Getting the Scoop on Pre-Clovis Poop - The Investigations Continue

A history resource article by Mary Harrsch © 2015

Ancient American.  Photo by Mary Harrsch © 2004.

Recently, one of my friends posted a Smithsonian Magazine article to my Facebook timeline about new DNA research linking prehistoric Amazon populations in Brazil to prehistoric Australians. Researchers think a non-Mongoloid common ancestral group that had originally migrated from Africa traveled to south Asia. From there, the group branched off with some of the group migrating north to Siberia while the rest migrated south to New Guinea and Australia.  The non-Mongoloid Siberian group eventually continued on to the Americas continuing their migration all the way into South America, apparently without leaving any remnants in North America. Furthermore, the DNA study appears to corroborate Brazilian Paleoindian skull studies performed in 2002.  In that study, Paleoindian skulls dating between 8200 and 9500 BP recovered in Brazil were compared to late Pleistocene/Early Holocene skulls recovered from sites in Australia and New Zealand.

"The Santana do Riacho late Paleoindians present a cranial morphology characterized by long and narrow neurocrania, low and narrow faces, with low nasal apertures and orbits. The multivariate analyses show that they exhibit strong morphological affinities with present day Australians and Africans, showing no resemblance to recent Northern Asians and Native Americans. These findings confirm our long held opinion that the settlement of the Americas was more complicated in terms of biological input than has been widely assumed. The working hypothesis is that two very distinct populations entered the New World by the end of the Pleistocene, and that the transition between the cranial morphology of the Paleoindians and the morphology of later Native Americans, which occurred around 8-9 ka, was abrupt. This, in our opinion, is a more parsimonious explanation for the diversity detected than a long, local microevolutionary process mediated by selection and drift. The similarities of the first South Americans with sub-Saharan Africans may result from the fact that the non-Mongoloid Southeast Asian ancestral population came, ultimately, from Africa, with no major modification in the original cranial bau plan of the first modern humans." - Walter Alves Nevesa, André Prousb, Rolando González-José, Renato Kipnis and Joseph Powell, Early Holocene human skeletal remains from Santana do Riacho, Brazil: implications for the settlement of the New World, Journal of Human Evolution 45 (2003) 19–42

But, although the Smithsonian article mentions a coprolite (fossilzed feces) study done here in Oregon in which fragments of human DNA were found dating to as far back as 14,340 B.P. and the DNA was found to share commonalities with modern Native Americans, there was no discussion about how the Oregon findings appear to contradict the theories put forward by the 2002 Brazilian skull researchers and later DNA studies that non-Mongoloid Paleoindians settled South America first and later Mongoloid groups became the ancestors of northern Native Americans.

As it turns out, I interviewed Dr. Dennis Jenkins of the University of Oregon back in 2009 about his coprolite studies for a website in London that is no longer online.  I've never been one to waste research so I am republishing it here for those who may not have read it back in 2009 and have an ongoing interest in these types of investigations seeking to discover ancient migration patterns from the Old World to the New.  At the end I have added updates about more recent ongoing investigations at Paisley Caves and elsewhere.

So, here once again is "Getting the Scoop on Pre-Clovis Poop!" originally published in 2009.

Looking out across the arid sagebrush-dotted landscape of southeastern Oregon makes a person wonder if there's anyone really out there.  When I lived there for seven years in the late 1970s and early 80s and worked as an economic development coordinator for a local county government, I actually heard the region referred to as  "the empty quarter".  But Oregon's high desert, part of the 200,000 square mile area known collectively as The Great Basin, is actually teaming with life and, as it turns out, even human life, for over 14,000 years.

In fact, a handful of shallow caves near Summer Lake, a large alkali bed in south central Oregon, have yielded human remains in the form of coprolites (fossilized feces) that return carbon dates of between 12,750 and 14,340 calendar years before present.  This finding appears to finally wield a death blow to the "Clovis first" school of thought that has ruled the chronology of settlement of the Americas since the mid-20th century.

Summer Lake in southeast Oregon's Great Basin country.  Photo by Mary Harrsch © 2015

The Clovis first theory was developed following the discovery of a number of sites in the 1930s containing artifacts from a Paleo-Indian culture who produced distinctive bifacial lanceolate spear points.   Found near Clovis, New Mexico in excavations between 1932 and 1937, remains of this prehistoric population group have been dated to near the end of the last Ice Age, originally thought to be about 13,000 years ago.  New radiocarbon dates by Michael Waters from Center for the Study of First Americans, Texas A&M University, and Thomas Stafford, Stafford Research, Inc, Boulder, Colorado, place Clovis remains from the continental United States in an even shorter time window (11,050 to 10,900 years ago).

