Bubonic Plague In China

Summary

Modern genetic techniques and assimilation of global historical accounts have revealed that the Black Plague that devastated Europe in the Middle Ages, originated in Asia and arrived via the Silk Road trade route.  To recap some key dates (all in the current era):

* Yuan Empire, China 1331
* Hebei Province, China 1334 (the province that surround the Beijing province in northern coastal China)
* Persia 1335
* Kyrgyzstan 1338-1339
* Kaffa, Crimea 1344
* Syria 1345-1348
* Mecca, Saudi Arabia 1349

Kublai Khan's Yuan Empire with a capitol in Beijing, included by 1294 CE, all of modern China except the Tarim Basin, all of Mongolia and Korea, and some of the adjacent territory in what is now Russia to the North of Mongolia and Manchuria. The Yuan Dynasty extended from 1271 CE to 1368 CE, not quite a century, and not long after the plague ravaged China. (The long lived Ming Dynasty originating in Southern China followed the Yuan Dynasty).

Analysis

The role of the expanding plague and the depopulation and chaos left behind in its wake also makes the rapid expansion of the Mongolian Empire resemble much more closely than is commonly realized, the expansion of European conquest in the New World following the arrival of Columbus, and small pox, in 1492 CE. The Golden Horde may have accumulated plague immunity by the time it reached Europe.

The backdrop of the plague also helps explain the population genetic impact of the Mongol Dynasty in Asia, since it swept into a population bottleneck that subsequently expanded. And, it explains the fall of the Yuan Dynasty in China itself.

Sources

According to one not particularly reliable source, which I nonetheless have no particular reason to doubt:

Many scholars believe that the Black Death began in north-western China, while others cite south-western China or the steppes of Central Asia. We do know that in 1331, an outbreak erupted in the Yuan Empire; it may have hastened the end of Mongol rule over China. In 1334, this disease killed 5 million people in Hebei Province - about 90% of the population.  As of 1200, China had a total population of more than 120 million, but a 1393 census found only 65 million Chinese surviving. Some of that missing population was killed by famine and upheaval in the transition from Yuan to Ming rule, but many millions died of bubonic plague.

From its origin at the eastern end of the Silk Road, the Black Death rode trade routes west. At Central Asian caravanseries and Middle Eastern trade centers, it infected people all across Asia. . . .

Ibn al-Wardi, a Syrian writer who would later die of the plague himself in 1348, recorded that the Black Death came out of "The land of Darkness" (Central Asia). From there, it spread to China, India, the Caspian Sea and "land of the Uzbeks," and thence to Persia and the Mediterranean.  The Egyptian scholar Al-Mazriqi noted that "more than three hundred tribes all perished without apparent reason in their summer and winter encampments, in the course of pasturing their flocks and during their seasonal migration." He claimed that all of Asia was depopulated, as far as the Korean Peninsula. (Orent, 106)

The Central Asian scourge struck Persia just a few years after it appeared in China - proof, if any is needed, that the Silk Road was a convenient route of transmission for the deadly bacterium.  In 1335, the Il-Khan (Mongol) ruler of Persia and the Middle East, Abu Said, died of bubonic plague during a war with his northern cousins, the Golden Horde. This signaled the beginning of the end for Mongol rule in the region.  An estimated 30% of Persia's people died of the plague in the mid-14th century. The region's population was slow to recover, in part due to the political disruptions caused by the fall of Mongol rule and the later invasions of Timur (Tamerlane).

Archaeological excavations on the shores of Issyk Kul, a lake in what is now Kyrgyzstan, reveal that the Nestorian Christian trading community there was ravaged by bubonic plague in 1338-39. Issyk Kul was a major Silk Road depot, and has sometimes been cited as the origin point for the Black Death. It certainly is prime habitat for marmots, which are known to carry a virulent form of the plague.  It seems more likely, however, that traders from further east brought diseased fleas with them to the shores of Issyk Kul. Whatever the case, this tiny settlement's death rate shot up from a 150-year average of about 4 people per year, to more than 100 dead in 1338-39. 

