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:

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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.

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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.

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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).

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1) First, a post from the past: Theological incorrectness – when people behave how they shouldn’t….sort of .

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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.

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:

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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.

I 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:

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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):

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Image credit: Luna04

My post The paradigm is dead, long live the paradigm! expressed to some extent my befuddlement at the current state of human evolutionary genetics and paleoanthropology. After the review of the paper of possible elevated admixture with Neandertals on the dystrophin locus a friend emailed, “Remember when we thought everything would be so simple once we could finally see this stuff?” Indeed I do remember. The fact that things aren’t simple is very exhilarating, but it is also a major quash on theoretical clarity. Science is after all not a collection of facts, but it is in part facts which one can sieve through a analytic framework.

In hindsight with the relative robustness of ancient DNA results we can make some assessments about the role of human bias within particular heuristic frameworks over the past generation. From the mid-1980s up until 2000 it was victory after victory for the Out-of-Africa with total replacement model. The rise of mtDNA and Y chromosomal lineage studies seemed to buttress the idea of common descent from neo-Africans within the last 100-200,000 years for all human populations. There wasn’t much of a perturbation from this march toward paradigm ascendancy in the aughts, except that there were now also now a trickle of papers which claimed to phylogenetic “long branches” in the human genome. The 2006 Evans et al. paper, Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage, was probably the one that made the biggest media splash. But these were inferences. Subsequent analysis of the draft Neandertal genome seems to suggest that in fact the microcephalin allele in question did not introgress.

Case closed? Obviously not. Now we’re in a different era. The Evans et al. paper may have wrong in the specifics, but its general framework seems to likely have been validated: there are genetic lineages in the modern human genome which are not derived from the neo-Africans. But, let us remember that the overwhelming majority of the human genome is neo-African. A reasonable interval for non-Africans is 90-99% neo-African. But, a non-trivial minority has introgressed or admixed from other lineages. Out-of-Africa is mostly correct, but in some ways so is Multiregionalism. But how do we describe this? “Weighted multiregionalism”? “Mostly Out-of-Africa?” The old terms were nice because they were punchy and precise. If you look at Multiregionalism or Out-of-Africa in Wikipedia the newest results are noted, but it doesn’t seem that they’ve been integrated into the analytic narrative. Yet.

I have noted a few times that one thing you have to be careful about in two dimensional plots which show genetic variance is that the dimensions in which the data are projected upon are often generated from the data itself. So adding more data can change the spatial relationships of previous data points. Additionally, in 23andMe’s global similarity advanced plot you are projected onto the dimensions generated from the HGDP data set. There are some practical reasons for this. First, it’s computationally intensive to recalculate components of variance every time someone is added to the data set. Second, it isn’t as if the ethnic identity of any given individual is validated. What would you do if an alien sent in a kit and spuriously put “French” as their ancestry?

So, in reply to this comment: “Let me rephrase: is there any difference when you switch to the world-wide plot? I imagine not, or you would’ve mentioned it.” Actually, there is a slight difference. Below on the right you have a “world view,” with my position being marked with green, and on the left a “zoom in” for Central/South Asia in the HGDP data set.

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After 2010′s world-shaking revolutions in our understanding of modern human origins, the admixture of Eurasian hominins with neo-Africans, I assumed there was going to be a revisionist look at results which seemed to point to mixing between different human lineages over the past decade. Dienekes links to a case in point, a new paper in Molecular Biology and Evolution,  An X-linked haplotype of Neandertal origin is present among all non-African populations. The authors revisit a genetic locus where there have been earlier suggestions of hominin admixture dating back 15 years. In particular, they focus on an intronic segment spanning exon 44 of the dystrophin gene, termed dys44. Of the haplotypes in this they suggested one, B006, introgressed from a different genetic background than that of neo-Africans. The map of B006 shows the distribution of the putative “archaic” haplotype from a previous paper cited in the current one from 2003. As you can see there’s a pattern of non-African preponderance of this haplotype. So what’s dystrophin‘s deal? From Wikipedia:

Dystrophin is a rod-shaped cytoplasmic protein, and a vital part of a protein complex that connects the cytoskeleton of a muscle fiber to the surrounding extracellular matrix through the cell membrane. This complex is variously known as the costamere or the dystrophin-associated protein complex. Many muscle proteins, such as α-dystrobrevin, syncoilin, synemin, sarcoglycan, dystroglycan, and sarcospan, colocalize with dystrophin at the costamere.

