Category Archives: biogeography

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


Advertisements

Rivers in European Plague Outbreak Patterns, 1347-1760

by Michelle Ziegler

The era of big data is coming to historic epidemiology. A new study published this month in Scientific Reports took a database of 5559 European outbreak reports (81.9% from UK, France, and Germany) between 1347 and 1760 to analyze the role of rivers in the incidence and spread of plague. Their hypothesis was that river trade played a similar role as maritime trade in disseminating the plague but that the correlation would grow weaker over time as movement of goods over land became less expensive. In the 14th century, water transport was approximately ten times cheaper than land transport; the cost ratio diminishes to two to four times as expensive by the 18th century.  While it is not surprising that rivers had a role in disseminating the plague, the high correlation Yue, Lee, and Wu (2016) found between not only the proximity of the river but also its size and elevation is striking. Over 95% of the outbreaks occurred within 10 km of a ‘navigable’ river, defined as 5 m or greater in modern width and to differentiate maritime from riverine trade, excluded outbreak sites within 5 km of the maritime coastline. To ensure that rivers were suitable as trade routes, they only included rivers that linked two cities and excluded rivers that flowed into a lake without an outlet.

srep34867-f1
“Figure 1. Temporal and spatial distribution of plague outbreak in Europe in AD 1347–1760 (modifed from Büntgen et al 2012).” Yue, Lee, & Wu, 2016.http://www.nature.com/articles/srep34867/figures/1

If we drill down into their results more directly, then we find that 84% of the city centers were less than 1 km from a river with 79.5% of those being on a river at least 20 meters wide. By their calculations, the average river width was 84.6 m. This correlates well with increased traffic and goods following to and through cities on substantial rivers. It is worth nothing here that the specific examples they give in England, Fossdyke, River Great Ouse, and the River Derwent are either canals or fit into an extensive canal system.

Looking at relationships between the outbreak sites and geography also favors high traffic river routes. When they included a “spatial lag in the regression models” they showed that there is a “highly significantly correlation with the spatial lag (p <0.01), indicating that plague outbreaks were spatially dependent upon previous outbreaks in adjacent cities” (Yu, Lee & Wu, p. 2). There was also a negative correlation between elevation and plague incidence, which they attribute to a lack of navigable rivers at higher elevations noting that only 20 incidents were recorded above 1000 m over sea level.  They also tested their results with controls for population density and economic status which did not impact their results for the likelihood of plague incidence or the association between outbreaks and river width. This will have to be evaluated by those with more modeling experience than I have.

There are a few caveats. First, such studies are only as good as their database. Yue, Lee and Wu used the digitized database constructed by Büntgen et al (2012) that was itself based on a 35-year-old archive published in French. I’ll leave its scrutiny to historians. They also do not address potential biases in all such databases, such as the likelihood that urban sites are recorded at a higher frequency than rural sites or that the political climate can impact the survival of records. Indeed, economic records are likely to note pestilence as a factor affecting commerce. While the environmental destruction of an enduring war could increase plague incidence, the high level of records from the ’30 years war’ needs a historian’s eye to evaluate. They also note that they are using measurements of modern rivers and canals that may have been significantly different in the past, modified by both natural processes such as silting or flooding and man-made changes such as straightening, dredging, or canal development.

They also assume there were no European reservoirs, which we now know is not true. Ancient DNA studies have indicated that there were at least two strains descended from the Black Death circulating within late medieval Europe (Bos et al, 2016;  Spyrou et al, 2016). The European reservoir(s) have not yet been located. However, relatively few of the incidents reported in the database are likely to be actual zoonotic events linked directly to a local sylvatic (wild) reservoir, plus many known reservoirs outside of Europe are found at high elevation (for example in Tibet or Madagascar) and so are unlikely to be in this particular database given the absence of sites at higher elevations. Once a new outbreak emerges from a high elevation reservoir and comes off the mountain so to speak, then its transmission by rivers is as likely as a strain entering from outside of Europe. On the other hand, if cities or even river networks are the actual reservoirs, it would significantly affect their results.

River and canal networks or large river ports could function as reservoirs. River ports are similar to coastal maritime ports in that they have wharfs, warehouses and nearby markets that would support large rodent populations. Barge traffic would specialize in transport of grain and other foodstuffs attractive to rodents.  Yue, Lee, and Wu  (2016) state that they did not query their database for the effect of flooding because they could not accurately predict where floods would occur, that flooding is not predictable based solely on river width. Flooding along these river and canal systems is something that needs to be investigated because it would force rodents out of their normal shelter and could be related to human outbreaks (as the plague of 589 in Rome probably was). Floods could also carry infected rodents or fleas downstream on floating debris.

This study is an interesting jumping off point for future work. The database needs to be evaluated by historians and perhaps subdivided into smaller time periods. Division of the database into regional studies would also allow local archaeology and ecology to be more informative on precise outbreaks. I’m looking forward to all of the questions big data studies like this one open up!