Although specific numbers and anecdotes are hard to come by, different chronicles note that Central Asian cities like Talas, in modern-day Kyrgyzstan; Sarai, the capital of the Golden Horde in Russia; and Samarkand, now in Uzbekistan, all suffered outbreaks of the Black Death. It is likely that each population center would have lost at least 40% of its citizens, with some areas reaching death tolls as high as 70%. 

In 1344, the Golden Horde decided to recapture the Crimean port city of Kaffa from the Genoese, Italian traders who had taken the town in the late 1200s. The Mongols under Jani Beg instituted a siege, which lasted until 1347, when reinforcements from further east brought the plague to the Mongol lines.

An Italian lawyer, Gabriele de Mussis, recorded what happened next: "The whole army was affected by a disease which overran the Tartars [Mongols] and killed thousands upon thousands every day." He goes on to charge that the Mongol leader "ordered corpses to be placed in catapults and lobbed into the city in hopes that the intolerable stench would kill everyone inside."

This incident is often cited as the first instance of biological warfare in history. However, other contemporary chroniclers make no mention of the putative Black Death catapults. A French churchman, Gilles li Muisis, notes that a "calamitous disease befell the Tartar army, and the mortality was so great and widespread that scarcely one in twenty of them remained alive." However, he depicts the Mongol survivors as surprised when the Christians in Kaffa also came down with the disease.

Regardless of how it played out in fact, the Golden Horde's siege of Kaffa certainly did drive refugees to flee on ships, bound for Genoa. These refugees likely were a primary source of the Black Death that went on to decimate Europe.

European observers were fascinated but not too worried when the Black Death struck the western rim of Central Asia and the Middle East. One recorded that "India was depopulated; Tartary, Mesopotamia, Syria, Armenia were covered with dead bodies; the Kurds fled in vain to the mountains." However, they would soon become participants rather than observers in the world's worst pandemic.

In "The Travels of Ibn Battuta," the great traveler noted that as of 1345, "the number that died daily in Damascus [Syria] had been two thousand," but the people were able to defeat the plague through prayer. In 1349, the holy city of Mecca was hit by the plague, likely brought in by infected pilgrims on the hajj.

The Moroccan historian Ibn Khaldun, whose parents died of the plague, wrote about the outbreak this way: 

Civilization both in the East and the West was visited by a destructive plague which devastated nations and caused populations to vanish. It swallowed up many of the good things of civilization and wiped them out... Civilization decreased with the decrease of mankind. Cities and buildings were laid waste, roads and way signs were obliterated, settlements and mansions became empty, dynasties and tribes grew weak. The entire inhabited world changed.

This source cites, as its sources:

* Benedictow, Ole Jorgen. The Black Death, 1346-1353: The Complete History (2004).
* Marshall, Robert. Storm from the East: From Ghengis Khan to Khubilai Khan (1993).
* McNeill, William Hardy. Plagues and People (1976).
* Orent, Wendy. Plague: The Mysterious Past and Terrifying Future of the World's Most Dangerous Disease (2004).

Wikipedia cites:

* As evidence of the genetic origin of the plague in China, Nicholas Wade (31 October 2010). "Europe’s Plagues Came From China, Study Finds". The New York Times. Retrieved 1 November 2010. This report was actually based upon: G. Morelli et al. (2010) Nature Genetics. December; 42 (12):1140-1143. doi:10.1038/ng.705.

* Regarding the Lake Issyk Kul outbreak in Kyrgizstan, Raoult; Drancourt (2008). Paleomicrobiology: Past Human Infections. Springer. p. 152.

* The Cambridge History of China: Alien regimes and border states, 907–1368, p.585 for the proposition ("In the 1330s a large number of natural disasters and plagues led to widespread famine, starting in 1331, with a deadly plague arriving soon after."), and

* Kohn, George C. (2008). Encyclopedia of plague and pestilence: from ancient times to the present. Infobase Publishing. p. 31. ISBN 0-8160-6935-2, as evidence of an early Chinese outbreak ("The 14th-century plague killed an estimated 25 million Chinese and other Asians during the 15 years before it reached Constantinople in 1347.", i.e. from 1332-1347 CE).

