The flying wing into a graph

If you are going to use ADMIXTURE, you really need to read the original paper, Fast model-based estimation of ancestry in unrelated individuals (it’s not gated, so there’s no excuse). Though the original Jonathan Pritchard paper from 2000, Inference of Population Structure Using Multilocus Genotype Data, is probably sufficient. Unfortunatey there’s a problem with these model-based barplots: people have a real hard time not reifying them excessively. Let’s call it “Plato’s revenge.” But really Plato only elaborated what’s obviously a pretty standard-issue cognitive tick: we like to think in absolute categories. This is most of the problem with “does race exist” discussions; you always need to move past the idea of Platonic constructions, which are by necessity social.

That’s what’s nice about PCA. It’s a visual representation of the underlying variation in the data, and the clusters are not pre-specified. Unfortunately fixing the parameter as K = 5 magically means for most people that there are actually 5 real populations. And “most people” even includes a lot of geneticists.

So I’m going to do an experiment, and move away from model-based clustering, and use TreeMix to explore data. This of course behooves us to make sure we read the original paper, Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data. I have done so, and three elements jump out at me:

- “This Gaussian model was first introduced by Cavalli-Sforza and Edwards [1], and the motivation for this model is outlined in Nicholson et al. [33], if the amount of genetic drift between the two populations is small (at most on a timescale of the same order as the effective population size), then the diffusion approximation to a Wright-Fisher model…”

- “We do not model the boundaries of the allele frequencies at zero and one, nor do we consider new mutations. This means that this model will be most accurate for alleles that were at intermediate frequency in the ancestral population.

- “The contribution of each parental population is weighted; if we assume admixture occurs in a single generation….

This first post is something of an experiment. I have a data set (unfortunately some of the data is not public, so I won’t be posting the Dropbox link this time) which is mostly skewed toward Northern Europeans. Using PCA I removed individuals which were outliers and generated some reasonable clusters around the centroids of particular nations (i.e., the national clusters are those with individual’s whose ancestors were all from a given nation, to the best of their knowledge).

The clusters are:

- E_Africa (HapMap Masai, with some outlier removal)
- England (I selected individuals who were distant from the Irish, without being German)
- Finland
- Germany (I selected individuals which were basically North German; the Netherlands to Saxony)
- Ireland
- Italy (these individuals are Southern Italian; from Roman down to the Naples, but excluding Sicily)
- Mbuti_Pygmies (HGDP)
- Mozabite (HGDP, some outlier removal)
- N_Amerindian (HGDP, Pima and Maya; some outlier removal)
- S_Amerindian (HGDP, Surui and Kariatana; some outlier removal)
- NE_Asia (HapMap and private data for Japanese and Koreans)
- N_India (HapMap and 1000 Genomes Gujarati and Punjabis)
- N_WestAsia (Armenians and Turks)
- Papuan (HGDP)
- Poland (Removed all Jews from this data)
- Scotland (tried to remove individuals too close to Irish and English; this was not easy)
- SE_Asia (1000 Genomes Dai and Vietnamese)
- S_India (1000 Genomes Tamil and Telugu)
- Spain (1000 Genomes and private data)
- Sweden
- S_WestAsia (private data, Saudis and Kuwaitis, pruned from those with recent African ancestry)
- W_Africa (1000 Genomes Yoruba and Esan)
- Yakut (HGDP)

The merged data set has 290,000 SNPs. It’s missingness is 0.25% (0.0025). But there are over 5,000 individuals in the data set, and that could hide some major biases in the distribution of missingeness (e.g., the small number of HGDP Papuans could have a lot of these). So I decided to remove all SNPs that had any missingness in the data. That’s ~40,000 markers. That means all 40,000 of these markers are present as calls in all 5,000 individuals in the data. For PCA 40,000 is actually pretty good, so here are the first 6….

 

pc1pc2PC3PC4PC5PC6The magnitude of the dimensions are: 245, 142, 34, 27, 16, and 12. The first two, which form the “wing” shape which we’re all familiar with, represent Africa vs. everyone else, and then western vs. eastern Eurasia. These are not set in stone. Remember, what PCA does is yank out independent dimensions which explain the variation in the data. If you overload the data with a particular type of variation then it could change the rank order. Or, if you throw in a very inbred group then their component is going to be so salient.

Since can’t read the PCA plots, you should click on them. They’ll pop out into something more readable. PC 3 separates out Eurasia north to south. This is a much smaller dimension than west to east. I think that fits intuition. The fourth PC separates the Amerindian groups. Really it’s a Surui vs. non-Surui axis. I really like PC 5 and PC 6, because they show the different European clusters more visibly. The issue is that there’s very little genetic variation in Europe when judged on a world-wide scale. But the lower components are starting to capture it. I’m not going to lie, ggplot’s default color scheme is hella confusing. I’ll tell you that the two populations away from the rest are Indians, with North Indians closer to Europeans than South Indians. And way up to the top right are Papuans. One way I like to think of these sorts of patterns post hoc is that the Indians are pointing to a “ghost population.” They’re not Papuans, but they have some distant affinity to Papuans….

Next I decided to run TreeMix. First with the full 290,000 SNP data set. Then the 40,000 which are 0% missingeness. I ran them each 10 times and outputted them. I set them for 5 migrations. I’ll leave them without comment, except this:  the problem I have with TreeMix is that I’m reassured when I see a migration edge that I’m expecting, but don’t know what to make of those which are surprising. The reason is that the algorithm can’t lie, but it can only work with the data and assumptions that go into it. When Joe Pickrell first came out with his TreeMix results there was a weird arrow going from the Amerindians to the Europeans. No one really knew what to make of this, though it wasn’t entirely surprising (something like this shows up in ADMIXTURE plots well, and I saw it in Noah Rosenberg’s microsatellite STRUCTURE work as far back as 2005). After the fact we know can make sense of it. TreeMix was showing us the impact of the “Ancestral North Eurasians” as best as it could. The Amerindians of the New World have the highest proportion of this ancestry, an the people of Northern Europe some of the highest fractions in the Old World. So it drew a migration edge from the former to the latter. When you put in the Mal’ta (or Yamnaya) data into TreeMix that “spurious edge” disappears….

 

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Open Thread, 8/2/2015

51aBlSPDX8L._SX342_BO1,204,203,200_After my post, Do Colored People Exist if There Are No White People to Observe Them?, I’ve gone to finishing up The Making of Modern Japan (I’d stopped about halfway through my read). One interesting aspect about Japanese history during the Tokugawa period is that though the nation was relatively isolated from European influences, there was much more interaction with Korea and China.

My wife sent me this link, A Four-Year Old Reviews the French Laundry. Impressed that she actually tried mos of the items. Related, The Great Sushi Craze of 1905, Part 1: The Unexpected History of Japanese Food in America, From Edo Bay to the Bowery.

Reich + Ancient DNA Willerslev + 1000 Genomes South Indian data

There’s a lot of genetic data out there. Many of the Reich lab data are downloadable. Additionally, Martin Sikora gave me a pedigree file with a lot of the ancient genotypes in their recent paper (much appreciated since pulling genotypes out of a lot of big sequence files of varied coverage was going to take some  time and care). I merged the two together. But for whatever reason the Reich data set did not include anything from the South Indian samples from the 1000 Genomes. Since I have those, I decided to add a bunch. These are Telegu and Tamil speakers who are neither Brahmins nor scheduled castes and tribes (for those curious, the Velama map pretty well on PCA to the “South Indians” I culled from the 1000 Genomes).

You can download it here. It’s a 200 MB tarball. It’s in plink format. I did a minor allele frequency filter out 0.05, and got it down to 385,000 SNPs. Please note: these data vary greatly in quality on the individual level. A lot of the ancient samples are missing a lot of positions, so keep that in mind when you analyze them (e.g., if you run PCA some of the dimensions are pretty obviously just ancient samples missing lots of markers in a systematic manner). Finally, there are non-human outgroups in the data. For example if you run a PC analysis without subsetting PC 1 will separate Marmoset from humans, with other primates and ancient samples in spanning the gap. If you leave in ancient populations, a lot of them are going to be of much lower quality than the run-of-the-mill population.

Below are the samples by population and size. Most of the labels are from the Haak et al. data set. Obviously they’re a little idiosyncratic, but I figure you can figure it out. Please note that the .fam file has population labels in the family ID column. I added them manually where they didn’t exist (e.g., the Willerslev data and the 1000 Genomes did not have them, so I added them where appropriate).

Group N
S_India 136
Yoruba 70
Turkish 56
Spanish 53
Druze 39
Palestinia 38
Han 33
Basque 29
Japanese 29
Sardinian 27
BedouinA 25
French 25
Ulchi 25
Burusho 23
Chukchi 23
Eskimo 22
Russian 22
Tubalar 22
Brahui 21
Mozabite 21
Balochi 20
Biaka 20
Greek 20
Hungarian 20
Makrani 20
Yakut 20
BedouinB 19
Pathan 19
Yukagir 19
Egyptian 18
Kalash 18
Mayan 18
Sindhi 18
Adygei 17
Mandenka 17
Bell_Beaker 15
Unetice 15
Yamnaya 15
Hazara 14
Papuan 14
Pima 14
HungaryGam 13
Orcadian 13
Somali 13
AA 12
Bergamo 12
Icelandic 12
Karitiana 12
LBK_EN 12
Masai 12
Corded_Ware 11
Khomani 11
Nganasan 11
Norwegian 11
Sicilian 11
SwedenSkog 11
Ami 10
Armenian 10
Balkar 10
Belarusian 10
Bougainvil 10
Bulgarian 10
Chuvash 10
Croatian 10
Czech 10
Dai 10
English 10
Estonian 10
Even 10
Georgian 10
Han_NChina 10
Kalmyk 10
Kusunda 10
Lithuanian 10
Mbuti 10
Miao 10
Mixe 10
Mixtec 10
Mordovian 10
North_Osse 10
Selkup 10
She 10
Thai 10
Tu 10
Tujia 10
Tuvinian 10
Uygur 10
Uzbek 10
Yi 10
Zapotec 10
Abkhasian 9
Atayal 9
Chechen 9
Daur 9
Iranian_Je 9
Jordanian 9
Koryak 9
Kyrgyz 9
Lezgin 9
Libyan_Jew 9
Naxi 9
Nogai 9
Oroqen 9
Ukrainian 9
BantuSA 8
Cambodian 8
Cypriot 8
Esan 8
Hezhen 8
Iranian 8
Kinh 8
Kumyk 8
Lahu 8
Lebanese 8
Luhya 8
Luo 8
Maltese 8
Mansi 8
Mende 8
Punjabi 8
Saudi 8
Surui 8
Syrian 8
Tajik_Pomi 8
Tunisian 8
Tuscan 8
Yemenite_J 8
Aleut 7
Algerian 7
Altaian 7
Ashkenazi 7
Bengali 7
Bolivian 7
Ethiopian 7
Finnish 7
French_Sou 7
Georgian_J 7
Karasuk 7
Motala_HG 7
Tunisian_J 7
Turkmen 7
Xibo 7
Albanian 6
BantuKenya 6
Gambian 6
Hungary_Vatya 6
Iraqi_Jew 6
Itelmen 6
Korean 6
Mongola 6
Moroccan_J 6
Saharawi 6
Yemen 6
Afanasievo 5
Armenia_LBA 5
Cochin_Jew 5
GujaratiA 5
GujaratiB 5
GujaratiC 5
GujaratiD 5
Hadza 5
Ju_hoan_No 5
MTurkish_J 5
Quechua 5
Spanish_No 5
Andronovo 4
Kikuyu 4
Piapoco 4
Russia_Iron_Age 4
Scottish 4
Sintashta 4
Spain_EN 4
Spain_MN 4
Tlingit 4
Armenia_MBA 3
Australian 3
Baalberge 3
Benzigerod 3
Datog 3
Dolgan 3
FTurkish_J 3
Hungary_Maros 3
Italy_Remedello 3
Mezhovskaya 3
Sweden_Nordic_BA 3
Athabascan 2
Botocudo 2
Canary_Isl 2
Denmark_Nordic_BA 2
Denmark_Nordic_LN 2
Greenland 2
MiddleDors 2
Nivkh 2
Okunevo 2
Russia_LBA 2
Sweden_Nordic_LN 2
AG2 1
Alberstedt 1
Aleutian 1
Altai 1
Ancient_De 1
Ancient_Ne 1
Birnirk 1
Chimp 1
Clovis 1
Denisovan 1
Denmark_Nordic_LBA 1
Denmark_Nordic_MN_B 1
EBA 1
Esperstedt 1
Germany_BA 1
Gorilla 1
Halberstad 1
hg19ref 1
Hungary_MBA 1
Iceman 1
Italian_So 1
Karelia_HG 1
Karsdorf_L 1
Kazakhstan_Sintashta 1
Kostenki14 1
LaBrana1 1
LateDorset 1
LBKT_EN 1
Lithuania_LBA 1
Loschbour 1
MA1 1
Macaque 1
Marmoset 1
Mezmaiskay 1
Montenegro_Iron_Age 1
Montenegro_LBA 1
Orang 1
RR 1
Saami_WGA 1
Samara_HG 1
Saqqaq 1
Spain_EN_r 1
Starcevo_E 1
Stuttgart 1
Sweden_Battle_Axe 1
Sweden_Battle_AxeNordic_LN 1
Sweden_Iron_Age 1
Thule 1
Ust_Ishim 1
Vindija 1

