Razib Khan One-stop-shopping for all of my content

October 31, 2010

30,000 full human genomes by January 1st, 2012?

Filed under: Genomics — Razib Khan @ 11:37 pm

That seems to be the inference one can make from this thorough article in Nature, Human genome: Genomes by the thousand. Last summer I pointed to a projection of ~50,000 in 2011. Nature’s current tally is ~3,000 genomes sequenced. Though issues of accuracy are still important to remember, it’s pretty striking isn’t it only 10 years on from the Human Genome Project how far we’ve come? Over a one year period there will be a shift of about an order of magnitude. Though that may be a drop off from 2009-2010, which is likely to have been two orders of magnitude. Totally not rational, but I’m feeling a touch lame at only having 500,000 SNPs done.

Below are the charts from last summer….


genomeseq1
genomseq2

(link acknowledgement, Dan Vorhaus)

Leigh Van Valen Obit in The New York Times

Filed under: Biology,Leigh Van Valen — Razib Khan @ 3:22 pm

If you haven’t, check out the Leigh Van Valen obituary in The New York Times. I hadn’t been aware of the breadth of his work, and the disciplinary range he showed over his career.

On the “liberal gene”

Filed under: Behavior Genetics,Genetics — Razib Khan @ 1:54 pm

Jim Manzi has already posted on the warranted skepticism of DRD4 being reported in the press as the “liberal gene.” Here’s the original paper. The main issue I have is not with the original research, but the inevitable confusions in the media which always arise. First, we know that complex behavioral phenotypes such as religiosity and personality seem to be heritable. That is, a set of genetic variants within the population seems to track the variation in the trait (just as with I.Q.). But, it’s been a much longer haul to actually connect a specific genetic locus to said variation, though the dopamine related genes are always brought forward as candidates. Additionally, particularly when it comes to politics there’s the norm of reaction looming. One might grant that same genetic variation which predisposes Swedes in Sweden to being on the Left or the Right is operative among ethnic Swedes in Minnesota, but most of the difference is actually between population, and a function of the differing environmental milieus of the Upper Midwest and Scandinavia (though perhaps there were strong selection effects operating upon those who chose to leave Scandinavia for the USA). Finally, as with personality, there’s the problem of characterizing the phenotype in the first place in political orientation. Not insoluble in my opinion, but far less clear than something like height, or even intelligence.

The big picture is that variation on most complex behavioral traits has some upstream genetic correlates. And, we can get some sense of the magnitude (or lack thereof) of the effect in a given environment. But like fMRI the introduction of DNA probably adds more glitz than substance at this point. We’ve long known many traits which we think as purely reflective and environmental have a partial biological basis in disposition. Clearly an area to be continued….

October 30, 2010

Election 2010 Predictions

Filed under: Politics — Razib Khan @ 10:20 pm

800px-SarahPalinElonFor Congress, I think that the breakdown will be:

Senate – 50 Republicans, 50 Democrats

House – 240 Republicans, 195 Democrats

My reasoning? I just took FiveThirtyEight’s numbers and shaded them a bit to the Republican side. There’s no point in making predictions unless you predict something novel and a bit off expectations. Additionally, since the readership here leans a little Left I am inclined to tweak you guys a bit and make the political Götterdämmerung even more terrifying, though I didn’t want to push my luck and give you an implausible value which you’d reject on the face of it.

Image Credit: Therealbs2002, Wikimedia Commons

Have ADMIXTURE run on your genetic data

Filed under: Genetics — Razib Khan @ 9:51 pm

The last 24 hours of the initial sample collection phase of the Dodecad Ancestry Project are upon us. So if you have raw 23andMe data, you got a day to send it in, if you’re of the following groups:

-Greeks (not necessarily from Greece: Cypriots, Pontic Greeks from the former USSR, North Epirotes, Griko speakers from Italy, -Muslim rumca speakers from Turkey, etc. are all accepted)
-People from the Balkans
-People from Anatolia
-People from the Caucasus
-Italians
-Non-Indo-European speakers from Europe (e.g., Finns, Hungarians, Basques)
-Scandinavians and Icelanders
-Iranians
-Armenians
-Jews from Italy, the Balkans, or Anatolia
-Assyrians
-Arabs

The point of the project is to get a better picture of genetic variation in Eurasia, especially in undersampled groups.

The global human – II

Filed under: Culture,Faces — Razib Khan @ 9:15 pm

global2A reader pointed me to a second composite image of a “global human.” It is “a composite itself from four composite of Northwest European, South & West Asian, East Asian and African faces….” I was very taken aback by this face, because it was familiar: staring back at me is a younger variant of the faces of my maternal uncles! I asked a friend who has met my family their impression of the photo without a preface, and they immediately wondered if it was a stylized representation of one of my mother’s male relatives.

The possible impossibility of truth and the importance of incorrectness

Filed under: Knowledge,philosophy — Razib Khan @ 11:54 am

In the post below on the genetic history of India, or earlier when discussing the revisions of European prehistory, one general trend that is cropping up is that the future seems more complex and muddled than we’d presumed. This introduces the real possibility that in the foreseeable future we won’t be able to opine with any credibility about the nature of the pre-literate past, because our tools are good enough to falsify simple models, but not powerful enough to distinguish between the set of more complex models. In contrast, ten years ago when it came to the expansion of farming in Europe on offer we had simple and clear dichotomies; demic diffusion of Anatolian farmers vs. cultural diffusion of farming techniques along trade routes. Ten years ago when it came to India we are mooting the possibilities between elite transmission of Indo-European language, versus demographically significant migrations into South Asia bringing the Indo-Aryan dialects.