* But, Wikipedia notes the lack of a clear medical description of the bubonic plague in China until 1644, relying on Sussman GD (2011). "Was the black death in India and China?". Bulletin of the history of medicine 85 (3): 319–55. doi:10.1353/bhm.2011.0054. PMID 22080795.

There is another Wikipedia article here that specifically addresses the migration of the Black Plague.  It cites regarding the Chinese Outbreak:

* McNeill, William H. (1976). Plagues and People. New York: Anchor Books. ISBN 0-385-12122-9.

The Collapse of Harappan Civilization Marked By Leprosy, TB and Violence

Indus River Valley civilization cities like Harappa grew from about 2200 BCE to 1900 BCE, only to suffer a collapse that brought down the civilization.  New archaeological studies point to infectious diseases like leprosy and tuberculosis, an arid climate change shift and interpersonal violence often marked by crushed skulls as characteristic of its final days.

Robbins Schug's research shows that leprosy appeared at Harappa during the urban phase of the Indus Civilization, and its prevalence significantly increased through time. New diseases, such as tuberculosis, also appear in the Late Harappan or post-urban phase burials. Violent injury such as cranial trauma also increases through time, a finding that is remarkable, she said, given that evidence for violence is very rare in prehistoric South Asian sites generally.

"As the environment changed, the exchange network became increasingly incoherent. When you combine that with social changes and this particular cultural context, it all worked together to create a situation that became untenable," she said. 

The results of the study are striking, according to Robbins Schug, because violence and disease increased through time, with the highest rates found as the human population was abandoning the cities. However, an even more interesting result is that individuals who were excluded from the city's formal cemeteries had the highest rates of violence and disease. In a small ossuary southeast of the city, men, women, and children were interred in a small pit. The rate of violence in this sample was 50 percent for the 10 crania preserved, and more than 20 percent of these individuals demonstrated evidence of infection with leprosy.

Evidence of class divides and violent deaths are in strong contrast to relatively egalitarian and peaceful earlier periods of the Indus River Valley civilization, suggesting that its high culture's desirable features were unable to sustain themselves in the face of the pressures created by a prolonged and severe drought.

The study also notes that the expanding scope of Harappan trade brought more infectious agents in touch with its urban areas.

The underlying article which is the source for the brief review above has a very rich and generally well supported context for the finds such as the following (citations omitted):

The Harappan Civilization developed in the context of a semi-arid climate that was pervasive in South Asia for the latter half of the Holocene. Since it was first proposed as a factor in the demise of the Indus Civilization, debates about the role of climate and environmental changes have raged on but it has become increasingly clear that by 2800 B.C., aridity levels in the Indus Valley were broadly similar to contemporary levels until a period of destabilized environment—fluctuating rainfall, increased seasonality, and accelerate channel migration—began in the Indus Valley after 2000 B.C. From 2200-1700 B.C., a significant rapid climate change event in South Asia saw disruptions in monsoon rainfall and significant changes in fluvial dynamics along the Indus Rivers, including the Beas River. 

Increasing aridity initially occurred in the context of a flourishing interaction sphere that spanned West and South Asia in the third millennium B.C. Historical records from Mesopotamia describe regular trade with ‘Meluhha’ (the Indus Valley) from 2400-2000 B.C. Harappans manufactured etched, biconical carnelian beads, shell, faience and steatite ornaments, ivory, copper, and ceramic items, cotton, silk, jute, cloth, barley, oil and other perishables. Exports focused on raw materials for these products, items which have been recovered from sites around the Persian Gulf region; Harappan seals have also been recovered; and cylindrical seals resembling those from Mesopotamia have been recovered at Indus urban centers as well.
Participation in the interaction sphere facilitated a period of rapid urbanization at the city of Harappa, creating a dense and heterogeneous population in the ancient city. Cities are political, economic, and ceremonial centers that can offer opportunities unavailable in the hinterlands. Technology, production, and consumption transformed Indus society, particularly in period IIIC, when population growth was at its fastest rate: high levels of immigration disrupted the formerly organized settlement pattern; houses in the core areas of the city spilled over onto the streets and ‘suburban’ areas sprang up on low mounds to the west and northwest of the city center. 

