Populaiton genomics of mutualistic Bacteria

1. Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medicae

2. Silly microbiologist, genomes are for mutualists

Some comments:

• The genomes were sequenced to ~ 100x coverage with on an Illumina GAIIx.
• Reads were then aligned to reference genomes of close relatives of the sequenced strains.
• These alignments were then used for various comparative and population genetic analyses
• As far as I can tell no de novo assemblies were done
• I am quite confused about their methods for detecting putative regions that have undergone horizontal gene transfer:
• In the methods: "We identified genes likely to have experiencedrecent horizontal gene transfer by comparing the ratio ofpolymorphisms that were shared between species to fixeddifferences between species. Based on the whole-genomedistribution of this ratio (Figure S3) we identified putativelytransferred genes as those with a ratio of shared polymorphisms tofixed differences >0.2."
• Not sure how/why this should work.  Not saying it is a bad idea - I just don't really understand it.
• They also examine various population genetic parameters including possible selection, SNPs, Tajima's D, and more.