Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica. Archive package of additional figures, tables and data

Concoct 7 - Eleven MAGs Contigs. Concoct 8 - Alignments and phylogenies of SCGs across the Tree of Life. Date estimation 1 - Date randomization tests for the temporal signal in multiple replicate data sets that were analysed by BEAST Date estimation 2 - Linear regression plots (TempEst [37]) of root-to-tip genetic distances to the MRCA of two sets of modern genomes plus Ragna (red), Tepos-14 and Tepos-35 (green) [19] versus their dates of sampling.

Date estimation 3 - Comparison of MRCA dating estimates by BEAST using ancient plus modern, and only modern strains Date estimation 4 - Raw Maximum Clade Credibility trees as well as a summary of the mutation rates from BEAST inferences. ParaC Pan-genome 1 - Gain and loss of genomic islands shown on a maximum-likelihood radial phylogeny derived from 61,451 non-repetitive core SNPs within the Para C Lineage plus Birkenhead ParaC Pan-genome 2 - Summary statistics for pan-genomic contents of Ragna plus 219 modern genomes of the Para C Lineage ParaC Pan-genome 3 - Gene gain/loss events and numbers of pseudogenes by sub-lineage ParaC Pan-genome 4 - The pan-genome of the Para C Lineage based on 6,665 single copy genes from 220 genomes.

ParaC Pan-genome 5 - Sequences, original gene names and annotations of the reference sequences for 6,665 pan genes in the Para C Lineage. ParaC Pan-genome 6 - Pseudogenes associated with sub-lineages and clades of the Para C Lineage. ParaC Pan-genome 7 - Genomic islands and plasmids.

ParaC Pan-genome 8 - Data and script for extracting rate of gene gain/loss and pseudogenes from the branches of an ML tree. See readme.txt for instructions. ParaC genome SNPs 1 - Numbers of mutational and recombinational SNPs per clade within the Para C Lineage plus Birkenhead ParaC genome SNPs 2 - SNPs in the core genome of the Para C Lineage plus Birkenhead.

ParaC genome SNPs 3 - Maximum likelihood phylogeny and inferred geographical origins based on 61,451 non-repetitive core SNPs from the Para C Lineage plus Birkenhead. ParaC genome SNPs 4 - Venn diagram of substitutions scored as recombinational by RecHMM, ClonalFrameML and Gubbins. Salmonella supertree 1 - Metadata for 2,964 representative genomes in Salmonella enterica subsp.

I. Salmonella supertree 2 - A species tree (ASTRID) based on 3,002 core gene trees from 2,964 representative genomes from S. enterica subsp. I. Salmonella supertree 3 - A RAxML maximum likelihood phylogeny based on a 2.8 Mbp concatenate of 3,002 core genes from 2,964 representative genomes from S. enterica subsp. I Workflow - Workflow to reconstruct the Ragna genome