CaneToadMaxentPoints

Comma-delimited file with points used for MaxEnt

popmap

Tab-delimited file: first column is sample name, second column is the population assignment

StantonGeddes2013_Medicago_nodule_occupancy

Spreadsheet of nodule occupancy data, described in more detail in README file

R script for accession phenotypes

R markdown script used to generate the accession means that were used in the genome-wide association analysis using the TASSEL program

R script for nodule occupancy accession phenotypes

R script to calculate rhizobia strain nodule occupancy for genome-wide association analysis

Select and resequence data package

This zipped set of files includes all intermediate data sets and major scripts used to create the results and figures in the paper. See Readme file for additional info

Genotype calls from Stacks for Tasmanian devil RAD-seq

This VCF file contains raw genotype calls produced by Stacks as described in Epstein et al. 2016. Very briefly, the genotyping workflow was quality control -> PCR de-duplication (for paired-end samples) -> Alignment to reference -> Filter out MAPQ < 40 -> Stacks

StantonGeddes2013_Medicago_plant_data

Spreadsheet of plant phenotype data collected in greenhouse experiment for genome-wide association study. Column headings are: block, pot (individual plant ID), trtmnt (rhizobia treatment applied to the plant, either "rhz_12" for a mixture of two rhizobia strains, or "control" for no rhizobia), HM_accession (Medicago HapMap accession), height_1 (height recorded at about two weeks), leaves_1 (number of leaves at about two weeks), height_2 (intermediate height measurement), height_3 (final height before harvest), branch_3 (number of branches on plant before harvest), flowering date (date first flower observed), nodule_above (number of nodules counted in top 5 cm of roots), nodule_below (number of nodules below 5 cm of root growth). More information is available in the R markdown script "StantonGeddes2013_script.Rmd" that accompanies this file

Neighbor-joining trees showing relationships among 32 <i>S. meliloti</i> (blue squares) and 12 <i>S. medicae</i> (red circles).

<p>A) chromosomes, B) pSymA and pSMED02, and C) pSymB and pSMED01. Trees were constructed using sequences from coding regions only. The length of the branch separating <i>S. medicae</i> from <i>S. meliloti</i> strains is shown at a scale that is 5% of the true scale. The 24-strain <i>S. meliloti</i> group is marked by asterisks. All branches had 100% bootstrap support unless otherwise indicated. Branches with <80% bootstrap support were collapsed into polytomies. An identical tree with strain identifications is provided as <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002868#pgen.1002868.s002" target="_blank">Figure S2</a>.</p

Total number of SNPs, nucleotide diversity (mean θ_π) and mean <i>D_T</i> for all data and for gene regions separated by species and replicon.

<p>Data are only from genes for which >90% of the sites have unambiguous base calls from ≥80% of the strains and were not identified as recently transferred between <i>S. meliloti</i> and <i>S. medicae</i>.</p