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Chrysostom, Against the games and the theatres, now online in English

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Mark Vermes has completed for us an English translation of Contra ludos et theatra (PG 56, columns 261-270), which I have put in the public domain.  I’ll make an HTML version later, but you can get a PDF and a DOCX from Archive.org here:

http://archive.org/details/ChrysostomAgainstTheGamesAndTheTheatres

As always, you are free to use or distribute this for any purpose, personal, educational or commercial.  I hope it’s useful!

 


Doctor Who Shoes on my Christmas List

Turkish Seller Offers Erdfrisch papyri on EBay

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The Scripture blogs are now discussing freshly-surfaced papyri, this time a sale on eBay. The current threads seem to begin with a post on The Quaternion (An Academic Blog about the New Testament and Early Christianity: Manuscripts, Texts, and Contexts, run by Brice Jones):
 Just today (29 October 2012), a seller on eBay posted anauction with the title, “Greek-Coptic Roman Rare Egyptian Uncial PapyrusFragments.” This seller (“mixantik”), who is from Turkey, has been auctioning hundreds of ancient Coptic and Greek papyrus fragments in lots on eBay for at least a year. I have contacted this seller on several different occasions to inquire about some of his papyri. He tells me that all of his papyri come from Egypt, although it is not clear precisely where in Egypt. But it is clear that someone has discovered a very large quantity of papyri. A colleague has suggested to me that perhaps the locals are continuing to find papyri in Oxyrhynchus, which is a possible scenario. The papyri that are sold by this dealer are 100% authentic; this can be verified by an analysis of the handwriting from the images the seller posts on eBay—usually very good images. I check eBay daily, with the search phrase “papyrus fragment,” to see if this seller (or any other) is auctioning off papyri. This seller's previous lots have sold for pennies, anywhere from $20 to $300.
Yes, and I see from his feedback that the owner of a certain "responsible antiquities collectors" discussion list has recently been one of his customers (#320890937385), I wonder whether he applied his own list's "Code of Ethics" to these purchases? Yes I mean Tim Haines. Other dealers are also recognizable in the list of those leaving feedback.

In the comments we read:
Most of his fragments are in fact Greek. It would seem that, given the quantity of Greek fragments that he has sold over the last year or so, someone has made a big find. In the images he posts, there is dirt all over the papyri, which tells me these are coming straight from the ground.

Anyway "Mixantik" is (despite the claim to be based in the USA) based in Istanbul, and formerly traded under the name of "Yasasgroup" (on eBay Jan-Oct 2008), but as "Mixantik" since Oct 2008. Both in his former incarnation, as well as the first months of operation under the new name is eBay sales consisted mainly of Ottoman antiques, but also Coptic antiques (including pages ripped from 11th and 14th century Bibles), so potentially originally coming from Egypt (less likely Sudan) - so how are they coming on the market? From January 2009 alongside these items, the first pieces of Coptic textiles start to appear in the descriptions attached to the feedback, some clearly labelled "Roman Egypt". From February 2009 the first papyrus fragments started coming onto the market. So they've been sold for three years right under everybody's noses, along with all sorts of other stuff, with a marked Egyptian bias. The current spate of the increased participation of 'dugups' in this dealer's offer dates back to June 1010. This dealer has also sold a fossil or two (one to Tim Haines). A few days ago he sold something which he described as "Oxyrhynchus papyri fragments" - dealer's blague or the actual provenance?

There is a firm called "Yasasgroup" in Istanbul, this imports and exports building materials, stone, marble, fibreglass mat etc. One wonders whether any of their products come from Egypt. Notably a "Yasasgroup" has a series of Photobucket pics of papyrus fragments here (cached). What, if any, is the connection between the building supplies firm and the antiques/antiquities dealer?

Very probably 'Mixantik', whoever he is, is doing nothing contrary to current Turkish law. Turkey however loudly demands its antiquities back from other countries, one might legitimately ask what Turkey is doing to prevent Turkish dealers selling off the antiquities from other countries (like dismembered medieval Coptic bibles and dugup antiquities from Egypt), and sending them out of the country further afield, to the USA to Britain (Mr Haines) and others. "Mixantik" has been selling masses of what look very much like freshly surfaced archaeological material for three years at least - and are the Turks doing anything about it? If they are not, then why do they expect others to listen to their demands to send back stuff which is not-exactly-freshly-surfaced?

