This is an essay written for submission to the science journal *Nature* in 2016. It was rejected, and since it was in response to a piece that originally appeared in *Nature*, I saw no reason to attempt to place it elsewhere. I am posting it now (January 2024), because it has become newly relevant to understand the London 6330 genome as representing a separate strain of Yersinia pestis in circulation in 14th century Europe. While much has changed in plague research in the past eight years (many points I make here I would no longer subscribe to), it is important from a historical perspective to understand the order in which different pieces of knowledge became available. (Note that the several instances of “phenotype” here should be corrected to “genotype.”)
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Abstract
Due to discovery of a provenancing error in a 2011 study, announced here, one of the genomes assumed to be from the East Smithfield Black Death Cemetery seems instead to have been involved in a separate epidemic event, the “second mortality” of 1360-63. Here I demonstrate that this London genome, 6330, should be redated, and I show that samples coming from another site in the Netherlands that present with the same genotype also have not been sufficiently provenanced to tie them specifically to the Black Death. This redating does not in itself challenge the genetic implications of the 2011 study or others that have relied on it. But, drawing on arguments of both biological and historical plausibility, I argue that a subsidiary claim that the pestis secunda strain reflects a European genetic development that then, in later centuries, went back to central Asia, is a less than parsimonious explanation of the evolution of one of the most lethal killers in human history.