Achtman on Plague Evolution


Mark Achtman who led the international team that assembled the phylogenetic tree for Yersinia pestis participated in a Royal Society meeting on ‘Immunity, infection, migration and human evolution’ in June 2011. Achtman’s contribution placed plague evolution within the context of other ‘monomorphic’ pathogens.

Here are some of my notes from his published contribution:

I’ve redesigned the phylogenetic tree given in Achtman, 2012 and the original paper, Morelli et al, 2010 below so that it works better online and is hopefully easier to read. This diversity is based primarily on single nucleotide polymorphisms (SNPs), similar to genetic fingerprints that usually do not affect function. The right branch (branch 2) of including the ‘medievalis’ isolates (2.Med1 and 2.Med2) evolved along the Silk Road after the Black Death. The left branch is much more diverse including Antiqua strains (1.Ant1) that are closest to the root species. The far left cluster of ‘orientalis’ strains (1.Ori1-3) represent the global spread of the third pandemic. The dates given here come from Acthman (2012), and may be a bit optimistic.

Major branches of the Yersinia pestis pedigree. ya= years ago. Not to scale, after Achtman, 2012 and Morelli et al, 2010.
Table showing the 18 genetic changes that differentiate the branches of Yersinia pestis along with some aDNA results from Haensch et al, 2010.


Achtman, M. (2012). Insights from genomic comparisons of genetically monomorphic bacterial pathogens Philosophical Transactions of the Royal Society B: Biological Sciences, 367 (1590), 860-867 DOI: 10.1098/rstb.2011.0303

Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner DM, Feldkamp M, Kusecek B, Vogler AJ, Li Y, Cui Y, Thomson NR, Jombart T, Leblois R, Lichtner P, Rahalison L, Petersen JM, Balloux F, Keim P, Wirth T, Ravel J, Yang R, Carniel E, & Achtman M (2010). Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nature genetics, 42 (12), 1140-3 PMID: 21037571

Haensch S, Bianucci R, Signoli M, Rajerison M, Schultz M, Kacki S, Vermunt M, Weston DA, Hurst D, Achtman M, Carniel E, & Bramanti B (2010). Distinct clones of Yersinia pestis caused the black death. PLoS pathogens, 6 (10) PMID: 20949072