Clovis spear point.  Image courtesy
of Wikimedia Commons.

The Clovis people were skilled hunters who stalked large mammals, particularly mammoths and mastodons, evidenced by numerous finds of the skeletal remains of these late Pleistocene animals intermixed with Clovis weapon points.  In fact, the Clovis people were considered to be such lethal hunters that they have been placed at the center of the Pleistocene overkill hypothesis used to explain the extinction of these animals from the North American continent. This may be an oversimplification, however, as research has shown the Clovis people utilized over 125 species of plants and animals including extinct bison, mastodon, sloths, tapir, paleolama, horse and a host of smaller animals.

As years passed and no validated archaeological evidence dated earlier than the Clovis period (using the somewhat limited dating methods available at the time) were discovered, the Clovis first theory became solidly entrenched. However, it began to unravel as early as 1961 with the discovery of a child's skull in Taber, Alberta, Canada, carbon dated to 30,000 y.b.p.  The dating of the skull was immediately dismissed as erroneous as were artifacts at Crows Nest Pass (Alberta) dated to 23,000 y.b.p., stone choppers and scrapers below the glacial deposits in Grimshaw, Bow River and Lethbridge (Alberta) dated to 40,000 - 20,000 y.b.p. and human-worked mammoth bones found by Canadian archaeologist, Jacques Cinq-Mars, in 1978-79 at the site of Bluefish Caves in the Yukon Territory.  A bone spear point from the Bluefish site was finally radiocarbon dated in the early 1990s to 28,000 y.b.p.  But, Cinq-Mars research was ignored by mainstream anthropologists so he was unable to obtain funding for follow-up research until 2008.  I was actually surprised that so many Canadian finds appear to have been totally omitted from lists of potential pre-Clovis sites, even though core ice sample studies in the late 1970s indicated Arctic ice was only 17,000 years old in areas that could have served as corridors to the North American continent during earlier epochs.

More publicity was awarded to controversial sites in the US where researchers had to focus their dating efforts on contextual remains rather than human artifact samples until Dr. Dennis Jenkins of the University of Oregon recovered human coprolites from a cluster of dry rock caves 150 miles south of Bend, Oregon (USA) in 2002.

Dr. Dennis Jenkins excavating Paisley Caves.
Image courtesy of the University of Oregon.

Throughout most of the first half of the 20th century, coprolites were considered relatively worthless and were usually discarded when found in archaeological excavations.  But in 1946, botanist Eric Callen was asked to search for evidence of maize in human coprolites recovered by archaeologist Junius Bird from a pre-Colombian excavation at Huaca Prieta in the Chicama Valley of Peru. Although Dr. Callen, then a professor of plant pathology at McGill University in Montreal, did not find any maize pathogens in Bird's samples, he became intrigued with the information he did discover and soon switched to archaeology focused exclusively on coprolites.  Needless to say, Dr. Callen, despite his degree from the University of Edinburgh, was ridiculed for what many of his colleagues considered to be bizarre research.  But the importance of knowledge gained from the study of excrement was revealed with advancements in genetic studies in the late 50s and 60s and now Dr. Callen, who unfortunately died prematurely of a heart attack on a dig in 1970, is recognized as the father of human coprolite analysis.   But back to the coprolites in question!

Paisley Caves was not targeted as a potential pre-Clovis site.  In fact, the remote site, plundered by pot hunters in modern times, was first excavated in 1938 by Dr. Luther Cressman, founder of the University's Department of Anthropology and former husband of world-famous anthropologist, Margaret Mead.  Cressman's team trenched caves 1, 2 and 3 of the 8 caves and rockshelters that comprised the site.  They evaluated three stratigraphic levels, examining sediments above Mazama ash, in the ash, and below the ash. (Mount Mazama was a stratovolcano in the Oregon Cascade Range that erupted in approximately 5,677 B.C. with a force estimated at 42 times more powerful than that of Mt.St. Helens in 1980.  Crater Lake, the centerpiece of Crater Lake National Park, is nestled in the remnants of Mazama's caldera.)  They discovered a few human artifacts in apparent association with the remains of extinct late Pleistocene camel, bison, and horses but Cressman's finds were largely ignored because of what was subsequently viewed as a lack of adequate documentation.