I think that such models are wrong, because there are major parameters left out of the picture. Now in the world we see around us the possibility of really achieving plausible consensus around a positive truth has decreased significantly, because the causal possibilities are proliferating. A model then becomes synonymous with a story. But to admit that it may be that we can’t know is still a greater improvement on the delusion that we did know.

These are general observations. R. A. Fisher’s attempt to transform evolutionary biology into a deterministic set of laws as powerful as those of thermodynamics seems to have failed; at least beyond a trivial level. The importance of history and contingency, of specific detail, muddles the general insight which we can derive in evolutionary processes. But if there is no general insight to derive then we shouldn’t be deriving it, should we? False confidence in knowledge we think we have is a far greater sin than the admission of ignorance.

October 29, 2010

Open Thread – October 30th, 2010

Filed under: Blog,Price Equation,The Price of Altruism — Razib Khan @ 11:27 pm

Oren Harman, author of The Price of Altruism is on BHTV. Recommended.

Coon and friends

Filed under: Blog,Coon,South Park — Razib Khan @ 11:24 am

This week’s episode of South Park was OK, but I really loved this take off on a scene from A Clockwork Orange:


My Dodecad results

Filed under: 23andMe,Anthroplogy,Dodecad,Genetics,Personal genomics — Razib Khan @ 10:51 am

A few days ago Dienekes opened up the Dodecad project to a wider range of Eurasians. I decided to send my 23andMe sample to Dienekes ASAP, and the results came back today. I’m DOD075. Dienekes also just put up an explanation of the 10 ancestral components he’s generating from ADMIXTURE (along with tree-like representations of their distances). Below I’ve placed myself in the more local context of populations to which I’m close to:

ADMIXTURE10

Here are all the populations.

Karnataka is a state in northwest South India, and can be taken as somewhat representative of the Dravidian populations. The purple component is a South Asia distinctive element. Using the terminology of Reich et al. it would be the ancient stabilized hybrid population which came out of the admixture of Ancient North Indians (ANI) and Ancient South Indians (ASI). On the margins I assume there’s just noise popping out; e.g., the “East Asian” sliver among the Kannada speakers from South India. On the other hand, the Burusho have shown evidence of East Asian admixture in other studies I’ve seen. They have a bit of the derived East Asian EDAR variant for example.

As for me, no surprise that I have a lot of “East Asian” for a South Asian. Since Dienekes is more interested in Western Eurasia he didn’t go to the point of dividing the East Asians into a northern and southern branch. I’m pretty sure I’d be in the southern branch, along with the Miaozu sample (more well known as Hmong to Americans). The bigger question is how atypical for an east South Asian I am. There is a certain basal load of East Asian ancestry among northeast South Asian Indo-Aryan speakers. Another question is whether my East Asian component can be attributed to the Mundari substrate absorbed by Indo-Aryans in northeast India, or by a more recent admixture of Tibeto-Burmans. Some of both surely, but knowing my family’s long residence on the eastern margins of the Indo-Aryan speaking domains of South Asia, cheek-by-jowl with Tibeto-Burmans, I believe I am likely to have some recent Burmese ancestry. Specifically through my paternal grandfather.

Finally, though it is just as likely to be nothing, I have a bit more “Southern European” than the other South Asians. I assume this is from my great-grandfather who was from Delhi, and part of the polyglot Muslim religious intellectual class of that city. His physical type, which my maternal grandmother inherited, was clearly West Asian. He probably had non-trivial Persian or Central Asian ancestry.

Friday Fluff – October 29th, 2010

Filed under: Blog,Friday Fluff — Razib Khan @ 8:25 am

FF3

1. First, a post from the past: Atheism, Heresy and Hesychasm. I used to post about religion a lot more, especially in the fall of 2006. That was back when ScienceBlogs was small enough and tight enough to have a back & forth discussion among the weblogs pretty easily. I also was working a lot of hours at my job at the time and that imposed a sort of tight discipline on me, I remember hustling off posts after work, before sleep, and on Saturday (into schedule queue).

2. Weird search query of the week: “dave mirra wife.” I had no idea who Dave Mirra was before I saw that query.

3. Comment of the week, in response to Daily Data Dump – October 25th, 2010:

White bread tastes good because its a more neutral base on to which to add other flavours. This is something you hicks will never understand.

4) OK, so last week’s poll didn’t work. In that it didn’t record any responses. Rather than do polls, I’ll just throw out a question, and let people answer if they so choose: which science blogs do you read? And do you have one yourself?

5) And finally, your weekly fluff fix:

worriedhustle

October 28, 2010

Daily Data Dump – October 28th, 2010

Filed under: Blog,Daily Data Dump — Razib Khan @ 10:57 am

A very special note: I endorse Christie Wilcox for 2010 Blogging Scholarship.

A map of human genome variation from population-scale sequencing. This paper is getting a lot of play. A taste of things to come from the 1000 Genomes Project. It’s OA, so check it out.

Difficulties in Defining Errors in Case Against Harvard Researcher. I think Marc Hauser will be an emeritus professor by the time the case involving his alleged misconduct is resolved.


Where did all these monkeys come from? – Fossil teeth may hint at an Asian origin for anthropoid primates. We were all Asians before we were all Africans! Before that perhaps were all Laurasians and/or Gondwanans. How about Pangaeans?

Sugar-Sweetened Beverages and Risk of Metabolic Syndrome and Type 2 Diabetes. “…individuals in the highest quantile of SSB intake (most often 1–2 servings/day) had a 26% greater risk of developing type 2 diabetes than those in the lowest quantile.” Genetic background probably matters in terms of the effect size.