UPDATE Thursday evening:
several "mixantik" auctions have just disappeared, they were of tightly-rolled muddy papyrus scrolls with some letters (?) visible on the outside he called them "dead books".  The scale used in the photos was a CD, better - I suppose - than the fag packet in other of his photos.

Vignette: EBay Pappy fragment, going for a song. 



Winning Ugaritic

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Jim West announced on his blog today that I was the winner of his giveaway of the brand new volume An Introduction to Ugaritic by John Huenegard. Since he said that I had the most compelling answer regarding why I deserved the book, it seemed it might be worth sharing what I wrote. I realize that my having the “most compelling answer” may be a polite way of saying that, of the very small number of entries in his giveaway, mine was the least lame by a very tiny margin.

Here’s what I wrote, in answer to his three questions:

1- In a few paragraphs describe how you came to be interested in Ugaritic.

The answer to this question requires multiple paragraphs. If there is one thing that I have learned from my undergraduate students, it is that one can always postpone the substance of what one has to say by including an introductory paragraph which does nothing other than postpone the matter at hand.

I am interested in Ugaritic for many reasons. I have long been fascinated with the texts that provide earlier parallels to stories and concepts we find in the Bible, and so I have been interested in Ugarit and the texts recovered there ever since I was an undergraduate. With my recent focus on Mandaic and other dialects of Aramaic, I have been focusing more attention on Semitic languages, and would love to be able to explore Ugaritic as well.

But in the final paragraph, I will confess the real reason for my interest in the volume. I am primarily a New Testament scholar. Most NT scholars know Koine Greek and little else. I would like to be the one cool guy in gatherings of NT scholars who knows Ugaritic.

2- Are you presently in University or Grad School and pursuing Ugaritic studies?

No – who would be so foolish as to pursue Ugaritic in grad school, when one can devote that time to major languages and learn Ugaritic on one’s own with the help of a handy volume like the one you are giving away?

3- If you’re chosen as the completely random winner based on your responses to the first 2 questions above, what will you do with the volume?

If I win I promise that I will never use the volume for the purpose of propping up table legs, swatting flies, or corporal punishment. I will, on the other hand, read it over and over again until I know Ugaritic!

 

Is the State Department Cultural Heritage Center Worth Funding with Money Borrowed From China?

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During one of the presidential debates, Republican Presidential Candidate Mitt Romney said his test for whether a federal program should be continued is whether it was worth funding with money borrowed from China.   Whether Romney wins the presidency or President Obama is reelected, the next Administration will face some hard choices about what programs are really worth funding. 

If the State Department is forced to start watching its pennies, I'm not sure its Cultural Heritage Center could really justify its worth compared to other worthy State Department programs.

The Center caters exclusively to a small group of academics and foreign cultural heritage bureaucrats.   The money it hands out to foreign countries to fund archaeological projects could probably be better spent on things like supplies of clean water or fighting aids.

Moreover, the actual public support for its program to restrict the import of cultural goods is quite slim.  And the net result of its activities has simply been to give foreign collectors and cultural goods dealers a competitive advantage.  While Americans face stifling red tape requirements that preclude entry of  thousands upon thousands of cultural artifacts, foreign collectors and dealers face no such hurdles and go about their business as usual.

Perhaps, the best thing to do would be to eliminate the Cultural Heritage Center and transfer CPAC and the decision making regarding import restrictions to the Department of Commerce.  Commerce is well suited for handling trade issues and would likely not take the anti-business stance that seems ingrained in the State Department bureaucracy.   

Will this happen anytime soon?  No, but hopefully federal budget makers will start asking some hard questions about exactly what the Cultural Heritage Center does for the American taxpayer.  Certainly, the Fourth Circuit Court of Appeals recently suggested that it might be time for Congress and the Executive Branch to pay more attention to what the Cultural Heritage Center is doing.

