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Jean M
10-22-2015, 10:03 PM
Simon Rasmussen et al., Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago, Cell, Volume 163, Issue 3, p571–582 (22 October 2015) http://www.cell.com/abstract/S0092-8674%2815%2901322-7

Highlights

Yersinia pestis was common across Eurasia in the Bronze Age
The most recent common ancestor of all Y. pestis was 5,783 years ago
The ymt gene was acquired before 951 cal BC, giving rise to transmission via fleas
Bronze Age Y. pestis was not capable of causing bubonic plague


Summary

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.

This paper was revealed to be in the offing at the LAG conference in Jena, I hear. So I've been looking out for it, but Dienekes got there first! http://dienekes.blogspot.co.uk/2015/10/bronze-age-plague.html

6397


Another recent paper finds that Yersina Pestis repeatedly arrived in Europe from Asia:
Boris V. Schmid, Ulf Büntgen, W. Ryan Easterday, Christian Ginzler, Lars Walløe, Barbara Bramanti and Nils Chr. Stenseth, Climate-driven introduction of the Black Death and successive plague reintroductions into Europe, PNAS, vol. 112, no. 10 (March 10, 2015), pp. 3020–3025.

Jean M
10-22-2015, 10:32 PM
The host individuals from which Y. pestis was recovered belong to Eurasian Late Neolithic and Bronze Age cultures (Allentoft et al., 2015), represented by the Afanasievo culture in Altai, Siberiab (2782 cal BC, 2794 cal BC, n = 2), the Corded Ware culture in Estonia (2462 cal BC, n = 1), the Sintashta culture in Russia (2163n cal BC, n = 1), the Unetice culture in Poland (2029 cal BC, n = 1), the Andronovo culture in Altai, Siberia (1686 cal BC, n = 1), and an early Iron Age individual from Armenia (951 cal BC, n = 1).

RISE00 Estonia Sope Corded Ware 2575–2349
RISE139 Poland Chociwel Unetice 2135–1923
RISE386 Russia Bulanovo Sintashta 2280–2047
RISE397 Armenia Kapan EIA 1048–885
RISE505 Russia Kytmanovo Andronovo 1746–1626
RISE509 Russia Afanasievo Gora Afanasievo 2887–2677
RISE511 Russia Afanasievo Gora Afanasievo 2909–2679

Jean M
10-22-2015, 10:39 PM
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).

DMXX
10-23-2015, 01:44 AM
Could Yersinia and other infections have something to say about the Indo-European migrations, I wonder? Dispersals from the common homeland, fleeing that outbreak zone, only to serve as vectors for the bacteria themselves?

I also wonder whether this has any association with the aridisation of the steppes around that rough time period.

Gravetto-Danubian
10-23-2015, 02:04 AM
As I wrote on Eurogenes' thread:


I suspect plague night have preceded the Bronze Age populations. It’s certainly a more sound explanation of why there was a late Neolithic collapse- from central Anatolia to Scandinavia - without resorting to some of the more "imaginative", empirically questionable scenarios

This hypothetical plague appeared to have hit G2a men most of all. On the Y-chromosome lies the male-specific immunohistocompatability complex Y-HC, involved with T cell (CD8 and CD4 T cells) regulation. If not related to that, then it must also have been related to the overcrowded conditions of densely populated tell settlements and tepe, living in close quarters with animals, etc.

Residual WHGs were more resilient because they were less densely populated and continued a broader economy, similar with the eastern pastoralist groups who moved in the wake of this population collapse into scantily uninhabited land in Central Europe. The low density persisted well into the MBA.

Tomenable
10-23-2015, 08:42 AM
Could Yersinia and other infections have something to say about the Indo-European migrations, I wonder?

It seems so.

Perhaps they facilitated the Indo-Europeanization, like later smallpox and other diseases facilitated European colonization of the Americas.


I suspect plague night have preceded the Bronze Age populations. It’s certainly a more sound explanation of why there was a late Neolithic collapse- from central Anatolia to Scandinavia - without resorting to some of the more "imaginative", empirically questionable scenarios

It probably preceded the main wave of immigrants - just like in the Americas smallpox usually hit the locals decades before conquistadores.

Jean M
10-23-2015, 11:03 AM
Science Daily: http://www.sciencedaily.com/releases/2015/10/151022124532.htm

Plague in humans 'twice as old' but didn't begin as flea-borne, ancient DNA reveals

New research dates plague back to the early Bronze Age, showing it had been endemic in humans across Eurasia for millennia prior to first recorded global outbreak, and that ancestral plague mutated into its bubonic, flea-borne form between the 2nd and 1st millennium BC.

They say the new evidence that Y. pestis bacterial infection in humans actually emerged around the beginning of the Bronze Age suggests that plague may have been responsible for major population declines believed to have occurred in the late 4th and early 3rd millennium BC.