What’s old is new in our genomes

The_10,000_Year_Explosion_(Cover)Over at Nature Ewan Callaway has a piece up, Neanderthals had outsize effect on human biology. The upshot is that the few percent of archaic admixture in modern humans, who descend from a Neo-African group ~50,000 years ago, may have significance functionally, and been driven by adaptation. This is not surprising. Greg Cochran and Henry Harpending discussed this dynamic in their The 10,000 Year Explosion (speaking of Greg, he is having a fund raiser). Though not entirely analogous, the work of plant evolutionary geneticists also indicates that we might expect this sort of phenomenon, whereby adaptive variants are absorbed from substrate as populations expand (for a somewhat different angle, though related, see How species evolve collectively: implications of gene flow and selection for the spread of advantageous alleles; I doubt it’s a coincidence that a lot of the deep understanding of evolutionary genetics I have comes from people working on plants).

A few years back I groused to Nick Patterson that the initial Neandertal genome paper in 2010 was overly skeptical of the possibility of admixture resulting in adaptive variants entering the modern human genome pool from archaics. Nick’s argument was simply that they hadn’t detected any such variants at that time, so it was a straightforward thing to report. If you listen to what Ed Green and company stated in the media they were very careful how they parsed their statement in regards non-neutral variants. My rejoinder was that on prior grounds it is hard to imagine that out of a few percent of the genome there wasn’t at least a few significant adaptive alleles.

As Callaway reports above that turned out to be right. I think the original research was a bit too conservative by relying only on empirical results when the theory here seems quite strong. Additionally, I would actually take some issue with the title in the Nature piece. Some of the same researchers have found reduced Neanderthal admixture proportions on the X chromosome, suggesting selection against Neanderthal variants in the admixed genome (a phenomenon common during hybridization between diverged lineages), which is predominantly Neo-African. In other words, the few percent might actually be less than what one might have concluded based on a census count and the genealogy a few generations out of the initial admixture event. It doesn’t really make sense to say that Neanderthal’s had an outsized effect when it is likely that their distinctive variants were also purified somewhat from the genome initially. Perhaps one might say that they had an outsized effect after you control for the fact that deleterious variants from Neanderthals were removed from the equation early on. As it is, and I think as implied in the article, we don’t know enough about the number of functional archaic alleles to adduce whether they have more impact or not. Rather, Neanderthals gave us all things under the sun.

World history as a window on the human condition

k8493The argument I made in my post below is pretty straightforward and transparent if you read even a little bit of world history. Most of the assertions of post-colonial theorists collapse under even the barest of inspection with an empirical mindset. The problem though is most people don’t have much comparative historical or anthropological data to sift through the theory. To give a concrete example, a good friend of mine is an academic from the Arab world. When discussing differences between American society, and his own, he often posits the construct of “Western culture.” My objection to this reflex is always to suggest that what he thinks of as distinctive about “Western culture” is actually a feature shared by many other societies…and Arab culture is distinctive in its own ways. There are ways that all cultures are peculiar, and ways in which it shares features with other cultures.

5180z9XRWsL._SY344_BO1,204,203,200_The bigger problem is that it is not uncommon to have knowledge of Western culture and history, at least to a cursory level, and also the knowledge of a non-Western culture and history. Therefore, there’s a reoccurring theme of dyadic juxtapositions between the “West and the Rest”, where the West is fixed constant, while the rest is a variable. It doesn’t take a genius to realize the problems with this. You can’t make comparisons between the ethnic cleansing practiced by the Manchus in Dzungaria in the 18th century with that on the nascent American frontier if you never examine the tension between Inner Asian civilization and that of China.*

So how would get an appropriate education on world history? Works such as J. M. Roberts’ The History of the World are useful, but often they are stretched thin. A great deal of “Big History” is really just too top-level. Rondo Cameron’s A Concise Economic History of the World is obviously too focused on one particular phenomenon. Rather, I’d suggest that Power and Plenty and After Tamerlane are appropriate balances between broad generality, and thick specificity. Interestingly both of them focus on the world at a 1,000 year scale or so. Long enough to see trends, but not so long as to make all assertions diffuse.

What do readers think? What has been useful to you?

* The Manchus could never have obliterated the Dzungarian Mongols were it not for their capture of the resources of the Chinese state-system, the rise of military technology which eliminated many of the strategic advantages of nomads, an collusion of the Russian Empire.

Indo-Europeans, red in tooth & claw

Lord Indra

Lord Indra

51WnxzkxMTL._SX312_BO1,204,203,200_The Indo-European Controversy: Facts and Fallacies in Historical Linguistics, by Asya Pereltsvaig and Martin Lewis is a pretty one-sided monograph. The reason, as admitted by the authors, is that they believe a certain sector of academia and the middle-brow reading public are not exhibiting enough skepticism about the application of Bayesian phylogenetics in linguistics. To a great extent The Indo-European Controversy: Facts and Fallacies in Historical Linguistics is a book length rejoinder to a paper published in 2003 to great acclaim, Language-tree divergence times
support the Anatolian theory of Indo-European origin
. It’s basically a short letter to Nature. When this paper came out I did not have academic access to such things, and there weren’t online resources (like Twitter) to allow one to make an end-around to academic paywalls. So I remember actually going down to the local college library, and getting a paper copy of the edition of Nature, and reading just like that. In fact that may very well be the last scientific paper i read on paper. And, I went in search of that paper because of an article I saw in The New York Times by Nick Wade, A Biological Dig for the Roots of Language. Pereltsvaig and Lewis correctly peg Nick Wade’s influence in my opinion. My own passing interest in the topic was triggered by coverage in the media. There are other papers of note which follow in the tradition of the 2003 letter to Nature. In particular, I recommend Mapping the Origins and Expansion of the Indo-European Language Family, in Science. If you don’t know much about Bayesian phylogenetic, read the supplements.

5140FASZyJL._SX330_BO1,204,203,200_The heart of the argument Pereltsvaig and Lewis seems to be that some key assumptions in the model that Bayesian phylogeneticists are using to make inferences about the emergence and spread of Indo-European languages are wrong. And, those incorrect assumptions lead to empirical results which are also wrong. Though it was difficult for me to follow much of the deep dive into technical linguistics (thanks for that Asya!), some of the problems with inferences are pretty easy to see. They note that in the supplements of the 2012 paper (second one above) the Romani language is placed as an outgroup to the other members of the Indo-Aryan family. This seems wrong to Pereltsvaig and Lewis, and from what I know it is wrong. Linguistic consensus is that Romani dialects are related to those of Northwest India. It turns out that the genetics favors this, as their South Asian ancestry does seem to derive from Northwest Indian populations. We can go on with details in this vein, but what’s the root of the problem?

One of the major issues brought up in The Indo-European Controversy: Facts and Fallacies in Historical Linguistics is that these Bayesian phylogenetic models utilize lexical information as data inputs. In particular, a set of a few hundred cognates. There are two issues. First, the choice of cognates might be biased, or at least bias the output. Second, vocabulary may not be the best foundation on which to generate a phylogeny of language. Rather, something like grammar may be more phylogenetically informative. The authors of the above works under criticism actually state they’re trying to use grammar as an input too. But in any case, the tendency for vocabulary to be exchanged between nearby groups, irrespective of their phylogenetic origin, is presumably the reason that the Romani languages drifted far enough away from the other Indo-Aryan languages to seem like an outgroup. No matter how ingenious your method, if your input data is biased or not informative, your output is not likely to be useful. Pereltsvaig and Lewis allude to the fact that linguistics has not found their “atoms” yet. I’d state it differently: linguistics lacks its DNA sequence. Using a biological analogy, these linguistic applications of Bayesian phylogenetics are attempting to discern evolutionary history from phenotype.

9780631205661_lThe second major problem with the papers coming out of the Bayesian phylogenetic tradition in linguistic history is an incorrect model assumption: that populations expand purely through diffusion-like processes. If you read the detailed methods it’s pretty clear that they’re converging on the joint posterior probability of tree given the data as well as the geographic distribution assuming a demic diffusion framework. The Indo-European Controversy tackles extensively the historiography of migrations, or lack thereof. Before World War II archaeologists naively traced migrations through the change in cultural forms, while after World War II the backlash became so strong that the null was always that pots, rather than people, were on the move. And, when people were on the move in pre-state societies, it was envisaged in almost a mechanical fashion, as individuals on the farming frontier had higher fertility, and so endogenous growth simply swamped out other groups like European hunter-gatherers. Part of its appeal isn’t just ideological, it’s an elegant model. Historical detail and contingency isn’t relevant, and inter-group conflict can be sidestepped. It’s all about endogenous growth of a population assuming particular resources, until it hits a Malthusian limit in the locality.

Unfortunately this model is almost certainly wrong for human history. Ancient DNA has revolutionized everything, because it is shown just how punctuated demographic shifts can be. Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity highlighted this dynamic a few years back. More recently, Population genomics of Bronze Age Eurasia and Massive migration from the steppe is a source for Indo-European languages in Europe indicate discontinuity. I want to emphasize the term discontinuity, as this is very different from gradual diffusion. Rather than a methodologically individualistic model, where higher fertility in farmsteads or at least villages gradually resulted in the transition from one group to another, a more likely I’d been is inter-group tension, conflict, and amalgamation. In some cases, near total replacement. It may not have been always violent, rather, agriculturalists on the Malthusian margins may not have been able to withstand the shock of a new culture arriving and sequestering critical resources (an analogy I’m thinking is the massive collapse of Roman culture in the Balkans whenever the imperial limes withdrew toward the coasts; without state support and scaffold the way of like the Latin peasantry just wasn’t feasible, so they quickly migrated or died off).

For example, it looks as if the Uygurs are not descended in large part from the first Indo-Europeans on the fringes of western China. I took the data the Reich lab posted and ran TreeMix on it. After reducing the number of populations, I ran TreeMix on it. Below are 10 plots. The West Eurasian ancestry of the Uygurs is not overwhelmingly Northern European-like. Weirdly the graphs below suggest it is somewhat less Northern European than the West Eurasian ancestry contributing to the Hazara! Though that may be an artifact of some sort. The point is that as suggested by many scholars it seems highly likely that the Indo-European population of the Tarim basin was a composition, and that Tocharians and Indo-Iranians were both present. And,  probably did not appear at the same time.