The evolution of the marine phosphate reservoir. “We propose that these two factors are intimately linked; a glacially induced nutrient surplus could have led to an increase in atmospheric oxygen, paving the way for the rise of metazoan life.” Interesting stuff.

The global human

Filed under: Culture,Faces — Razib Khan @ 9:55 am

Paul Conroy sent me a link to a Dutch article which purports to illustrate what the average human male’s face looks like. From what I can gather this is a weighted average by population. Click through and tell me what you think. Seems plausible enough to me.

Sons of the conquerors: the story of India?

munda2

The past ten years has obviously been very active in the area of human genomics, but in the domain of South Asian genetic relationships in a world wide context it has seen veritable revolutions and counter-revolutions. The final outlines are still to be determined. In the mid-1990s the conventional wisdom was that South Asians were a branch of a broader West Eurasian cluster of peoples, albeit more distant from the core Middle Eastern-North-African-European-Caucasian clade. The older physical anthropological literature would have asserted that South Asians were predominantly Caucasoid, but with a Australoid element admixed in at varying proportions as a function of geography and caste. To put it more concretely, and I think accurately, a large degree of South Asian physical variety can be defined along the spectrum between A. R. Rahman and Nawaz Sharif. The regional and caste truisms are only correlations. Subrahmanyan Chandrasekhar was a Tamil Brahmin, but experienced anti-black racism in the United States. I think that is reasonable in light of his appearance.

ResearchBlogging.orgThis rough & ready mainstream understanding, supporting by classical genetic markers, was overturned in the early years of the 21st century. One line of thought argued that South Asians were much more distinctive from the broader Western Eurasian cluster of peoples. Representative of this body of work is a paper like The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. These researchers tended to start with the female lineages, mtDNA, and then supplement that with Y lineages, the paternal descent. A separate line of evidence, generally drawn from Y chromosomal results, indicated that there were deep connections between the people of India and those of Central Eurasia, in particular via the R1a haplogroup. Additionally, one aspect of the first set of results which was very surprising was that it actually placed South Asians closer to East, not West, Eurasians. But by the end of the aughts the uniparental studies had been supplemented by a range of results produced from SNP-chips, which looked at hundreds of thousands of genetic variants. These studies seemed to support the older view of South Asians being closer to West Eurasians than East Eurasians. Finally last year a paper came out which posited that almost all South Asian populations were actually an ancient stabilized hybrid between two groups, a European-like population, “Ancient North Indians” (ANI), and another group which is no longer present in unadmixed form, “Ancient South Indians” (ASI), of whom the Andaman Islanders are distant relatives. Though there was a slight bias toward ANI as a whole, the fraction of ASI increased as one went southeast, and down the caste ladder. The distinctive “South Asian” ancestral group in other words then may actually be conceived of as a compound of these two elements; an admixture of the native substrate against a European-like genetic background.

Strangely it sounds an awful lot like the older idea of a Caucasoid population with Australoid admixture. We know now that the connection between the tribal peoples of India, and the indigenous groups of South and Southeast Asia as a whole, to those of Australia and Melanesia, is tenuous at best. So the term “Australoid” is not really informative, and may even mislead. And in terms of historical linguistics I don’t think we’ve solved the problem by appealing to an “Aryan invasion.” The high fraction of ANI among South Indian tribal groups who are isolated from even Dravidian caste groups is a clue to the likelihood that the admixture event is very ancient, and probably precedes the arrival of the Aryans to the Indian subcontinent.

But there are more than two actors in this game. In Reconstructing Indian population history the authors acknowledge that their model is stylized, that reality is more complex. Additionally, they perceive in their data that some tribal groups from northeast India have an element which is outside of the purview of a two-way admixture event. They discarded this set from their broader analysis because this seemed to be a restricted phenomenon to these groups. A new paper in Molecular Biology and Evolution re-injects this third element into the picture. Population Genetic Structure in Indian Austroasiatic speakers: The Role of Landscape Barriers and Sex-specific Admixture:

The geographic origin and time of dispersal of Austroasiatic (AA) speakers, presently settled in South and Southeast Asia, remains disputed. Two rival hypotheses, both assuming a demic component to the language dispersal, have been proposed. The first of these places the origin of Austroasiatic speakers in Southeast Asia with a later dispersal to South Asia during the Neolithic, whereas the second hypothesis advocates pre-Neolithic origins and dispersal of this language family from South Asia. To test the two alternative models this study combines the analysis of uniparentally inherited markers with 610,000 common SNP loci from the nuclear genome. Indian AA speakers have high frequencies of Y chromosome haplogroup O2a; our results show that this haplogroup has significantly higher diversity and coalescent time (17-28 KYA) in Southeast Asia, strongly supporting the first of the two hypotheses. Nevertheless, the results of principal component and “structure-like” analyses on autosomal loci also show that the population history of AA speakers in India is more complex, being characterised by two ancestral components – one represented in the pattern of Y chromosomal and EDAR results, the other by mtDNA diversity and genomic structure. We propose that AA speakers in India today are derived from dispersal from Southeast Asia, followed by extensive sex-specific admixture with local Indian populations.

Some background is necessary here. South Asia is notoriously linguistically diverse, but, that diversity can be bracketed into several broad families. First, the Indo-European languages are represented by Indo-Aryan and Iranian dialects (and Germanic, if you include English). Second, the Dravidian languages are found across the subcontinent, from Brahui in Pakistan to Malto in Bangladesh. But they’re really the dominant languages in the southern cone of South Asia. That being said it seems likely that historically their distribution extended far into the north, with Brahui in western Pakistan being a relic of that period, as well as the fragmented tribal groups in Central India. There is also evidence down to historic periods of a Dravidian-speaking substrate in Maharashtra. And purely from a philological perspective it seems clear that many Indo-Aryan languages evolved within a Dravidian linguistic substrate.

