Anthropology.net

A new study of over 600 mtDNAs from 20 American and 26 Asian populations is shedding some unique insight on how the Americas were peopled. As you may have been taught, it was thought that the Americas were founded by a not so diverse founding population or two. Before this paper, only about 70 left their genetic print in modern descendants, a very small but effective founder population.

But, there are new results, which were published almost two months ago, that show that there was much more genetic diversity in the founder population than was previously thought. I didn’t catch it until I saw both Razib and Science Daily report on it a couple days ago.

The paper, “Beringian Standstill and Spread of Native American Founders,” was published in the freely accessible PLoS One. Beringia is a fancy way of naming the Bering Land Straight that once connected the north east Asia continent to north west America continent.

One of the more interesting lines of evidence they found from their sequence comparison and their revised phylogenetic map is that the ancestral population literally chilled out in Beringia for a long time. The authors estimate about 15,000 years. That’s long enough so that specific mutations accumulated which separated the New World founder lineages from the Asian sister-clades.

The other more interesting thing that was uncovered was that the founding haplotypes are uniformly distributed across North and South America. They do not show a nested structure from north to south. That means that after what the authors are terming the Beringian standstill and what I’m calling the Beringian chillout, the initial North to South migration was very swift. It was not a gradual diffusion.

And as Razib pointed out in his post, during the last 30,000 years, there was a lot more bouncing back and forth from Northeast Asia and North America. The analysis shows that there was a series of back migrations to Northeast Asia as well as forward migrations to the Americas from Beringia, “more recent bi-directional gene flow between Siberia and the North American Arctic.”

Overall, this study tells us a lot on how people were moving about in the northern hemisphere. But what about oceanic travel, and the recent chicken population genetic similarities? They seem to have made some cultural if not genetic contribution to populations here.

Related sidenote, I like how this study one ups an older PLoS paper, which I reffered to above (the 70 people one). If you want, check out that paper, “On the Number of New World Founders: A Population Genetic Portrait of the Peopling of the Americas.”

The BBC reports on the discovery of a very abundant collection of fossils unearthed at an ancient hyena den in the Granada region of south-east Spain. The site is named Fonelas P-1, and it is very important. How so? It falls right in between the Pleiocene and Pleistocene which is when early Homo is thoght to have made one of the first migrations out of Africa.

Currently, the site has yielded over 4,000 very diverse fossils including, gazelles, wolves, wild boar, lynx, sabretoothed cats, giraffes and zebras… as well as hyenas.

The official date hasn’t come back yet, but Fonelas P-1 is thought to be about 1.8 million years old. No hominins have been found yet but I wouldn’t be surprised if they do find one. With such a diverse and abundant list of fauna, Fonelas P-1 would have been the perfect place to attract hominins. Also, there are many similar fauna represented in Fonelas collection and those found early tool making sites in East Africa.

So keep your eyes out for Fonelas P-1. It should be a really interesting European site for paleoanthropology and paleontology.

A few weeks back, Kambiz posted an article, ‘US Army is Embedding Anthropologists’, which discussed whether or not it was prudent, or even desirable for trained anthropologists to assist the US military in its current operations in Iraq and Afghanistan; last night I read what I consider to be an outstanding addition to the discussion of this issue, in a post to Anthro-L, which was submitted by Jeff Bristol. Having obtained the author’s permission to reproduce it here, I hope this will add a unique perspective to the many words that have been said and written on this subject over these past weeks.

I’m an anthropology student who has recently left active duty in the US Army and who served as a Farsi linguist, so while I am definitely not quite yet a professional in our field, I think I still have somewhat unique perspective on this issue. I was also deployed to Afghanistan on active duty and served in Iraq as a civilian contractor in order to finance finishing my degree. I’ve read a lot of the articles that have been recently published about the HTS/HTTs (the military acronym for the anthropology teams in the field) and I have to agree with Ken’s statement that a boycott of counter-insurgency efforts would be a great loss, not just to the military and the US, but to anthropology and the countries we are occupying as well. Whether we like it or not, the wars and actions in Iraq and Afghanistan are a reality and it seems to me that the US gov’t has made a real reach out to enact better, more enlightened policy through the hiring of ‘experts in culture.’