Antiquities trade in Nigeria: Looting in the midst of crisis

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Samarkeolog has a post on 'Antiquities trade in Nigeria: Looting in the midst of crisis', November 1, 2012. Good stuff as usual, not sure about this bit though:
African nations’ cultural objects have been harvested by foreign powers; attacked by religious movements and political factions; and, sometimes under duress, reduced to commodities and sacrificed for subsistence or survival [...] In addition to these activities, communities have been gouged by economic forces; they have been forced to tear their archaeological heritage out of the ground and sell it in order to subsist.
So why looting and not prostitution, nicking cellphones or selling kidneys? I do not think anyone is "forced" to sell knocked-off Nok heads or dugup pots, it surely is a choice. We too easily impose our own ideas of "heritage" on people to whom it is basically a foreign concept - see C.A. Folorunso, 'The Practice of Archaeology in Nigeria' pp 807-826 in L. Lozny 'Comparative Archaeologies: A Sociological View of the Science of the Past' (Springer 2011:ISBN:9781441982247), a book I recently had the misfortune to review.

Gays as God’s Gift

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Saturday Morning Breakfast Cereal provides a wonderfully satirical take on depressingly common assertions by preachers and pundits. If gays and lesbians were indeed the cause of hurricanes and earthquakes, imagine how that power could be harnessed for good…

HT Pharyngula

Open Access Journal: Marsh Bulletin


Mandaeans and Other Marsh Arabs

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Via Access to Mideast and Islamic Resources, I learned of the Marsh Arabs Heritage Project, which looks at the cultural, religious, and social life of the marshlands of Southern Iraq, including the Mandaeans, but also Muslims, Jews, Christians, Yezidis and others.

The pdf downloads appear not to have been added yet, but there is in essence an entire book online. Those interested in the people of that region and their heritage will find it interesting!

Hobbit banned as title of lecture on prehistoric ‘hobbit’

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hobbit

Powered by Guardian.co.ukThis article titled “Hobbit banned as title of lecture on prehistoric ‘hobbit’” was written by Alison Flood, for guardian.co.uk on Tuesday 30th October 2012 15.59 UTC

It was, perhaps, inevitable that Homo floresiensis, the three-foot-tall species of primitive human discovered on the Indonesian island of Flores, would come to be widely known as “hobbits”. After all, like JRR Tolkien’s creation, they were “a little people, about half our height”. But a New Zealand scientist planning an event about the species has been banned from describing the ancient people as “hobbits” by the company which owns the film rights to The Hobbit.

Dr Brent Alloway, associate professor at Victoria University, is planning a free lecture next month at which two of the archaeologists involved in the discovery of Homo floresiensis in 2003, Professor Mike Morwood and Thomas Sutikna, will speak about the species. The talk is planned to coincide with the premiere of The Hobbit film, and Alloway had planned to call the lecture “The Other Hobbit”, as Homo floresiensis is commonly known.

But when he approached the Saul Zaentz Company/Middle-earth Enterprises, which owns certain rights in The Hobbit, he was told by their lawyer that “it is not possible for our client to allow generic use of the trade mark HOBBIT.”

“I am very disappointed that we’re forbidden … to use the word ‘Hobbit’ in the title of our proposed free public event … especially since the word ‘Hobbit’ is apparently listed in the Oxford English Dictionary (and hence apparently part of our English-speaking vocabulary), the word ‘Hobbit’ (in the Tolkien context) is frequently used with apparent impunity in the written press and reference to ‘Hobbit’ in the fossil context is frequently referred to in the scientific literature (and is even mentioned in Wikipedia on Homo floresiensis). I realise I’m in unfamiliar word proprietry territory (as an earth scientist) … so I’ve gone for the easiest option and simply changed our event title.” said Alloway.

The event is now called “A newly discovered species of Little People – unravelling the legend behind Homo floresiensis”.

“Certainly, this name change won’t diminish the curiosity of the New Zealand public nor our collective enthusiasm for the Hobbit – whichever form you might be interested in knowing more about – the movie/book fantasy version or the fossil version found in Flores,” said Alloway.