IndianHazUyg.1 IndianHazUyg.2 IndianHazUyg.3 IndianHazUyg.4 IndianHazUyg.5 IndianHazUyg.6 IndianHazUyg.7 IndianHazUyg.8 IndianHazUyg.9 IndianHazUyg.10

So a second question that came to has to do with the origin of the Indo-Aryans, and the genetic history of the Indian subcontinent. About five years ago I told John Hawks that I was skeptical of too much European-like contribution to the Indian population because not enough European pigmentation alleles were segregating in the population. My inference was based on a wrong assumption. It turns out that the earliest steppe dwellers were not particularly pale of mien going by their genetic architecture on pigmentation loci. My objection has no basis, because the modern European phenotype is very new, and likely post-dates the arrival of Indo-Europeans to India. Additionally, there is suggestive evidence of a steppe connection, such as the widespread presence of the “European” allele for lactase persistence in Northwest India. This allele is new, and swept up in frequency very recently. Its presence in Northwest India almost certainly indicates non-trivial demographic connections.

The blogger at Eurogenes has illustrated the dynamic, but it’s pretty obvious that Northwest Indian populations have some affinity to the Yamnya population in particular. Below are the results from TreeMix using a narrower set of population than above. Notice how Pathan tends to move toward the Yamnaya…..

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Indian.9

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But why the affinity to the Pathan, and not the Iranian samples? Who knows. I’ll pull down the data set from the Willerslev lab soon, but I think ancient DNA from India is going to have to answer the question. But I’m curious how the “Out of India” people spin this, because they will have a ridiculous rationale….

Human Genomics “out of the box”

51qciM4cBhL._SX258_BO1,204,203,200_A friend of mine proudly told me recently that she’d purchased an unabridged edition of The History and Geography of Human Genes. Turns out that there are some affordable used copies floating around (under $50, like the Atari 2600!). Flipping through the old unabridged edition I had to admit: a lot of the assertions derived from classical autosomal markers hold true. It might be that all you really need to get “up to speed” is an annotated version. Also, I’d get rid of the synthetic maps, which no one uses anymore (there are some methodological reasons, as well as the fact that they just didn’t turn out to be a very intelligible visualization).

Of course things have changed between then and now. Thanks to open data you can do much more powerful analysis than you find in The History and Geography of Human Genes on your notebook computer in a few hours. So I had the idea for this post a few hours ago…and thought perhaps I’d accompany it with a few TreeMix plots. Below are the 1000 Genomes data, with 250,000 markers (I pruned by intersecting with HGDP markers as well as those with very low missingness):

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Open Thread, July 26th, 2015

51WnxzkxMTL._SX312_BO1,204,203,200_Been reading The Indo-European Controversy: Facts and Fallacies in Historical Linguistics, by Asya Pereltsvaig and Martin Lewis. To a great extent it is a book length response to the research program which made such a big splash with the 2003 Nature paper, Language-tree divergence times support the Anatolian theory of Indo-European origin. I’m over half-way through. Some of it has been hard going, as I’m not very familiar with the details of linguistic science (I get very confused when linguists start using technical terminology for accent changes; anything beyond dipthong). On the other hand, I know a decent amount about the nuts and bolts of Bayesian phylogenetics, and their critique are cogent so far.

9rj62eTo be fair I’m broadly sympathetic to Pereltsvaig and Lewis’ program. There are a decent number of references to genetics in the work, though it looks like they were in final revisions before Massive migration from the steppe is a source for Indo-European languages in Europe. But even without the genetics, I think the case is pretty strong that a simple version of Colin Renfrew’s Anatolian demic diffusion doesn’t work. The contortions necessary to make it plausible in Anatolia during the Bronze Age are too implausible.

If The Indo-European Controversy is a bit too technical, I do recommend everyone check out The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World. David Anthony’s work is probably a lot more relevant today because of the findings from genetics. Even if a Steppe-only model can’t explain everything, evidence of massive population replacement in Northern Europe really does overturn any naive idea that Germanic languages somehow derive from the LBK culture….

Do colored people exist if there are no white people to observe them?

TaylorSwiftApr09William Dalrymple in The New Yorker has a reflection up on the 1947 partition of the subcontinent, The Great Divide. It is fine so far as it goes. He reminds us of the scale of the tragedy, millions of deaths, as well as the depravity of the barbarity, as “infants were found literally roasted on spits.” Some day I will have to educate myself about this period, as I only have vague recollections of reading fragments of Freedom at Midnight as a child. I recall stopping at the point where the authors reported how a group of men broke into an obstetrics unit at a hospital and took a newborn who had just breathed their first and smashed its brains out on the walls, while the mother and hospital staff watched in horror. That was enough to get a flavor of the “action.” Fortunately my family did not suffer during this period, Bengal was relatively quiet in comparison to the atrocities washing over Punjab (as many of you are aware, my family experienced more hardship in the 1971 war, though as they were relatively privileged Muslims who were also not very involved in the arts or politics they were not actively targeted).

But there is one section whose assumptions and implications rub me the wrong way. Let me quote:

In the nineteenth century, India was still a place where traditions, languages, and cultures cut across religious groupings, and where people did not define themselves primarily through their religious faith. A Sunni Muslim weaver from Bengal would have had far more in common in his language, his outlook, and his fondness for fish with one of his Hindu colleagues than he would with a Karachi Shia or a Pashtun Sufi from the North-West Frontier.

Many writers persuasively blame the British for the gradual erosion of these shared traditions. As Alex von Tunzelmann observes in her history “Indian Summer,” when “the British started to define ‘communities’ based on religious identity and attach political representation to them, many Indians stopped accepting the diversity of their own thoughts and began to ask themselves in which of the boxes they belonged.” Indeed, the British scholar Yasmin Khan, in her acclaimed history “The Great Partition,” judges that Partition “stands testament to the follies of empire, which ruptures community evolution, distorts historical trajectories and forces violent state formation from societies that would otherwise have taken different—and unknowable—paths.”


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Ten years ago I read Nicholas Dirks’ Castes of Mind. It is a work of history which shows how many caste identities were fashioned de novo under the impetus of British bureaucratic taxonomy. Though Dirks is too subtle to assert that the caste system was created by the British, the general thrust of the work is clearly one which emphasizes the role of recent historical contingency in establishing the social order of South Asia as we understand it. The subhead is after all: “Colonialism and the Making of Modern India.” The British are then the agents who operate upon the formless void of the Indian subcontinent’s amorphous peasant culture. They came, they saw, and they created. Even when I read Castes of Mind I was moderately skeptical of the narrative, as there had been enough genetics done to suggest that South Asian populations were stratified by caste. By this, I mean that caste status as much, or more, than geography predict the genetic structure of Indian society. It was already evident, for example, that South Indian Brahmins were closer to North Indian Brahmins than they were to South Indian Dalits when it came to genetic relatedness. Brahmins and Dalits are two caste groups which are clear and present throughout South Asia (the “middle castes” tend to vary from region to region, and the classical warrior and trader castes are not present in South India, though there are notionally Sudra groups which occupy their roles). Even those who prioritize the role of the British would accept that the Brahmin and untouchable categories predate the reification of the colonial period. But what the latest genetics is telling us is that caste endogamy has been a feature of Indian life for at least 2,000 years, and perhaps longer. Not only are Brahmins distinct from Dalits, but castes with a less clear position in the classical varna typology, such as the Reddy group of South India, clearly have had long histories as a distinct group. The genetics should make us skeptical of claims that the British were the dominant causal force in shaping caste as a ubiquitous feature of Indian life.

And so with religion. The contemporary revisionism, which now is approaching mainstream orthodoxy, is that South Asian religious life before the arrival of the British, and the Western outlook more generally, was characterized by a quietist syncretism where communal boundaries were fluid to the point of identity being a flimsy veil which could be shed or shifted dependent upon context. An alternative history then might be proposed of a united subcontinent, where Hindus and Muslims were coexistent, or, perhaps where a Hindu and Muslim identity did not even exist. The cognitive psychologist Pascal Boyer likes to characterize a theory as “information for free.” You don’t really have to know anything, you can simply deduce from your axioms. Though this model obviously integrates ethnographic and historical realities, it constructs a post-colonial fantasy-land, where South Asian religiosity was without form or edge before the arrival of Europeans and their gaze collapsed the wave function. Before the arrival of Europeans people of color were tolerant of religious diversity, varied sexual orientations, and practiced gender egalitarianism. In other words, India was like the campus of Oberlin college, except without the microaggressions, and more authentic spirituality!

51J39W7ZRFL._SX306_BO1,204,203,200_The first problem with this narrative is empirical and specific. Before white Europeans arrived in South Asia to roil and upend its social order, and transform its culture, there was already a ruling race of self-consciously white people doing just that. They were the Turks, Persians, and a lesser extent Arabs, who introduced Islam to the subcontinent. As alluded to in Dalyrmple’s piece in some ways Islam was conceived of as a sect of the foreigners by the natives, as well as the Muslims themselves. This is not an entirely strange state of affairs, in the first century or so of the existence of Islam the religion was the tribal sect of the Arab ruling caste of the Caliphate. Only with the rise of the Abassids and maturation of Islamic civilization as a pan-ethnic and post-ethnic concept did the “converted peoples,” in particular the Persians and Turks, become full members of the Ummah and turn it into the universal religion that we understand it today (though even today there is an ethnic dimension in Islam, for example, the Islamic State accepts that the Caliph must be an Arab of the Quraysh tribe).

For many centuries Islam in South Asia recapitulated this pattern, whereby those who descended from converts were received as second class citizens (and still called “Hindus,” which simply meant a native of Hindustan). And to this reality must be added the dimension of race, for the Muslims from the west viewed the native peoples as black, and many elite families with origins in Persia and Central Asia maintained their endogamy for generations partly as a matter of racial hygiene. When Muslim elites did intermarry with the descendants of converts, it was invariably with those descended from high caste groups. The Mughal Emperors wed women from a Hindu background, but these were often the daughters of powerful Rajputs, whose values and armies fused with the Muslim invaders to create what we understand as Islamicate civilization.

Yet there are many other stories besides the standard one of the rise and fall of Mughal India. Islam arrived on the southern coast via traders from the Arab world, and has a distinctive flavor because of that fact. In Crossing the Threshold: Understanding Religious Identities in South Asia, the author shows how the arrival of Islam in the subcontinent often involved a complex and heterodox process of cultural interaction mediated by esoteric strains of the Ismaili sect. It is not relevant for the purpose of this post to review the nature of Ismaili Islam, but it is important to note that Sunnis view this group as deviant and marginally Muslim. With the arrival of the Mughals there began a long period of persecution of Ismailis in the Indian subcontinent. Both Crossing the Threshold and Mullahs on the Mainframe, an ethnography of a particular Ismaili sect in Gujarat, indicate that many of the Sunni Muslims of the subcontinent may be descended from people who entered Islam via Ismailism. Under the Mughals heterodox Muslim sects like the Ismailis were under more pressure and subject to more persecution than non-Muslims. In Gujarat this resulted in mass conversions to Sunni Islam. In other regions it might have resulted in a “compromise” state of shifting to a Twelver Shia identity, which though not Sunni, was generally accorded more respectability than Ismailism. These people would be anticipating the life of Muhammad Ali Jinnah, whose recent ancestors (most accounts state his grandfather) converted from Hinduism to Ismailism, but who himself was an entirely irreligious man who avowed a Twelver Shia faith for purposes of formality.

The author of Crossing the Threshold suggests that for many centuries there existed in the subcontinent under the more tenuous and patchwork pre-Mughal Islamic rulers many liminal communities, who straddled the line between Muslim and Hindu. So long as the Muslims of the Indian subcontinent viewed themselves as strangers in a land which offered them opportunities for profit, there was a certain freedom in being viewed as an amorphous black-skinned mass of “Hindus” whose only importance was in the tax that they provided their overlords. The Mughals changed that. Though they were in origin Timurid princes from Central Asia, their long ascendancy in the subcontinent produced a genuine synthesis with the indigenous substrate. By the later years of the dynasty their symbolic and ceremonial roles as Emperors of India became so entrenched that even resurgent Hindu groups such as the Marathas retained the Mughals as figureheads, much as the Zhou dynasty persisted for centuries after its genuine preeminence had faded.

