More Evidence of plague in LN/BA steppe populations

Angela

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This time it's in Europe, not Central Asia.

See:
http://biorxiv.org/content/early/2016/12/15/094243

"Molecular signatures of Yersinia pestis were recently identified in prehistoric Eurasian individuals, thus suggesting Y. pestis might have caused some form of plague in humans prior to the first historically documented pandemic. Here, we present four new Y. pestis genomes from the European Late Neolithic and Bronze Age (LNBA) dating from 4,500 to 3,700 BP. We show that all currently investigated LNBA strains form a single genetic clade in the Y. pestis phylogeny that appears to be extinct today. Interpreting our data within the context of recent ancient human genomic evidence, which suggests an increase in human mobility during the LNBA, we propose a possible scenario for the spread of Y. pestis during the LNBA: Y. pestis may have entered Europe from Central Eurasia during an expansion of steppe pastoralists, possibly persisted within Europe until the mid Bronze Age, and moved back towards Central Eurasia in subsequent human population movements."

"it is assumed that
plague affected human populations in three pandemic waves. The first, the Plague of Justinian,starting in the 6th century AD, was followed by multiple epidemic outbreaks in Europe and theMediterranean basin, and has been associated with the weakening and decay of the Byzantineempire (Russell, 1968). The second plague pandemic first struck in the 14th century with theinfamous ‘Black Death’ (1347-1352), which again spread from Asia to Europe seemingly alongboth land and maritime routes (Zietz and Dunkelberg, 2004). It is estimated that this initialonslaught killed 50% of the European population (Benedictow, 2004). It was followed byoutbreaks of varying intensity that lasted until the late eighteenth century (Cohn JR, 2008). Themost recent plague pandemic started in the 19th century and began in the Yunnan province ofChina. It reached Hong Kong by 1894 and followed global trade routes to achieve a nearworldwide distribution (Stenseth et al., 2008). Since then plague has persisted in rodentpopulations in many areas of the world and continues to cause both isolated human cases andlocal epidemics."

"Our perception of the evolutionary history of Y. pestis was changed substantially by arecent report of two reconstructed genomes from Central Asian Bronze Age steppenomads/pastoralists (~4,729 cal BP and ~3,635 cal BP, respectively) and molecular Y. pestissignatures in an additional five individuals from Eurasia (~4,500 to 2,800 BP) suggesting thepresence of plague in human populations over a diffuse geographic range prior to the firsthistorically recorded pandemics. Phylogenetic analysis of the two reconstructed Y. pestisgenomes from the Altai region shows that they occupy a phylogenetic position ancestral to allmedieval and extant Y. pestis strains, though this branch was not adequately resolved."

"In our dataset we identified four strong positives from three different locations datingfrom the Late Neolithic to the Early Bronze Age: one sample from the Lithuanian site Gyvakarai(Gyvakarai1), one sample from the Estonian site Kunila (KunilaII) and two samples fromAugsburg, Germany."

"The four prehistoric genomes presented here are the first complete Y. pestis genomes from theLate Neolithic and Bronze Age in Europe. They form a distinct clade with the previouslyreconstructed Central Asian Bronze Age Y. pestis genomes, confirming that all Late Neolithicand Bronze Age genomes reconstructed so far originated from a common ancestor. The oldestgenome RISE509 (Rasmussen et al., 2015) occupies the most basal position of all Y. pestis."

From a later period, but you get the idea:
the-triumph-of-death-by-pieter-bruegel-the-elder-16th-century-oil-on-picture-id450085209


Well, that about seals the deal for me. No wonder it didn't matter that Corded Ware had no bronze weapons until the very end, and barely even any copper.


Maybe by the time they crossed the Alps most of it had burned out?
 