The work was conducted by an international team including researchers from the universities of Copenhagen, Denmark, and Cambridge, UK, and the findings are published today in the journal Cell.

"We found that the Y. pestis lineage originated and was widespread much earlier than previously thought, and we narrowed the time window as to when and how it developed," said senior author Professor Eske Willerslev, who recently joined Cambridge University's Department of Zoology from the University of Copenhagen....
Researchers concluded these early strains of plague could not have been carried by fleas without ymt. Nor could they cause bubonic plague -- which affects the lymphatic immune system, and inflicts the infamous swollen buboes of the Black Death -- without the pla mutation.

Consequently, the plague that stalked populations for much of the Bronze Age must have been pneumonic, which directly affects the respiratory system and causes desperate, hacking coughing fits just before death. Breathing around infected people leads to inhalation of the bacteria, the crux of its human-to-human transmission.

Study co-author Dr Marta Mirazón-Lahr, from Cambridge's Leverhulme Centre for Human Evolutionary Studies (LCHES), points out that a study earlier this year from Willerslev's Copenhagen group showed the Bronze Age to be a highly active migratory period, which could have led to the spread of pneumonic plague.

"The Bronze Age was a period of major metal weapon production, and it is thought increased warfare, which is compatible with emerging evidence of large population movements at the time. If pneumonic plague was carried as part of these migrations, it would have had devastating effects on small groups they encountered," she said.

"Well-documented cases have shown the pneumonic plague's chain of infection can go from a single hunter or herder to ravaging an entire community in two to three days."

Mbantua
10-23-2015, 11:55 AM
I am a microbiologist, retired now, but I thought everyone knew that Y. pestis home was the Eurasian steppes mostly in Asia, and by extension the steppes where the Indo-Europeans are said to come from in far eastern Europe. Steppes, grasslands and prairies are Rodent heaven, and rodents have fleas or ticks or some other disease transmitting vector. Wherever people live they make it suitable for rodents and other pests. Ever wondered why Northern Europeans have a greater immunity to the Plague? The steppes north of the Caucasus region is the homeland of Indo-European and Northern Europeans. The two go together like a hand in a glove.

I was amazed by Dienekes' revelation about Y. pestis, but he is not a microbiologist but some internet dilettante.

George
10-23-2015, 12:26 PM
I am a microbiologist, retired now, but I thought everyone knew that Y. pestis home was the Eurasian steppes mostly in Asia, and by extension the steppes where the Indo-Europeans are said to come from in far eastern Europe. Steppes, grasslands and prairies are Rodent heaven, and rodents have fleas or ticks or some other disease transmitting vector. Wherever people live they make it suitable for rodents and other pests. Ever wondered why Northern Europeans have a greater immunity to the Plague? The steppes north of the Caucasus region is the homeland of Indo-European and Northern Europeans. The two go together like a hand in a glove.

I was amazed by Dienekes' revelation about Y. pestis, but he is not a microbiologist but some internet dilettante.

I'm beginning to wonder whether this should be factored in as a possible explanation for the mysterious disappearance of the classical Trypilian civilization and its mega-proto-cities. With an apparent population diminution of some 60/70% within a relatively short time span. But this was still pre-BA, in the second half of the 4th millennium BCE. On the borderland of the steppes. Were their huge communities rodent-infested with serious sanitation problems to boot?

Jean M
10-23-2015, 12:29 PM
I was amazed by Dienekes' revelation about Y. pestis...

What revelation? Dienekes makes only a brief comment of his own on this paper:


This paper used the same data as the Allentoft et al. paper, but instead of focusing on the human DNA recovered from ancient Eurasians, it went looking for interesting stuff in the non-human DNA (the stuff that is usually thrown away).

The result: 2,800-5,000 year old Yersinia pestis from Europe to the Altai. It will be cool to look at even older remains than the Bronze Age, but this already pushes the date for plague by a couple thousand years, and implicates steppe people in its earliest spread.

Dienekes no doubt has Internet alerts running (as I do myself) to pick up new DNA papers. He posts about them, as do several other bloggers, thus providing a useful service in the same way that this forum does, with its pinned threads for new papers. We don't have to agree with the commentary that bloggers sometimes attach to the news to find the alerts useful. It is up to us to evaluate the papers for ourselves.

Tomenable
10-23-2015, 06:05 PM
I'm beginning to wonder whether this should be factored in as a possible explanation for the mysterious disappearance of the classical Trypilian civilization and its mega-proto-cities. With an apparent population diminution of some 60/70% within a relatively short time span. But this was still pre-BA, in the second half of the 4th millennium BCE. On the borderland of the steppes. Were their huge communities rodent-infested with serious sanitation problems to boot?