Pleistocene mastodon hunt courtesy of Pinterest.

New excavations were launched in 2002.  Dr. Jenkins' team focused on the recovery of in situ bone and cultural materials and photographed all large mammal bones and artifacts found in situ.  They sampled the soil around all specimens thought to be from the Pleistocene era and employed a newer dating method, obsidian hydration, to provide information about the surrounding context.

Although radiocarbon dating has been around since 1949, obsidian hydration as a dating technique was introduced by geologists Irving Friedman and Robert Smith in 1960.  Obsidian hydration is based on the fact that obsidian, a volcanic glass formed by the rapid cooling of silica-rich lava, has a saturation point of 3.5 percent.

Obsidian contains about 0.2 percent water. When a piece of obsidian is fractured, atmospheric water is attracted to the surface and begins to diffuse into the glass. This results in the formation of a water rich hydration rind that increases in depth with time. The hydration process continues until the fresh obsidian surface contains about 3.5 percent water. This is the saturation point. The thickness of the hydration rind can be identified in petrographic thin sections cut normal to the surface and observed under a microscope. Friedman and Smith reasoned that the degree of hydration observed on an obsidian artifact could tell archaeologists how long it had been since that surface was created by a flintknapper. - Chronological Methods 10 - Obsidian Hydration Dating, University of California, Santa Barbara.

Cave 1 yielded sage brush charcoal dated to 8440 y.b.p., human feces dated to 7540 y.b.p, and a basketry fragment, and a few point fragments, the oldest of these artifacts was a butcher-cut artiodactyl (deer, pronghorn, or mountain sheep) rib dated at 11,930 y.b.p.  In Cave 2, charcoal remains were discovered at a depth of more than a meter below the Mazama ash layer and was associated with stone-working debris and tools of various kinds including a short length of sagebrush rope, a wooden peg, a pumice abrader, and scrapers.  The rope returned a radiocarbon date of 12,000 y.b.p. and a butcher-cut sage grouse bone an age of 13,860 y.b.p.

In Cave 5, dense cultural remains were found to depths of a meter and a half below the Mazama ash layer.  Processed sinew and grass fiber thread was unearthed at a little over 1 meter below the ash layer.  The grass fiber thread produced a carbon date of 12,750 y.b.p.

Mural of prehistoric camelids that roamed Oregon in the late .
Pleistocene.  Photographed at the John Day Fossil Beds
Visitors Center by Mary Harrsch.

But the best was yet to come for in Cave 5, remains of prehistoric camelids (camels and llamas) were recovered along with human coprolites in the same layer.  An ankle bone from one of the animals produced a carbon date of 14,290 y.b.p., corresponding to the date produced by the fossilized coprolites.

Samples from the coprolites from Cave 5 were sent to Dr. Eske Willerslev in Copenhagen for DNA analysis.  Dr. Willerslev had developed a new technique to recover DNA from dirt and ice.  When Willerslev successfully extracted DNA from the samples, they were submitted to three labs in Germany and Sweden to obtain independent results.  All three returned dates of approximately 14,300 years ago.  The results were presented at a special conference of prehistoric archaeologists last February and was, for the most part, widely embraced.  But, a cadre of researchers at none other than Dr. Callen's own McGill University questioned some of the methods used to produce the findings recently in a July 2009 issue of Science magazine.  Questions focused primarily on the presence of canine DNA possibly indicating the feces were not human and  possible unidentified sources of contamination, either directly or through leeching  associated with human urine seepage through the cave deposits.   Jenkins and Willersley pointed out that canine and human cohabitation could have occurred at the site so the presence of canine DNA would not be surprising.  But the questions surrounding contamination were more difficult to resolve.

"We were particularly concerned about leeching," explains Dr. Jenkins, "especially since rodent feces comprise almost 80 percent of the excavation material.  But we tested the coprolites for wood rat DNA and found no trace of it.  If there had been no leeching of rodent DNA into the coprolites with their presence in the environment so high, there is little reason to suspect leeching from subsequent human visitations.  Lithic debris was generally found to be very sparse and the proportion of tools to debitage unusually high. This pattern suggests that occupations were generally limited to very brief stays and that the site was not generally a destination camp."