516ZEEEK2XL._SX332_BO1,204,203,200_But over the 150 years that the Mughals dominated South Asia with their armies they also changed the nature of Islam in the subcontinent in many ways. The Naqshbandi Sufi ordered was associated with the dynasty, and objected when rulers such as Akbar bent or rejected what they perceived to be Islamic orthodoxy. And the Naqshbandi were in a place to judge what was orthodox, as they were an international order with branches across Sunni the Muslim world. The historian S. A. M. Adshead discusses the role of what he calls the “Naqshbandi International” in binding the Islamic world back together after the shattering of the Mongol invasions in Central Asia in World History.

China was another zone of Naqshbandi influence. Unlike India China proper had (and has) never been ruled by Muslims. After period of prominence under the Yuan (Mongols) the Muslim groups became another minority, tolerated by the Han Chinese, but viewed with curiosity and confusion. While the Muslims of what is today called Xinjiang were part of the Turkic world, and even when conquered by the Manchus ruled as a separate domain from China, those resident in the east were relatively isolated, and swam in a Han sea. The Dao of Muhammad: A Cultural History of Muslims in Late Imperial China tells the story of the intellectuals among the Muslims of eastern China, who were confronted with accommodating the reality that they existed at the sufferance of non-Muslims, and could only advance to prominence and prosperity playing the game according to the rules of the Han majority. At the popular level in places like Ningxia there emerged Muslim apocalyptic movements which bore a striking resemblance to heterodox variants of Pure Land Buddhism. But among the intellectuals there arose the conundrum of how to render compatible orthodox Islam and Neo-Confucianism. So long as China was reasonably isolated from the rest of the world, this process occurred without interruption, and followed its own logic. What emerged can reasonably be described as a synthesis between Islam and Neo-Confucianism which resembles in its broad outlines the sort of fusion which occurred in early Christianity after the ruling elites took up the religion and imparted upon it their own philosophical presumptions. Just as some Christians perceived in their religion the completion of the project of the ancient Greek philosophers, so Hui Muslim intellectuals in the cities of eastern China in the 18th century saw in Islam not the overturning of Chinese culture, but its extension and perfection.

Suffice it say this tendency among Chinese Muslims did not give fruit to a vital modern tradition. Several waves of Islamic reform have blasted into China from the outside world, first from Central Asia, and later from the Middle East proper in the age of modern transport and pilgrimage. The Islamic-Confucian synthesis in its full elaboration was a stillborn sect. Similarly, the Islamic-Hindu synthesis championed by the Mughal prince Dara Shikoh and prefigured by his great-grandfather Akbar, was forestalled by the emergence of Aurangzeb. Remembered as pious and steadfast by many modern day Muslims, he is reviled by Hindus, and most Western historians who perceive that the sun set on religious pluralism with his defeat of his brother seem to take a dim view of him. But Aurangzeb was closely associated with the Naqshbandi over much of his life, and he may be less important to the broad social movement of South Asian Muslims being drawn into an international system, with a standard set of beliefs and practices, than we think. Rather, Aurangzeb’s actions may have been consonant with both the indigenization of Islam in the subcontinent, as it struck deep roots and elbowed aside the native religious traditions which had heretofore been beneath notice, and reached out to foreign Muslim traditions so as to make it world normative.

513yXnWcqDL._SX322_BO1,204,203,200_Though I began talking about the Indian subcontinent, the dynamic may be more general. In The Next Christendom: The Coming of Global Christianity, Phillip Jenkins notes that though many claims are made for indigenous African churches, that is, those which have no connection to global denominations and movements and tend to more freely integrate African practices, as African societies become more Christianized they tend to become more mainstream and orthodox in their affiliation. What Jenkins is observing is that with development and modernity indigenous and local practices tend to fade into the background, as African Christians become influenced by the ideas and traditions of Christians from other regions of the world. Individuals who consider themselves part of a religious community start to adhere to the practices and norms of that community’s history.

In India there are still liminal communities in the mode envisaged by Crossing the Threshold. The Meo people of Northwest India are classic exemplars, as they are Muslims who maintain many Hindu traditions. But the trend even among the Meo is to become progressively “more Muslim,” and those Meo who leave their homeland tend to assimilate into the conventional Sunni Muslim milieu and lose their distinctiveness. The Ismaili Khoja community of India is another example of a Muslim group with many Hindu customs and beliefs which has become more “orthodox” within historical memory. In this case the arrival of their spiritual leader, the Aga Khan, from Iran in the 19th century seems to have triggered an Islamic reformation of views and mores. And just as there may have been many groups which moved toward a more standard Muslim identity, there were likely those who became more self-conscious in their Hinduism, as that tradition coalesced as a negation of the exclusive confessionalism of Islam. The Hussaini Brahmins may be a case of the latter. Conventional Hindus in most ways, they customarily participated in Shia Ashura, and have an origin story which places them at Karbala on the side of the sons of Ali. As noted above it was not unknown for high caste Hindus to enter Islam and intermarry with the Muslim nobility. Over time their Hindu origins may have been obscured, as they constructed wholly Muslim narratives. The Hussaini Brahmin community might illustrate a case where the process was halted, and reversed, albeit with a retention of some of their Islamic practices and beliefs. In Crossing the Threshold the argument is made that it the critical aspect for the Sunni Muslim eminences enforcing the new orthodoxy was that Muslim and non-Muslim be clear and distinct categories. Therefore, better a Hindu than a heretic.

51k6n6ma-NL._SY344_BO1,204,203,200_What have I left out of the story? Note that white Europeans are notably absent from the narrative. To some extent this is an artificiality. European “factories” were present on the margins of Mughal India. Jesuits supplanted Muslims as astronomers in the court of Ming China, and were disputants on religious topics in the court of Akbar the Great. Christianity, Islam, and Buddhism, were all closely associated with each other in Central Asia, to the point where it is difficult to tease apart the arrows of causality. In China it seems likely that some varieties of Christianity with ultimate roots in Persia and Central Asia were subsumed into strands of Pure Land Buddhism. But, the point is that history and peoples are subject to general patterns and dynamics, and European colonialism may be thought of as just one important contingent factor. A critical one, but one factor nonetheless.

41JdP75Eu8L._SX321_BO1,204,203,200_It is hard to deny the influence of European culture and Christianity on Indian national and religious worldviews. Consider Hindutva. Conceived of as a form of Hindu racial nationalism by Vinayak Savarkar, himself an atheist who advocated the dismantling the caste system, it is difficult to understand it without considering the dominant winds of culture in the early 20th century. Those winds invariably blew out of Europe. The colonial imprint, the mirrored reflection of British racial nationalism, is hard to deny. Today the intellectual descendants of Savarkar promote bizarre beliefs like the idea that ancient Hindus had flying machines and nuclear weapons, and that astrology is a true science and Ayuvedic medicine is superior to that of the West. It is hard not to see in these beliefs a funhouse distortion of Western trends, such as Christian Science and Creationism. Similarly, the Islamic Creationism of Harun Yahya is explicitly indebted to the American evangelical movement!

And yet within South Asia the broad trend of confessionalization predates the arrival and dominance of Europeans. It seems entirely likely that a division between Islam and what became Hinduism in the subcontinent was inevitable, as modernity and globalization seem to produce crisper identity groups, which are not diffuse, inchoate, and locally rooted. Yes, illiterate peasant naturally practice syncretistic traditions, but when the illiterate peasant becomes a town dweller a different sort of religious practice takes hold. There is a reason that the city-dwelling Christians of the Late Antique world were contemptuous of the marginally Christianized peasantry, the pagani. The last European people to convert to Christianity were the Lithuanians, in the late 14th century. But the peasantry retained enough of their customary religion that veneration and recollection of sacred groves seem to have persisted down to early modernity.

51W2mxRBC9L._SX326_BO1,204,203,200_The Reformed Dutch scholar Atonie Wessels wrote a book titled Europe: Was it Ever Really Christian? His thesis is that from an orthodox Protestant perspective which privileges the beliefs and practices of the individual, it can be argued that much of the European peasantry was operationally pagan down to the Catholic and Protestant Reformations of the 16th and 17th century, followed by the secularization of the continent that began after the Peace of Westphalia. In short, during the period after the fall of Rome and Renaissance the elites were steadfastly Christian, but peasants were only nominally so, with their spiritual life dominated by superstitions rooted in local traditions. In contrast, the emergence of Protestant and Catholic identities during the Reformation resulted in a broad based Christian feeling and identity among the populace. So much so that when the Hohenzollerns converted to Calvinism in the early 17th century their subjects remained steadfast in their Lutheranism. But as the populace became more conventionally Christian, the elites began their long slide toward secularism, finally resulting the rise to power of Frederick the Great, who in matters of religion was apathetic at best.

The European example is important, because it shows that even without exogenous European colonialism confessionalism occurs as a society modernizes. The seeds of this confessionalization are clear in South Asia even before the rise to power of the British raj, as Hindu rulers such as Shivaji privileged their own native traditions as against that of the Muslims, while earlier the rulers of Vijayanagar had served as patrons of Hindu traditions while the north of the subcontinent was dominated by Muslim polities. It does seem fair to state that Sanatani is not comprehensible without it dialectic with Islam. But, it is important to note that Buddhism as an organized religion with a missionary impulse predates Christianity by centuries. Obviously institutional religious identity in the subcontinent is not dependent upon the idea of Europeans and Muslims. What differed with the arrival of Islam is that it was a Weltanschauung which was not digestible to the native cultural traditions.

Though the various Muslim ruling warrior castes held themselves aloof from the people of India, being within the subcontinent, but not of it, it seems inevitable they presumed that their domains were now a permanent part of the Dar-ul-Islam, just as Iran or Central Asia was. Certainly Ibn Battuta could travel in an entirely Muslim India, which operated in parallel with the practices of the vast majority. Over time no doubt the Muslims assumed that the subcontinent would be won over as Iran had. It is hard to remember now, but in the first few centuries of Islamic rule there were periodic anti-Muslim nativist religious eruptions which attempted to overthrow the Muslims, who were perceived as aliens. Prophets arose which told of a time when Islam would fall, and the old religion of the Iranians would come back to the pride of place that it had had. A detailed exploration of this lost world can be found in Patricia Crone’s The Nativist Prophets of Early Islamic Iran, but these movements always make cameos in even traditional works of early Islamic history, such as Hugh Kennedy’s When Baghdad Ruled the Muslim World. But by 1000 A.D. the majority of Persian peasants were Muslim, and Zoroastrianism and its affiliated movements slowly went into their long decline (though still retaining influence through various heterodox Islamic and post-Islamic religious movements).

61H+zZL41QL._SY344_BO1,204,203,200_In India you have a world where the vision of the Iranian prophets came to be, where Islam which seemed eternal and ever waxing in numbers and influence, lost its hold on power and native dynasties which championed local religious traditions arose. There are many differences between the situation of Iran and India. In no particular order, India is far more populous than Iran, local non-Muslim rulers always managed to retain independence at the far corners even at the height of Islamic power and dominion, and the cultural distance between the Muslims and the natives of India was arguably greater than that between the Arabs and the Persians. Even though the Iranians and northern Indians share Aryan cultural roots and influence, reflected in language and religious ideas, those are distant affinities. In contrast, the Arabs had long been present on the margins of the western Iranian world, and the ecology of much of Iran and Mesopotamia was familiar to them.

One peculiarity of the historiography of India under the Muslims is that many scholars claim that local intellectuals, mostly Brahmins, behaved as if their conquerors did not even exist. This sort of involution though may be less strange than seems on first inspection. Ashkenazi Jews in Central and Eastern Europe are to a great extent a people without a history, as their intellectual class devoted its energies to Talmudic commentary, not recording the history of their people. India was massive, and transformations were pregnant within its cultural matrix in response to the Islamic challenge. The Sikh religion seems an obvious case of synthesis, albeit one which while that of Hindu reformist movements such as Arya Samaj seem to sublimate the external variables.