After 1900 B.C., in the Late Harappan phase, population density was diminished and settlement focused largely in the core areas of the city. Declining sanitation conditions and an increasingly disorganized settlement plan indicate disruptions to authority were systemic. Disruptions in the exchange network also occurred after 2000 B.C. at a time when West Asian trading partners were responding to their own rapid climate change event. At this point, Magan and Dilmun are mentioned more frequently in Mesopotamian writings while references to Meluhha largely disappear and material evidence of trade interactions declines. Large-scale depopulation of Indus cities in the Late Harappan phase weakened Indus society. Late Harappan settlements flourished in Gujarat and Rajasthan while only a handful of settlements remained occupied in the Beas River Valley.

These finds include those from Cemetery H, which corroborates and dates a transition in funerary practices closely associated with the appearance of Indo-Europeans in the region that is mentioned in early Rig Vedic materials, which are some of the earliest written materials from the region.

Ultimate source: Gwen Robbins Schug, K. Elaine Blevins, Brett Cox, Kelsey Gray, V. Mushrif-Tripathy. Infection, Disease, and Biosocial Processes at the End of the Indus CivilizationPLoS ONE, 2013; 8 (12): e84814 DOI:10.1371/journal.pone.0084814

Why Did Asians Become Asian?

Razib, at Gene Expression has an interesting post on a gene that shows strong signs of selective pressure in East Asia prior to the migration of the founding population of the Americas called EDAR based on a paper published in Cell, Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant. 

Razib notes that the authors of the Cell paper fail to make a convincing argument for what selective pressure was involved.  Neither their climate adaptation theory, nor their sexual selection for small breast and lusterous black hair theory withstand serious scrutiny.  I advance another hypothesis which I believe is a more convincing explanation for this selective swep and another striking East Asian racial type defining mutation (low levels of body hair), although it is a hypothesis to be tested rather than a proven theory.

The Selective Sweep At The EDAR Locus Was A Protective Response To Bubonic Plague.

My hypothesis is that the EDAR gene and low levels of body hair were protective against flea carried bubonic plague, an extremely lethal disease with its origins in China.  This disease became a powerful selective pressure in East Asia when the domestication of dogs provided a vector for this flea borne disease in human communities. 

These communities also became more vulnerable to the plague because their transition to behavioral modernity in the Upper Paleolithic revolution led to the formation of semi-sedentary communities who fished and hunted other coastal animals, and this in connection with the advantage conferred on them by domesticating dogs allowed them to live in villages with population densities sufficient to sustain plague outbreaks.

The communities of semi-sedentary fishing and foraging villages with domesticated dogs where the bubonic plague outbreaks began were probably similar in diet and social organization to those of the early Jomon people of Japan, the Comb Ceramic and Pitted Ware people of Northeast Europe, the Paleo-Eskimos of Greenland, the Inuit and the Native Americans of the Pacific Northwest. 

The mass deaths in Inuit communities from exposure to diseases carried by Basque whalers who were their first contact with Europeans supports the hypothesis that these communities had sufficient population density and intercommunity trade links to sustain a major outbreak of bubonic plague without causing it to fizzle out by killing people before the disease could be spread.

Bubonic plague acts on the lymph system.  The derived EDAR allelle might have been protective because lymph nodes are warehouses for the immune system, so a higher frequency of lymph nodes would strengthen immune response, and because small breasts would have reduced the volume of vulnerable plague targeted lymph tissue there making women with smaller breasts more likely to survive a plague infection. 

The hair type phenotype associated with the derived EDAR allelle, and also one or more other allelles coding phenotypes for low levels of body hair which are a racial type defining East Asian allelle, may have reduced the vulnerability of people with this phenotype to infection with the plague's flea vector.