The researchers also evaluated the fecal samples for Native American haplogroups and found both A and B groups associated exclusively with Native American populations.  To remove any doubts about sample contamination from researcher contact, all team members were tested for the presence of Native American haplogroups A and B. None were found in any of the 67 people who had come into contact with the samples during the research process.

Armed with new Bureau of Land Management and National Science Foundation research grants, Dr. Jenkins and his team suited up in full isolation garb in 2008 to recover more coprolites from the Pleistocene aged deposits.  New field workers were again tested for Native American genetic markers.

"We collected over 300 new coprolites bringing our total collection to over 1100," Jenkins exclaims, "We're collecting all coprolites we find whether or not we suspect they are human.  Some may be wolf, or bear, or dog.  But, we feel our chances to find human remains increases each time we find one so we're gathering every one employing stringent collection protocol to protect against contamination of ancient coprolites with modern DNA.  During the excavations we also found a toothed comb-like bone implement that we are very excited about and are anxious to learn its radiocarbon age.  Of course we realize the bone itself could be much older than the point in time it was fashioned into an artifact but we approach each challenge as they come."

Thomas Stafford also visited the site and took numerous samples.  His research firm, based in Boulder, Colorado, will apply revolutionary chemical pre-treatment techniques to finds including the extraction and freeze drying of urine from samples to exclude material seepage that may be impacting radiocarbon dates.

"Artifacts may actually be older than radiocarbon dates indicate if there is contamination from urine produced at a later time," Jenkins explains.  "Such analysis is extremely expensive but results will be that much more precise."

Portrait of Modoc chief Yellow Hammer by
E.A. Burbank, 1901.  Image courtesy of
Wikimedia Commons.

Perhaps the aspect of his research that is the most gratifying to Jenkins is that it is viewed positively by local Native American tribes.  "Members of  The Klamath Tribes (Klamath, Modoc, and Yahooskin Paiute) are enthusiastic supporters of our work here," Jenkins observes, "they are proud of their heritage and thrilled that we've put the little community of Paisley on the world map.  They tell me, 'Dennis, we told you we have been here forever!' You will find even older evidence of our ancestors.'"

After the passage of the Native American Graves Protection and Repatriation Act almost 20 years ago, much of the research on early remains was stopped. Prehistoric remains became bones of contention between archaeologists and tribal members culminating with a court battle that erupted over the posssession of the 9,300 year old Kennewick Man. Now, coprolites are seen as the key to the future study of ancient American population groups.

Jenkins, like Dr. Callen before him, sees enormous potential in his collection of prehistoric poop.  "Once you start digging into these coprolites, you realize you've got data that can't be found anywhere else.  These people weren't just mammoth hunters, they were eating chicken-sized sage grouse, rabbits, and many different kinds of plants!"

Jenkins hopes that between his archaeology and Willerslev's genetic detective work, they may eventually be able to identify genetic links that can be mapped and used to create a more accurate theory about the spread of humans across the Americas.  Who knows, perhaps they will even be able to relieve PaleoIndians of the blame for extinction of America's megafauna too!

Update - After Jenkins initial findings were published in the May 2008 journal Science, another research team led by Ainara Sistiaga, an archaeologist from MIT, analyzed the fossilized excrement and pointed out the material contained too high of percentage of plant material to be excrement from a human.

Sistiaga’s team used gas chromatography and mass spectrometry to scan the scat for types of sterols — fatty molecules found in both plants and animals. When plants are digested, they produce byproducts called phytosterols. Animal tissues, meanwhile, contain cholesterol — which the human body also manufactures on its own — and it, in turn, is metabolized into a compound called coprostanol. 

“Humans, because of their omnivorous diet and their high levels of cholesterol biosynthesis, will always have a predominance of coprostanol, the intestinal product of cholesterol,” Sistiaga said. 

But while coprostanol usually makes up about 60% of the sterols in human droppings, she said, the study finds that nearly 70% of the sterols in the Paisley Cave feces are plant-based. 

“Even in the case of a vegetarian diet — unusual in an Upper Paleolithic society — the cholesterol and coprostanol values are too small to derive from a human,” she [Sistiaga] said. - Blake De Pastino, Western Digs (2013)

The Sistiaga team analyzed the original coprolites found in 2008, though.  In 2012, Jenkins led another team back to Paisley Caves and recovered projectile points, animal bones and more coprolites that dated to 13,200 B.P. - still older than dates the Brazilian team estimated for northern Paleoindians.