The oldestgenome RISE509 (Rasmussen et al., 2015) occupies the most basal position of all Y. pestis."
Rise 509 is Sintashta 2100 BC, right? That's after Corded Ware expansion and are away geographically. So, we can't really blame Yersinia Pestis for being a secret weapon of IEs going deep into Europe.
 
the European neolithic population collapsed earlier, some 5.5 ka
strangely, that is about the time the wheel was invented which should have brought progress

ncomms3486-f2.jpg

http://www.nature.com/articles/ncomms3486

could it be that the genomes in the study were the first onces who had build up resistence against this early form of pestis?
 
The Black Death needs rats to propagate (with its fleas) to propagate, as from human to human is not usual: once the pest kills all rats, the fleas migrate to the dogs, once done, they jump to humans, so it's a kind of city pest, as rats have its "ecosystem" in the markets and in the trash. I don't think it's an "IE plague" but a consequence of the develoment of unplanified urban life.

The picture is that of "The Triumph of Death", by Bruegel (XVI Century), so the author didn't saw the Black Death; he was just painting how the death is for all, no matter if farmer or king.
 
Rise 505, according to the authors, is the youngest sample, and derives from a back migration of the plague from Europe east. Still, Le Broc, you're right, these particular samples are from after the initial movements of steppe people into Europe. However, this is what the authors have to say:

"1. The first scenario assumes that plague was introduced multiple times to Europe from a common reservoir between 5,000 to 3,000 BP. Here, the bacterium would have been spread independently from a source, most likely located in Central Eurasia, to Europe at least four times during a period of over 1,000 years (Figure 1), travelling once to Lithuania, once to Estonia, and two times to Southern Germany.

2. The second scenario assumes that plague entered Europe once, established a reservoir within or close to Europe from which plague circulated, and then moved back to Central Eurasia and the Altai region/East Asia during the Bronze Age (Figure 1). This hypothesis of persistence mirrors that which has been proposed to explain the presence of plague in Europe during the notorious second pandemic (Spyrou et al., 2016)."

"With these few genomes available it is difficult to disentangle the two hypotheses; however, interpreting our data in the context of what is known from human genetics and archaeological data can offer some resolution. Ancient human genomic data point to a change in mobility and a massive expansion of people from the Caspian-Pontic Steppe related to individuals associated with the ‘Yamnaya’ complex, both to the East and the West starting around 4,800 BP."

"The first indication of plague in Europe is found in the Baltic region and coincides with the time of the arrival of the steppe component (Allentoft et al., 2015)."

"The two Late Neolithic Y. pestis genomes from the Baltic in this study were reconstructed from individuals associated with the Corded Ware Complex (Gyvakarai1 and KunilaII). The Baltic Y. pestis genomes are genetically derived from the strain that was found in the ‘Andronovo Complex’ from the Altai region, suggesting that the disease might have spread with steppe pastoralists from Central Eurasia to Eastern and Central Europe during their massive range expansion. The younger Late Neolithic
Y. pestis genomes from Southern Germany are genetically derived from the Baltic strains and are found in individuals associated with the Bell Beaker Complex."

"The patterns in human genetic ancestry and admixture and the temporal series within the LNBA Y. pestis branch therefore support scenario 2, suggesting that Y. pestis was introduced to Europe from the steppe around 4,800 BP. Thereafter, the pathogen became established in a local reservoir within or in close proximity to Europe, from where the European Y. pestis strain was disseminated back to the Altai region in a process connected to the backflow of human genetic ancestry from Western Eurasia into the Altai."

"On account of the chronology, the ancient Y. pestis phylogeny, and known patterns of human mobility, we find stronger support for the second scenario."

"The manifestation of the disease in Europe could have played a major role in the processes that led to the genetic turnover observed in the European human populations that might have harbored different levels of immunity against this newly introduced disease. Testing these hypotheses will require more extensive assessment of both human and Y. pestis genomes from the presumed source population before and after the migration from the steppes, as well as in Europe during this period of genetic turnover."