• This article was amended on 1 November 2012 because the first paragraph and a quotation from Dr Brent Alloway referred to the Saul Zaentz Company/Middle-earth Enterprises as “representatives of the Tolkien Estate”. While the Saul Zaentz Company/Middle-earth Enterprises hold the film rights and some other rights to certain of JRR Tolkien’s literary works including The Hobbit, they are not representatives of the Tolkien Estate. The Estate has also asked us to clarify that it was not approached concerning Dr Alloway’s lecture.

guardian.co.uk © Guardian News & Media Limited 2010

Published via the Guardian News Feed plugin for WordPress.

Come, be Impressed by My Papyri

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If you follow the feedback to some of dealer Mixantik's papyrus sales, you can find out what happened to some of them. At least one guy appears to have bought several as-yet-unread fragments as a job lot and then gone to a local craft shop or home funishings store and bought some cheap  frames. He then put a fragment in each and then flogged them individually through eBay as "framed manuscript fragments, look good in your den" - in other words cool geegaws that look good on the wall. He made a profit and the buyer thinks he will look terribly eroodyte (a different slant on the "let me show you my etchings" come-on). When the owner tires of pretending to be erudite, or dies, whichever happens first, how many of these tatty yellowing fragments in a cheap 99-cent frame get deposited in a museum, and how many end up in the trash, or car-boot sale?

Is this really the correct way to treat a precious manuscript heritage?  Laws exist to prevent this happening, but private collectors - and buyers generally - have no interest in abiding by them (or even finding out what they are). Thus it is that information is lost, object disappear into private collections, and we are all the poorer for the loss.

Vignette: The ignoble fate of some dugup antiquities - to be sold for a few dozen dollars to thoughtless nerds who want some cool interior decoration accessories (photomontage from ebay pages).  A decent photograph would be just as decorative and atmosphere-forming. Meanwhile, evidence and associations are destroyed. And nobody gives a damn.

Sounds and Symbolism from the Netherworld:Acoustic Archaeology...

Neolithic monument unearthed in Cornwall

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Slate disc with incised decoration on both sides. Image: Cornwall Council

Archaeologists working at the site of the future Truro Eastern District Centre (TEDC) in Cornwall, southwest England, have discovered the fragmentary remains of a prehistoric enclosure built around 5,500 years ago.

Aerial view of the site. Image Cornwall Council Aerial view of the site. Image Cornwall Council

An important discovery

Initial surveys of the site were carried out in 2009, with a condition of the planning approval being to carry out further archaeological research. Preliminary findings from the excavations, led by Cornwall Council’s Historic Environment Service, suggest the eastern end of the site may represent a henge or possible causewayed enclosure dating to the early Neolithic period (circa 3800 to 3600BCE).

A causewayed enclosure was a sizeable circular or oval area enclosed by a large bank and ditch,” said Dan Ratcliffe from the Council’s Historic Environment Service. “These sites date to the early Neolithic – a period which also saw the first introduction of agriculture to Britain, the domestication of animals, the manufacture of pottery, and the first appearance of large communally built and used ceremonial monuments. Both the construction of the site and the activities within and around it probably served to bring communities together.”

Understanding causewayed enclosures

Angela Bilardi with Laura Ratcliffe (both from the Historic Environment Projects team) excavate the pit containing the slate disc. Image: Cornwall Council Angela Bilardi with Laura Ratcliffe (both from the Historic Environment Projects team) excavate the pit containing the slate disc. Image: Cornwall Council

Recent research in the British Isles indicate that causewayed enclosures were constructed within a relatively short time frame. The concept seems to have originated in mainland Europe spreading quickly through France, Germany, Scandinavia and into the UK. Using the latest in dating techniques along with statistical analysis of C14 results, it has been shown that causewayed enclosures in Ireland appeared earlier than those in Kent, with those in Essex coming in at a slightly later period.

Around 80 sites with evidence of causewayed enclosures are known across southern Britain. The find at Truro – if it is a causewayed enclosure – is the first to be discovered to the south west of the border between Dorset and Devon although the ‘tor enclosures’ at Carn Brea and Helman Tor are thought to have been built at the same time and may have served similar functions.