If you find all this fascinating and would like to learn even more about early prehistory, I would encourage you to check out Dr. Brian Fagan's course, Human Prehistory and the First Civilizations, available from The Great Courses.

References:

Thompson, H. (n.d.). A DNA Search for the First Americans Links Amazon Groups to Indigenous Australians. Retrieved August 4, 2015, from http://www.smithsonianmag.com/science-nature/dna-search-first-americans-links-amazon-indigenous-australians-180955976/#HKuLwpk60s9BOo5g.01

Neves, W., Prous, A., González-José, R., Kipnis, R., & Powell, J. (n.d.). Early Holocene human skeletal remains from Santana do Riacho, Brazil: Implications for the settlement of the New World.Journal of Human Evolution, 45(2003), 19-42. Retrieved August 4, 2015, from http://www.museunacional.ufrj.br/arqueologia/docs/papers/Prous/nevesprous2003skeletalremains.pdf

A. Sistiaga, F. Berna, R. Laursen, & P. Goldberg (2014). Steroidal biomarker analysis of a 14,000 years old putative human coprolite from Paisley Cave, Oregon Journal of Archaeological Science DOI: 10.1016/j.jas.2013.10.016

M. Thomas P. Gilbert, Dennis L. Jenkins, Anders Götherstrom, Nuria Naveran, Juan J. Sanchez, Michael Hofreiter, Philip Francis Thomsen, Jonas Binladen, Thomas F. G. Higham, Robert M. Yohe II, Robert Parr, Linda Scott Cummings, & Eske Willerslev (2008). DNA from Pre-Clovis Human Coprolites in Oregon, North America Science DOI: 10.1126/science.1154116

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Mysterious burial of fetus with 17th century Danish Bishop

A history resource article by Mary Harrsch © 2015

Although I usually read and write about the study of Egyptian mummies, I received a press release about Lund University's current research on the mummy of it's 17th century founder, Bishop Peder Winstrup and was intrigued when I read that a 5 - 6 mo. old human fetus was found under the Bishop's feet in his coffin.  Apparently the researchers will be conducting DNA testing to see if the child was related to the Bishop.

Peder Winstrup, a bishop and prominent historical figure in Scandinavia, was one of the founding fathers of Lund University. He died in 1679 and was buried in the famous cathedral in Lund a year later. The coffin, together with its contents, constitutes a unique time capsule from the year 1679 with a well-preserved body, textiles and plant material.

Usually the internal organs would have been removed; in this case, however, the body was not embalmed in a traditional manner but simply dried out naturally. The good condition of the body seems to be the result of several factors in combination: constant air flow, the plant material in the coffin, a long period of illness resulting in the body becoming lean, death and burial during the winter months of December‒January and the general climate and temperature conditions in the cathedral.

In December Peder Winstrup underwent a CT scan at the University hospital in Lund. The preliminary results show that the body is relatively well preserved and it was possible to identify most of the internal organs.

The first results show dried fluid and mucus in the sinuses, indicating that Winstrup had been bedridden for a long period before he died. Calcifications in the lung could indicate both tuberculosis and pneumonia. Plaque was also found in the left coronary artery of the heart, the aorta and the carotid artery, indicating that the bishop suffered from atherosclerosis.

“The gall bladder also has several gallstones, which could indicate a high consumption of fatty food”, says Caroline Ahlström Arcini, an osteologist working on the project.

Peder Winstrup, who lived to the age of 74, also suffered from osteoarthritis in both the knee and hip joints. In addition, he had lost a number of teeth. Traces of caries were found in a couple of the remaining teeth, which would indicate that he had access to sugary foods.

“His right shoulder was slightly higher than his left, due to an injury to a tendon in the shoulder. This would have limited Winstrup’s mobility, making it difficult for him to carry out simple everyday tasks such as putting on a shirt or combing his hair with the comb in his right hand”, says Caroline Ahlström Arcini.

Unexpected discovery of a foetus

An unexpected discovery that emerged from the CT scan was a four- or five-month old foetus, well hidden in the coffin under Winstrup’s feet. Nobody knows who put the foetus there.