It seems to me that the anthropology community can either take up the offer and try to help make what may be called a very unpalatable situation better by extending the insights that only it can provide, or sit back on its hands and let the gov’t execute its policies that even if well-intentioned would be otherwise misinformed. I think we can all agree that misinformed action is the worst thing that can happen not just for our country, but for the civilians in the occupied countries as well. It is inarguable I think that their lives that are more impacted by decisions made over there than ours.

Until this initiative started the only ‘experts in culture’ in the countries were people like myself who received language training at the Defense Language Institute (DLI) in Monterey. While I and my military linguist former colleagues receive an undoubtedly high level of language training at the DLI, our cultural training extends only so far as what the native teachers there impart to us and what those of us who are honestly interested in the culture of the people who speak our respected languages (not necessarily in the majority, but not a small minority by any stretch of the imagination. Many of them are much like myself: people who joined the military and picked this particular career field either because we are interested deeply in foreign cultures and wanted some ‘real world’ time and a break from school or because we are interested in language and linguistics) pick up on our own.

While this may not be an inconsiderable level of knowledge, which is certainly added to by the practice of working with the language and its native speakers on a daily basis while deployed, we certainly do not have an anthropologist’s knowledge of cultural theory and foundations. For my part I had always intended at the end of my five-year contract to get out of the military and pursue anthropology. While my time as an ‘expert in culture’ was nice in the sense that it gave me to a chance to learn and grow in my understanding of the languages and cultures of Middle East and Central Asia and play the anthropologist in a sense, I could not have provided the insight I think I can now and will be able to provide with greater utility in the future.

If anthropologists boycott the occupations in the Middle East, nothing overseas will change. Institutions in the two countries we are attempting to build stability in will continue to be built on lines which may or may not be compatible with the cultural and social systems in existence within them. If these systems are not in harmony with the cultural environment in which they are created they will accordingly fail. On the other hand, if anthropologists enter the mission there, perhaps their greater insight will lead to more compatibility and stability in Iraq and Afghanistan as the reforms and reconstruction efforts will be guided in such a way as to allow for the social needs and norms of the people we are trying to help (and do not be mistaken, the soldiers, sailors, arimen and marines and their officers overseas want to help the people in those countries if for no other reason than because they want to come home and not go back).

It should be noted that in the beginning of our occupation in Iraq (I was in the military then and served from June 2001 until June of 2006) the insurgency was almost nonexistent. Soldiers and marines on patrols would often stop by neighborhood cafes for a coffee, hand candy out to kids and had a relatively strong dialogue with the local people. All things that every soldier, sailor, marine and airman in Iraq want.

Unfortunately (and most soldiers who were in country, not myself but many friends of mine, will blame, shout and curse Paul Bremmer for this) the reconstruction policy in the country started off on the wrong cultural foot. In an effort to sweep out the old and bring in the new, almost every shaykh in the country was arrested for one reason or another, creating massive destabilization in the traditional tribal power structure and forcing people, as a result of the disruption of power structure in place and operating even under Saddam, to side with insurgents and other elements in direct reaction against the disrupting influence. This also led to the idea that things may have been better off before. This is a reality that most people on the ground now understand and regret, and one reason why anthropologists are being brought into the fight. If they had been there in 2003 maybe things would have remained relatively peaceful, and Iraq could be a very different country today. Afghanistan has obviously been more successful, but the native power structures in that country were left more intact and less was intrinsically altered.

As for the anthropologists playing an ‘Emily Post’ role in the military, for now I am sure that is the case. That was often the role my fellow linguists and myself found ourselves playing, so it is to be expected the anthropologists currently serving are seen in their cultural capacity as ‘super-linguists’ in a way. The difference obviously is, in many cases (I would like to think I was an exception), Emily Post was the only role my fellow linguists and myself were able to play, not being versed in the theories of culture, but rather only its practice. The good thing here is that the army will adapt as it gains a better understanding of the ‘skill set’ (to use the military term) that anthropologists can bring to the mission, and the military will. The one thing I have noticed about dogmatic systems having spent six years, including my time as a contractor, immersed in them is that when told to learn how to use a new tactic or tool and apply it, it will be learned. The military has a surprising number of bright people to figure it out.