A very unusual discovery on-site of a slate disc decorated on both sides and thought to date to the later Neolithic. Image: Cornwall Council A very unusual discovery on-site of a slate disc decorated on both sides and thought to date to the later Neolithic. Image: Cornwall Council

Cataloguing the finds

Now, the team will catalogue their finds, process samples and prepare to write a report on their work, but before then, they will carefully re-bury the partially excavated site to protect it for future generations.

Among some of the remarkably well preserved finds are large sherds of Late Neolithic Grooved Ware pottery (a type of pottery that is first produced in Orkney at the opposite end of the UK) and an unusual slate disc which is engraved on both sides. One side has a distinctive chequerboard pattern while the other has lozenges with arrowhead decoration. It is apparent that this artefact has been deliberately placed within a pit, but it is too early to posit a firm theory about it’s function or deposition.

Often, but not always, Grooved Ware is found within ceremonial and ritual locations, possibly acting as a receptacle for fermented drinks. It ranges in size from drinking cups to large straight sided vessels.

Late Neolithic Grooved Ware pottery discovered during the excavations.  Image: Cornwall Council Late Neolithic Grooved Ware pottery discovered during the excavations. Image: Cornwall Council

Preservation for future investigation

“While it is important that we take the opportunity to learn more about our findings now, best practice is for the site to be preserved for future generations of archaeologists who will have better technologies to understand it than we do today,” said Dan Ratcliffe from the Council’s Historic Environment Service. “Scientific analysis of evidence recovered during the excavations is expected to take some years after the sample excavation has concluded.”

Tim Wood, Cornwall Council’s assistant head of transportation, says: “The proposed development has sufficient flexibility in the design to ensure that the construction above does not interfere with the archaeological remains.” 

Source: Cornwall Council

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Not praising, burying: Cambridge day

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I will be spending the day at Fitzwilliam Museum in Cambridge tomorrow as part of the 'Not praising, burying' event [details]. At the start of the day I will be reflecting on the central themes of Artful Crafts. It strikes me that one of the central themes has been the way that Greek pottery has been removed from its ancient context and placed in an artificial "artistic" world that has promoted "important" creators. And museums and collectors have sought to acquire works by major names: Artful Crafts preceded the return of material to Italy from North American private collections.

I will be drawing attention to a Paestan krater once owned by Dr John Disney (founder of the Disney Chair of Archaeology) and acquired by the Fitzwilliam nearly a century after Disney's founding benefaction.

Next week the McDonald institute will be hosting a seminar to reflect on tomorrow (see also BBC).

Bookmark and Share so Your Real Friends Know that You Know

Lire demain – Reading tomorrow

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Last summer the University of Lausanne held a conference on the new forms of publication offered by Digital Humanities: From Ancient Manuscripts to the Digital Era). Now the proceedings of the conference have been published:

Taking advantage of the topic which was the theme of the conference, the editors choose to publish several versions of the proceedings. The videos from the main conferences were released quite soon after the venue on the conference’s main webpage (Humanités digitales@unil ). These are now also available in the more conventional paper-edition of the proceedings. The e-book version however covers the whole venue and contains 38 contributions.


Logos Bible Software 5 is Here

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Logos Bible Software has released the new version of their flagship project: Logos 5.

It incorporates some massive changes in datasets and built in resources while keeping much of the user experience quite similar to Logos 4. I had originally intended to have a useful post ready this evening surveying how tools for studying Greek have changed and have been improved, but prior commitments in thesis writing and a couple other undisclosed Greek projects have held me back. So that’s still in process right now (sorry). Ideally, it will be up by tomorrow. We’ll see.

The most exciting thing about Logos 5, in my opinion, is all the effort they have put into meaningful access to content. It isn’t about searching a massive number of books any more. It’s about finding useful information for specific questions. It’s about making the semantic web real within Logos. The Bible Sense Lexicon is an incredibly exciting project and a great example of creating structured and meaningful information and making it easily accessible.