Next, in the far north there are languages of Tibetan provenance and affinity. These are explicable in their origins and relationship. But in the northeast third of the Indian subcontinent there are a two groups of Austro-Asiatic languages. The prefix “Austro” is indicative of the symbiotic relationship between historical linguistics and physical anthropology in the early 20th century (most famously illustrated in the transplantation of the social-linguistic term Aryan from a South Asian and Iranian context, to a racialized Northern European term). The map at the top of this post shows the distribution of the Austro-Asiatic languages, as well as their subdivisions. There is clearly an eastern and western wing to the group, but most scholars assume that this is an artifact of the historical eruption of the Burman and Thai peoples out of the southern fringes of the Chinese Empire and into mainland Southeast Asia.

800px-Ramakrishna_Mission_Cherrapunjee_106Within India the Austro-Asiatic languages fall into two broad categories: the Munda and the Khasi. The Khasi inhabit the massif which separates Bengal and Assam. Their culture and society is at some variance from the norm in India (they are matrilocal, and animist or Christian). A close relationship to the people to the east is clear in both their language and their physical appearance. The Khasi, and other groups such as the Garo, are of the family of peoples and ethnicities which have arrived from the east and north relatively recently, making the transition from the world of Tibet and Burma to India. This is evident in the face of the Khasi child in the image to the left. Once passing out of their lands of origin these populations have assimilated to different degrees to the Indic domain. The Tripuri people for example retain a Tibeto-Burman language, but are adherents of Vaishnav Hinduism (my own family were once subjects of the Manikya dynasty). The Ahom of Assam were totally assimilated by the Indo-Aryan substrate. Like the Bulgars of Bulgaria their only influence was in the ethnonym that they contributed to their subjects. A quick survey of my own genetics, and those of other South Asians of eastern origin on 23andMe, clearly shows the influence of assimilated Tibeto-Burmans. One Bangladeshi Muslim individual clearly carries an East Asian Y chromosomal haplogroup.

The Munda are a somewhat different case. In older historical literature on South Asia there is some consideration that the Munda may be the earliest inhabitants of India; predating the Dravidians. Some readers of South Asian origin also point out that in the early Indo-Aryan language there may be more evidence of Munda, than Dravidian, influence. But the eastern connections of the Munda languages seem clear, albeit less explicable than those of the Khasi or the Tibeto-Burman peoples of the far northeast. If the Munda are the indigenous people then it stands to reason that the Mon-Khmer languages derive from South Asia. On the other hand the vast majority of the Austro-Asiatic languages exist in Southeast Asia, and, the Munda themselves have been hypothesized as being the bearers of rice-culture from the east.

This is where genetics comes into play. There has already been evidence of an eastern influence in the genes of the Munda from other researchers, so what this paper does is look at that in detail, instead of discarding it as a minor effect which muddles the broader picture. I’ve reformatted figure 3 to show how the groups relate to each other. On the left is a PCA. Most of the variance is west-east, ~6%, while some of it is north-south, ~1%. On the right is a bar plot generated from ADMIXTURE. I’ve edited out many of the populations. Focus on the Austro-Asiatic groups from India.

munda1

In the PCA you see the SE-NW axis of ANI-ASI admixture which is the primary aspect of genetic variation within South Asia. Numerically Dravidian and Indo-Aryan groups along this axis are the vast majority of South Asians. But the Munda and other Austro-Asiatic groups are not trivial; there are strong suggestions that the eastern Indo-Aryan groups, Oriya, Bengali, and Assamese, are to some extent shaped by influence from the Austro-Asiatic elements. The closer connection of the Khasi to East Asian populations is clear on the PCA. But the fact that the South Indian samples are further along axis-Y than the Munda are indicative of admixture in the Munda population. Looking at the bar plot that’s clear. The dominant dark-green signature of South Indian ancestry is also predominant among the Munda, and found at non-trivial amounts among Iranian, Khasi, and Southeast Asian populations, but the Munda clearly have an eastern component which is not found in South Indians. This is probably the element which perturbs them on the PCA.

But this just tells us the relationships in terms of total genome content. It doesn’t necessarily tells us the historical sequence of admixture events or the direction of migration. In fact the evidence of Indian ancestry in Southeast Asia could be suggesting migration from South Asia to the Southeast Asia (there is plenty of cultural evidence of transmission, though the presumption is that the demographic movements were marginal). They note in the paper that one phenomenon which could be obscuring and confusing our understanding is that much of gene flow occurs through isolation-by-distance (IBD). Village-to-village dynamics. In contrast to this you have folk wanderings, which result in a “leapfrog” aspect. The Hazara and Uyghur are both cases of leapfrogging, as their genetic makeup can’t be explained easily by IBD. So here the connections between the Munda and Southeast Asians, and the broader relationship between Southeast Asians and South Asians, could be IBD, or perhaps reflect deep ancient common ancestry. Perhaps the ASI group spanned the region from the Arabian Sea to the South China sea, and were only later overlain by ANI and East Asian populations.

To explore these questions the authors tunneled down to a more fine-grained scale, and looked at uniparental lineages as well as a gene at which recent selection seems to have operated upon East Asians in distinction to other groups, EDAR. Though uniparental lineages are only partially informative in terms of ancestry, they are very amenable to dating because of their haploid inheritance patterns. And the relationships between the branches of the termini can give us historical information.

