a metadata mapping file (mapping.txt) for all the samples

Genome assembly and annotations for Sodalis lineage SLEU

Genome was assembled using metagenomic techniques and annotated using the RAST server

Representative sequences for 16S OTUs identified in this study.

Sequences with names beginning with "denovo" are less than 97% similar to Greengenes representative sequences at this similarity level. All other sequences are those from Greengenes release 13_8

Genome assembly and annotations for Sodalis lineage SAL1

Genome was assembled using metagenomic techniques and annotated using the RAST server

Genome assembly and annotations for Sodalis lineage SAL2

Genome was assembled using metagenomic techniques and annotated using the RAST server

2017_ArcilaHernandezetal_ExperimentalColonies_Dryad

2017_ArcilaHernandezetal_ExperimentalColonies_Dryad is a csv file with data by block and treatment for assays on ant foraging, stable isotopes, morphology, colony size, and count data of 16S sequences obtained with qPCR and 454 pyrosequencing

2017_ArcilaHernandezetal_wildcolonies_Dryad

2017_ArcilaHernandezetal_wildcolonies_Dryad is a csv file with count and weight data of worker and reproductive ants in wild colonie

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)

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