I know a lot of people that work with languages at the same level I do (or higher) tend to be rather cynical about how tools for using Greek and Hebrew are present in Bible Software packages, but Logos also put significant effort into academic projects and they’re only able to do it because of the pastoral and layperson user base that they have to support such projects. Steve Runge’s Lexham Discourse Greek New Testament is an important example of this. Another is the SBLGNT. Personally, I’d rather work with them to improve how language study is done in the future than merely dismiss them. And, well, that’s what I have been doing and will continue to do so.

I’ll have more thoughts on Greek databases and changes and advancements in the coming few days (because there are some important ones), which is probably just fine. It looks like users are swamping Logos’ servers right now anyway…


Filed under: Biblical Studies, Greek, Libraries, Linking, Logos Bible Software, Other, Scholarship

ALDER paper and software (Loh et al. 2012)

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A new paper has appeared on the arXiv that introduces ALDER, a method for testing for admixture and inferring its parameters (when it happened and the proportions of the two mixing populations). You can get the software from here.

I have already tried it and I can confirm two claims in the paper (i) it's extremely fast, and (ii) it is conservative in the sense that it's test fails even when an f3 test of admixture indicates admixture. Here is a plot of one case where it detected admixture, ASW as CEU+YRI, I got the output on the right, which shows a very clear pattern of exponential decay. I also tried a different experiment using Mozabites as the admixed population. The results are quite interesting:

Test SUCCEEDS (z=10.39, p=2.7e-25) for Mozabite with {CEU30, YRI30} weights

DATA: success (warning: decay rates inconsistent) 2.7e-25 Mozabite CEU30 YRI30 10.39 6.75 11.39 55%  17.45 +/- 1.68 0.00037417 +/- 0.00003187 28.63 +/- 3.84 0.00005311 +/- 0.00000787 16.21 +/- 1.42 0.00023789 +/- 0.00001752

DATA: test status p-value test pop ref A ref B 2-ref z-score 1-ref z-score A 1-ref z-score B max decay diff % 2-ref decay 2-ref amp_exp 1-ref decay A 1-ref amp_exp A 1-ref decay B 1-ref amp_exp B

Notice that the 1-reference decay using CEU is 28.63 and with YRI it is 16.21, while the 2-reference (both CEU and YRI) is an intermediate 17.45. I believe that this is capturing the same behavior as Jin et al. (2012), according to which:
There was an almost complete absence of recent gene flow from European populations to the Mozabite gene pool (Figure 6A). For the Sub-Saharan African ancestral component, there were more long CSDAs at the tail of empirical distribution than those in the HI model, which confirmed that recent gene flow from African populations had contributed to the Mozabite gene pool (Figure 6B). 
This is also what ALDER is telling us, since the decay using CEU is more "abrupt" (hence lack of long segments of admixture that might indicate recent admixture), while that using YRI is less so (and hence recent Sub-Saharan admixture has contributed longer segments).