As for the anthropologist in uniform carrying a weapon, it is a wide piece of Army philosophy that regardless of a person’s job specialty he or she is a soldier first, meaning that he or she must be prepared to defend both themselves and their comrades should the need arise. While I am surprised the anthropologist was in uniform as there are ways around that requirement, they would never be allowed to enter a possibly dangerous situation without one. One a cultural note, however, being armed in Afghanistan has no negative connotations in the minds of the people there. In fact it would be expected of anyone associated with the military.

I never had any negative reactions while I was in the country for having a weapon and I was often with the populace and found myself generally carrying two. I always found most of the people where I was, which was not in the south where heavy fighting occurs, to be generally genuinely friendly, especially when they learned I spoke Persian. In fact, my Tehranian accent usually led to interesting questions about which member of my family was Iranian (I am very Northern European-looking and always identified myself as an American). Contractors on the other hand are not necessarily required to be armed (for myself I would want at least a pistol which is easily concealed if I were in a war-zone, but I guess in some sense once a soldier always a soldier), so perhaps that would be a better way to go. Who knows, but I’m sure it’s one thing the military will figure out as this program develops. For one thing, the pay would be a lot better. I know there aren’t many anthropologists if any making the kind of money contractors do overseas.

In any case, it may be a while before we start to see the results of this change in policy in the two countries; maybe as much as a year or longer. It will take a while for the anthropologists to get fully integrated into greater military strategy, and then a little longer until the projects they begin and advise on start to build in momentum and importance, but I think nothing bad can come of it. The US isn’t leaving Iraq and Afghanistan because the AAA decides to boycott (in fact, let’s be honest, it may not even be a blip on the radar), so it’s either let the association’s members do what they want, or keep valuable help away not just from the gov’t, but also from the people in the countries which we all would like to rebuild.

Jeff Bristol

Rather than add comments of my own to Jeff’s post, I’ve decided on this occasion to post this ‘as is’, in the hope that those with more insight regarding this contentious issue, will feel prompted to add comments of their own to this post. Tim

I’m sure at least Afarensis will be happy to know that his undergraduate advisor, Bill Bass and the body farm he has built has debuted on Boing Boing today. It is not everyday that anthropology makes it on that site.

Boing Boing ultimately links to an article by Allan Bellows of Damn Interesting, who followed Bill Bass around and documented his research. For anyone interesting in part of the dirty work behind forensic anthropology, do check out Allan’s descriptive and entertaining post. 

Both P-ter of Gene Expression and John Hawks have covered the new publication on blood type O and malaria resistance. This is a very well studied marker and very important to human evolution because it has been a major selective force on the human population.  I even isolated my own blood type alleles recently and I’m happy to confirm that I’m O for both alleles because this new paper says how blood type O is more resistant to malaria. 

Here’s the link to the paper, which is currently open access, “Blood group O protects against severe Plasmodium falciparum malaria through the mechanism of reduced rosetting.” 

Many thanks to Adam James at freelancejournalists.org, for alerting us to this latest development in the fortunes of the Hadzabe tribe of Tanzania, whom it would appear, despite having the odds stacked against them, appear to have pulled off a spectacular victory in their attempt to retain domain over their traditional hunting grounds, which looked set to be taken over by helicopter-borne Saudi royals, who considered themselves to be in need of new recreational hunting grounds. Here’s some detail from his article…

One of Africa’s last hunter-gatherer tribes has won a “great victory” after an Arab royal family dropped plans to use the people’s ancestral land for commercial hunting.

A company acting on behalf of Crown Prince Sheikh Mohamed of the United Arab Emirates has pulled out of a deal made two years ago with the Tanzania government to hunt wildlife in 2,267 square kms of remote bush in the Yaeda Chini region of Tanzania, east Africa.

Campaigners feared if a hunting concession was granted to the company then the 400-estimated Hadzabe hunter-gatherers of Yaeda Chini would have been criminalised as poachers and driven off land their ancestors have lived on for 10,000 years.