61LXo6U7a4L._SX331_BO1,204,203,200_Though the British may have been a proximate cause for the communal conflicts that tore apart the subcontinent in 1947, they were not the deep cause. As Victor Lieberman observes in Strange Parallels: Europe, Japan, China, South Asia, and the Islands, after 1000 AD there arose several polities dominated by cultural aliens, such as that of the Muslims in India, the Tai in Southeast Asia and the Manchu in China. But unlike the latter two cases the Islamic elites never sufficiently rooted themselves in the local culture to establish a coherent and unified national identity. While the Manchu racial sense of distinctiveness persisted down to their overthrow, their cultural assimilation to most Han mores was so total that rulers such as Kangxi Emperor arguably became exemplars of Confucian rulers. Though the Tai imposed their language of the Mon and Khmer people whom they conquered, they produced a genuine cultural synthesis by patronizing the Theravada Buddhism of their subjects and espousing it as their national religion. While the kings of Thailand patronized Brahmins to give their rule a tincture of Hindu legitimacy, the Mughals were styling themselves as Padishahs.

If Dara Shikoh had defeated Aurangzeb and the British had never brought India into their Empire, would history have been different? I would like to hope so, but I doubt so. Akbar had attempted to create a new religion, but it did not last beyond his life. By the 17th century what was becoming Hinduism, and Indian Islam, were already sufficiently developed that they were becoming cultural attractors. Not through cognitive bias, but the weight of inertia of their cultural history and precedent. The transition from Akbar, to Jahangir, to Shah Jahan, and finally Aurangzeb, is one from an individual who brooked the displeasure of Naqsbhandi shiekhs, to one who worked hand in hand with them. An alternative vision is one where the heirs of Akbar turn their back on their dreams of Fergana, and rely upon Rajputs to dominate their lands instead of a mix of Central Asians and native Indians, Hindu and Muslim. Perhaps the Mughals would have become indigenized enough that they would transform into that they would have become fully Indian in their religious identity. Ultimately the answers of history are more complex than can be dreamed in your post-colonial philosophy, and the white man is neither nor the devil, but a subaltern of historical forces.

Amazonians may have Andaman-like admixture

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Recently had a discussion with a reporter at a major publication about genetic genealogy, and how genomics and ancient DNA has changed everything about what we know about the human. Though I did put in the caveat that it seems the New World has a mildly simpler history that aligns with what we’d somewhat expected or seen. I was wrong. It turns out that indigenous people of the Amazon have a few percent of ancestry derived from a population with the closest affinities to those of Australasia.

Screenshot from 2015-07-21 10:46:26The plot to the left roughly shows groups which share haplotypes when comparing the Mixe people of Mexico to other Amerindians. The stronger red shading shows an affinity between pairwise groups due to the putative admixture event. What you can see that various Australasian groups, as diverse as the Andaman Islanders and and Papuans show elevated signals of affinity with particular groups from the Amazon in comparison to the Mixe.

The model is outlined in the figure at the top. What you can see is that a there was admixture into one of the first groups which arrived in the Americas. This group already had ancient Siberian ancestry. It then seems to have absorbed some ancestry from another group with affinities to the peoples of Australia. Because the dominant ancestral component of the hybrid group was similar to the sister American lineage a wide range of ancestral fractions from this group into the peoples of the Amazon are compatible with the statistics yielded by the data. Up to 85 percent, or as low as 2%. The lower the fraction of admixed “First Americans” into the Amazonian groups in question, the higher the Australian element in that group, as that ancestral element only spans a 1-2% range. In other words, if the admixed First American group contributed only 2% to the modern Amazonians, it would be in large part descended from the Andaman-like group.

This detail matters because of what is brought up in the discussion of the paper, and has been mooted elsewhere: a lot of the older skeletons from this region of South America look different. One model, which the authors are skeptical of, is that admixture happened in the New World. That is, and outrider group of First Americans absorbed and older population which arrived earlier to the region. But Kennewick Man tells us that morphology is only a rough guide. The Anzik Clovis result did not yield any evidence of Andaman-like admixture. That means either there was structure coming into the New World. Or, the admixture happened here.

From the patterns in the genome the admixture is old. But the confidence interval is big. It is not detectable by those methods sensitive to recent admixtures. It is older than 4,000 years. But, it is clearly post-Neandertal admixture. So younger than 50,000 years. In fact, the admixture graph at the top of this post suggests that this admixture post-dates that with the ancient Siberians. That means it is highly likely it probably dates to no older than ~20,000 years, since you need some time for the various Eurasian groups to actually diverge from about 40,000 years ago onward.
dstatThe authors used a variety of methods to test this affinity that they detected. The ancestry fractions were low, so they wanted to see if the result was robust. It sees to be. I won’t get into the details, but I want to post the D-statistic table from the extended data. It uses a slightly different method the map above. Basically they’re testing explicit trees, and showing deviations from random drift along the independent paths which are compatible with gene flow across the tips of the tree. Admixture.

It strikes me that D-statistics show a lot more affinity with South Asians broadly. Why weren’t the signals as strong as in the Chromopainter analysis above? I have no idea, but perhaps it might have to do with the fact that South and Southeast Asians are themselves admixed between the Andaman-like group, and other populations (West and Northeast Eurasians respectively). This may have made higher to detect the haplotypes in question. Additionally, the Ami, an indigenous people of Taiwan also show up on this list. What this implies is that a broad constellation of eastern peoples who diverged from the ancestors of Northeast Eurasians were widely present in the past. In South and Southeast Asia descendants of these people were probably dominant down deep into the Holocene. The elevated signatures in groups like the Andaman Islanders and Papuans may be due to the fact that these groups are relatively pristine.

gr3In 2011 the Reich group published a paper which actually suggested that there were multiple waves of old Southeast Eurasians with the Andaman Islanders being remnants of a group which contributed a secondary signal of admixture into the peoples of Oceania. This was published at about the same time as a whole genome analysis which suggested that Oceanians were descended from an earlier migration out of Africa, and not admixed. There are other groups which are supporting multiple out of Africa events now. The plot is getting thick and complicated.

I only bring this up because much of the current work uses copious data to test explicit models. The authors are constraining the sample space of models, and if you select between ten models, it may still be that the best fit is not a really good fit to the “real” model of what actually happened. One reason ancient DNA has been revolutionary is that it has forced researchers to consider models that they would have otherwise thought ludicrous. There were long suggestions for example of common ancestry between Amerindians and Europeans…but these ideas were often discarded as implausible. There are all sorts of details in relation to modeling assumptions which give valid results which are nevertheless inaccurate.

It is turning out that reality is crazier than our imaginations. Hold tight.

CiteGenetic evidence for two founding populations of the Americas, Skoglund et. al., Nature (2015) doi:10.1038/nature14895

Documentary about ISIS’ escaped slaves

The full documentary from which this clip is extracted is at the Frontline website. I wasn’t really excited about watching this, but I made myself do it. The topic is very disturbing. Most of the film is about the modern day “underground railroad” out of ISIS territory of Yezidi women and children escaping slavery. The scene above is of what looks like a three year old girl who was captured by ISIS along with her mother and one year old brother describing beheadings, which she obviously witnessed. Apparently in disputes with her brother she threatens to cut his head off. The mother of the children tells of her time in one of the slave houses filled with women, and attempting to intervene when one of their ISIS guards started raping a nine year old. Apparently the guard declared that “this was allowed” by his religion. The narrator did not elaborate that the dominant accepted Hadith tradition is that the Prophet Muhammed consumated the marriage to his favorite wife Aisha when she was nine years old.*

Later on in the documentary there is a scene with teenage foreign fighters kicking back and just shooting the shit. The general implication is that they were all raised in Europe. They’re basically horsing around and joking like young men are wont to do. First, they amusingly describe mass killings of Yezidi men. Then later they start making lurid humorous references to Yezidi slave girls.

The truly disturbing aspect is that the body language and the overall mien are so startlingly familiar, but the topics are depraved. I think this goes to the heart of the fact that though we like to dismiss ISIS fighters as sociopaths, they really aren’t. Rather they are motivated by existential and ideological factors. An analogy to Nazi dominated Germany is probably warranted. Most Germans did not start out as Nazis, but during the early conquest years most seem to have conformed to the new dispensation. There are documented instances for example of nurses who were known to toss Jewish children out of the upper stories of hospitals as a way to kill them quickly and free bed up beds for non-Jews, who after World War II went right back to their old profession.

The-Black-Book-of-CommunismISIS seems nihilistic because its aims and means are so alien to the norms of modern civilization, broadly construed. But the same could have been said of the Khmer Rouge regime of the 1970s, or the the Nazi dominion in World War II. And, unlike these two groups international Commmunism for decades managed to appeal to Western intellectuals who believed in its ultimate goals, even if they blanched at the methods of Lenin and then Stalin. They had a dream, and what’s a hundred million broken eggs to make that beautiful omelette?

* No matter if this is true or not, the problem for us in the year 2015 is that may ISIS fighters taking this hadith at face value to justify the rape of nine year old girls.

A Population Geneticist’s Apology

9780981519425_1Brian Charlesworth, co-author of the magisterial Elements of Evolutionary Genetics, won the Thomas Hunt Morgan Medal from the Genetics Society of America this year. An open access copy of his speech, What Use Population Genetics?, is now online at Genetics. In the speech he makes the case toward are a more broad audience, which include people working in molecular and developmental areas far removed from population genetics, why his field is important and critical to the broader scholarly enterprise.

First, he argues that without a good intuition for population genetic dynamics, one can not model evolutionary process very well. Of course that intuition only comes over time absorbing population genetics and gnawing problem sets. But you have to put the work in to talk cogently about evolutionary biology in its most broad scope. Charlesworth suggests that those who don’t know population genetics “run the risk of making mistakes such as asserting that rapid evolutionary change is most likely to occur in small founder populations.” The issue here is that selection is powerful in very large populations. Not so much in smaller ones. I’ve personally encountered this confusion many times from biologists who are not population geneticists. But, I do want to also admit that genetic drift can cause rapid allele frequency changes, so even here I would say that some people might quibble a bit with Charlesworth on the specific details (I am not one to dispute this particular assertion for the record; I know what he meant).

Second, he addresses the nature of transposable elements (TE) in the genomes of organisms, and why they are so common, and where they are so common, as well as the role of PRDM9 in recombination. Pervasive features of the genome may, or may not, have adaptive origins. That means evolutionary genetics has to step into the fray and address the long term dynamics. Intersecting the frameworks of evolutionary genetics, and the structural constraints of molecular genetics, Charlesworth illustrates how population genetics sheds light on the biophysical character of genomic features, as well as the distribution of those features. If evolutionary biology is the science of why. Population genetics is how. Molecular genetics may be thought of in this schema as the is.

Finally, though Charlesworth alludes to it in passing only at the end of his speech, I think it is critical to remember that the post-genomic era is upon us, and it is incumbent upon us to think in in population terms. The style of analysis which is common in population genetics lends itself easily to big data analyses. I recall a conversation with a young researcher last year at ASHG where he told he was moving from population, to medical, genetics. And yet when his most recent publication came out I had to observe that it was fundamentally a work of medical population genomics. You can take the geneticist out of the population, but you can’t take the population out of the geneticist.

Regulatory barriers to small-scale GMO production

FileStack_retouchedAfter my post on GMO and its enemies the usual suspects have been on the attack, accusing me of being a shill for Monsanto. The reality is that I’m a mammalian evolutionary genomicist. I don’t work in applied agricultural genetics, though I have no problem with that discipline. In fact, I’m a big fan. And, because of where I’m based out of I know people who work in and on GMO, and I know their motivations. I can tell you that they sincerely think their research is going to help people. In fact, feed people.

41rxx-UtsWL._SY344_BO1,204,203,200_Nevertheless, a common refrain is that objections to GMO have to do with objections to capitalist mass agriculture. The issue isn’t the science of GMO, but big ag. As you know, I don’t buy this. But let’s set that aside. This spring one of the panels at the Biotechnology Literacy Project (BLP) Boot Camp had to do with government regulation of GMO. I was shocked by the greatly increased regulatory hurdles that GMO face in comparison to more traditional techniques (it’s analogous to what gene therapy studies have to go through).* This enormous overhead imposed by regulation means that small operations, in particular academic laboratories, can’t do viable research on GMO that can get funded. Though CRISPR technology opens up myriad possibilities of modification of food plants studied by a few labs here and there, no researcher can devote the resources necessary to jump through all the hoops placed in front of this work.