This is interesting too:
"The presence of Y. pestis may have been a promoting factor for the increase in mobility of human populations (Rasmussen et al., 2015)."

Do they mean to imply that even though the steppe people might have had some degree of immunity to it they were fleeing it?

In that regard, the authors aren't definitive as to whether it was as virulent as Justinian's version or the Black Death. I would think it wasn't, just because the steppe people did survive it. I would also assume there were differing levels of immunity to it.

@Bicicleur
We can't just look at those first incursions to the south. Plus, we don't have very many genomes from there. When did the Central European groups fall? Baden is still genetically "Old Europe".

@Berun,
It was found in steppe pastoralists, initially and after the back flow, who probably practically slept with their flocks. They didn't have an "urban" life.

I know very well who painted the picture and when. It helps not to be so literal.
 
But they must have inhabited some kind of towns like that of Arkaim or some closed area, rats need their ecosystem and herders mobile tents are not one. Maybe sheeps? First notice then... in fact i don't catch how it would spread. The Black Death arrived in a ship from the Black Sea... maybe merchant's wagons could be an ecosystem? Something is not fitting all it.

About thr picture the same author did one of the Tower of Babel, very famous, but I think that no archaeologist took it as example for ziggurats...
;)
 
They weren't merchants either in those early periods. You're mixing up your time periods.

They presumably carried all their possessions in those carts as they moved around following their animals, and perhaps small children. Seems like a perfect breeding ground to me, as indeed were merchants' wagons in the Middle Ages. In that case, some suggest that the fleas lived in the wool, or in blankets. So, towns that thought they could keep it at bay by refusing entry to people from plague areas let it in with goods.

By all means let's be literal...a plague pit in Venice...

2_461.jpg


See:
http://news.nationalgeographic.com/news/2007/08/photogalleries/massgrave-pictures/photo2.html

It might not have been this virulent in the late neolithic. They got inconsistent results. It will need more testing.

If it was pretty virulent even then, look what one bacterium can do. It would have helped take down MN Europe, damaged the Byzantine Empire, and caused untold harm in Europe for centuries. At the height of the Black Death, perhaps half the population of Europe died. In one of my ancestral villages the death toll was 90%. You can read the priest's notes and still feel the horror.

This seems to be repeated over and over again throughout history. Look at the New World and what happened to the Amerindians because of smallpox, measles, etc.

In some areas 80-90% of the native peoples died.
http://www.sciencemag.org/news/2016/11/european-diseases-left-genetic-mark-native-americans
 
This is their map of the spread:
Spread of plague in Europe.jpg

The map is hard to read, but I think the earliest northern sample where they found it is about 2500-2200 BC?

I don't know if they have the right vector. They keep on talking about rats, but the original vector for the Medieval plague was some other kind of rodent, wasn't it, a steppe one?

If I have time, I'll read it again.

Ed. Yes, the original hosts for the Medieval plague were animals like marmots. At some point it jumped to rats. I wonder if in the LN it could have jumped to squirrels? People ate squirrels didn't they, especially in times of hunger?

https://en.wikipedia.org/wiki/Black_Death
 
why was it the native americans got european diseases to which the conquistadores had grown imune, but the conquistadores didn't get diseases from native americans?

I think it takes a certain population density before diseases can spread
 
This is their map of the spread:
View attachment 8283

The map is hard to read, but I think the earliest northern sample where they found it is about 2500-2200 BC?

I don't know if they have the right vector. They keep on talking about rats, but the original vector for the Medieval plague was some other kind of rodent, wasn't it, a steppe one?

If I have time, I'll read it again.

Ed. Yes, the original hosts for the Medieval plague were animals like marmots. At some point it jumped to rats. I wonder if in the LN it could have jumped to squirrels? People ate squirrels didn't they, especially in times of hunger?

https://en.wikipedia.org/wiki/Black_Death

well don't we need more data before drawing large conclusions?
 