The following figure shows the relationship and distribution of a particular Y chromosomal haplogroup which the Munda carry, and other South Asians tend not to, which connects them to the east:

munda3

The haplogroup is O2a (M95). The results from the Y chromosomal data are not clear, though they do seem to reject the model whereby Southeast Asian O2a lineages derive from Indian ones. But it does not seem as if you have a scenario where one founder lineage entered into South Asia from Southeast Asia, there are too many disparate branches of O2a found among Indians. Additionally, the coalescence time (back to last common ancestor) is deeper in Southeast Asia, but still deep in South Asia among the Munda. From this it seems that the origin of Austro-Asiatic languages in South Asia can be rejected, but the details of the emergence of Austro-Asiatic in South Asia can not be clearly perceived as of yet. From what I can gather the authors themselves do not necessarily believe that their results in this domain are robust (insensitive to varying the model’s assumptions even marginally).

An interesting point though is that the mtDNA, the female lineage, does not seem to diverge from other South Asians much at all. I find it intriguing that this is the same pattern we see along the major NW-SE axis of variation. It seems that mtDNA lineages unite South Asians, while the Y lineages separate them (by caste and region). The generality has many exceptions, but it points to a peculiar sex mediated admixture process from both the northwest and northeast. Men on the move have reshaped the genetics and culture of South Asia, but the mtDNA lineages still point to an ancient Eurasian group with distant but stronger affinities to the east than the west. The mtDNA are likely the purest distillation of ASI.

Finally, they look at frequencies of variants of EDAR among the South Asian groups. EDAR is in some ways diagnostic of East Asian ancestry; it seems that a variant which produces thick straight hair emerged relatively recently among East Asians.  Here’s the result from the HGDP browser:

edar1

edar2The G allele exhibits co-dominance, so the GA phenotype has intermediate hair-thickness between AA and GG. Haplotype structure based tests of natural selection have indicated that the derived G allele is recent. The map to the right shows the frequency of the derived G variant by population group. The bubble size is proportional to frequency, while the colors represent language groups. Again the Khasi and Tibeto-Burman groups are as you’d expect, they exhibit a relatively high frequency of the derived variant. The Hazara are a group which only came into being within the last 1,000 years through an admixture event. The Tharu seem to have their origins in Nepal’s transitional zone, and all the Nepali populations have significant admixture with Tibetan groups even if they themselves are not Tibetan in language and culture. The interesting result are the Munda. The Dravidian groups lack the derived EDAR variant, as do Indo-European groups without a plausible East Asian source of admixture. But within the Munda the derived variant is found in proportions ~5%. This is far lower than the 60% among the Tibeto-Burmans of the northeast, or the 40% among the Khasi, but it is significant. And this result allows the authors to reject the IBD model of connection for Austro-Asiatic groups, because the Munda harbor the variant which other South Asian groups in their environs do not. Gene flow predicated on linguistic affiliation at such a remove seems implausible, so the most parsimonious explanation is that the Munda languages arrived in India from Southeast Asia as part of a leapfrog folk wandering.

But why the low frequency of the derived variant? Obviously the Munda have admixed with the local substrate, so dilution would be one explanation. Another could be that when the Munda left East Asia the frequency was lower. Additionally, whatever selective forces were driving the frequency up may have abated in South Asia, and it could be that there was selection against the derived variant! Whatever the truth of it the existence of the derived EDAR variant among the Munda would be like finding the European LCT variant among an East Asian population: clear evidence of long distance gene flow and population movement.

So where does this lead us? First, let me observe that some of the authors on this paper are the same ones who argued for a predominantly indigenous origin for South Asians in the early 2000s based on mtDNA variation. In this paper they seem to be leaning against an indigenous origin for the Munda, or at least refuting the conjecture that the Munda are ur-Indians par excellence. I didn’t go into the details of the coalescence times because they’re rather a mess, but EDAR is probably a “tipping point” in arguing for a relatively recent exogenous origin for the Munda. The strong sex asymmetry in genetic variation is also suggestive, we have plenty of evidence of historical examples of genetic leapfrogs occurring through men-on-the-move. The asymmetry also seems to exist among the Khasi and other Tibeto-Burmans in India’s northeast (figure 2 of the paper).

The arguments about the history, culture, and genetics of South Asia have traditionally been disputed along the Aryan-Dravidian axis. I’m not interested in rehashing that aspect, but these data point us to another reality: on India’s northeast frontier there’s another component. As an ethnic Bengali myself I’ve always been somewhat aware of this. Some of my relatives and family acquaintances look much more like Garos than other South Asians. This component is even more evident on the face of Assamese and Nepali, whose languages are Indo-Aryan and religion is Hinduism, but whose appearance bespeaks a more variegated background. On some level South Asians from these regions are aware of their peculiarity, even if it isn’t spoken of much. I have read that in the wake of the victory of Japan over Russia in the early 20th century Bengali intellectuals expressed in public their pride at their Asiatic ancestry. With the rise of China in the 21st century I suspect more South Asians from Nepal, Bengal, and Assam, will rediscover that aspect of their background which links them to the east, and not the west. The genetics is just telling us what we already knew.

Citation: Gyaneshwer Chaubey, Mait Metspalu, Ying Choi, Reedik Mägi, Irene Gallego Romero, Pedro Soares, Mannis van Oven, Doron M. Behar, Siiri Rootsi, Georgi Hudjashov, Chandana Basu Mallick, Monika Karmin, Mari Nelis, Jüri Parik, Alla Goverdhana Reddy, Ene Metspalu, George van Driem, Yali Xue, Chris Tyler-Smith, Kumarasamy Thangaraj, Lalji Singh, Maido Remm, Martin B. Richards, Marta Mirazon Lahr, Manfred Kayser, Richard Villems, & Toomas Kivisild (2010). Population Genetic Structure in Indian Austroasiatic speakers: The Role of Landscape Barriers and Sex-specific Admixture Mol Biol Evol : 10.1093/molbev/msq288

Link acknowledgement: Dienekes Pontikos.