In any case, enough with my own preliminary experiments. From the paper itself, there are interesting applications of the new methodology for Sardinians, Japanese, and Central African Pygmies:
Both Central African Pygmy populations in the HGDP, the Mbuti and Biaka, show evidence of admixture (Table 1), about 28 +/- 4 generations (800 years) ago for Mbuti and 38 +/- 4 generations (1100 years) ago for Biaka, estimated using San and Yoruba as reference populations (Figure 2A,C). The intra-population heterogeneity is low, as demonstrated by the negligible affine terms. In each case, we also generated weighted LD curves with the Pygmy population itself as one reference and a variety of second references. We found that using populations French, Han, or Yoruba as the second reference gave very similar amplitudes, but the amplitude was significantly smaller with the other Pygmy population or San as the second reference (Figure 2B,D). Using the amplitudes with Yoruba, we estimated mixture fractions of at least 15.9 +/- 0.9% and 28.8 +/- 1.4% Yoruba-related ancestry for Mbuti and Biaka, respectively. 
For Sardinians:
We detect a very small proportion of Sub-Saharan African ancestry in Sardinians, which our ALDER tests identified as admixed (Table 1; Figure 3A). To investigate further, we computed weighted LD curves with Sardinian as a test population and all pairs of the HapMap CEU, YRI and CHB populations as references (Table 2). We observed an abnormally large amount of shared long-range LD in chromosome 8, likely do to an extended inversion segregating in Europeans (PRICE et al. 2008), so we omitted it from these analyses. The CEU–YRI curve has the largest amplitude, suggesting both that the LD present is due to admixture and that the small non- European ancestry component, for which we estimated a lower bound of 0.6+/-0.2%, is from Africa. The existence of a weighted LD decay curve with CHB and YRI as references provides further evidence that the LD is not simply due to a population bottleneck or other non-admixture sources, as does the fact that our estimated dates from all three reference pairs are roughly consistent at about 40 generations (1200 years). Our findings thus confirm the signal of African ancestry in Sardinians reported in MOORJANI et al. (2011). The date, small mixture proportion, and geography are consistent with a small influx of migrants from North Africa, who themselves traced only a fraction of their ancestry ultimately to Sub-Saharan Africa, consistent with the findings of DUPANLOUP et al. (2004).
Moorjani et al. (2011) had estimated 2.9% admixture in Sardinians occurring at 71 +/- 28 generations, so the new results appear to be different, perhaps on account of the the treatment of the chromosome 8 inversion or the ability of ALDER to pick the distance threshold (hard-set at 0.5cM in rolloff) adaptively. Also, note that ALDER is able to estimate admixture proportions based on the amplitude of the weighted LD, whereas in the previous test the proportions were calculated using an F4 ratio test which did not take into account East Eurasian-like gene flow into the CEU population, and considered both CEU and Sardinians as having experienced no Asian-related gene flow.

So it appears that the African admixture in Sardinians is real, but may be both lower and later than previously estimated. In a recent experiment, I "scrubbed" possible segments of African ancestry in Sardinians, and this diminished their African ancestry from 3.1% to 1.8%. If we consider the 1.8% to be the spurious admixture due to Asian-related gene flow into northern Europe, then African admixture in Sardinians will be the remainder 1.3%, and perhaps lower due to the very "intensive" nature of the scrubbing procedure.

globe4 estimates African admixture in Sardinians as 0.8%, with some heterogeneity in its apportionment in 28 different individuals (left), with three individuals appearing as outliers and the remainder randomly distributed around the 0.8% median. The outlier individuals are HGDP01062, HGDP01076, and HGDP01071; the last of these is not included in the curated version of HGDP released by Patterson et al. (2012). ALDER includes a facility for detecting heterogeneity in admixture, but I did not see this particularly discussed in my first scan of the paper. In any case, it now appears that different methods converge on a small African admixture in Sardinians, and the 1200-year old age estimate seems consistent with medieval history.


The paper also deals with the Japanese: 
Genetic studies have suggested that present-day Japanese are descended from admixture between two waves of settlers, responsible for the Jomon and Yayoi cultures (HAMMER and HORAI 1995; HAMMER et al. 2006; RASTEIRO and CHIKHI 2009). We also observed evidence of admixture in Japanese (Table 1), and while our ability to learn about the history is limited by the absence of a close surrogate for the original Paleolithic mixing population, we were able to take advantage of the one-reference inference capabilities of ALDER. We observed a clear weighted LD curve using HapMap JPT as the test population and JPT–CHB weights (Figure 3B). This curve yields an estimate of 45 +/- 6 generations, or about 1,300 years, as the age of admixture. To our knowledge, this is the first time genome-wide data have been used to date admixture in Japanese. As with previous estimates based on coalescence of Y-chromosome haplotypes (HAMMER et al. 2006), our date is consistent with the archaeologically attested arrival of the Yayoi in Japan roughly 2300 years ago (we suspect that our estimate is from later than the initial arrival because admixture may not have happened immediately). Based on the amplitude of the curve, we also obtain a (likely very conservative) genome-wide lower bound of 41 +/- 3% “Yayoi” ancestry using formula (12) (under the reasonable assumption that Han Chinese are fairly similar to the Yayoi population). It is important to note that observation of a single-reference weighted LD curve is not sufficient evidence to prove that a population is admixed, but we did find a pair of references with which the ALDER test identified Japanese as admixed, which, combined with previous work and the lack of any signal of reduced population size, makes us confident that our inferences are based on true historical admixture.
This is a useful application of the idea that you don't need both reference populations to estimate admixture. If a population A experiences gene flow from another B, then A will become more like B over time, and allele frequency differences between A and B will diminish but will continue to reflect differences between the local and introgressing element. This idea was first used by Pickrell et al. (2012), and a new variation of it is used in the current paper.

