Thursday, 22 October 2015

Bronze Age origins of bubonic plague

Study finds evidence of Yersinia pestis bacterium in 5,000-year-old human teeth

Three pandemics of bubonic plague have occurred in historical times: the first began with Plague of Justinian from AD 541 to 544, continuing intermittently until AD 750 AD; the second began with the Black Death from AD 1347 to 1351, continuing in waves including the Plague of 1665-66 into the eighteenth century; and the third which started in China in the mid-nineteenth century and triggered a series of outbreaks worldwide during the first half of the last century. The Black Death alone killed 30 to 50 percent of the European population. Deaths totalled at least 75 million, more than the number of deaths during World War I and II combined.

The cause of this deadly disease was identified as the flea-borne bacterium Yersinia pestis in 1894 by Swiss biologist Alexandre Yersin. More recently, genetic studies have suggested that it diverged from the more widespread but less virulent Yersinia pseudotuberculosis anywhere between 2,600 and 28,000 years ago.
In a newly-published study, researchers investigated the origins of Y. pestis by sequencing ancient bacterial genomes obtained from the teeth of Bronze Age people across Eurasia dating from 2,800 to 5,000 years ago. Their findings indicate that the flea-borne strain that caused the historic period plague pandemics evolved from a less virulent strain that was present in human populations long before any records of plague outbreaks.

The strains infecting Bronze Age Eurasian populations lacked the Yersinia murine toxin (ymt) gene, which encodes a phospholipase D protecting the bacterium inside the flea gut, so enabling fleas to act as vectors. Similarly, mutations associated with the development of bubonic plague and evading mammalian immune systems had not yet occurred. Not until around 3,000 years ago did highly virulent, flea-borne strains emerge.

The researchers also estimated the divergence from Y. pseudotuberculosis at 55,000 years ago, twice as early as previous maximum estimates. The Bronze Age strains began to diverge from one another 5,800 years ago. Although they could not cause bubonic plague, they could still cause pneumonic and septicemic plague and these might have been responsible for population declines between the late fourth and early third millennium BC. Large scale population movements and social changes during the Bronze Age might have facilitated plague outbreaks, but not on the scale of the historical era flea-borne pandemics.


Rasmussen, S., Allentoft, M., Nielsen, K., Orlando, L. & Sikora, M., Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago. Cell 163, 571-582 (2015).x

Friday, 16 October 2015

Modern humans were in China 100,000 years ago

Assignment of fossil teeth from Fuyan Cave to Homo sapiens is ‘unequivocal’

Ever since genetic evidence emerged to support the ‘recent Out of Africa’ model of modern human origins, the orthodox view is that until around 60,000 years ago modern humans were confined to Africa and a short range extension into Southwest Asia. The latter is thought to have been brought to an end as colder, more arid climatic conditions set in around 90,000 years ago. The model has been challenged by archaeological evidence suggesting that modern humans were established on the Arabian Peninsula 125,000 years ago and had reached India 77,000 years ago.

What has up until now been lacking is unequivocal fossil evidence significantly earlier than around 45,000 years old. Controversial evidence had previously been reported from two sites in southern China. An age of up to 139,000 years old has been claimed for the Liujiang Skull, discovered in 1958, but the exact geological position of the find was not documented and the skull could actually be as little as 30,000 years old. A lower jawbone and two molar teeth from Zhirendong (‘Homo sapiens cave’) in Guizhou Province have been securely dated to 106,000 years old, but it is not certain that these remains belonged to a modern human.

However, the discovery has now been reported of 47 teeth at the newly-excavated site of Fuyan Cave in Daoxian, Hunan Province. Uranium series dating of associated stalagmite fragments gave a minimum age of 80,000 years old for the teeth and faunal dating gave a maximum age of 120,000 years old. The teeth were compared with those of Late Pleistocene humans from Europe, Asia and Africa and were found to fall consistently within the Homo sapiens size range. They are generally smaller than other Late Pleistocene samples from Asia and Africa, and are closer to European Late Pleistocene samples and the teeth of present-day people. They resemble the latter far more closely than they do the teeth of Neanderthals or Homo erectus.

The announcement adds a radical new dimension to the history of modern human dispersals in Eurasia.

Liu, W. et al., The earliest unequivocally modern humans in southern China. Nature 526, 696-699 (2015).x

Wednesday, 14 October 2015

Ancient DNA reveals more extensive Neolithic back migrations to Africa from Eurasia

Sequenced genome of 4,500-year-old Ethiopian male provides genetic baseline for researchers

Modern humans are generally accepted to have originated in Africa, and the genomes of native Africans is therefore of great importance in reconstructing early migrations as our species dispersed around the world as it provides a baseline against which later events can be viewed. A problem for geneticists is the back migrations from Europe and Southwest Asia that have occurred within historical times, which act as a confounding factor when working with genetic data from present-day populations.

One way by which the problem could be solved is to obtain ancient DNA from prehistoric human remains, but this has proved difficult with only mitochondrial DNA being obtained up until now. However, in 2012, archaeologists excavated the burial of an adult male in Mota Cave, a riverside cave discovered the year before in the highlands of southwestern Ethiopia. Radiocarbon remains established that the remains were 4,500 years old, predating Eurasian migrations and the dispersal of Bantu farmers which spread agriculture across much of sub-Saharan Africa.

Conditions in the cave favoured the survival of ‘Mota’s’ DNA and it proved possible to sequence his genome. It was found that he was closely related to present-day Ethiopian populations, and in particular to the Ari, a group of Omotic speakers from southern Ethiopia, located to the west of the highland region where Mota lived. This was unsurprising and confirmed the view that there had been population continuity in this relatively isolated region over the last 4,500 years.

The researchers then searched for the source of the later Eurasian admixture by assuming that the present-day Ara genome is a genetic mix of Mota plus the source. It was found that the closest match was with Neolithic LBK farmers from Stuttgart and with present-day Sardinians. The latter are known to be the closest contemporary match to early Eurasian Neolithic farmers. The implication is that the genetic backflow into Africa came from the same source as the Neolithic expansion into Europe from Anatolia. These farmers were presumably responsible for the archaeologically-attested arrival of wheat, barley and other domesticated Southwest Asian crops in Africa around 3,000 years ago.

The next step was to use Mota as an African genetic baseline and the Neolithic LBK as the source of the Eurasian component to estimate the magnitude and geographic extent of historical migrations, without having to use present-day populations. It was found that the Eurasian genetic backflow was substantially higher than previously believed, with an additional 4 to 7 percent of the genome of most African populations tracing back to a Eurasian source. The geographical impact was also far greater than previous estimates suggest, extending all the way to West and South Africa. Even the Yoruba and Mbuti, often used as baselines in genetic studies, were found to have a significant Eurasian component, albeit less than in East Africa.

The Mota data has thus proved to be extremely informative about Neolithic migrations and obtaining even earlier African genomes would be highly desirable. Unfortunately, the African climate does not favour the preservation of DNA, but it is to be hoped that as sequencing techniques improve more ancient African genomes will become available.

Llorente, M. et al., Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent. Science 350 (6262), 820-822 (2015).