Which type of operations can handle this regulatory straight-jacket? You guessed it: Monsanto. That explains one reason so many mass production crops are GMO. That’s big ag’s bread & butter. So will anti-GMO activists, who are concerned with industrial agriculture, and not the genetic technology, argue for changing the regulations to make academic research more viable and accessible for small and medium sized labs? To my knowledge no one in that community is pushing for this.

* If you engage in some Google punditry you’ll encounter documents which suggest that GMO research approval is easier in the USA than elsewhere. This is true. But, from talking to those who work in the field it’s still a big haul for a normal sized laboratory.

Open Thread, July 19, 2015

51gYdVvOoQL._SX379_BO1,204,203,200_Occasionally I get emails from students about how they should go about becoming a biologist who studies evolution. As if I would know. But sometimes the blind seek guidance from the blind! The number one thing I tell them though is that you need mathematical and computational skills today. This is true to some extent even if you are going to be mostly a bench biologist. You don’t want to be the person who’s always relying on someone else for basic analysis. With that, let me note that my friend Vince Buffalo’s book, Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools, is finally out, and I’d recommend it to anyone who wishes to bone up in this area. I’ve read a draft, and it’s definitely useful for any undergraduate or aspiring graduate student in getting you ahead of the curve if you haven’t already done work in this area. It will probably save you some time on Stackoverflow once you get there.

hd5C-sZ3_400x400Speaking of friends, it looks like N of Everyone Kick Starter is going to hit its minimum threshold, and will get funded in their campaign. They’ve also now put a demo up of the Reader on their website. Check it out. You can get a flavor of the direction the firm wants to push scientific publishing. This space will get shaken up at some point, so it’s always useful to keep an eye on it.

9780199589883I’m still slowly making my way through A New History of Western Philosophy. I do most of my reading on the Kindle. When I bought the book, and frankly when I started reading it, I did not understand that it was over 1,000 pages. Additionally, the author does not scrimp on detail. He engages in laborious exposition on items such as how Aristotle’s philosophical thoughts on motion were affected by the constraints of expression in the Greek language of particular concepts.

So why do I read this stuff? I’m a scientist (sort of). I come from a scientific background. From the first I assumed that I would pursue science in some way as an adult. Later on I branched out and explored history and geography. In all of these subjects older works are generally superseded or integrated. You don’t need to read Gibbon’s Decline and Fall to know the general outline of Roman history. Michael Grant’s more recent The History of Rome will do. Similarly, you don’t need to read The Origin of Species to understand evolution (though to be fair, I think in hindsight that it is valuable, after reading it a second time as an adult with a better understanding of evolutionary biology). Just get the Doug Futumya text, Evolutionary Biology, if you want to be technical. Or, What Evolution Is from Ernst Mayr if your taste is more toward something palatable for the generalist audience. That will spare you Charles’ Darwin’s groping attempts at concocting a theory of inheritance.

Philosophy is different. When I encountered philosophy, and I was 20 by the time I seriously engaged the topic, I was shocked by the fact that there was a whole field where the ideas of men who lived over two thousand years ago were still relevant. Let me quote Machiavelli:

“At the threshold, I take off my work-day clothes, filled with dust and mud, and don royal and curial garments. Worthily dressed, I enter into the ancient courts of the men of antiquity, where, warmly received, I feed on that which is my only food and which was meant for me. I am not ashamed to speak with them and ask them the reasons of their actions, and they, because of their humanity, answer me. Four hours can pass, and I feel no weariness; my troubles forgotten, I neither fear poverty nor dread death. I give myself over entirely to them. And since Dante says that there can be no science without retaining what has been understood, I have noted down the chief things in their conversation.”

51K-gkZ7rAL._SX327_BO1,204,203,200_Many, such as Steven Pinker in The Blank Slate, have wondered about our reliance on dead philosophers as authorities on the human condition. In  The Blank Slate Jean-Jacques Rousseau is something of a villain. In agreement with Pinker I believe that most of Rousseau’s conjectures about human nature* have been roundly refuted. Additionally, attempts to construct social arrangements based on Rousseau’s understanding of human nature have failed, sometimes horribly so. More broadly, Pinker has offered that one reason that why the ancients are relevant in philosophy is that the discipline is characterized by the problems which are intractable. They are those domains which remain to philosophy as a discipline after science has carved out huge swaths of its traditional territory. I don’t deny the truth of much of what Pinker says, but when you read Aristotle and Xunzi’s political philosophy, it is hard to deny that their insights are far more relevant and useful than those of Plato or Jean-Jacques Rousseau. And, like good music and art sometimes distance allows us to perceive better the wheat from the chaff. The philosophers who remain relevant and prominent from antiquity were often those of particular genius and creativity. And that is only evident with the passage of historical time.

Obviously I wasn’t anticipating how many comments my post on country rap would generate. I do want to enter into the record that if you use an ethnic slur like “cracker” I’m not going to post the comment. You can just send me an email. I don’t think these slurs are elevating for the conversation.

Finally, on that post, some people seem to think I was casting aspersions on lower class people. That was not my intention at all. Additionally, though I don’t interact with that sort of person much today, I did grow up with a lot of lower and lower middle class rural whites. I even spent time working on a mule farm owned by a friend’s mother. As they say, class isn’t about money. And the poor and working classes have their own folkways in any case. My point is that just because there are particular folkways that are common among a certain class, they don’t have to “own” those tendencies, and can try and transcend them. But we as a culture don’t really engage in this sort of aspiration toward a higher and ennobling state. This actually has its flip case in the flaunted debauchery of the likes of Paris Hilton, who rub in Middle America’s face their exemption from bourgeois norms due to their class status.

* The representation of his conjectures about human nature, for those who note that there is some revisionist work which argue’s he’s been misrepresented.

Between the millennia and generations


Iron Age and Anglo-Saxon genomes from East England reveal British migration history
Stephan Schiffels, Wolfgang Haak, Pirita Paajanen, Bastien Llamas, Elizabeth Popescu, Louise Lou, Rachel Clarke, Alice Lyons, Richard Mortimer, Duncan Sayer, Chris Tyler-Smith, Alan Cooper, Richard Durbin

108_322When I first realized of the possible utility of genetics toward anthropology and history I came up against a major problem in addressing extremely fine-grained questions: the tools did not have the power to probe very small genetic distances, constrained in time and space. After reading Norman Davies massive The Isles I was to understand that the Anglo-Saxon transformation of Britain into England was a matter of elite cultural emulation. What did genetics have to say about this? The answer was “not much.” In an earlier era of a few dozen classical autosomal markers or just mtDNA and Y chromosomal fast evolving microsatellites genetics was not powerful enough to distinguish between extremely close European populations. In The History and Geography of Human Genes L. L. Cavalli-Sforza notes that Europe is the most homogeneous of his continental groups where he had many samples. If you remove outliers like the Finns and Sicilians, this is very true today when we have whole genomes. Though conventional whole-genome SNP panels can distinguish Northern European population clusters they are packed very tightly together.

Using the Human Origins Array data set the authors of Iron Age and Anglo-Saxon genomes from East England reveal British migration history projected the genootypes of ancient samples from the Iron Age and the Anglo-Saxon period upon modern groups. As you can see the Northwest European data sets are packed so close it’s hard to discern structure. In the era of pre-genomic phylogeography it was nearly impossible. To answer whether the Anglo-Saxon migration was a mass folk wandering or a tiny mercenary elite one would have to distinguish Germano-Scandinavian heritage from that of the native British, and the reality is that these are all very close groups. We now know that the ethnogenesis, at least in a genetic sense, of Northern Europeans as a whole seems to date to the Bronze Age, on the order of 4,000 years ago. Therefore, to pick up genetic structure you are by and large focusing on only two to three thousand years of drift between these groups! This explains why the older methods were so under-powered. There just wasn’t much raw material for them to work with; not enough time had passed for the populations to diverge.

nedPLOTA few months ago the PoBI project finally published, and revealed local structure across the British Isles. The authors concluded that in England proper a minor, but substantial, proportion of the ancestry derived from the Anglo-Saxons. That is, Germans. The authors used SNP data sets. That is, less than a million markers in the genome (and out of the twenty to thirty million SNPs in the human genome). But, they had a massive sample coverage from which to extract insights from.

51IQSePVDRL._SY344_BO1204203200_This preprint takes a different tak. They take whole genome sequences from ancient subfossils. What they lack in sample size, they make up for in marker set (some of the coverage is high enough that they probably got decent calls), as well as the fact that they are sampling individuals who are from the source cultures in question. Celts, Anglo-Saxons during the invasion period, and also during a some what later epoch. Their results in nearly perfectly in line with those of PoBI. Using their samples as representative they estimate that ~30 percent of the eastern English ancestry is German. A lower proportion is found in Wales and Scotland.

The figure above illustrates this finding. A key point about this paper is to emphasize that since they are using whole genome sequences they can focus on rare alleles. Because the alleles are at low frequency they’re likely to be younger, and if they are younger they are also more likely to yield the power to discern differences between very genetically close groups, such as the Germans and the British. In the plot above you see that the Anglo-Saxon samples are shifted left, while the Iron Age samples are shifted to the left. What this shows is that the Iron Age samples tend to share more rare alleles with the Spanish IBS data set from the thousand genomes, while the Anglo-Saxons share more alleles with the Dutch.  Eastern England and Wales and Scotland occupy positions that you’d expect.

Furthermore, the authors utilized the program rarecoal to explicitly model the population history of Britain using their data. This will be a major feature of future work in this area, as researchers drill-down to a very fine grain and ask precise questions which good quality whole genomes and robust phylogenetic packages can actually tackle.

There is still much that needs to be worked out on this topic. There’s only so much you can say from these handful of individuals. But even with these finite samples much was extracted. The authors observe that one of their Anglo-Saxon era individuals, buried in an Anglo-Saxon fashion, clustered perfectly with the British Iron Age individuals. Additionally, this individual was outfitted in a manner which suggested they were very high status within Anglo-Saxon society. But the authors did not connect this with the fact that all their Anglo-Saxon individuals were female. Hypergamy is entirely typical in human societies, and it is plausible that large numbers of migrating German men arrived on British shores without a wife and family in toe. In the years after the Norman invasion it was not uncommon for noble Saxon houses to give their daughters to an invader. And so the Anglo-Norman aristocracy arose as a synthesis between distinct paternal and maternal lineages. A similar scenario likely played out during the invasions of the Dark Ages.

The cognitive roots of genophobia

Over at Slate Will Saletan has a very long piece Unhealthy Fixation: The war against genetically modified organisms is full of fearmongering, errors, and fraud. Labeling them will not make you safer. The survey is useful if you are unfamiliar with the topic, though it will be sadly familiar to the rest of us. Saletan makes two observations which I think need highlighting. First, he asserts that “But the deeper you dig, the more fraud you find in the case against GMOs. It’s full of errors, fallacies, misconceptions, misrepresentations, and lies.” Basically it’s a shell game, and the reason is that those who oppose GMO obfuscate the fundamental roots of their objections (consciously or subconsciously). Saletan notes:

Third, there are valid concerns about some aspects of GE agriculture, such as herbicides, monocultures, and patents. But none of these concerns is fundamentally about genetic engineering. Genetic engineering isn’t a thing. It’s a process that can be used in different ways to create different things. To think clearly about GMOs, you have to distinguish among the applications and focus on the substance of each case. If you’re concerned about pesticides and transparency, you need to know about the toxins to which your food has been exposed. A GMO label won’t tell you that. And it can lull you into buying a non-GMO product even when the GE alternative is safer.