“You can only speculate as to whether it was one of Winstrup’s next of kin, or whether someone else took the opportunity while preparing the coffin. But we hope to be able to clarify any kinship through a DNA test”, says Per Karsten.

The next step will be investigations into the textiles in the coffin, as well as further study of the body. Tissue samples from the internal organs are to be removed, among other things. In addition, the extensive plant material in the coffin will be investigated.

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Typhus, Typhoid Fever or Avian Influenza? What plague killed the father of the Parthenon?

A history resource article by Mary Harrsch © 2015

Portrait of Pericles 1st century BCE Roman
copy of 5th century BCE Greek original from
Lesbos.  Image courtesy of Wikimedia Commons

Note: this is a crosspost from one of my other history blogs, History's Medical Mysteries.

"Fever, headache, sore throat, and vomiting developed in a 65-year-old man.  He had been in excellent health until approximately 1 week earlier, when he had sudden onset of headache, ocular erythema, and halitosis.  On the third day of illness, he began to sneeze and cough, and noted bilateral pleuritic chest pain.  On the sixth day, he developed projectile vomiting of dark, bilious fluid.  At this time, he complained of fever so intense that he would not allow himself to be covered with even the lightest clothing.  He also complained repeatedly of intense thirst.  Although he drank copious amounts of water, his thirst persisted, worsened by frequent vomiting."

Thus begins a study to determine what may have caused the death of the famous Athenian stateman, Pericles, as a clinical exercise at a 2000 clinical pathologists' conference at the University of Maryland School of Medicine. Each year, a team of practicing pathologists and historical consultants select a famous individual from the past whose manner of death remains speculative and attempts to derive a definitive cause of death.

The death of Pericles is examined by Drs. David T. Durack, MD, Robert J. Littman, PhD, R. Michael Benitez, MD and Philip K. Mackowiak, MD. Their paper, Hellenic Holocaust: A Historical Clinico-Pathologic Conference was published in the American Journal of Medicine in 2000 (Volume 109: pages 391-397).

Phidias showing the Parthenon frieze to Pericles, Aspasia, Alcibiades and Friends
by Sir Lawrence Alma-Tadema, 1868.  Image courtesy of Wikimedia Commons.

Thucydides reported that desperate patients racked with thirst and fever plunged into cisterns and wells seeking relief. Of the few survivors, some lost fingers and toes from peripheral gangrene, others suffered blindness, and there were also reports of survivors experiencing a complete loss of memory.

Bust of the Greek general and
historian, Thucydides at the
Royal Ontario Museum.  Image
courtesy of Wikimedia Commons.

Research indicates the disease originated in Africa then spread to the Persian Empire and ultimately to a beseiged Athens via the port of Piraeus where it attacked a population of almost 400,000 condensed into 4 square miles. But which variety of plague was it?

What do the experts say? (PDF of original article reprinted with permission)

Update: In 2006, a research group led by Manolis Papagrigorakis of the University of Athens extracted pathogen DNA from three teeth recovered from skeletal remains found in the ancient necropolis of Kerameikos dated to approximately 430 BCE and assumed to be victims of the great plague.  The only pathogen Papagrigorakis and his team could identify was a strain resembling Salmonella enterica serovar Typhi (typhoid fever).  Papagrigorakis' report that appeared in May 2006 in Volume 10, Issue 3, Pages 206–214 of the International Journal of Infectious Diseases entitled DNA examination of ancient dental pulp incriminates typhoid fever as a probable cause of the Plague of Athens (full text) was immediately refuted by Beth Shapiro and Andrew Rambaut of the Henry Wellcome Ancient Biomolecules Centre at Oxford University as well as M. Thomas P. Gilbert of the Niels Bohr and Biological Institutes, University of Copenhagen in a letter (full text) to the same journal.

Shapiro points out, "The authors’ diagnosis is based on a similarity score, resulting from BLAST comparisons between their amplified fragments and published sequences. Specifically, the authors report a 7% divergence between their sequences and S. enterica serovar Typhi, and 8% divergence between their sequence and the next most closely-related Salmonella strain, S. typhimurium. Based on the closer match to S. enterica, the authors conclude that ‘‘[if] another, yet unknown pathogen... was the actual cause of the Plague of Athens, it would have to be closely related to S. enterica and definitely closer than S. typhimurium.’’