The Hadzabe, who live in small groups and are believed to number less than 1,000 in total in Tanzania, are the closest cultural relatives to the San bushmen of the Kalahari in Botswana.

I must admit that after months of seeming silence, I was somewhat pessimistic regarding the final outcome of this battle, as it appeared that the deal had been done, and that in due course the surrounding landscape would have been echoing to the sound of Saudi helicopter-gunships massacring the big game on the ground below. And although there was a considerable amount of opposition expressed on the Web and elsewhere, the overall impression I had was that as there didn’t appear to be a concerted effort to defend the Hadzabe, their days as hunter-gatherers were strictly numbered. But as we can see, the company behind the recreational hunting initiative, UAE Safaris Ltd., have themselves decided to head for the hills, though not without a few parting shots in the direction of the world’s media…

A UAE Safaris statement read: “To suggest or imply that the company operations included restricting or preventing Hadzabe tribesmen from continuing their traditional hunting practices is incorrect – traditional hunting practices are subject only to Tanzanian law.”

“However, a commercially motivated misrepresentation of the company’s intentions and activities has been continuously perpetuated by certain interest groups. This has regretfully caused us to review the long term sustainability of our planned program in the entire region resulting in our reluctant withdrawal.”

Read the rest of this entry »

Razib beat me the the punch on the new news that some Neandertals had red hair. He’s managed to write a very thorough and informative post over at Gene Expression. Check it out. Paul Rincon, a reporter for the BBC also has news of this, here.

This is a very curious finding and the entire study will be published in Science by tomorrow. Here’s an inactive link to the publication. It should start working once Science decides its time. All I have to share with you is the following excerpt, plucked from Razib’s post,

“The melanocortin 1 receptor (MC1R) regulates pigmentation in humans and other vertebrates. Variants of MC1R with reduced function are associated with pale skin color and red hair in humans primarily of European origin. We amplified and sequenced a fragment of the MC1R gene (mc1r) from two Neanderthal remains. Both specimens have a mutation not found in ~3700 modern humans. Functional analyses show that this variant reduces MC1R activity to a level that alters hair and/or skin pigmentation in humans. The impaired activity of this variant suggests that Neanderthals varied in pigmentation levels, potentially to the scale observed in modern humans. Our data suggest that inactive MC1R variants evolved independently in both modern humans and Neanderthals.”

Based upon Razib’s discussion on the author’s unique discovery a of non-synonymous substitution in the Neandertal MC1R of an A to a G which encodes the amino acid Arginine instead of Glyceine…. A SNP not found easily found in modern humans, I decided to look up what SNPs are known for modern humans’ MC1R. Currently, about 153 SNPS are known for modern humans’ MC1R. I haven’t bothered to translate all 153 sequences to see which ones show up an arginine where a glyceine was, but I’m pretty sure the authors did that, and screened their Neandertal specific SNP to this public data, before they published their paper.

This unique SNP reduces expression of the protein which MC1R produced, and a loss of function on MC1R, which results in fair skin and red hair. The really strange thing is that, like I said, this SNP ain’t found easily in modern humans. But in the two Neandertal samples they found, from Spain and Italy, this SNP was present.

A related curiosity is how this publication comes a week after the findings with FOXP2. One of the lead authors of the Neandertal FOXP2 paper is Carles Lalueza-Fox, is first author of the red haired Neandertal paper. It is somewhat remarkable how the FOXP2 paper got published in Current Biology, while very similar, related study from at least one of the same authors gets published in Science. Some, like myself, consider a study on hair color to be way less impacting than a study on the evolution of a language associated transcription factor. Anyways, not a very astute observation… who really knows why Science went the superficial route.

Eric at The Primate Diaries has posted the latest edition of Four Stone Hearth, which as he rightly points out, is the first edition of its second year. And a roaring start it is to this second year, with an impressive array of contributions from around the blogosphere, including entries from a few blogs that were hitherto unknown to me, particularly in the Cultural and Linguistic Anthropology sections, so I’ll look forward to checking out these sites, as well of course all the other entries in the Archaeology and Biological/Evolutionary sections.