According to Wikipedia, Japanese skeletons of the Kofun period resemble those of modern Japanese, so perhaps the age estimate is a little younger than the actual period of admixture. In any case, perhaps admixture between populations carrying varying amounts of Yayoi/Jomon ancestry was not instantaneous, so ALDER is not picking up the beginning of a continuous process that lasted for several centuries.

Finally, there is a reference to another paper currently in submission: "MOORJANI, P., N. PATTERSON, P. LOH, M. LIPSON, and OTHERS, 2012 Reconstructing Roma history from genome-wide data. In submission." Given that the Roma likely possess really old West Eurasian admixture related to "Ancestral North Indians", as well as really recent European admixture after they migrated to Europe, and perhaps even intermediate West/Central Asian admixture as they made their way from India to the west, this seems like a very complicated case, involving admixture at different time scales, and between different but related populations, so it will be interesting to see how it will all fit together.

To conclude, ALDER seems like a very practical tool for studying admixture in human populations, so I'm sure it will prove quite useful in the future.

arXiv:1211.0251 [q-bio.PE]

Inference of Admixture Parameters in Human Populations Using Weighted Linkage Disequilibrium

Po-Ru Loh, Mark Lipson, Nick Patterson, Priya Moorjani, Joseph K. Pickrell, David Reich, Bonnie Berger

Abstract

Long-range migrations and the resulting admixture between populations have been an important force shaping human genetic diversity. Most existing methods for detecting and reconstructing historical admixture events are based on allele frequency divergences or patterns of ancestry segments in chromosomes of admixed individuals. An emerging new approach harnesses the exponential decay of admixture-induced linkage disequilibrium (LD) as a function of genetic distance. Here, we comprehensively develop LD-based inference into a versatile tool for investigating admixture. We present a new weighted LD statistic that can be used to infer mixture proportions as well as dates with fewer constraints on reference populations than previous methods. We de?ne an LD-based three-population test for admixture and identify scenarios in which it can detect admixture that previous formal tests cannot. We further show that we can discover phylogenetic relationships between populations by comparing weighted LD curves obained using a suite of references. Finally, we describe several improvements to the computation and fitting of weighted LD curves that greatly increase the robustness and speed of the computation. We implement all of these advances in a software package, ALDER, which we validate in simulations and apply to test for admixture among all populations from the Human Genome Diversity Project (HGDP), highlighting insights into the admixture history of Central African Pygmies, Sardinians, and Japanese.

Link

Looting Them and US

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The Wall Street Journal article discussed in the post above (Justin Scheck, 'Artifact Prices Draw Looters' Wall Street Journal November 2, 2012) also mentions the case of a California collector Norman Starks who had been accused of disturbing Indian artefacts on Federal land though he was in the end not convicted. The newspaper explains that the looting of ancient sites for collectables: 
troubles tribal members, who generally say that Indian artifacts should remain where they are. "This is our identity," said Darrel Cruz, cultural-resources director for the Washoe Tribe of Nevada and California. [...]  In recent years, his tribe has encountered disturbed graves and stolen petroglyphs, he said. 
 There is an interesting "them and us" thread running through this. Here the ancient artefacts in US soil are being preserved not for "us all", but for a "them living among us who are disturbed by it". This might go some way to explaining some of the (to us Europeans) odder opinions one comes across in a US milieu about cultural property and who it "belongs to", which seem at odds with other US statements and opinions about everybody's place in the world.

1912-2012 Εκατό χρόνια έρευνας στην προϊστορική Μακεδονία

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December 22, 2012 - 9:29 AM - συνέδριο
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