@Bicicleur,

It's a good question, and one that's been asked before, including by Jared Diamond. The broad answer is that Europeans had stronger immune systems. The question is why was that the case. One explanation is as you described, which is population density. I don't much buy that one, as the Inca and Aztec populations certainly had population density. Those areas were very different from North America, yes? People like Jared Diamond propose that Europeans had a closer relationship with their domestic animals than New World cultures had with llamas, for example. (Measles, chicken pox, flu, are all connected to exposure to animals.) I'd have to refresh my memory. Were llamas their only domestic animals? I'd say the biggest factor might be one of the ones listed in the article below, which is that Europeans had a stronger immune system because of the migrations and admixture which were so much a part of their history and not just because it exposed them to so many different pathogens. The Native Americans were very isolated for, what, 14-15.000 years?

After delving more into it, and not just relying on the abstract, I conclude we need more data to know when and where it first actually appeared in Europe proper, how it was transmitted, how virulent it was, whether there were varying levels of immunity, etc. However, these two papers in combination have convinced me personally that this pathogen originated in the Central Asian steppe (as did the subsequent Medieval plague), and came to Europe with the steppe pastoralists. I don't see how the data can be interpreted any other way, but I have an open mind about it.
 
I've read several times that the first farmers must have been exposed to many diseases because of close contact with their animals, but afaik there is no actual proof of that yet.

The fact that Europe always has been exposed to immigration from abroad is IMO an important factor indeed.
Every time the plague came during historical times it came in from Asia, didn't it ?
But when I think about it, shouldn't the same have happened in India e.g. ?
Would something like that have gone undocumented in India?
 
something doesn't fit in the scenario that the pestis would have been spread by corded ware

the oldest genome infected in the study is RISE 509 which is Afanasievo
Afanasievo, Yamna and Poltavka are all R1b and autosomal similar : no EEF, lots of EHG and also an important share of CHG

Poltavka outlier, Potapovka, Sintashta, Srubna, Andronovo and Corded Ware are are all R1a and autosomal similar : also lots of EHG, but with EEF and a reduced share of CHG
therefore it has been suggested that Corded Ware people had their origin not in eastern Europe, but in western Europe

on the other hand, as both groups were speaking IE language, there must have been contacts between both groups
 
I don't have doubts about the Black Death, I only was pointing out that it would be better to show a scientific paper or a contemporary picture instead than a picture dealing were the Death is the principal actor.

There were merchants as is the unique way to understand what are doing Maykop copper axes in the steppes and Balkans other than invasion. In fact speaking about trade, just trade of furs would be a vector to spread the pest. In fact the date of spread coincides with the first true Neolithic cultures in Eastern Europe and Central Asia, so that if Yersenia was latent in a HG clan, the trade of furs would spread it (just remind how in Neolithic Europe there was an active trade of obsidian, shells, and precious stones).
 
@Bicicleur
Sorry, I forgot to link to that study discussing why Europeans didn't pick up more diseases from Native Americans.
http://www.todayifoundout.com/index.php/2014/03/native-americans-didnt-wipe-europeans-diseases/

I did quickly look up whether they had a lot of domesticated animals in the sense that Europeans had them, and the answer is that they actually didn't, which surprised me.

"In ancient Mexico, the dog, turkey, and duck were the only domesticated livestock;sheep, goats, pigs, cattle, and horses were introduced by the Sapnish. The Aztecs' basic diet therefore tended towards vegetables and fruits, supplemented by game animals, fish, turkeys, and other birds, and various kinds of insects."

http://www.foodtimeline.org/foodmaya.html

So, this may indeed be an important reason, as well as the repeated migrations that occurred in Europe.

Just coincidentally, I've been doing some reading about Louis XIV of France and his court. Measles was a scourge still then, not the mild childhood disease it became. Le Grand Dauphin died of it, his daughter-in-law Marie Adelaide, and then his son the Dauphin. In the space of a very short time the entire line of succession came down to one little boy, the future Louis XV. Meanwhile, Louis XIV himself and most of his court escaped. So, even at this late date, there were still people in Europe for whom it was a fatal disease. However, among Native Americans, perhaps 90% of a village would die.

