Category Archives: molecular biology

Medieval Historians Taking Genomics into Account

At the International Congress on Medieval Studies at Kalamazoo (Kzoo) last month, I couldn’t help feeling that we have reached a turning point. I went to four sessions that engaged in genomics, human and/or bacterial, in some way. Granted, these are a tiny proportion of the 500+ sessions offered, but I have learned that if you can string together so many sessions on any topic related to your work, it’s a really good Congress.

Before and After 1348: Prelude and Consequences of the Black Death session, Kalamazoo, 2017. Pictured: Monica Green and Robert Hymes (Photo: Nukhet Varlik, used with permission)

The tone was set in the very first session when Philip Slavin brought up human epigenetics in his discussion of 14th-century famine. This was followed the next day with three sessions on the Black Death and 14th-century crisis. The two Contagions society sessions went very well. Carenza Lewis talked about her ceramics landscape survey that showed how deep the 14th-century demographic loss actually was. Fabian Crespo introduced the audience to the human immune landscape and how it can be fruitfully approached (including by epigenetics).  I will post on the roundtable on Bruce Campbell’s The Great Transition later this summer. The third plague session, Before and After 1348,  organized by Monica Green focused on Asia and generated a vigorous discussion.   I also attended a fifth session that focused on more traditional biological anthropology, ie. mostly osteology.

This turn hasn’t come all of a sudden. Historians began paying more attention to bacterial genomics a little over a decade ago when plague aDNA first hit the news. Michael McCormick, Lester Little, and Monica Green have all been instrumental in bringing science to the attention of historians. Three edited volumes stand out for putting genomics in front of historians: Lester Little’s Plague and the End of Antiquity: The Pandemic of 541-750 (2007), Linda Clark and Carol Rawcliffe’s Society in the Age of Plague (2013), and Monica Green’s Pandemic Disease in the Medieval World: Rethinking the Black Death* (2015).

On the other hand, scientists have also edited collections of papers that should make the science more accessible to historians. Didier Raoult and Michel Drancourt have edited two volumes, Paleomicrobiology (2008) and Paleomicrobiology of Humans (2017). Ruifu Yang and Andrey Anisimov edited a more technical volume, Yersinia pestis: Retrospective and Perspective (2016) that should summarize the state of the science  (as of 2016) for more advanced readers in the humanities.

Of the monographs, the historian’s usual primary venue,  books addressing genomics or using genomics as a springboard are limited. With at least three appearing in 2016 by Nükhet Varlik, Ole Benedictow, and Bruce Campbell, this should change soon. At this point, I should mention that genomics is already becoming useful to historians of other diseases, especially leprosy and tuberculosis. Historians are also becoming reinvigorated to provide context for plague and other diseases that may be of interest to geneticists and biological anthropologists. Varlik’s edited collected Plague and Contagion in the Islamic Mediterranean  (2017) is the most recent to provide context for a variety of diseases in an understudied area.

*Green’s volume was first published as a double inaugural issue of the journal The Medieval Globe and then published as a hardback book by ARC Medieval Press.

Presentations on the Plague from the European Association of Archaeologists, Vilnius, Lithuania, 2016

I just discovered that most of the presentations from the “Plague in Diachronic and Interdisciplinary Perspective” session of the Europan Association of Archaeologists meeting in Vilnius, Lithuania on 2 September 2016 are now on YouTube.  I think I have collected them all here. Enjoy 3 hours of plague talks!

Introduction-Plague in diachronic and Interdisciplinary perspective by Marcel Keller

From Mild to Murderous: How Yersinia pestis Evolved to Cause Pneumonic Plague by Wyndham Lathem (30 min)

Reconstructing ancient pathogens – discovery of Yersinia pestis in Eurasia 5,000 Years Ago by Simon Rasmussen (15 min)

Plague in the eastern Mediterranean region 1200-1000 BC? by Lars Walloe (15 min)

Placing the Plague of Justinian in the Yersinia pestis phylogenetic context by Jennifer Klunk (15 min)

A demographic history of the plague bacillus revealed through ancient Yersinia pestis genomes by Maria Spyrou (15 min)

Analysis of a High-coverage Yersinia pestis Genome from a 6th Century Justinianic Plague Victim by Michal Feldman (15 min)

