Analyzing the Black Death by Phylogenetics

Yersina pestis is a bacterial species that causes a deadly disease known as the Plague. Currently, outbreaks of the Plague occur in very few parts of the world, but ancient outbreaks had a major role in shaping human history. In the 14th century, a Plague outbreak referred to as the Black Death swept through Europe as shown on the map in Figure B4-6, killing 30 million people – over a third of the population – and causing perhaps as many to flee, further spreading the disease. In addition to its impact on the genetic structure of modern European populations, the Black Death affected European art and culture; stories and songs about the Black Death are common, and plague statues to commemorate survivors are found in many European cities.

Figure B4-6

A few years ago, modern genomic technology examined the Black Death. Victims of a medieval Plague outbreak were exhumed from East Smithfield in London; DNA from the infecting bacteria was extracted from their teeth and the genomes were sequenced. The sequences of those strains were compared with sequences from present-day plague outbreaks; sources of these modern outbreaks are represented by green dots on the map in Figure B4-7. A phylogenetic tree representing the genetic relatedness of the strains was constructed based on 1,694 informative positions across the genome.

Figure B4-7

Present-day strains that cause the plague differed from Black Death strain by fewer than 100 nucleotide sites. As shown in Figure B4-7, the 14th century East Smithfield strain shared an ancestral node with present-day strains, with the exception of lineages from Asia, strongly suggesting that a single lineage was responsible for medieval strain and all non-Asian outbreaks since. As the tree calculations placed the East Smithfield strain an ancestral node, the Black Death strain is the probable ancestor of modern disease-causing Yersinia pestis.

Further reading: Bos KI, et al. Draft genome of Yersinia pestis from victims of the Black Death. Nature. 2011 Oct 12. doi: 10.1038/nature1054