Yes, it seems to be the consensus that the medieval plague came from the steppes as well. As I mentioned above, the current theory is that the first host was the marmot. It's just another rodent, like a squirrel. In Russia and Asia it's still hunted for fur. I'm sure it's also eaten. One question is whether at the period we're talking about transmission required eating it or handling the blood and body parts when skinning it and working the fur, or whether it had already made the jump to transmission by fleas. Obviously, if it could spread through flea bites, it could spread more quickly. However, the hemorrhagic fevers of Africa can spread and be devastating just through the handling of the bodies (and its discharges) of the people affected. The only way to stop the spread, really, is quarantine.

It did spread to India in the 17th century, not in the 14th, and we know so little about India from a data point of view at the earlier periods.
https://contagions.wordpress.com/2011/11/26/did-india-and-china-escape-the-black-death/

That sample you mention is the oldest sample in this paper. You have to look at the prior paper. It's a Willerslev, Rasmussen, Allentoft paper.

See: Rasmussen et al 2015

http://www.cell.com/abstract/S0092-8674(15)01322-7

"The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics."

So, we're talking about samples from 3000 BC so far as the oldest found, but that doesn't mean they won't find older ones. I think the estimation for the illness itself is about 5500 years ago, so 3500 BC, but I'm always skeptical about these dates.
 
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thx Angela, I find this quite interesting
I glanced at the Willersev paper and I will read it later.
In figure 1 I see their oldest genome is also Afanasievo.

It looks like early farmers must have gotten sick by contact with their animals and have grown immune to it.
But that was probably some 10.000 year or so ago.
Would first farmers in Europe have spread diseases to European HG then? Same in Africa and the Indus Valley.
 
I have another question, Angela.

I'm not a specialist but my understanding is that the researchers have amplified and checked certain loci in the genomes to see whether these individuals had grown immune to pestis. Is that correct?
 
thx Angela, I find this quite interesting
I glanced at the Willersev paper and I will read it later.
In figure 1 I see their oldest genome is also Afanasievo.

It looks like early farmers must have gotten sick by contact with their animals and have grown immune to it.
But that was probably some 10.000 year or so ago.
Would first farmers in Europe have spread diseases to European HG then? Same in Africa and the Indus Valley.

I find it fascinating too. In fact, I've been fascinated by the plague pandemics since university. One summer I went through the archives of my ancestral villages looking specifically at that period, and that's how I found that 90% mortality rate in one of them. Of course, as a student of Italian, I've also read The Decameron numerous times, which also piqued my interest.
https://en.wikipedia.org/wiki/The_Decameron

There are a number of really great reads on it.

The Great Mortality:
https://www.theguardian.com/books/2005/apr/09/featuresreviews.guardianreview15

This is a fictionalized version of it:
https://en.wikipedia.org/wiki/Year_of_Wonders

This is about the earlier Plague of Justinian: Justinian's Flea
https://www.theguardian.com/books/2007/may/05/featuresreviews.guardianreview9

As to the immunity question I didn't find any specific comment, although perhaps a geneticist would be able to see the answer in the data. Maybe the older paper has something? Just going by what was true of things like measles and small pox death rates in Europeans of the 17th century versus Native Americans in the 17th and 18th centuries, I'd say that with some passage of time the percentage of people with total or partial immunity increases. It does take some time to cull the herd, though. In populations exposed for the first time, and especially if they are "stressed" for other reasons, like malnutrition, the death rates are going to be much higher.