Greek warriors depicted on a 5th century BCE gravestone.
Permanent collection of the British Museum.
Photographed by Mary Harrsch © 2012

"This statement, however, is simply not true. Although the Athens sequence is indeed slightly more similar to S. enterica, the two cited Salmonella species are actually much more closely related to each other, with less than 1% divergence for the sequenced gene. In fact, if a simple phylogenetic analysis is performed, the ancient sequence is shown to fall outside both S. enterica and S. typhimurium, as well as several other Salmonella species (Figure 1). While this analysis confirms that the Athens sequence is possibly Salmonella, it demonstrates clearly that it is not typhoid (97% bootstrap value). Based on the evolutionary timescale inferred for Salmonella and E. coli, the Athens sequence and typhoid would have shared a common ancestor in the order of millions of years ago."

Then, in 2013, a thesis, entitled A novel offering of Avian Influenza as the causative agent of the Plague of Athens: contextual and paleopathological analysis of the 5th century BCE Plague of Athens via primary resources and modern DNA sequence-based identification strategies of dental pulp from a mass grave at Kerameikos, was published by Karen Spence.  Although Spence was less critical of the Papagrigorakis team's conclusions, she pointed out that the sequencing procedure used would not have identified any RNA-based pathogens.  She acknowledged the Maryland pathologists' conclusions that human-to-human communicated influenza would not have had a high enough mortality rate to be a good match for the Athens pathogen (which had an estimated mortality rate of 25%).  But, she proposes that zoonotic avian influenza passed from domestic poultry to humans would have.  Spence points out that when refugees from the surrounding countryside flooded into Athens, they probably brought smaller animals with them like pigs and chickens.  She proposes that some of the poultry were carriers and quickly infected other birds in the confined quarters.  The animals then passed the disease to their human caregivers.  Birds often carry the pathogen without succumbing to the disease themselves.  Even if some of the birds died, they were probably eaten, due to the conditions of the siege.  She postulates that an infected reservoir of birds would have retained the pathogen over a long period of time accounting for several years of plague rather than a flare up that would quickly die down as in the case of human-to-human transmitted influenza.

Roman mosaic of doves drinking from a bowl from 2nd century BCE
Greek original by Sosos recovered from Pompeii.
Photographed at the Capitoline Museum in Rome, Italy by Mary Harrsch
© 2009 

Although Spence makes a convincing case, she indicates in her table comparing symptoms of  the Athenian plague with Typhoid Fever and Avian Flu that neither pathogen usually results in the survivor pathologies described by Thucydides.  It is the survivor pathologies that are carefully addressed by the Maryland pathologists in their conclusion that the most likely causative pathogen was typhus and why I find the Maryland analysis most convincing.

Since avian flu cannot be transmitted from human to human, I was also skeptical that Pericles, a wealthy statesman, would have had contact with chickens, other than to eat one.  Likewise, I would doubt his household steward would resort to obtaining a dead chicken from a lower class meat market that may have procured diseased carcasses. I also question why the disease would first appear in Piraeus, the port, as most refugees came from the surrounding countryside. The affliction was also reported as previously occurring in Ethiopia and Persia.  Neither location suffered from siege concentrations where poultry may have been in particularly close contact with humans.

Of course there is the possibility the besieged Athenians imported poultry as a protein food source since they no longer had access to cattle that were left behind in the fields. But it is more likely that being a seafaring people, they would have relied upon fish instead.

However, I appreciated the comparative table Spense uses to clearly demonstrate typhoid fever's lack of many of the attributes of the plague described by Thucydides.  I would have liked to have seen such a table covering all 29 pathogens that have been proposed over the last 150 years of study.

In my research I also found an interesting article about new DNA extraction techniques developed in just the last five years that were used on victims of the Justinian plague at the Ancient DNA Centre of McMaster University in Hamilton, Canada.  It made me wonder if the new method would be more successful with the Athenian samples.  I would also like to see an attempt made specifically on adult females from the Kerameikos remains. Thucydides recorded that caregivers suffered an extremely high rate of infection and mortality and in ancient Athens, as today, most caregivers would have been female. There did not seem to be any reference to gender in the Papagrigorakis report. If gender was not considered I think this could be a significant barrier to more conclusive results.

The idealized Spartan warrior, Leonidas
Image courtesy of Wikimedia Commons.  Edited by Mary Harrsch.