Other hard selective sweeps on allelles that confer resistence to diseases, are documented in recent human evolution (e.g. malaria), and hard sweep on the genes for lactose persistence can to some extent also be seen as genes enhancing immune capacity via better nutrition.  So the hypothesis that EDAR conferred selective fitness by conferring disease resistence is a plausible one. 

But, since the timing of the EDAR selective sweep was clearly too early for it to be driven by the Neolithic revolution, and very low population density terrestrial hunter-gatherer populations who moved very slowly before horses were domesticated are ill suited to harboring infectious disease outbreaks which tend to quickly run their couse and fizzle out, they must have arisen in more tightly tied, higher population density communities. 

Upper Paleolithic fishing villages whose prosperity is also enhanced by the use of domesticated dogs could account would have had nearly Neolithic population densities.  Their use of domesticated dogs would simultaneously provide a bubonic plague flea vector in a community where the rat vector of the bubonic plague flea Middle Ages was not available (since there were no large human grain stores for the rats to plunder) and explain why this happened 30,000 years ago around the time that the dog was domesticated, rather than at some earlier or later point in prehistory.

The hypothesis that EDAR conferred resistence in particular to bubonic plague rather than some other disease is driven by the particularized importance of the lymph system that the derived EDAR allelle appears to enhance to bubonic plague in particular relative to other lethal infectious diseases.

Why Don't Finns and Russians Have The Derived EDAR Allelle?

How do I explain the absence of the derived EDAR allelle in Northeast European populations who show clear genetic signs of East Eurasian genetic contributions, probably through linguistically Uralic populations distingished by the Y-DNA haplogroup N which is a sister clade to the dominant Asian Y-DNA haplogroup O?

The Last Glacial Maximum sterilized Northern Asia, killing off the plague and killing or exiling all of its modern humans.  North Asia was repopulated from one or more genetically East Eurasian refugia, probably including Tibet and the Altai Mountains, that had become isolated from coastal China before the selective sweep took place ca. 30,000 years ago in response to a series of bubonic plague outbreaks.

These refugia included the place of origin in North Asia of Y-DNA haplogroup N whose population did not undergo the selective sweep for the derived EDAR allelle that coastal villages in China from which this mutation expanded did, perhaps because these nomadic terrestrial hunter-gatherers lacked the relatively high population densities in semi-sedentary villages of the fishing people in which this mutation arose, or perhaps because the colder climate there was protective.

Even if the derived EDAR allelle was present in low frequencies in the North Asians who repopulated North Asia, genetic drift and founder effects could have purged it from the populations who made East Eurasian genetic contributions to Northeastern Europeans, because the derived EDAR allelle was not actively conferring selective advantage in either the tundras of Siberia or in Europe, where bubonic plague did not arrive until the 14th century from a Chinese source via Siberia's Southern fringe.

The story of Y-DNA haplogroup N securing its current distribution in a counterclockwise expansion from Southeast Asia is wrong according to this hypothesis.  Instead, haplogroup N subsequently introgressed into the Han Chinese population before or in the early phases of the East Asian Neolithic revolution and expanded with its rice and millet farmers, all of the way to to South Asia where Munda rice farmers carried its most far flung extension.

Later North Asian populations acquired the ubiquitous EDAR allelle from their expanding Han Chinese neighbors to the South who in the Neolithic era that followed the East Eurasian genetic introgression into Northeast Europe, brought higher density settlements that were subject to EDAR alllelle selective pressures associated with the periodic plague outbreaks that followed Han Chinese trade routes into North Asia.

Caveats.

The biggest gap in this theory is that I have no idea whether the derived EDAR alllele (or the derived allelle for low levels of body hair found in East Asians) would have indeed been protective against death from bubonic plague.  But, this is something that should be relatively easy to examine once the question is well posed.  If it isn't protective, we need to find out what the gene did that did confer selective advantage, because neither the climate conditions theory, nor the small breast fashion fad theory make sense to explain such a powerful selective sweep.

DNA phylogeny evidence already in print should be able to establish whether the hypothesis regarding the Northeast European infusion of East Eurasian DNA is consistent with the evidence.