In terms of transmission by flea bite at this time, the authors maintain it is possible but they cannot be not sure.
"Based on the genetic characteristics of the LNBA genomes (i.e. lack of ymt, still functional pde2 and rcsA as shown by previous work, Rasmussen et al., 2015), functional ureD which will kill 30-40% of the flea vectors) it seems unlikely that Y. pestis was able to use a flea vector in a blockage-dependent model. However, since neither of these genes seem to be required for EPT, it is possible that LNBA Y. pestis was transmitted by a flea vector via EPT."

As to virulence, there is this:
"This indicates that LNBA Y. pestis could potentially cause a pneumonic or a less virulent bubonic form."

This all sounds pretty serious to me.

Oh, I forgot to quote this above:
"The MRCA of all Y. pestis was dated to 6,295 years(95% HPD interval: 5,063-7,787 years). This estimation overlaps with those previously made by Rasmussen et al. (2015)(5,783 years, 95% HPD interval: 5,021–7,022 years) suggesting a Holocene origin for plague.".
 
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my understanding of the Rasmussen study :

the Bronze age pestis was not as deadly as the later historical plagues, as it lacked certain mutations
we don't know how deadly it was
this form of pestis was not apt to spreading by fleas

From our findings, we conclude that the ancestor of extant Y. pestis strains was present by the end of the 4th millennium BC and was widely spread across Eurasia from at least the early 3rd millennium BC. The occurrence of plague in the Bronze Age Eurasian individuals we sampled (7 of 101) indicates that plague infections were common at least 3,000 years earlier than recorded historically. However, based on the absence of crucial virulence genes, unlike the later Y. pestis strains that were responsible for the first to third pandemics, these ancient ancestral Y. pestis strains likely did not have the ability to cause bubonic plague, only pneumonic and septicemic plague. These early plagues may have been responsible for the suggested population declines in the late 4th millennium BC and the early 3rd millennium BC (Hinz et al., 2012, Shennan et al., 2013).

only the youngest of all , in Armenia :

RISE397ArmeniaKapanEIA1048–8850.250.406.88
did posses the ymg mutation which would make it much more deadly and possibly the ancestor of later historical outbreaks

furthermore :

We investigated the origin of Y. pestis by sequencing ancient bacterial genomes from the teeth of Bronze Age humans across Europe and Asia.

So these are bacterial genomes, not human, but the bacterial genomes survive on the hosts teeth for 5000 years.
 
There seems to be a slight difference of opinion between the two sets of authors then, with this paper holding fleas could have been a vector.

Both seem to agree the strains prevalent at this time could have caused pneumonic plague, but differ as to whether they could have caused bubonic plague, yes?

Just so we know the difference.

"The three types of plague are the result of the route of infection: bubonic plague, septicemic plague, and pneumonic plague. Bubonic plague is mainly spread by infected fleas from small animals.[1] It may also result from exposure to the body fluids from a dead plague infected animal.[3] In the bubonic form of plague, the bacteria enter through the skin through a flea bite and travel via the lymphatic vessels to a lymph node, causing it to swell. Diagnosis is made by finding the bacteria in the blood, sputum, or fluid from lymph nodes.[1]"
https://en.wikipedia.org/wiki/Bubonic_plague

"
Primary pneumonic plague results from inhalation of fine infective droplets and can be transmitted from human to human without involvement of fleas or animals. Untreated pneumonic plague has a mortality rate from 90-100%....Pneumonic plague can be caused in two ways: primary, which results from the inhalation of aerosolised plague bacteria, or secondary, when septicaemic plague spreads into lung tissue from the bloodstream. Pneumonic plague is not exclusively vector-borne like bubonic plague; instead it can be spread from person to person. There have been cases of pneumonic plague resulting from the dissection or handling of contaminated animal tissue. This is one type of the plague formerly known as the Black Death.[2]"
https://en.wikipedia.org/wiki/Pneumonic_plague

They're both horrible, of course, but I suppose one difference is that for bubonic plague, trade goods could spread it, but with pneumonic plague, you really need the movement of people, which would actually tie in with what they're proposing.
 

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