Addendum: This is more a speculative comment, so I will tack this on to the body of the main post. Here’s my current very tentative model for how South Asians came to be. At some point after the last Ice Age 10,000 years ago the ANI arrived, and hybridized with the ASI, who are descendants of the older original Out of Africa wave to South Asia. After this, but before the Aryans, the Munda arrived from the northeast, and pushed into lands inhabited by ANI-ASI groups. 4,000-3,000 years ago the Indo-Aryans arrive, and impose themselves as an elite on the ANI-ASI hybrid population, before being assimilated biologically and imparting their language to the Indian majority. I don’t know where Dravidian came from, but perhaps it was the language of the ANI (its existence in fragments all across the swath of the northern Indian subcontinent is suggestive, as well as possible connections to ancient Elamite, the language of Bronze Age southwest Iran). Eventually the Aryanized ANI-ASI marginalized the Munda in northeast India and drove them to the highlands. Finally, the Tibeto-Burmans arrived in the historical period.

Image Credit: Wikimedia Commons

October 27, 2010

The future shall belong to the odorless!

Filed under: Asians,Body Odor,Genetics — Razib Khan @ 2:16 pm

My blog post prompted this response:

He notes research hypothesizing a link between high latitudes and the dry earwax gene, and also research that suggests that the dry earwax gene, something that would seem to have little selective impact, may be linked to the same gene that regulates body odor. Low body odor might conceivably confer the 1% per generation selective advantage that would appear to be necessary to account for the current mix of those genes over the 50,000 years the distinction between Asia and the rest of the world is appeared to have evolved.

People can interpret results however they want, it’s a free country. In fact I do so all the time. But I want to enter into the record that I’m skeptical of this particular model of negative selection against stinkiness.

Daily Data Dump – October 27th, 2010

Filed under: Blog,Daily Data Dump — Razib Khan @ 12:08 pm

In Mideast House of Cards, U.S. Views Lebanon as Shaky. Some of the problems here are structural demographics. The institutions of Lebanon’s democracy were formed when Maronite Christians were the plural majority, followed by Sunni Muslims, then Shia Muslims, and finally minorities such as the Greek Orthodox and Druze. Today the likely plural majority are the Shia, followed by the Sunnis and Maronites. Add on top of this the fact that the Shia tend to be poorer, and, have an invested international backer in Iran. The connection between the Iranian Shia and the Lebanese Shia has traditionally been closer than between the Iranian Shia and the Iraqi Shia.

Saudi Border With Yemen Is Still Inviting for Al Qaeda. Interesting coincidence that I posted on this issue last week. I think my libertarian friends such as Will Wilkinson and Bryan Caplan will get their wish for relatively open borders in the 21st century as a matter of pure probable prediction (there will be exceptions, I suspect Japan may be one). The future will be something more like the United Arab Emirates, though I hope we’ll be able to effect some humanitarianism on the margins, as well as mitigate the popularity of ugly modernist mega-structures.


Steve Hsu has an interesting weblog. He’s a physicist at the University of Oregon with an interest in various other topics, including behavior genetics and psychometrics. He also looks things up.

Dusk in Autumn is a weblog by an individual who goes by the handle “agnostic.” He doesn’t post often, but when he does it is generally interesting and quirky. He is a callipygiaphile.

reaction norm keeps pumping out content. Don’t burn yourself out dawg.

Australian Aboriginal people are one?

Filed under: Aboriginal Genetics,Anthroplogy,Australia,Genetics — Razib Khan @ 12:22 am

ozlang2Richard Broome’s Aboriginal Australians is one of those books which I own which I finally managed to finish recently. It was a quick overview of Australian Aboriginals and their relationship with the settler society, and later in modern Australia. From what I could tell it was a serviceable introduction, though it took a persistent preachy tone whereby one was repeatedly reminded that the Aboriginals were an ever-peaceful people in harmony with nature, notwithstanding their regular burnings of the landscape and inter-tribal brawls. They were in timeless equilibrium with the land that they loved before the white man arrived to destroy their idyll with the shock of modern civilization. The narrative is presented as if the Aboriginals were almost totally static, and perfectly optimized to the environment that was Australia. I personally think this sort of model makes indigenous people less than human, even if it turns them into angels instead of beasts. Of course it’s probably impossible to not have a strong perspective in this sort of material, and I suppose this  type of treatment evens out the ledgers of the past. But one can discern the major themes from the subtle and not-so-subtle polemic easy enough.

One aspect of Aboriginal culture which I have wondered about is its perceived uniformity. The Dreamtime is discussed as if it’s a cultural universal among Australian Aboriginals. Is it? A little poking around indicates that Aboriginals seem to share the idea, though with variations. How’d that come to be? Broome’s model seems to assume that the Dreamtime has deep roots in Aboriginal culture, but we know that the roots likely don’t preexist their arrival in Australia, the people of New Guinea and Melanesia don’t have the concept. It may be that they lost the concept, but I doubt that all of them would. Rather the Dreamtime’s ubiquity in Australia may reflect demographic and cultural change within Australia since the arrival of modern humans ~50,000 years ago.