The concrete and coherent objection to GMO which lies just under the surface of the arguments put forward by activist groups like Greenpeace is that they are part of the agricultural-industrial complex. But as many have observed, if the problem with GMO is their connection to big agriculture, then why aren’t the arguments simply recycled from those used against industrial agriculture? There are two issues. First, there is broad popular suspicion of “genetically modified organisms.” Using GMO as a hook, and engaging in FUD, is more effective than arguing against corporate agriculture. Second, as Saletan implies in the piece, even anti-corporate concerns aside there are genuine concerns rooted in the idea that there is something “wrong” with genetically modifying organisms (in fact, with the emergence of cheap CRISPR, we’re potentially at the precipice of small scale agricultural innovation, though right now it is unlikely to happen because of regulation).

This sentiment is very broad, and, it is not ideological. Or at least it wasn’t as of 2006, when the EATGM question on for the GSS was asked, with over 900 respondents. It asks:

Which statement best describes your own view about eating foods that have been genetically modified? 1. I don’t care whether the food I eat has been genetically modified. 2. I am willing to eat genetically modified foods, but would prefer unmodified foods if they are available. 3. I will not eat food that I know has been genetically modified.

The results:

Screenshot from 2015-07-18 16:02:54

As you can see, there’s no ideological difference. The slightly greater skepticism of Democrats can probably be attributed to socioeconomic considerations. The less educated, the poorer, and women, are all more skeptical of GMO. These are more well represented among Democrats as demographics, and some of these are the most liable to vote and identify Democrat despite not being particular socially liberal (e.g., poorer minorities).

gmo1But that’s nearly 10 years ago. I’m not sure that the lack of ideological polarization will be so evident now. As documented by Saletan, and earlier in Slate by my friend Keith Kloor, the really high octane activists and public intellectuals behind the anti-GMO push are on the cultural Left. Last year Oregon had a GMO food labeling ballot measure. It lost narrowly. But as you can see in the scatter plot to the left there is a very tight correlation between a county being Democratic and favoring labeling. Second, there was an earlier go around on the same topic in 2002. That measure was destroyed at the polls. If trends continue it seems entirely likely that labeling will succeed in Oregon in the next go around. Americans intuitively are biased toward transparency as a good.

Screenshot from 2015-07-18 16:22:39The fact is that the majority of the public remains skeptical of GMO foods. And large majorities support labeling. Which prompts one to ask: why did the labeling measures not pass in Oregon and California? I think the critical aspect here is that attitudes of skepticism toward GMO are wide but shallow beliefs. Only a small minority of individuals have very strong views on the topic. Those opposed who have very strong opposition tend to come from the liberal intelligentsia. Anyone who has been involved in science and policy around this topic (I have friends who work on GMO crops) will vouch for this. Similarly, those enthusiastic tend to be a small number of plant scientists (who also, tend to be politically liberal on the whole). It is true that large agricultural firms are pro-GMO, but here’s the reality: big ag is making money, it doesn’t need GMO. In fact, because of public sentiment and preference big ag naturally sees organic labeling as a profit center!

DescartesBabyOnce the issues of GMO become salient, as in the ballot measure here on the West coast, then people become more cautious. Anti-labeling arguments start to be more persuasive, and those with business interests that might intersect with agriculture might come to different opinions, as the precautionary principle starts cutting in other directions. GMO has not become culturally polarizing. Yet. Most peoples’ opinions are inchoate and instinctive. I believe they derive from folk biological intuitions about essences. Ultimately it’s about the fact that people don’t understand genes in any prosaic sense, but they think that they’re somehow magically involved in the nexus of who we are in a deep and fundamental sense. That’s why the translocation of fish genes into tomato are so uncomfortable for people; they imagine that the essence of the fish is somehow being mixed with the essence of the tomato, and that just feels wrong. Genophobia of this sort is comprehensible in a cognitive anthropological framework. Just as we are likely wired for Creationism, I think we’re wired for being very skeptical of the concept of GMO, because of the implicit connotations of muddling categories which we view was fundamental. And, just like Creationism, we can overcome these deep intuitions. Much of natural science in the modern world consists of overcoming and updating of deep intuitions.

410tL5IwqTL._SX329_BO1,204,203,200_But, the deep intuitions can be harnessed toward political movements. In the United States Creationism is not just a sentiment and intuition, but a formalized social-political project which fuses some elite suspicions of scientific naturalism with populist skepticism of common descent. Modern Creationism has a particular intellectual pedigree, but it works with the raw material of gut human feeling. Creationist sentiment is old, as old as our species. But Creationism as a potent political movement is new, and its affiliation with the edges of American conservatism is actually a feature of the past generation. It has a history of how it got from where it was, to how it got to where it is. In American Grace Robert Putnam and David Campbell report data that political and religious affiliation co-vary and influence each other (with the former often effecting the latter!).

I am mildly optimistic that this will not happen with GMO, and that is because scientists are anti-anti-GMO, and, politically liberal. It seems very likely that a GMO food labeling measure will pass in the near future. And I believe that this will galvanize a backlash among scientists on the whole. Something similar happens on the Right with Creationism. Whenever the movement actually scores a victory elite Republicans, who invariably accept the science of evolutionary biology, become alarmed and roll back gains made by Creationists. Unlike evolution, GMO are not just abstractions in a laboratory. When GMO becomes pervasive enough, or at least the knowledge of how pervasive they are becomes more common, then the public will likely make peace with their reservations, just as they have with in vitro fertilization.

The domination of demotic chic

51MzSp6UPlL._SY344_BO1,204,203,200_Probably because I’m reading the perspectives of ancient philosophers such as Plato who had very specific and clear views of human excellence, I’m struck now by the rise of brashly demotic artistic forms, and how they push their way into our public space. Consider the rise of country rap, which is one of the more bizarre cultural syntheses to arise out of the dialectic discourse which permeates American society. Country music has traditionally been dominated by rural white Americans, and reflects a conservative ethos which is notionally aligned with traditional values. Rap, in contrast, emerges out of a hip-hop urban milieu which is oppositional to broader American society, distrusting authority rather than celebrating it.

When the Moonshine Bandits “We’re all country” came on my Spotify I was curious about Sarah Ross rapping about how she’s from Jersey, but still country. And, there are explicit shout-outs to blue collar life. They seemed to be owning a denigrated lifestyle and class background. So I looked up the video. The aesthetic was shocking to me. To be entirely frank, it seems to celebrate a gritty slovenliness as the best of all things. Eternal Budweiser, mac & cheese, and poor muscle tone. Many hip-hop and bro country music videos are gauche in their crass superficiality, but at least ultimately there’s often a nod to an aspiration toward excellence, in wealth, in accruing attractive females, in being in shape. You don’t see any of this in the above video. It’s a valorization of the demotic, the pedestrian. Average looking people coalescing together to get inebriated. No symposium, that.

The genetic structure of East Asians

There was a question about East Asian genetic structure. There have been a fair number of papers published on the issue. But over the years I’ve assembled a pretty large personal data set from public sources, as well as stuff people have sent me. I decided to look at the East Asian individuals and how they relate to each.

First, I focused on the major ethno-national groups (or ones of particular interest and relevance, such as Mongols). Second, I LD pruned the data set down to 96,000. Third, I did some outlier removal. For example, I wanted to include some Kalmyk data, but it turns out all the Kalmyk have European admixture at some level. And a subset of individuals from Cambodia and Vietnam are ethnic Chinese. Those were removed.

I ran ADMIXTURE K = 5 unsupervised. Treemix k = 500 and global rearrangements on, and rooted with Cambodians.

Eigenvalues 7.59041, 4.04862, 3.00559, 2.60692 and 2.01554.

Asian1

Asian2

Asian3

Asian4

AsianTreeix.9

AsianTreeix.8

AsianTreeix.7

AsianTreeix.6

AsianTreeix.5

AsianTreeix.4

AsianTreeix.3

AsianTreeix.2

AsianTreeix.1

Asian_htm_m40027816

First, the evidence of gene flow into the Han ethnicity, or the absorption of the Han of local substrate, is clear in these results. Second, I’m pretty sure that the weird affinity between Yakut (the northernmost Turks) and Cambodians has to due with admixture into both groups from non-East Eurasians that is old. In the case of Cambodians something Indian-like, and for Yakuts something more like “Ancient North Eurasians.”

How East Bengalis got East Asian

51KHpfTVbiL._SY344_BO1,204,203,200_Let’s start at the beginning. If you read a book about Indian history in the 1980s it might begin with this sort of stylized narrative: in the beginning where the Mundas. Then there were the Dravidians, then finally the Aryans (and as an afterthought various East Asian groups on the fringes of north and eastern South Asia). The thesis, broadly, was that the Munda people, who speak an Austro-Asiatic language, were the closest that South Asia had to genuine aboriginals. The oldest of old. Supporting this contention is the fact that the languages of the Munda people, with distant affinities to Cambodian and Vietnamese, are alien in comparison to Dravidian and Indo-Aryan (if Dravidian has any connections outside of the subcontinent, they are always posited to the west. The Munda languages clearly have eastern connections). The supposition then was that from the Munda arose various peoples of Southeast Asia. To cut to the chase this model is probably wrong. The genetic structure of South Asia seems to have arrived at its current outlines relatively recently. In regards to the Munda people their origin is in Southeast Asia. Their Y chromosomal lineages and autosomal heritage both imply this. Additionally, they carry the East Asian derived variant of EDAR. Though much of their culture is almost certainly exogenous, and of relatively recent vintage, they are clearly highly admixed with the South Asian substrate. In particular, the fusing of an ancient West Eurasian population (“Ancestral North Indians”, or ANI) and a deeply rooted indigenous group with distant affinities further east (“Ancestral South Indians”, or ASI).

Chaubey, Gyaneshwer, et al. "Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture." Molecular biology and evolution 28.2 (2011): 1013-1024.

Chaubey, Gyaneshwer, et al. “Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture.” Molecular biology and evolution 28.2 (2011): 1013-1024.

One of the reasons that the ancient character of Munda residence in South Asia was persuasive is that their seem to be resident in upland zones, perhaps refuges from later arrivals. Their fragmented distribution is a tell that they occupied wider territories than is the case today. One thesis is that the Gangetic plain was inhabited by Munda people before the Indo-Aryans arrived. Rather than Dravidians, the indigenes in the Vedas may have been Mundas. But I’m interested in a more parochial question: can Munda ancestry explain the high fraction of East Asian ancestry in Bengalis, particular eastern Bengalis?

We can address this question a bit with genetics thanks to the resources we have in terms of population coverage. As readers know I’ve started to work with the 1000 Genomes data set. Luckily it has a large number of Bengalis within it. Meanwhile, the Estonian Biocentre has put its genotype data online, and there are Munda samples in there. I merged the data together, and removed pretty much all missing alleles. At the end of it I had 185,000 SNPs. To explore the questions I had I decided to look at several populations. Bengalis and Telegu speakers (their genetic position would put them as “middle castes”; not Brahmins, but not Dalits or tribals). Georgians (from the Caucasus) as an outgroup. For East Asian groups, Burmese, Cambodians, Filipinos and Dai. Finally, a small number of Munda. I plotted them on a PCA and removed those individuals who were not easily assigned to a cluster. The first PCA: MundaPC1 This isn’t really telling you much you don’t know. Let’s look at PC 3 now: Rplot As you can see the Munda show a cline toward the Cambodians. This makes sense if the Munda descend from Austro-Asiatic agriculturalists. The Austro-Asiatic expansion in Southeast Asia probably dates to 4,000 years ago or so. That might put a ceiling on how early the Munda arrived in Sout Asia. In these results the Filipinos are representative of Austronesians, who likely have their roots in Taiwan and the Fujian coast, while the Dai are the forerunners of the Thai who arrived in Southeast Asia over the last few thousand years, taking over the uplands of Burma and Laos, and swallowing the Khmer civilization which once flourished in the Chao Phraya basin. But it’s hard to make out what’s going on with the Bengalis…to me it isn’t clear that they’re shifted as much toward the Cambodians as they should be if the Asian ancestry was due to Munda being absorbed by Indo-Aryan speaking farmers. Next I ran Admixture. I ran supervised and unsupervised and they showed the same qualitative result. Below is a bar plot of the unsupervised result, K = 5. plinkAA_htm_mf149510

The Munda ancestry which is labeled East Asian here is overwhelmingly Austro-Asiatic. That is not the case with the Bengalis, who exhibit a range of fractions. There is very little Austronesian ancestry, which is something one might expect. But, there’s a balance of Austro-Asiatic and Daic ancestry in many individuals, though there is variation (my mother has one of the strongest Austro-Asiatic skews among the Bengalis, while my father is among the most Daic; previous runs of admixture consistently show that her East Asian is more Southeast Asian than his, which has suggestions of Northeast Asian). This is not consistent with Munda being the sole source of East Asian ancestry in modern Bengalis.1 Using rolloff based methods researchers have estimated that admixture into Bengalis occurred on the order of 1,000 years ago. There’s nothing here that would contradict that, and the admixture can easily be explained by the Burmese in the data above, or Khasi and Garo people, who live to north and and east of Bengalis. Finally, I ran TreeMix on the data. I removed the Georgians and Filipinos because they didn’t add much. Additionally, for kicks I broke apart the Bangladeshis into two groups defined by the 25 most Daic, and 25 least Daic. Below are the ten plots from the ten runs.

