More aDNA from the Black Death

 

Green dots indicate sites examined. Dotted lines are likely transmission routes for the plague in 1347-1353. (Haensch et al, 2010, Fig. 1, Click to enlarge).

 

An international team has confirmed Yersinia pestis biomolecules in Black Death era* ‘plague pits’ (Haensch et al., 2010). Ancient DNA (aDNA) specific for Yersinia pestis and the Yersinial F1 antigen were discovered in skeletons from recognized plague pits in the Netherlands, England, and France. German and Italian skeletons tested positive for Y. pestis antigens but did not yield DNA. Their work supports Pusch et al.’s (2004) claim that the antigen test is significantly more sensitive than amplification of aDNA, as expected based on the antigen’s abundance per cell and durability. This is now the fourth group to amplify Y. pestis aDNA from skeletons of the first or second pandemic periods, and the third group to find Y. pestis antigens. So far there are no papers that I know of reporting difficulties with the antigen test. Given that the antigen test appears to be more sensitive, and is likely cheaper, faster and easier to use, it may become the primary tool for testing ancient remains for archaeological purposes.

The DNA isolates were large enough to allow the amplification of several Y. pestis specific DNA markers to classify these samples relative to modern strains. The diagram below illustrates the evolution of Yersinia pestis from its parent species Yersinia pseudotuberculosis.

 

New aDNA markers (green boxes) placed on the Y. pestis phylogenetic tree (Haensch et al, 2010).

 

A phylogenetic tree diagrams the genetic relationships between clones or strains. The size of the nodes gives a relative indication of the abundance of the marker tested. Perhaps the easiest way to describe a phylogenetic tree is to say that it is a branch of a tree of life for a specific species that includes extinct species/strains. Small Things Considered has a post this week further explaining the terminology and relationships within a phylogenetic tree.  Today phylogenetic trees are constructed primary by comparative genetics. This is still very early days for the plague phylogenetic tree. Unless the evolution of Y. pestis is a major interest of yours, I would wait until a great deal more data is available before paying much attention to the phylogenetic tree.  Haensch et al used more and different markers than previous groups so the placement of aDNA from previous groups on this diagram may or may not be in conflict; they are placed on the same clade. In looking ahead Haensch et al. explain that further genotyping of this clade will need to be done to resolve their isolates with that of earlier groups.

“These tests should involve further genotyping of large, global collections of extent lineages in combination with extensive palaeogenetic analysis of other mass graves from the historical routes traveled by the Black Death and Justinian’s plague. Such analyses are very promising because they could potentially fully reconstruct the history of ancient plague pandemics withing the modern phylogeographical context of Y. pestis.” (Haensch et al., p. 6)

DNA from ancestral strains of Y. pestis should put fears over contamination with modern DNA finally to rest.

The number of unique clones found in aDNA does give an indication of how many sources and transmission lines existed in the past. Haensch et al. isolated two distinct clones of Y. pestis from the 14th century suggesting that the main wave of the Black Death pandemic had at least two sources. The discovery of the same clone in 14th century mass graves from Hereford England and in southern France at Saint-Laurent-de-la-Cabrerisse puts to rest the notion that the plague was different in northern Europe. A distinctly different strain in the Netherlands also suggests that northern Europe was infected more than once.

The paper is available to everyone in the open-access journal PLoS Pathogens here.

* The sites from England, France and the Netherlands were all 14th century, consistent with the main waves of the Black Death. The German and Italian sites were 16th-17th century. The three control sites ranged in date from 7th century to 17th century.

Haensch, S., Bianucci, R., Signoli, M., Rajerison, M., Schultz, M., Kacki, S., Vermunt, M., Weston, D., Hurst, D., Achtman, M., Carniel, E., and Bramanti, B. (2010). Distinct clones of Yersinia pestis caused the Black Death. PLoS Pathogens, 6 (10)

Pusch CM, Rahalison L, Blin N, Nicholson GJ, & Czarnetzki A (2004). Yersinial F1 antigen and the cause of Black Death. The Lancet infectious diseases, 4 (8), 484-5 PMID: 15288817