Dystrophin is the longest gene known on DNA level, covering 2.4 megabases (0.08% of the human genome) at locus Xp21. However, it does not encode the longest protein known in humans. The primary transcript measures about 2,400 kilobases and takes 16 hours to transcribe; the mature mRNA measures 14.0 kilobases….

Dystrophin deficiency has been definitively established as one of the root causes of the general class of myopathies collectively referred to as muscular dystrophy. The large cytosolic protein was first identified in 1987 by Louis M. Kunkel…after the 1986 discovery of the mutated gene that causes Duchenne muscular dystrophy (DMD) ….

OK, so we’ve established that this is not an obscure gene. Here’s the abstract of the new paper:

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Yesterday the first batch of results from 23andMe’s v3 chip came online. Instead of 550,000 SNPs you get ~1 million. The difference is pretty clear when you look at the raw SNPs. Under Account → Browse Raw Data, I can enter LCT, and this is what I see:

I’m line #2. A sibling is line #1. Looking at this sort of stuff makes it really likely I’ll upgrade. My main rationale for not upgrading is that there’s diminishing marginal returns for ancestry related stuff. Speaking of ancestry, let’s compare my sibling’s ancestry painting to my own.

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Participants So Far. Zack reports 10 people of South Asian ancestry have sent their raw data. His coverage seems OK, but he only has multiple samples from Punjabis. I know some people who will be sending their data in soon, and I’m going to swap my parents in for me, so Bengalis will go from N = 1 to N = 2, but please spread the word. Better coverage in eastern and southern South Asia is really needed.

Why Rich Parents Don’t Matter. Jonah Lehrer references my post When genes matter for intelligence. This is a possibility which I think needs to be more widely spread by the mainstream media: “Eliminating such inequalities in the early years of life would simply create a new kind of inequality, driven by genetics.” When people fret about the relative lack of class mobility into Ivy League universities compared to the 1960s, they might consider if the mobility of that era was simply a function of the relatively recent removal of previous discriminatory barriers. Once those barriers are gone for a few generations there’s no reason to expect that the “peak churn” would match the transition phase.

US equivalents. Comparing the aggregate GDP of American states to nations around the world.

Human Prehistory and Genetics Wiki. I don’t “do” the wiki thing myself, but in case you’re interested.

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Last week I announced the Harappa Ancestry Project. It now has its own dedicate website, http://www.harappadna.org. Additionally, it has its own Facebook page. For Zack to get his own URL he needs about 10 more “likes,” so please like it! (if you are so disposed) Finally, from what I’ve heard the first wave of the 23andMe holiday sale results are coming online this week. Actually, one of the relatives who I purchased the kit for is in processing currently, so I know that we should have a bunch of new people in the system very, very, soon.

Speaking of people, last I heard Zack had gotten about a dozen responses. That’s enough to start an initial round of runs, but obviously he needs more people. More importantly, the goal here is to get better population coverage. One of the things we know intuitively and also from the most current research is the existence of a lot of within-region population variation in South Asia which is structured by community. In other words, a sample of 30 people, where you have 3 from 10 different communities exhibiting geographical and caste diversity is going to be far more useful right now than 300 Jatts from Indian Haryana. Getting 300 Jatts for Haryana would be interesting in that it would give you a window into intra-communal variance, but there’s diminishing returns on the inferences you could make about South Asians as a whole.

If you know someone who has done the 23andMe testing and has preponderant ancestry from South Asia, Iran, Burma, or Tibet, please forward the the URL for the Harappa Ancestry Project. If you are a 23andMe member, and involved in the forums, it might be useful to post a comment thread on this project, as the people you share genes with would see it.