To estimate the time of the recombination event (tRE), as well as the time of the most recent common ancestor (tMRCA) for each parental strain, we studied separately the genomic partition spanning the recombinant element from nt 5787 to 5991 (ALN2-1) and the partition covering the rest of the ORF (ALN2-2) that is the 59 region (nt 1 to 5786) together with the 39 region (nt 5992 to 10245) flanking the recombinant portion. The same uniform prior was fitted on the root height as before. For individual genes in ALN2-2, prior distributions for the MeanRate parameter were derived from posteriors in BEAST inference 1 with substitution and clock models unlinked during the analysis.