The next edition of Four Stone Hearth will be with us in two weeks’ time, and on this occasion will be hosted by Sam Wise over at Sorting Out Science on November 7th. So until then, enjoy reading the current edition, and many thanks to Eric for compiling such a good collection of posts, as well as to everyone who kindly submitted content.

See you all on November 7th.

A quick reminder to anyone and everyone considering submitting content for the forthcoming 4SH – this from Martin at Aardvarchaeology…

Wednesday 24 October will see the Four Stone Hearth blog carnival appear in all its archaeo/anthro glory at The Primate Diaries. If you have read or blogged anything good on those themes lately, then make sure to submit it to Eric ASAP. (You are encouraged to submit stuff you’ve found on other people’s blogs.)

There’s an open hosting slot on 5 December and further ones closer to Christmas. All bloggers with an interest in the subject are welcome to volunteer to me.

If you’re a regular reader of this site, there are some times when my university doesn’t come through for me, such as its reluctance to subscribe to Nature and Science. But there are other times when my university really shines, such as on Friday afternoon, when I visited the Joint Genome Institute’s Production Genomics Facility in Walnut Creek, California because one of my classes arranged a tour.

Aside from being one of the largest dedicated DNA sequencing operations in the world, the JGI’s Production Genomics Facility is remarkable because it is helping sequence the Neandertal genome. The specific JGI scientists, James Noonan, Doug Smith, Joe Alessi, Feng Chen, Darren Platt, and Edward Rubin along with others, published the first 65,000 or base pairs of the Neandertal genome last year in this publication, “Sequencing and Analysis of Neanderthal Genomic DNA,” and they continue to make some headway.

I didn’t get to meet Noonan and Rubin, unfortunately. But I did get to see their facilities and the methodology they use to sequence any genome. They use a tried and true method of sequencing DNA which involves shearing all the genomic DNA first. Then, they insert the fragments of DNA into vectors of various sizes. This creates libraries that are important for scaffolding which is a way of rearranging fragments into a genome once sequencing is done. The vectors are shocked into bacteria, who, after platting and incubating, replicate with the vectors inside. The bacteria grow into colonies which are picked and the vectors are removed. Another round, or 30, of amplification is done with PCR and the samplesare labeled with florescent dyes and cleaned up to be sequenced.

The DNA is loaded into machines to be sequenced via capillary electrophoresis. This is called the Sanger method which reads the florescently labeled DNA fragments. These fragments, of varying size, are reassembled like a puzzle. The overlapping pieces help piece together the puzzle just as one uses the edges of a puzzle to create a framework. Once that’s done, the genome is finished and annotated.

This is all done at the JGI’s facility in Walnut Creek. It’s a really breathtaking operation, not only because it’s all done in house but because it is almost fully automated. Once the genome is sheared up and inserted into vectors, machines basically take over. I was in the room full of the sequencers, the Sanger machines, and I was nearly floored with how amazing it was. Even the platting of bacteria is automated. The coolest thing was the machines that pick off the bacteria. The robots take a photo of the plate and determine the ‘right’ colony to be plucked. Then an arm with a bunch of needles delicately picks up the bacteria.

I did get to see the 454 sequencing machines, which they currently have two of. I’ve introduced 454 before, because they are playing a vital role in sequencing the Neandertal genome. 454 is really good at sequencing small fragments of DNA, something which the Sanger machines can’t do well. An experiment was being loaded up while I was there. I was shocked to hear each usage of the machine requires over $5,000 worth of reagents to complete.

Also in their new technologies department was a Solexa/Illumina sequencer, which is kinda of a competitor to 454. They both use massive parallel sequencing of millions of fragments, but the Solexa is more or less continuous. Each experiment with Solexa instrument creates over 1 terabyte of data. That’s a crazy amount! The informatics there must be inundated.

Anyways, I was completely enamored. The US Department of Energy really has a gold mine of an institute there. If you live in the area, or ever visit the East Bay area, definitely check them out. They give tours to the public and educate you thoroughly. They also send you off with a lot of schwag, which is always nice.