Harappa Ancestry Project, t-minus one day

Zack is going to post the first batch of results from HAP tomorrow. It looks like he’s going to be using mostly the merged HGDP, HapMap, SVGP, and Behar data set, supplemented by a second set which also merges the Xing et al. sample (the intersection of Xing et al. with the other results is a much smaller number of SNPs, but, it includes a better coverage of various South Asian groups). He’ll initially be posting ADMIXTURE estimates as you’ve seen on Dodecad. I’m especially interested in the Anglo-Indian and Roma individuals which have sent Zack their samples. I don’t know of any genomic investigation of the former community, while the published research on Roma genetics doesn’t include SNP-chip results (usually they’re mtDNA, Y, or only a few autosomal markers). I’d be curious for possible evidence of homozygosity or linkage disequilibrium in the Roma individual due to the population bottlenecks which other studies have detected (I assume that’ll be in the future). The Roma are to a good approximation an admixture of India, West Asia, and European (often Balkan) groups, but, their history of endogamy and small founding groups experience rapid demographic expansion, are also critical to remember.

Here is the regional breakdown so far:

Read More

What do the people think?

With all the geopolitical tumult and news I was a bit curious to see what The World Values Survey could tell us about public opinion in Egypt and Tunisia. Unfortunately, Tunisia hasn’t been in any of their surveys, though Egypt has. So I thought it might be interesting to compare the USA, Sweden, Turkey, Egypt, and Iraq, for wave 5, which occurred in the mid-2000s. The main thing I took away from the exercise is to reflect that Americans are a more equivocal people than I had expected. Many of the questions have a 1 to 10 scale, and I’m providing the most extreme answers. So the low fractions for Americans for some questions point to a relative moderation on some topics…which is kind of weird when you are asking whether “People choosing their leaders is an essential characteristic of democracy.” Since that’s the definition of democracy broadly construed anything below a 10 out of 10 seems strange to me.

Read More

Around the Web – January 31st, 2011

The first month of 2011 is almost over….

Exiled Islamist Leader Returns to Tunisia. “…while Ennahdha was branded an Islamic terrorist group by Ben Ali, it is considered moderate by scholars.” I remember talking to a gay friend after 9/11 about Islam, and he began to repeat the pablum about how most Muslims were moderate and tolerant. I had to disabuse him of the notion that they would be as tolerant of him as the Christians at the local Congregationalist church. One can be moderate, but if the scale is set at one end of the broader distribution, that moderation can be quite extreme from the vantage point of an outsider. So a recent survey of British Muslims found that 0 out of 500 would accede to the position that homosexuality was morally acceptable. Certainly within the set of 500 there were many moderates on the issue, but the center of the distribution would probably not be what we’d consider “gay-friendly” (it might in fact be tolerance in a more pre-modern sense, where the majority suffers that the minority may exist, so long as they do not become undue burdens or flout public mores).

Selection is random. I don’t know if this is what the general population would term “random,” but it is an important point insofar as even if natural selection can be conceived as a deterministic process when you expand the parameters of population size and time to infinite, it still operates in a stochastic cauldron. That beings said, another point worth remembering is that selection is also stochastic insofar as it may operate over a set of equally fit adaptive peaks, and there’s no rhyme or reason to which peak selection may eventually drive the population toward (or, consider different genetic architectures which would lead to the same phenotypic value for a quantitative trait).

A Golden Age of Foreign Films, Mostly Unseen. I don’t know if this is relevant, but from what I have heard the “long tail” has not really panned out.

Read More

"Asian" in all the right places

mtDNA haplogroup G1a2

The pith: In this post I examine the most recent results from 23andMe for my family in the context of familial and regional (Bengal) history. I also use these results to offer up a framework for the ethnognesis of the eastern Bengali people within the last 1,000 years, and their relationship to other South Asian and Southeast Asian populations.

Since I received my 23andMe results last May I’ve been blogging about it a fair amount. In a recent post I inferred that perhaps I had a recent ancestor who was an ethnic Burman or some related group. My reasoning was that this explained a pattern of elevated matches on chromosomal segments with populations from southwest China in the HGDP data set. But now we have more than my genome to go on. This week I got the first V3 chip results from a sibling. And finally, yesterday the results from my parents came in. One thing that I immediately found interesting was my father’s mtDNA haplogroup assignment, G1a2. This came from his maternal grandmother, and as you can see it has a distribution which is mostly outside of South Asia. In case you care, I asked my father her background, and like my patrilineage she was a “Khan,” though an unrelated one (“Khan” is just an honorific). I received these results before the total genome assessment, and so initially assumed this confirmed my hunch that my father had some unknown recent ancestry of “eastern” provenance. But it turns out my hunch is probably wrong. In fact, my parents have about the same “eastern” proportion, with my mother slightly more! My expectation was that perhaps my mother would be around 25-30% “Asian,” and my father above 50%. The reality turns out that my father is 38%, and my mother 40%.