Reference:

Yue, R. P. H., Lee, H. F., & Wu, C. Y. H. (2016). Navigable rivers facilitated the spread and recurrence of plague in pre-industrial Europe. Scientific Reports, 1–8. http://doi.org/10.1038/srep34867

Büntgen, U., Ginzler, C., Esperf, J., Tegel, W., & McMichael, A. J. (2012). Digitizing historical plague. Clinical Infectious Diseases, 55(11), 1586–1588. http://doi.org/10.1093/cid/cis723

Bos, K. I., Herbig, A., Sahl, J., Waglechner, N., Fourment, M., Forrest, S. A., et al. (2016). Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus. eLife, 5, 17837. http://doi.org/10.7554/eLife.12994

Spyrou, M. A., Tukhbatova, R. I., Feldman, M., Drath, J., Kacki, S., de Heredia, J. B., et al. (2016). Historical Y. pestis Genomes Reveal the European Black Death as the Source of Ancient and Modern Plague Pandemics. Cell Host and Microbe, 19(6), 874–881. http://doi.org/10.1016/j.chom.2016.05.012

Expanding the Historical Plague Paradigm

When the first complete genomic sequence of Yersinia pestis was published on October 4, 2001 the world was naturally focused elsewhere, on anthrax bioterrorism — the Amerithrax incident was then in its second week– and the September 11 attacks were just over three weeks old. As the world redeveloped bioterrorism assessments and plans, plague was placed on lists along with anthrax, smallpox and yes, ebola as agents of national security concern and response.  Although plague produced more annual cases than most agents on the category A bioterrorism list, it was placed on the list primarily based on its historical reputation and past attempts to weaponize it (also based on its reputation). Yet, in 2001 there was a fierce debate ranging among historians and others on whether Yersinia pestis was the agent of the Black Death at all.

It would take another ten years before genomics would revolutionize our understanding of the historical plague. On October 12, 2011 the first draft sequence of an ancient plague genome was published. Finally, adding to the detection of Yersinia pestis DNA tests previously done on remains, the draft sequence isolated from the East Smithfield Black Death cemetery in London solidified consensus that Yersinia pestis is the agent of the Black Death pandemic.  Meanwhile, the phylogenetic tree of Yersinia pestis had been constructed based on the genetic sequence of isolates from all over the globe. Ancient and modern Yersinia pestis genomes were opening a new window into the history of the species.

As fundamental as genomic analysis is to the new understanding of historical plague, it is a skeleton of data that is open to many different historical interpretations. Science can’t adequately explain the historic plague epidemics alone; it takes historical context. In the inaugural double issue of The Medieval Globe,  Pandemic Disease in the Medieval World: Rethinking the Black Death (open access) begins this process. The eleven articles in this issue take the genetic identification of Yersinia pestis  as the agent of the Black Death as foundational and integrate modern biological and epidemiological information into a new global Old World assessment of the history of the Black Death and subsequent epidemics. Each of these articles lays the groundwork for future interdisciplinary work between historians, anthropologists, biologists, epidemiologists and others.

In my own contribution to this issue, “The Black Death and the Future of the Plague” I discuss why plague is still important in the modern world and for our future. Plague has played an integral role in the development of the re-emerging infectious diseases paradigm and is an agent of biosecurity concern. I review the current state of plague around the world, what we have learned about plague epidemiology and transmission, and how it can be applied to historic epidemics. I also make my case for why the study of the entire history of plague is uniquely important and why the sciences and humanities must move forward together.  I hope we can engage in a discussion on these issues here in the comments section, on twitter or by email.

My own interest and awareness of the issues surrounding the study of the plague was transformed when I had the great fortune to be invited by Monica Green to participate in a session at the American Historical Association annual meeting in New Orleans, January 2013. The group of plague scholars gathered there has largely remained in contact and expanded our network into an informal working group that has enriched all of our scholarship.  No one can become fully conversant with all of the disciplines involved in the study of even one epidemic, much less the entire history of the plague.  Working in disciplinary seclusion will not produce a satisfying paradigm or widespread consensus. It takes work, patience and some tolerance of how other disciplines work, but I have found it to always be worth it. I hope you will agree.

Some references for the milestones mentioned:

Parkhill, J., Wren, B. W., Thomson, N. R., Titball, R. W., Holden, M. T., Prentice, M. B., et al. (2001). Genome sequence of Yersinia pestis, the causative agent of plague. Nature, 413(6855), 523–527. doi:10.1038/35097083

Morelli, G., Song, Y., Mazzoni, C. J., Eppinger, M., Roumagnac, P., Wagner, D. M., et al. (2010). Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nature Genetics, 1–20. doi:10.1038/ng.705

Little, L. K. (2011). Plague Historians in Lab Coats. Past & Present, 213(1), 267–290. doi:10.1093/pastj/gtr014

Bos, K. I., Schuenemann, V. J., Golding, G. B., Burbano, H. A., Waglechner, N., Coombes, B. K., et al. (2011). A draft genome of Yersinia pestis from victims of the Black Death. Nature, 1–5. doi:10.1038/nature10549

Pandemic Disease in the Medieval World: Rethinking the Black Death. Edited by Monica Green. The Medieval Globe, 1 (1), 2014.