The Late Neolithic population crash in Europe coincides in time pretty well with the beginning of Indo-European expansion from the steppe. Let's also note that the Trypillian civilization bordered the steppe - so they could be the first ones to contract a disease from Indo-Europeans:

http://www.nature.com/ncomms/2013/131001/ncomms3486/full/ncomms3486.html

http://digitalcommons.wayne.edu/cgi/viewcontent.cgi?article=1059&context=humbiol

http://s30.postimg.org/4ncr0logx/Neolithic_demographics.png

parastais
10-23-2015, 07:12 PM
Interesting, it was also cooling around that time period before/at depopulation?

Tomenable
10-23-2015, 08:51 PM
Interesting, it was also cooling around that time period before/at depopulation?

Yes, indeed. Climate was getting colder in the 6th/5th millennia BC, as the Atlantic warm period ended:

https://en.wikipedia.org/wiki/Atlantic_(period)

Poor farmers - all bad things at once: cooling, disease, and from the steppe "horsemen of the Apocalypse" coming. :)

A Medieval prayer - 'From the air*, hunger, fire and war, Lord, save us' - would fit at that time too.

*Bad air = plague; and climate cooling of course meant lower crops for farmers.

=============================

About climate during the Neolithic period, I have also found this:

"Climate fluctuations and trajectories to complexity in the Neolithic: towards a theory":

http://arheologija.ff.uni-lj.si/documenta/pdf36/36_5.pdf

parastais
10-24-2015, 08:52 AM
Which kind of corresponds to what happened in Europe after 5th century AD. Bad weather and next plague.

Gravetto-Danubian
10-24-2015, 09:03 AM
Which kind of corresponds to what happened in Europe after 5th century AD. Bad weather and next plague.

As an aside, How well documented is the climate thing for the 5th cc AD ?

Jean M
10-24-2015, 10:24 AM
As an aside, How well documented is the climate thing for the 5th cc AD ?

Actually there were switches of climate from around AD 250-550 affecting the Roman Empire, which I cover in AJ with references. Crop failures would have led to food shortages, weakening resistance to disease. Plagues are recorded at intervals between AD 251 and 270. However I suspect that what parastais had in mind was the following sequence:


In 536 a volcanic eruption in the tropics threw enough dust into the atmosphere to cool the northern hemisphere for over a decade.
In 541 the Plague of Justinian broke out in Egypt in 541 and hit Constantinople the following spring, raging around the Byzantine empire from there.

parastais
10-24-2015, 11:51 AM
Actually there were switches of climate from around AD 250-550 affecting the Roman Empire, which I cover in AJ with references. Crop failures would have led to food shortages, weakening resistance to disease. Plagues are recorded at intervals between AD 251 and 270. However I suspect that what parastais had in mind was the following sequence:


In 536 a volcanic eruption in the tropics threw enough dust into the atmosphere to cool the northern hemisphere for over a decade.
In 541 the Plague of Justinian broke out in Egypt in 541 and hit Constantinople the following spring, raging around the Byzantine empire from there.

Thanks, that was for most part what I meant.
-------
I also recalled vaguely a graph showing also coolening before 536 which I thought was believed one of key reasons for fall of Rome, start of migration period and (one more paralel) Hunns from Steppe.
But I cant find good reference for that. Also Hunns did not replace y-dna lines of locals.
------
Relatively new Estonian study shows there oncatastrophical consequences for people around Baltic Sea on 536.
Curiously the study mentioned that whilst there was significant population loss in circum Baltics due to failed crops, it did not impact Finland which relied on hunting and fishing not agriculture...

Arame
10-24-2015, 01:53 PM
In 536 a volcanic eruption in the tropics threw enough dust into the atmosphere to cool the northern hemisphere for over a decade.

This event is documented by Armenian historians also. They call it foggy days that lasted 18 months.
https://en.wikipedia.org/wiki/Extreme_weather_events_of_535%E2%80%93536

One of my friends thinks an asteroid hit is more probable. He was part of Irish scientific group that was making a study about this event.
It can be the catalizator of the Justinian plague.

Bas
10-24-2015, 08:13 PM
Thanks, that was for most part what I meant.
-------
I also recalled vaguely a graph showing also coolening before 536 which I thought was believed one of key reasons for fall of Rome, start of migration period and (one more paralel) Hunns from Steppe.


Yes, the Rhine crossing which is believed to be one of the main reasons for the fall of the Roman empire. It is thought to be December 31st 405 or 406. Apparently the Rhine froze solid enough to cross and Germanic tribes swarmed across, eventually reaching Spain and North Africa. There is a phenomenon called the 'Roman Warm Period' that lasted from 250BC until 400AD, ending just before the Rhine crossing.

Tomenable
11-14-2015, 12:30 AM
IMO the first Neolithic culture devastated by Yersinia pestis plague from the steppe, were Trypillians, with their giant settlements:

http://rcin.org.pl/iae/Content/34704/WA308_45768_P319_OSIEDLA-GIGANTY_I.pdf

http://s21.postimg.org/b8b9tn9et/Trypillian_1.png

http://s9.postimg.org/drux643d9/Trypillian_2.png