Early medieval burials of plague victims: examples from Aschheim and Altenerding (Bavaria, Germany) by Doris Gutsmiedl-Schumann (15 min)

Fleas, rats and other stories – The palaeoecology of the Black Death by Eva Panagiotakopulu (15 min)

Plague in Valencia, 546: A Case Study of the Integration of Texts and Archaeology by Henry Gruber (15 min)

Germany and the Black Death: a zooarchaeological approach by M.A. Paxinos

Ötzi’s Lyme Disease in Context

One of the ancient DNA finds that continues to intrigue me is the discovery of Borrelia burgdorferi, the agent of Lyme disease, in Ötzi the 5300-year-old ice mummy from the Italian Alps. As far as I know, this is the only finding of B. burgdorferi in ancient remains of any date.  I discussed the initial report of these findings back in the summer of 2012. 


The more we learn about Ötzi’s environment and lifestyle, the less mysterious it seems. There are no signs of human habitation or land management in these high Alpine regions. Indicators of deforestation, farming, and pasture maintenance are lacking from lake sediment and pollen studies. Festi, Putzer and Oeggl (2013) found the first signs of human land management in the Ötztal Alps to began about 1000 years after Ötzi’s time. During the Copper Age, subsistence occupation of the valley floor was sufficient for the population of Ötzi’s time. They did minimal farming, and breeding of caprines (sheep, goats, and ibex). Festi, Putzer and Oeggl (2013) note that Ötzi’s mummy is the only piece of evidence for humans that high in the Otztal Alps before the Bronze Age.

Before Ötzi’s time, landscape management in the Mesolithic was to support red deer herds that were “in a state of semi-domestication by means of active hunting” (Rollo et al, 2002). (Native Americans managed deer populations in similar ways by promoting a landscape where deer thrive near their hunting grounds.) The importance of deer to Ötzi is underscored by everything about him from the red deer meat in his stomach to the roe deerskin that made up his quiver and antler in some of his tools (Rollo et al, 2012). Two different species of deer have been confirmed by genetic analysis.  Most of his clothing was made of sheep and goat skins (O’Sullivan et al, 2016).

The agent of Lyme disease, B. burgdorferi, is transmitted primarily by the tick Ixodes ricinus, common on deer, sheep, cattle, humans and dogs as adults and feed on rodents and small mammals as nymphs. Ticks often thrive at the forest edge where there are grasses for them to climb up to catch passing deer. It seems likely that they would also thrive in along upland forest edges as well. Ixodes ricinus is found throughout the Alps.  It is feasible that Lyme disease was a greater problem for humans when we relied on deer as a staple food.

Ötzi’s B. burgdorferi has yet to be confirmed by a second group. Interestingly, a recent study of B. burgdorferi’s phylogeny suggests that it originated in Europe and later spread to ‘post-Columbian’ North America (Margos et al, 2008). Although Lyme disease was only recognized in the 20th century, it is apparently an ancient disease caused by multiple Borrelia species. And Ötzi’s sequence has not been added to any phylogeny I’ve found, odd. Overlooked, or a problematic sequence?


Festi, D., Putzer, A., & Oeggl, K. (2013). Mid and late Holocene land-use changes in the Otztal Alps, territory of the Neolithic Iceman “Otzi”. Quaternary International, 353, 1–18.

Margos, G., Gatewood, A. G., Aanensen, D. M., Hanincová, K., Terekhova, D., Vollmer, S. A., et al. (2008). MLST of housekeeping genes captures geographic population structure and suggests a European origin of Borrelia burgdorferi. Proceedings of the National Academy of Sciences, 105(25), 8730–8735.

O’Sullivan, N. J., Teasdale, M. D., Mattiangeli, V., Maixner, F., Pinhasi, R., Bradley, D. G., & Zink, A. (2016). A whole mitochondria analysis of the Tyrolean Iceman’s leather provides insights into the animal sources of Copper Age clothing. Scientific Reports, 6, 1–9.

Rollo, F., Ubaldi, M., Ermini, L., & Marota, I. (2002). Otzi’s last meals: DNA analysis of the intestinal content of the Neolithic glacier mummy from the Alps. Proceedings of the National Academy of Sciences of the United States of America, 99(20), 12594–12599.