Image credit: f_mafra

Below are the “Ancestry Paintings” generated by 23andMe for my family (so far). What you see are the 22 non-sex chromosomes, which have two copies each, and assignments to “Asian,” “European,” and “African,” ancestry groups. The reference populations to generate these assignments come from the HapMap, the northern European sample of white Americans from Utah, Chinese from Beijing, Japanese from Tokyo, and ethnic Yoruba from Nigeria. What the assignment to one of these classes denotes is that that region of the genome is closest to that category in identity. It does not imply that your recent ancestry is European or Asian (African is probably a different matter, but there are many complaints about the results for African Americans and East Africans in the 23andMe forums). This caveat is especially important for South Asians, because we generally find that we’re ~75% European and ~25% Asian. All that means is that though most of our genetic affinity is with Europeans, a smaller fraction seems to resemble Asians more. Via “gene sharing” on 23andMe I can see that the Asian fraction varies from ~35% in South India and Sri Lanka, to ~10% in Pakistan and Punjab. This is not because South Indians have more East Asian ancestry than Punjabis. Rather, to a great extent the South Asian genome can be decomposed into two ancestral elements, one with a distant, but closer, affinity to populations of eastern Eurasia, and one with a close affinity to populations of western Eurasia. What some have termed “Ancient South Indians” (ASI) and “Ancient North Indians” (ANI). ASI ancestry, which is probably just a touch under 50% in South Asians overall, seems to shake out then as somewhat more Asian than European.* The fraction of ASI increases as one moves south and east in South Asia (and as one moves down the caste status ladder).

Read More

Harappa Ancestry Project, before the first wave

Zack has been posting his data sources, as well as how he filtered and formatted them, all this week. I assume that the first wave of results will be online soon. As of yesterday, this is what he had (I know he got some more today):

– Punjab 7
– Bengal 1
– Bihar 1
– Tamil 5
– Karnataka 1
– Anglo-Indian 1
– Roma 1
– Iran 3

Whole swaths of north-central India are missing. I am hopeful that more people will join in after the first wave of results are put out there. But, from what I have discussed with Zack it looks plausible that the very first wave will have a richer set of results because of the necessity of preliminary steps. So there’s some benefit in getting early. It’s really ridiculous to have literally 1 sample representing the 300 million people of Uttar Pradesh and Bihar. That’s 25% of South Asians represented by one person. I’ve gotten a commitment from one friend who was born U.P. to give his data up once it comes in, but there have to be others out there. (the Bengali N should go up to 2 when I swap my parents in for me)

The public data sources have Gujaratis, Tamils, Pakistanis (Punjabis, Pathans, Sindhis), and some South Indian groups (Tamil and Telugu). This leaves a blank spot on the North Indian plain.

Here’s the brief for the project again.

A 'leaky' model

John Farrell pointed me to this Anne Gibbons’ piece, A New View Of the Birth of Homo sapiens. Here’s some interesting passages:

The new picture most resembles so-called assimilation models, which got relatively little attention over the years. “This means so much,” says Fred Smith of Illinois State University in Normal, who proposed such a model. “I just thought ‘Hallelujah! No matter what anybody else says, I was as close to correct as anybody.’ ”

But the genomic data don’t prove the classic multiregionalism model correct either. They suggest only a small amount of interbreeding, presumably at the margins where invading moderns met archaic groups that were the worldwide descendants of H. erectus, the human ancestor that left Africa 1.8 million years ago. “I have lately taken to talking about the best model as replacement with hybridization, … [or] ‘leaky replacement,’ ” says paleogeneticist Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, lead author of the two nuclear genome studies.

I suppose ‘assimilation’ sounds too generic, but ‘leaky replacement’ seems more fitting for a building ‘super’. But it isn’t as if paleoanthropology has a Don Draper, a rogue with a way with words.

Here’s the infographic that went along with it:

Read More

American history in broad strokes

A comment below inquired about “good books” on American history. Unfortunately I don’t know as much about American history as I do about Roman or Chinese history. But over the years there have been several books which I find to have been very value-add in terms of understanding where we are now. In other words, these are works which operate with a broader theoretical framework, and aren’t just a telescope putting a spotlight on a sequence of facts.

Albion’s Seed. I read this in 2004, and it was a page turner.

The Cousins’ Wars. I had thought of Kevin Phillips as a political writer, but this was a very engaging and deep cultural history. My prejudice resulted in my not reading this until 2009.

What Hath God Wrought. This book focuses on the resistance of the Whigs and Greater New England to the cultural ascendancy of the Democrats and their “big-tent” coalition which included most of the South, the Mid-Atlantic, and much of the “Lower North” (e.g., the “butternut” regions of the Midwest settled from the Border South).

The Rise of American Democracy. This is a good compliment to the previous book, in that it takes the “other side,” that of the Democrats. In many ways this is the heir to Arthur Schlesinger’s Age of Jackson.

Throes of Democracy. A somewhat “chattier” book than the previous ones, it is still an informative read. It covers a period of history with the Civil War as its hinge, and so gives one the tail end of the Age of Sectionalism.