At the time of the plague, Athens was besieged by Sparta and male corpses from the ongoing conflict could have been included in the mass burial. Some historians would disagree on this point because death in battle would have a significant element of honor involved and mass burial of such individuals would have been particularly impious. But, a community in the grip of a severe plague where there were large accumulations of unburied corpses and a shortage of able bodied men to dispose of corpses, could have resorted to mass burial of at least some war casualties.  Thucydides said the population of Athens was so morally distressed by the plague that funerary rituals were "universally violated" (History of the Peloponnesian War - 2.52.3) - clearly supporting the possibility of mass burial, even of war casualties. Also, the Papagrigorakis study was conducted on only three teeth from randomly chosen victims apparently without regard to gender.  I would feel much more confident in the results if more victims were sampled.

Of course, we cannot even be sure the mass burial at Kerameikos was even a result of the so-called Athenian plague. Although excavators dated the burial fairly precisely to 430 - 426 BCE, dating methodologies are not so precise. The burial could be from an epidemic occurring before, concurrent with, or after the plague onset. The crowded siege conditions could have easily resulted in several concurrent diseases that would not necessarily include the pathogen responsible for the symptoms reported by Thucydides and observed in Pericles.

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Wreck from Ming Treasure Fleet Sought Off Kenya Coast

A Model of a 15th century Ming Dynasty Treasure Ship
dwarfs models of Columbus' Santa Maria and the later
clipper ship Cutty Sark built with the same scale. 
Photographed at the Ventura County (CA) Maritime Museum
by Mary Harrsch.

In a joint project of the National Museum of Kenya and Peking University, a team of 11 Chinese archaeologists will begin a £2m joint project to explore the Kenyan communities of  Lamu and Malindi for evidence of commerce with China dating back to the early 15th century.  Chinese marine archaeologists will also search for a rumored ancient ship wreck offshore.

"The sunken ship is believed to have been part of a mighty armada commanded by Ming dynasty admiral Zheng He, who reached Malindi in 1418. According to Kenyan lore, reportedly backed by recent DNA testing, a handful of survivors swum ashore. After killing a python that had been plaguing a village, they were allowed to stay and marry local women, creating a community of African-Chinese whose descendants still live in the area." - More: guardian.co.uk

Like many people (including many Chinese), I had never heard of this adventurous 7-foot-tall Chinese admiral before I read a fascinating article about his explorations in National Geographic in 2005 when the Chinese were celebrating the 600th anniversary of his voyages.  More and more evidence of the extent of his explorations continues to come to light and there is even speculation he reached the western shores of North America and/or South America, most notably in extremely controversial books published by retired British submarine commander, Gavin Menzies entitled 1421: The Year China Discovered the World and 1434: The Year a Magnificent Chinese Fleet Sailed to Italy and Ignited the Renaissance.

Chinese scientists have conducted DNA tests on Swahili inhabitants of Siyu village in Africa that indicated the people there had traces of Chinese ancestry thereby documenting the African connection.  Whether evidence that Zheng He ventured as far east as he did west remains to be seen.  It will be exciting, though, if they can find one of the actual ships that was part of Zheng He's fleet.

A couple of months ago I visited the Ventura County Maritime Museum down in Ventura, California and there I saw a scale model of a Ming treasure ship like those in Zheng He's fleet.  Beside the model were models built in the same scale of Christopher Columbus' ship the Santa Maria and the later clipper ship, "Cutty Sark" and they were tiny compared to the massive Chinese vessel.

When I read the National Geographic article, I was intrigued by the man himself as well.  Zheng He was born into a Muslim family in Kunyang in Yunnan province in 1371 C.E.  His father was descended from a Persian administrator of the Mongol Empire who was appointed governor of Yunnan during the early Yuan Dynasty.


In 1381 C.E. the Ming army attacked Kunyang and eleven year-old Zheng He, then called Ma He, was captured, castrated and sent to the Imperial Court.  His father was executed.  Yet, despite the murder of his father and his own mutilation, Zheng He, who still grew to towering height of 7 feet-tall, became a trusted adviser of the Yongle Emperor (r. 1403-1424) after Zheng He helped to overthrow the Jianwen Emperor.

National Geographic produced an excellent video about Zheng He and his voyages that I found on YouTube.  It is divided into ten parts.  As each video nears the end of its 9+minutes a link appears in the lower right hand corner to click to access the next part:



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