MTree.9 MTree.10 MTree.1 MTree.2 MTree.3 MTree.4 MTree.5 MTree.6 MTree.7 MTree.8

I don’t think breaking apart the Bengalis did any good. There were runs with the full fused sample, and the results were similar. It is clear that TreeMix also suggests that Munda are not a singular donor to Bengalis of their East Asian heritage. The donor is always shifted more toward other East Asian groups. Breaking apart the Bengalis into Austro-Asiatic and Daic skewed groups did result in the source of the gene flow being somewhat different. But not appreciably. I also ran the f3 and f4 statistics. There’s nothing surprising about who mixes with who…though it is notable that Burmese show nearly as high a gene flow from South Asians as Bengalis show from East Asians. There have long been suggestions of gene flow from India to Cambodia, perhaps associated with the ancient mediation of South Asian cultural forms across Southeast Asia. But the Burmese evidence of gene flow is tragically ironic in light of the fact that modern Burmese are virulently racist toward dark skinned Muslims who clearly have South Asian origins.

So what happened in Bengal? At the top of the post I have an illustration of The Rise of Islam and the Bengal Frontier, 1204-1760. The thesis of this book is that the Islamic nature of eastern Bengali is in large part due to its relatively recent settlement by Indo-Aryan farmers. Though Bengal has always been a marchland, on the fringes of Aryavarta, before the Islamic conquest of the 13th century its center of gravity, culturally and demographically, was in what is today in the Indian state of Bengal, to the west of Bangladesh. The author of The Rise of Islam and the Bengal Frontier, 1204-1760 suggests that Islamic elites were instrumental in opening up these lands, and the peasant cultivators who came to cultivate the new territory under their leadership were easily convinced to change their religious affiliations, as the old organically developed institutions of Hinduism and Buddhism were poorly moored in the virgin lands. To me this is reminiscent of Michelle Salzman’s data in The Making of a Christian Aristocracy, which suggests that Christian elites arose on the frontiers, rather than the old cores, under patronage of the new religious dispensation. In contrast the old Roman elite was relatively late to Christianity, as they were attached their own customs and traditions, which had thick and deep roots in the heartlands of the Roman world. Similarly, Hinduism (or what became what we term Hinduism) between the Doab and western Bengal seems to have resisted Islam’s attempt to destabilize local institutions and interpose itself as the dominant religious ethos of the sub-elites. Only the fringes of the west and east did Islam find purchase.

Finally, the high component of East Asian ancestry among the peasants of eastern Bengal are probably a function of the fact that there were groups from the east also pushing into the fertile territory. If the initial population density was low then a modest inflow at the early stages, ~1,000 years ago, could have a major long term impact. The crushing population densities of “Golden Bengal” was centuries into the future. A lack of cultural memory of this admixture is curious, but to a great extent shifting to the new religion meant that the proto-east Bengalis were creating a new identity. Things get lost….

How East Bengalis got East Asian

51KHpfTVbiL._SY344_BO1,204,203,200_Let’s start at the beginning. If you read a book about Indian history in the 1980s it might begin with this sort of stylized narrative: in the beginning where the Mundas. Then there were the Dravidians, then finally the Aryans (and as an afterthought various East Asian groups on the fringes of north and eastern South Asia). The thesis, broadly, was that the Munda people, who speak an Austro-Asiatic language, were the closest that South Asia had to genuine aboriginals. The oldest of old. Supporting this contention is the fact that the languages of the Munda people, with distant affinities to Cambodian and Vietnamese, are alien in comparison to Dravidian and Indo-Aryan (if Dravidian has any connections outside of the subcontinent, they are always posited to the west. The Munda languages clearly have eastern connections). The supposition then was that from the Munda arose various peoples of Southeast Asia. To cut to the chase this model is probably wrong. The genetic structure of South Asia seems to have arrived at its current outlines relatively recently. In regards to the Munda people their origin is in Southeast Asia. Their Y chromosomal lineages and autosomal heritage both imply this. Additionally, they carry the East Asian derived variant of EDAR. Though much of their culture is almost certainly exogenous, and of relatively recent vintage, they are clearly highly admixed with the South Asian substrate. In particular, the fusing of an ancient West Eurasian population (“Ancestral North Indians”, or ANI) and a deeply rooted indigenous group with distant affinities further east (“Ancestral South Indians”, or ASI).

Chaubey, Gyaneshwer, et al. "Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture." Molecular biology and evolution 28.2 (2011): 1013-1024.

Chaubey, Gyaneshwer, et al. “Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture.” Molecular biology and evolution 28.2 (2011): 1013-1024.

One of the reasons that the ancient character of Munda residence in South Asia was persuasive is that their seem to be resident in upland zones, perhaps refuges from later arrivals. Their fragmented distribution is a tell that they occupied wider territories than is the case today. One thesis is that the Gangetic plain was inhabited by Munda people before the Indo-Aryans arrived. Rather than Dravidians, the indigenes in the Vedas may have been Mundas. But I’m interested in a more parochial question: can Munda ancestry explain the high fraction of East Asian ancestry in Bengalis, particular eastern Bengalis?

We can address this question a bit with genetics thanks to the resources we have in terms of population coverage. As readers know I’ve started to work with the 1000 Genomes data set. Luckily it has a large number of Bengalis within it. Meanwhile, the Estonian Biocentre has put its genotype data online, and there are Munda samples in there. I merged the data together, and removed pretty much all missing alleles. At the end of it I had 185,000 SNPs. To explore the questions I had I decided to look at several populations. Bengalis and Telegu speakers (their genetic position would put them as “middle castes”; not Brahmins, but not Dalits or tribals). Georgians (from the Caucasus) as an outgroup. For East Asian groups, Burmese, Cambodians, Filipinos and Dai. Finally, a small number of Munda. I plotted them on a PCA and removed those individuals who were not easily assigned to a cluster. The first PCA: MundaPC1 This isn’t really telling you much you don’t know. Let’s look at PC 3 now: Rplot As you can see the Munda show a cline toward the Cambodians. This makes sense if the Munda descend from Austro-Asiatic agriculturalists. The Austro-Asiatic expansion in Southeast Asia probably dates to 4,000 years ago or so. That might put a ceiling on how early the Munda arrived in Sout Asia. In these results the Filipinos are representative of Austronesians, who likely have their roots in Taiwan and the Fujian coast, while the Dai are the forerunners of the Thai who arrived in Southeast Asia over the last few thousand years, taking over the uplands of Burma and Laos, and swallowing the Khmer civilization which once flourished in the Chao Phraya basin. But it’s hard to make out what’s going on with the Bengalis…to me it isn’t clear that they’re shifted as much toward the Cambodians as they should be if the Asian ancestry was due to Munda being absorbed by Indo-Aryan speaking farmers. Next I ran Admixture. I ran supervised and unsupervised and they showed the same qualitative result. Below is a bar plot of the unsupervised result, K = 5. plinkAA_htm_mf149510

The Munda ancestry which is labeled East Asian here is overwhelmingly Austro-Asiatic. That is not the case with the Bengalis, who exhibit a range of fractions. There is very little Austronesian ancestry, which is something one might expect. But, there’s a balance of Austro-Asiatic and Daic ancestry in many individuals, though there is variation (my mother has one of the strongest Austro-Asiatic skews among the Bengalis, while my father is among the most Daic; previous runs of admixture consistently show that her East Asian is more Southeast Asian than his, which has suggestions of Northeast Asian). This is not consistent with Munda being the sole source of East Asian ancestry in modern Bengalis.1 Using rolloff based methods researchers have estimated that admixture into Bengalis occurred on the order of 1,000 years ago. There’s nothing here that would contradict that, and the admixture can easily be explained by the Burmese in the data above, or Khasi and Garo people, who live to north and and east of Bengalis. Finally, I ran TreeMix on the data. I removed the Georgians and Filipinos because they didn’t add much. Additionally, for kicks I broke apart the Bangladeshis into two groups defined by the 25 most Daic, and 25 least Daic. Below are the ten plots from the ten runs.

MTree.9 MTree.10 MTree.1 MTree.2 MTree.3 MTree.4 MTree.5 MTree.6 MTree.7 MTree.8

I don’t think breaking apart the Bengalis did any good. There were runs with the full fused sample, and the results were similar. It is clear that TreeMix also suggests that Munda are not a singular donor to Bengalis of their East Asian heritage. The donor is always shifted more toward other East Asian groups. Breaking apart the Bengalis into Austro-Asiatic and Daic skewed groups did result in the source of the gene flow being somewhat different. But not appreciably. I also ran the f3 and f4 statistics. There’s nothing surprising about who mixes with who…though it is notable that Burmese show nearly as high a gene flow from South Asians as Bengalis show from East Asians. There have long been suggestions of gene flow from India to Cambodia, perhaps associated with the ancient mediation of South Asian cultural forms across Southeast Asia. But the Burmese evidence of gene flow is tragically ironic in light of the fact that modern Burmese are virulently racist toward dark skinned Muslims who clearly have South Asian origins.

So what happened in Bengal? At the top of the post I have an illustration of The Rise of Islam and the Bengal Frontier, 1204-1760. The thesis of this book is that the Islamic nature of eastern Bengali is in large part due to its relatively recent settlement by Indo-Aryan farmers. Though Bengal has always been a marchland, on the fringes of Aryavarta, before the Islamic conquest of the 13th century its center of gravity, culturally and demographically, was in what is today in the Indian state of Bengal, to the west of Bangladesh. The author of The Rise of Islam and the Bengal Frontier, 1204-1760 suggests that Islamic elites were instrumental in opening up these lands, and the peasant cultivators who came to cultivate the new territory under their leadership were easily convinced to change their religious affiliations, as the old organically developed institutions of Hinduism and Buddhism were poorly moored in the virgin lands. To me this is reminiscent of Michelle Salzman’s data in The Making of a Christian Aristocracy, which suggests that Christian elites arose on the frontiers, rather than the old cores, under patronage of the new religious dispensation. In contrast the old Roman elite was relatively late to Christianity, as they were attached their own customs and traditions, which had thick and deep roots in the heartlands of the Roman world. Similarly, Hinduism (or what became what we term Hinduism) between the Doab and western Bengal seems to have resisted Islam’s attempt to destabilize local institutions and interpose itself as the dominant religious ethos of the sub-elites. Only the fringes of the west and east did Islam find purchase.

Finally, the high component of East Asian ancestry among the peasants of eastern Bengal are probably a function of the fact that there were groups from the east also pushing into the fertile territory. If the initial population density was low then a modest inflow at the early stages, ~1,000 years ago, could have a major long term impact. The crushing population densities of “Golden Bengal” was centuries into the future. A lack of cultural memory of this admixture is curious, but to a great extent shifting to the new religion meant that the proto-east Bengalis were creating a new identity. Things get lost….

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