Freedom Just Around the Corner. By the same author, but covering a period of history overlapping more with Albion’s Seed.

The Age of Lincoln. This is not a “Civil War book.” It is of broader scope, though since the the war is right in the middle of the period which the book covers it gets some treatment. I’d judge this the “easiest” read so far of the list.

Replenishing the Earth. This is about the Anglo world more generally, but it is nice to plug in America into a more general framework. North America is not sui generis.

The English Civil War. This is obviously not focused on America, but it is a nice complement to Albion’s Seed, as it shows the very deep roots of the division between two of America’s folkways. The Cousins’ Wars serves as a bridge between the two, shifting as it does between both shores of the Atlantic.

I’m game for recommendations! I had a relatively traditional education in American history, and did very well in my advanced courses, but I knew very little before I read books like this.

The scions of Shem?

The media is reporting rather breathlessly a new find out of Arabia which seems to push much further back the presence of anatomically modern humans in this region (more accurately, the archaeology was so sparse that assessments of human habitation seem to have been made in a vacuum due to absence of evidence). Here is the major objection:

This idea is at odds with a proposal advanced by Richard Klein, a paleoanthropologist at Stanford University, that the emergence of some social or behavioral advantage — like the perfection of the faculty for language — was required for modern humans to overcome the surrounding human groups. Some kind of barrier had to be surmounted, it seems, or modern humans could have walked out of Africa 200,000 years ago.

Dr. Klein said that the Uerpmann team’s case for an earlier out-of-Africa expansion was “provocative, but in the absence of human remains, it’s not compelling.

The stone tools of this era are all much alike, and it is hard to tell whether early modern humans or Neanderthals made them. At the sites of Skhul and Qafzeh in what is now Israel, early modern humans were present around 100,000 years ago and Neanderthals at 60,000 years, but archaeologists cannot distinguish their stone tools, Dr. Klein said.

A warmer and wetter climate around this time let modern humans get as far as Israel but apparently no farther, and the new findings from Jebel Faya could represent a second limited excursion. But in this case, it is Africa that is expanding, or at least the African ecological zone, and not modern humans, Dr. Klein said. “The key issue is whether this is an early out-of-Africa movement, but if so, it was far more limited than the modern human expansion to Eurasia roughly 45,000 years ago,” he said.

Image credit: Maathias Kabel

In The Dawn of Human Culture Richard Klein argued that modern humans as we understand them today, protean and highly cultural creatures, are a product of a biological change which reordered our cognitive faculties. Klein pinpoints this change to the “Great Leap Forward” ~50,000 years ago. But, there is a large gap in time between anatomically modern humans, who were resident in Africa nearly ~200,000 years ago, and behaviorally modern humans, who engage in the symbolic cultural production which we perceive to be the hallmarks of humanity. As against this particular model there have always been “gradualists,” who argue that there was no discontinuous biological change which resulted in the shift toward hyperactive cultural production. Stephen Oppenheimer makes the case for this in his book The Real Eve. Oppenheimer suggests that there was a gradual and cumulative cultural evolution. He argues that a proper analogy might be the rate of cultural change in the 20th century vs. than in the 17th century. Obviously we know that genetic evolution can not explain most of the difference in rate of change across the two eras, but looking at archaeological remains from the two periods would make clear their stark differences to a third party observer to the point where I can’t help but think a biological rationale would seem plausible without any other information.

ResearchBlogging.orgI have no particular brief for either position in this post. I assume that both the biological and cultural models are too extreme now. The long term persistence of the Oldowan culture in much of the world implies to me that there may have been a biological chasm between hominin groups, and that the Oldowan “culture” was somehow biologically encoded. And yet I am not convinced that the gap between our Neandertal and neo-African ancestors was as great as Klein would have us believe. So now to the paper. First, let’s look at the abstract:

Read More

Neandertal (haplotype) in the family!

There is pretty much a 100% probability that I carry Neandertal origin genes, since I’m Eurasian. That being said, I hadn’t looked too closely into the matter in regards to my own genome, because the whole “which SNPs are Neandertal” issue has been pretty dicey. But after the “Neandertal dystrophin” paper sniffing for whether you carry a specific Neandertal haplotype got a whole lot easier. The authors provided the markers and their associated haplotypes within the paper. So if the B006 haplotye is Neandertal, by looking at your markers in 23andMe through the browse raw data feature you can figure out what your lineage is, and see if you are indeed “Neandertal” on that locus. Since it’s on the X chromosome, males will carry only one copy of the gene. On the other hand, if you’re a woman you’ll have two copies, so ascertaining what specific combination of markers you have spanning a particular genomic segment can be more difficult (the results are not “phased,” so you don’t know if the allele is from the mother or father on any given genotype). But inferring the sequence of markers on a strand of DNA is much easier if you have relatives to compare with.

As you know the results for my first sibling came back earlier this week. I decided to look at which haplotypes we carried. Below the fold are the SNPs (the links will take you to 23andMe, so if you are logged into your account it will take you to where you need to go):

Read More