A paper I reviewed last summer used a thick survey of SNPs to place Australian Aboriginals in their proper global genetic context. One of the major shortcomings of that paper was that it had a small sample size from one specific Aboriginal population, and, that population was heavily admixed with Europeans. With intermarriage rates on the order of 70-80%, and a large load of European ancestry already in the Aboriginal community, the number of “pure” Aboriginals will decline rapidly in the the coming century. So I was curious enough to look for a paper which surveyed a wider range of Australian Aboriginal people. I found one, from 2007, A comprehensive analysis of microsatellite diversity in Aboriginal Australians:

Indigenous Australians have a unique evolutionary history that has resulted in a complex system of inter and intra-tribal relationships. While a number of studies have examined the population genetics of indigenous Australians, most have used a single sample to illuminate details of the global dispersal of modern humans and few studies have focussed on the population genetic features of the widely dispersed communities of the indigenous population. In this study we examine the largest Aboriginal Australian sample yet analysed (N = 8,868) at fifteen hypervariable autosomal microsatellite loci. A comprehensive analysis of differentiation indicates different levels of heterogeneity among indigenous peoples from traditional regions of Aboriginal Australia. The most genetically differentiated populations inhabit the North of the country, in particular the Tiwi of Melville and Bathurst islands, Arnhem Land (itself divided into West and East Arnhem), and Fitzmaurice regions. These tribal groups are most differentiated from other Aboriginal Australian tribes, especially those of the Central Desert regions, and also show marked heterogeneity from one another. These genetic findings are supportive of observations of body measurements, skin colour, and dermatoglyphic features which also vary substantially between tribes of the North (e.g. Arnhem Land) and Central Australian regions and, more specifically, between the Tiwi and West and East Arnhem tribes. This study provides the most comprehensive survey of the population genetics of Aboriginal Australia.

Though not totally representative of the geographic expanse of Aboriginal peoples, the sample size here was still huge. But, they looked only at fifteen microsatellite. Microsatellites mutate fast and so have a lot of variation to draw upon, but fifteen is a rather low number compared to the 160,000 core SNPs used in the paper from last summer. So here you have a trade off between population converge and depth of the genomic survey.

Below are the primary results. First are the Fst values comparing regions, and sub-regions. Second a PCA which shows the relationship between populations. Finally, a fine-grained neighbor-joining tree which shows the geographical clusters.

My Australian readers can make more informed inferences, so I won’t say too much, aside from the impression that genetic distinction seems to correlate well with linguistic distinction. Here’s their conclusion:

The principal findings of this study are that the most differentiated tribal groups are located in three regions, West Arnhem Land, East Arnhem Land and Tiwi, all of which share borders with one another in the Central North of the continent. These tribal groups are most differentiated from other Aboriginal Australian tribes, especially those of the Central Desert regions, and also show marked heterogeneity from one another. These genetic findings are supportive of observations on body measurements….

Citation: Journal of Human Genetics 52, 712-728 (September 2007) | doi:10.1007/s10038-007-0172-z

Image Credit: Wikipedia Commons

October 26, 2010

Daily Data Dump – October 26th, 2010

Filed under: Blog,Daily Data Dump — Razib Khan @ 11:37 am

Just a heads up, I might be posting less later in the week and into the weekend. So might skip these at some point.

Are Democrats Overachieving in the Senate? Is Nate Silver is having a downward pressure on other political coverage? I don’t even bother checking the other analytical stuff in The New York Times; they’re just going to basically do souped-up trend stories with cherry-picked quotes from “experts” attempting a bit of man-bites-dog to product-differentiate. The basic outlines of what’s going to happen at the mid-terms is known, as well as the uncertainty. Beyond that most people are guessing and spinning. On the specific issue at hand, I’m not too versed in politics but I had assumed that the Senate was a less volatile institution in election-to-election change in party proportions because only 1/3 of it was up for election in a given year, vs. 100% of the House of Representatives. Silver points out that if the whole Senate was up for reelection we might be looking at filibuster-proof Republican majority, and an outside shot at veto-proof majority.

The Myth of Charter Schools. It’s basically a review of the problems with Waiting for “Superman”. I think this current educational enthusiasm is at a bubble-point, I noticed a few weeks back The New York Times published a downbeat assessment of Geoffrey Canada’s results with the Harlem Children’s Zone.


Evolutionary history of partible paternity in lowland South America. Basically these are cultures where there’s a high degree of expected paternity uncertainty and you simply distribute appropriate the probability of fatherhood explicitly. I found this section of interest: “Most importantly, why is partible paternity rare in the rest of the world and yet, so common in lowland South America? We suspect that the general lack of important heritable resources combined with a strong reliance on kinship and broad networks of social capital in the lowlands have prompted the bargaining and exchange of shared parentage.” From a male perspective then basically someone who is not your own biological child isn’t going to inherit much from you anyway, while in the short-term you might be able to gain social capital through the ties your wife forms with other men. This isn’t that shocking, Winston Churchill’s mother’s affairs supposedly aided in her husband’s and son’s political careers because of the contacts generated. Sex is social.

Moving away to get better. Interesting point that it is easier to get away from bullying in the United States because Americans move and reorder their social networks so often. I wasn’t a victim of bullying, but I know I’ve done the same. I see two or three friends from college about once a year. The last time I hung out with someone I knew from high school was in early February of 2006. I might be an deviated-from-the-norm case, but I’m not that atypical. And though moving and reordering social networks can have benefits, I think we don’t talk about the upsides to having stable networks and a familiar environment. I suspect that it decreases social anomie and increases trust.

DQB1*0602 predicts interindividual differences in physiologic sleep, sleepiness, and fatigue. See the summary at ScienceDaily.

