Bubonic plague, inbreeding Neanderthals and shipwrecked marble for a Roman-era temple

by Salman Hameed

[Updated below]

It is hard now to keep up with spectacular science news. Nevertheless, it is sometimes good to pause for a bit to appreciate the way scientists find clues about history. Here are three news items in the same issue of Science that I found riveting. This just reminded me of the crude nature of evolution-creation debates - and how those discussion take place in a parallel dumb universe ("where is the missing link?"; "Evolution is just a theory" etc.).

Here is the story of the bubonic plague. It was suspected that the Byzantine empire was hit by a bubonic plague that hastened its decline in the 6th century and later. This decline also facilitated the phenomenal expansion of Islam into the Byzantine territories. But do we know that this was a bubonic plague? Well now we do:

The Justinian Plague, which resurfaced regularly between the 6th and 8th centuries, is thought to have assisted the decline of the Roman Empire, but it has, until now, only been speculatively diagnosed as bubonic plague caused by the bacterium Yersinia pestis. Using stringent ancient DNA anticontamination protocols, Harbeck et al. have genotyped new material from the early medieval graveyard at Aschheim, Bavaria, dating from the 6th century. This graveyard contained 438 individuals, often in multiple burials—a sign of crisis. The amount of bacterial material available was scant, but Y. pestis was identified from one individual using five key single-nucleotide polymorphisms identified in recent phylogenies. Genotyping confirmed this isolate as basal to isolates from the 14th-century Black Death and the modern (19th-century) third pandemic and that, like the other pandemics, it originated in China or Mongolia.

Full article at: PLoS Pathogens 9, 10.1371/journal.ppat.1003349 (2013).

Then we have this phenomenal work of decoding of the Neanderthal DNA as well as another hominid group called the Denisovians. What is fascinating is that the researchers can tell not only that humans and Neanderthals interbred (yes - for those outside of Africa, about 2% of the DNA comes from Neanderthals), but that at least in some cases Neanderthal first cousins had offsprings:

Neandertals, the closest known relatives to modern humans, ranged across Europe to western Asia from perhaps 300,000 years ago until about 30,000 years ago. Their overlap in time and space with our ancestors had fueled debate about whether the two species had interbred. Then, in 2010, Pääbo's group published a low-coverage sequence (1.3 copies on average) of DNA from three Neandertal bones from Croatia, which showed interbreeding: About 2% of the DNA in living people from outside Africa originally comes from Neandertals (Science, 7 May 2010, pp. 680 and 710). 

That first Neandertal sequence was a huge accomplishment, as Neandertal DNA made up just a few percent of the DNA in the fossils, the rest being bacterial and other contaminants. Since then, the Leipzig group has found ways to zero in on human genetic material and to get more from degraded ancient DNA by using a sequencing method that starts with single, rather than double, strands of DNA. The approach provided a startlingly detailed view of the Denisovan pinkie bone (Science, 31 August 2012, p. 1028). 

But this powerful technique had yet to be applied to Neandertals. So Pääbo was thrilled when the DNA in the sample taken from the toe bone proved to be 60% Neandertal. The researchers were able to sequence each base 50 times over, on average—enough coverage to ensure the sequence is correct. This approach also provided low coverage of the genome from another fossil, a Neandertal baby's rib, more than 50,000 years old, from a cave in Russia's Caucasus region between the Caspian and Black seas. 

In a 10 p.m. talk to a full house, Pääbo offered some surprising results from the toe bone. For long stretches, the DNA from each parental chromosome is closely matched, strongly suggesting that this Neandertal was the offspring of two first cousins, he said. Comparing the data with those from the fossils from Croatia and the Caucasus showed that these populations were fairly separated from one another. The group also compared the chunks of Neandertal DNA found in living people with each of these three Neandertal samples. The closest match was with the Caucasus population, suggesting that interbreeding with our ancestors most likely occurred closer to that region.

Okay - so scientists, I think, are now invading the privacy of this inter-species relations. Do we really have to know what our ancestors were doing tens of thousands of years ago on those cold nights? ;) 

Actually we do.

Full story here (but you will need subscription). 

Okay - so moving on from our misbehaving ancestors to the shipwrecks carrying marble for temples. What is amazing here is that scientists can not only identify the dates of the shipwreck, but they can tell where the marble was quarried from and where it was headed. This is pretty cool (and Urdu speakers will know why Marble is called Sang-e-Marmar - the stone of the Marmara): 

Sometime between 100 B.C.E and 25 B.C.E., a wooden ship carrying almost 60 tonnes of

stone foundered in Aegean waters just off the coast of Turkey. It went down bearing its entire cargo, including eight massive drum-shaped blocks of white marble. Those blocks fit together to form part of a tapering column that likely stood more than 11 meters tall, plus a square uppermost piece: a Doric column. 

Two thousand years after the ship went down, archaeologists excavating what is now called the Kizilburun shipwreck have figured out exactly where the marble blocks came from and where they were heading, illuminating the marble trade in the Roman province of Asia Minor.
...
Carlson and classical archaeologist William Aylward of the University of Wisconsin, Madison. first set out to learn where the marble came from. As reported in a 2010 study in the American Journal of Archaeology, the team sent out samples of the marble for stable isotope analysis and other tests. The marble's values of the isotopes δ¹³C and δ¹⁸O and its spectroscopic details led them to Marmara Island, known as Proconnesos in Roman times, in the Sea of Marmara, the inland sea connecting the Aegean and Black seas. This island was the site of an important marble quarry when Asia Minor became a Roman province around 130 B.C.E. 

But where was the marble heading? The blocks' size and style suggest that the column was intended for a major public building, most likely a temple. Carlson and Aylward drew up a list of all the Doric-style monumental buildings under construction in the 1st century B.C.E. on coastlines south of the wreck site, the probable direction of travel away from the quarry. Then they searched for sites with a finished lower-column diameter of about 1.73 meters. They concluded that the marble was headed for the Temple of Apollo at Claros, where people in Roman times flocked to seek advice from oracles, just 50 kilometers from the wreck. That finding is "utterly convincing," says architectural historian Lothar Haselberger of the University of Pennsylvania. 

The data show that the quarry workers on Proconnesos were in close contact with the temple builders some 500 kilometers or more away, shaping the marble to the builders' exact specifications. The findings also show that the builders received columns in pieces in small shipments, hinting at a lengthy construction process. This information, says Carlson, "is the missing link that tells us a lot about this process."                   

Read the full story here (yes - subscription will be needed).                  

[Update - May 29th: So scientists can say quite a bit from DNA analyses about what humans and Neanderthals were doing tens of thousands of years ago, but according to the Council of Islamic Ideology in Pakistan, DNA analysis cannot be used as primary evidence in rape cases (it can be used as secondary evidence). Shame for that].