Tracking the potato pathogen

An increasing number of authors of scientific papers are writing good blog summaries of their work. The really great part is that the authors tend to give background details that help explain not only what the work means but also how it was done.

This week, one of the coolest new papers was the genetic characterization of the fungus that caused the Irish potato famine. Detlef Weigel describes the paper in a post at Haldane’s Sieve, a group blog devoted to describing open preprints in genetics and biology: “Our paper: The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine”. The post goes over the multidisciplinary team of researchers whose specialties were needed for the paper – from ancient DNA to pathogen genomics and systematics – and gives some neat details about the samples themselves:

Our conclusions are based on Illumina sequencing of 11 herbarium samples of infected potato and tomato leaves collected in Ireland, the UK, Continental Europe and North America and preserved in the herbaria of the Botanical State Collection Munich and the Kew Gardens in London. Both herbaria placed a great deal of confidence in our abilities and were very generous in providing the dried plants. The degree of DNA preservation in the herbarium samples was impressive, much higher than in other examples of ancient DNA, and the majority of recovered DNA was from the host plant, with some samples having in addition over 20% pathogen DNA. In contrast to recent studies of historic human pathogens, no target DNA enrichment was required. We compared the historic samples with modern strains from Europe, Africa and North and South America as well as two closely related Phytophthora species. Due to the 150-year long period over which the individual samples had been collected, we were able to estimate with great confidence when the various P. infestans strains had emerged during evolutionary time. Here, too, we found connections with historic events: the first contact between Europeans and Americans in Mexico falls exactly into the time window in which the genetic diversity of P. infestans experienced a remarkable increase. Presumably, the social upheaval following the arrival of the Europeans somehow led to a spread of the pathogen at the beginning of the sixteenth century, which in turn accelerated its evolution.

What a unique historical record of samples taken from potato plants across one hundred and fifty years. Now it has become possible for DNA investigation to trace down the evolutionary dynamics that led to one of the most famous epidemics in history. This kind of ancient DNA analysis, across multiple time layers to work out the diachronic record of changes in frequencies, has really developed during the last year or two.