‘dem bones tell strange tales

Filed under: Evolution,Genetics,Genomics,Human Evolution,Paleoanthropology — Razib Khan @ 12:16 am

There is a new paper in PNAS on remains from China which re-order and muddle our understanding of the emergence of anatomical and behavioral modernity in Eurasia. Human remains from Zhirendong, South China, and modern human emergence in East Asia:

The 2007 discovery of fragmentary human remains (two molars and an anterior mandible) at Zhirendong (Zhiren Cave) in South China provides insight in the processes involved in the establishment of modern humans in eastern Eurasia. The human remains are securely dated by U-series on overlying flowstones and a rich associated faunal sample to the initial Late Pleistocene, >100 kya. As such, they are the oldest modern human fossils in East Asia and predate by >60,000 y the oldest previously known modern human remains in the region. The Zhiren 3 mandible in particular presents derived modern human anterior symphyseal morphology, with a projecting tuber symphyseos, distinct mental fossae, modest lateral tubercles, and a vertical symphysis; it is separate from any known late archaic human mandible. However, it also exhibits a lingual symphyseal morphology and corpus robustness that place it close to later Pleistocene archaic humans. The age and morphology of the Zhiren Cave human remains support a modern human emergence scenario for East Asia involving dispersal with assimilation or populational continuity with gene flow. It also places the Late Pleistocene Asian emergence of modern humans in a pre-Upper Paleolithic context and raises issues concerning the long-term Late Pleistocene coexistence of late archaic and early modern humans across Eurasia.

I read the paper, and I really didn’t understand anything between the introduction and discussion. Mostly because it was a detailed exploration of anatomical details, and I’ve never taken an anatomy class. I basically rely on people like John Hawks to tell me what’s going on in that domain. He hasn’t blogged the paper (well, as of this writing), but he did give an assessment to National Geographic:

Still, the jaw and three molars were the only human remains retrieved from the Chinese cave, and the jaw is “within the range” of Neanderthal chins as well as those of modern humans, added paleoanthropologist John Hawks of the University of Wisconsin, Madison.

“If this holds up, we have to reevaluate” the human migration time line, he said.

“Basically, I think they’re right, [but] I want to see more evidence,” Hawks added. “I really, really hope that there can be some sort of genetic extraction from this [fossil].”

The issue of why this is relevant is covered well in the early portion of the paper:

…In eastern Eurasia, the dearth of diagnostic and well-dated fossil remains…has inhibited more than general statements for that region. Fully modern human morphology was established close to the Pacific rim by ∼40 kya, as is indicated by the fossils from Niah Cave in Sarawak…and especially Tianyuan Cave in northern China…The actual time of the transition has remained elusive, because the age of the latest known archaic humans in the region is substantially earlier…The eastern Eurasian age of the transition has been generally assumed to approximate that of western Eurasia (∼50–40 kya), although there have been claims supporting earlier dates for modern human presence in East Asia….

This scenario implies a long term (>100,000 y) restriction of early modern humans to portions of Africa with a brief ∼90 kya expansion into extreme southwestern Asia, followed by a relatively rapid expansion throughout Eurasia after ∼50 kya…The scenario also implies some form of adaptive threshold, roughly contemporaneous with the emergence of the Upper Paleolithic (sensu lato), and a marked behavioral difference between those expanding modern human populations and regional populations of late archaic humans (14).

It is in this context that three fragmentary human remains were discovered in 2007 at Zhirendong, South China…Because it is only well-dated diagnostic human remains that can document the timing and nature of human evolution and dispersal patterns (as opposed to archeological proxies for human biology or imprecise inferences from extant genetic diversity), the Zhirendong remains have the potential to shed light on these ongoing paleoanthropological issues.

jawOK, so the stylized orthodox model would be that anatomically modern humans arose in Africa ~200,000 years ago, and expanded out of Africa ~100-50,000 years ago. Full behavioral modernity emerged a bit later. In the broad outlines I think we can still go with this, but we have reached a level of fine-grained understanding of the evolutionary history of the human past that we need to consider adding detail to the margins of the story. The Denisova hominin, and perhaps H. floresiensis, are a good clue that the human family tree really was bushy, and that the past was filled with players unknown to us. The likelihood of Neandertal admixture also suggest that the other branches of the bush can’t be ignored and considered as without consequence for modern humans. There may be traces of other lineages in other human populations as well; there have long been claims based on inferences from some genetic data of modern populations, but the ability to compare to the Neandertal sequence gave those results from last spring particular credibility. But if the Neandertal admixture results become part of the consensus we should recalculate our probabilities of the other inferences.

linearSo how does it change things? One of the authors of the PNAS paper, Erik Trinkaus, has long made claims of hybridization from the fossil record, and this work falls in line with that tradition. The key here is the fossils seem to exhibit derived features, not ancestral ones. Derived features imply common ancestry of the populations which share the derived traits. If so, Trinkaus and company seem to be pointing to Alan Templeton’s “Out of Africa again and again.” On the other hand, I can’t but help think of Luke Jostins‘ plot of hominin cranial capacities as a function of time: separate lineages all seemed to be going on the same general path in terms of direction. I don’t make the claim here that H. sapiens sapiens was inevitable, but perhaps a common suite of traits which we associate with advanced hominin lineages, in particular the branch of which we are the terminus, were being selected for across the whole clade. In other words, perhaps anatomical modernity exhibits some element of convergent evolution, while behavioral modernity is the true hallmark of H. sapiens sapiens. It sounds crazy, and I don’t really believe it necessarily, but we live in crazy times. We had a neat and tidy story for 20 years between 1985 and 2005, but all good things have to end.

October 25, 2010

If you’ve done 23andMe….

Filed under: Uncategorized — Razib Khan @ 3:03 pm

The Dodecad ancestry project might be of some interest. In particular if you have ancestry from a gold-chain wearing culture.

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