Wednesday, May 29, 2013

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]. 


Asad M said...

Salman, just a silly question out of curiousity: would the offspring of a Sapien and a Neanderthal be able to reproduce coz usually the hydrid offspring of closely related mammals are sterile (e.g. horse & donkey or lion & tiger)? Also how many chromosome pairs did Neanderthal have? (I’m guessing 23 like us otherwise they wouldn’t have been able to produce anything at all).

Salman Hameed said...

good question. I will also get a more detailed answer from a biologist friend of mine and will get back. As far as I know, in most cases the hybrid offsprings are sterile - but not in all. But then there is also a question of how "species" are defined. But the details of these debates are beyond my understanding, but I do think the Neanderthal chromosomes are equal to humans. You should also check out "Inbreeding with Neanderthals> by Carl Zimmer.

Salman Hameed said...


Here is a response from evolutionary biologist. Charles Ross from Hampshire College:

Part 1:
Great question! The short answer, as you might expect, is "We don't know." In general, the fertility of hybrid offspring usually is variable both among individuals within a two-species hybrid cross, and among different combinations of hybridization between two species. That is, not all hybrid offspring are equivalent in their viability or fertility when two species cross, and hybridizations among different pairs of species may produce a variety of outcomes.

I think there really are two things to consider. First, Is it possible for Homo sapiens sapiens and Homo neanderthalensis to hybridize and what would be the state of the hybrid offspring? Second, how could we tell if this happened?

For the first question, we can consider the general phenomena of hybridization as well as the specific case of H. sapiens and H. neanderthalensis.
In general, hybridization is more prevalent among species than many people might guess. For information on this, see Arnold 1996, " Natural Hybridization and Evolution" and his later book in 2006, "Evolution Through Genetic Exchange", which compile some estimates on the extent of hybridization in nature. Overall, I believe he estimated about 19% of all species may have hybrid origins, with some groups approaching 50%. I don't have the books in front of me, so I can't say those numbers are accurate, but it probably is reasonable to believe that hybridization is not a rare occurrence. Additionally, the phylogenetic distance among hybridizing taxa can sometimes be moderately distant. That is, they don't have to be sister taxa. Rieseberg et al showed this with sunflowers, though I can't recall the specific journal article (2003?). While the results of hybridization are widely variable among cases, there are numerous cases where the hybrid offspring seem perfectly viable and fertile, with some hybrids even having higher fitness than their parental types in certain environments. Of course, there also are many cases where the hybrids exhibit some form of disfunction or unfitness. This usually takes the form of hybrid inviability or hybrid sterility, as in the case of sterile mules, which are the offspring of a male donkey and female horse (there actually are some cases of female mules siring offspring). These 'post-zygotic' barriers are almost always expressed more in the heterogametic sex (in this case, the male, who has XY sex chromosomes), something called "Haldane's Rule". There are many hypotheses about why Haldane's Rule exists, such as the expression of deleterious recessive alleles in a hemizygous state on the X, but overall it suggests some incompatibility among genomes of the hybridizing species. So, in general, hybridization doesn't appear to be a rare occurrence, and the outcome of hybridization is not always unfit offspring, though if the offspring do have low fitness, patterns of unfitness often take characteristic forms.

Part 2 coming up.

Salman Hameed said...

Charles Ross' response continues:
Part 2:

What can these patterns tell us about potential hybridization between H. sapiens and H. neanderthalensis specifically? From general patterns in nature, it certainly would seem possible, and it's hard to imagine why a hypothesis of isolation or hybridization should be preferred. However, there also are potential reasons why H. sapiens and H. neanderthalensis would not interbreed. Culture is a strong evolutionary influence and in Homo it clearly can affect things like mating preferences and non-random associations. Another potential barrier is the karyological (chromosomal) compatibility between the two species. H. sapiens have 46 chromosomes (23 'pairs'); great apes (and early Homo?) have 48 chromosomes. I don't think it is established how many H. neanderthalensis had, but if they had 48, hybridization could be difficult, though not impossible. For example, a horse has 64 chromosomes and a donkey has 62, though they can produce a mule with 63 chromosomes (though the sterility of the mule probably results from this). However, if there was a high level of synteny along various chromosomes that were different among species, it could be very possible to successfully hybridize and produce viable offspring. We know there is a high level of genomic synteny between humans and chimps, for instance (The second chromosome in humans is actually two in chimps), and though there are no human-chimp hybrids, it seems reasonable to think that even if H. neanderthalensis had 48 chromosomes, hybridizing and backcrossing with H. sapiens wouldn't be prevented by pairing chromosomes during metaphase. So, I would say that there is no 'genetic' reason to suspect H. sapiens and H neanderthalensis could or could not hybridize, though there might well be barriers at this level. Also, it would be hard to assert that a H. sapien - H. neanderthalensis hybrid would or would not be sterile. If there was some partial hybrid sterility, it likely would be expressed in male hybrids. However, hybridization itself could have been prevented by strong cultural barriers, but these may never be known.

For the second question about how we can tell if H. sapiens and H. neanderthalensis did in fact hybridize, the best evidence is currently emerging from comparing variation and characteristics of human and neanderthal genomes. We have lots of human genomes sequenced at this point, and Paabo and colleagues are sequencing the few neanderthal genomes available. They and others are looking for neanderthal 'genetic signatures' in our own genome. Finding genetic evidence of neanderthal genes in our genome is extremely hard to do, as we share at least 99.5% of our genome with neanderthals already due to recent divergence. That is, how do you know if a particular genetic variant is due to common ancestry or hybridization? It is possible, but it's like looking for a specific kind of needle in haystack of needles, which is why many researchers find the evidence equivocal. Consequently, thoughts about hybridization seem to flip back and forth with new evidence, but currently I feel there is some stronger evidence being presented, especially in conjuction with data from Denisovan genomes, suggesting that we did in fact hybridize with H. neanderthalensis, at least rarely. Here is a url of an article in Discover magazine that highlights some of the recent research in hominin hybridization:

Hope this gives some insight into the question. I apologize for the uncertainty in my answer, but I think that is the state of the evidence right now.

Charles Ross.

Asad M said...

Salman and Charles Ross, many thanks for taking the time to answer my question and for the Zimmer article link. I appreciate that we don’t have exact answers yet (and there’s a chance that we may never will) but we have learned a lot more about Neanderthals (and our own species) in the last decade alone and hopefully the works of Svante Paabo and other scientists will unravel a lot more clues in the near future.

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