As someone of you know the supplement on the Cardial ancient genome presents some really strange results. Look at the gene flow edges around the Mbuti. I have used TreeMix a fair amount, and I’ve seen some weird things of which I have not spoken. I’m sure others have as well. My assumption when I see something this peculiar is that it is an artifact of ascertainment bias or TreeMix just being TreeMix.
After the welter of novel analytic methods and ancient DNA I think perhaps we need to reconsider dismissals. Usually when you’re using TreeMix you’re looking for only a constrained set of the hypotheses. You pretty much ignore or shove aside “results” which bubble out of the word-work. But sometimes this marginalia can take center sage. When the original TreeMix paper came out it had a figure which indicated gene flow from the base of the Amerindian lineage to Russians. This was very peculiar. We now know what was happening. It was the signal of the admixture of the Ancient North Eurasians, represented by the Mal’ta boy. Similarly, the evidence of Austro-Melanesian admixture in some Amazonian peoples has been there in the SNP-chip data for years. It was just overlooked. Why? Because it didn’t make sense.
The examples are pretty numerous now. What is going on in my opinion is that the method of TreeMix is searching for the nearest proxy for donor populations when those populations are no longer present. That produces bizarre results in some cases, as the topologies confound our expectations. But the problem isn’t in the topologies, it’s in our interpretative framework. A reticulated genetic graph filled with implicit positions which are representative of extinct lineages which nevertheless contributed genes to extant lineages is going to be harder to unpack than our previous understanding. But what needs to happen is we need to update our understanding….
Because of the constant kvetching in the comments below about possible affinities between North Africans and Spaniards I was going to do some reanalysis of Botigue et al.’s data set, when this paper came out: A common genetic origin for early farmers from Mediterranean Cardial and Central European LBK cultures. This inference comes from a whole genome sequence of an ancient DNA sample. Specifically a 7,400 year-old Cardial individual (CB13) from the environs of modern Barcelona. The paper is open access, so read the whole thing yourself, it’s short. But the results are clear above. This individual has affinities with modern Sardinians more than any other modern groups. Second, come the Basques.
The balance of ancient DNA results are suggesting that there was a radical replacement of hunter-gatherers across Europe. These individuals of the early Neolithic seem to derive from the same source group, weather they were Cardial in the Western Mediterranean or LBK in Germany. And, they were admixed by the enigmatic “Basal Eurasians” and a European hunter-gatherer element. Using the CB13 the authors compared shared drift with various European hunter-gatherers. It turns out that CB13 shared the most with a Hungarian, not Iberian, hunter-gatherers. The implication is that we’re seeing a common mode of human cultural and genetic change: an initial stage of amalgamation giving way to endogamy. The later resurgence of “hunter-gatherer” ancestry that you see in Spain is probably attribute to the arrival of people from the North, likely Indo-European speakers. Notably, this individual had the derived allele SLC24A5 only
In any case, I also did a little analysis of North Africans, Spaniards, and Orcadians and French as token outgroups. All the plots here.
The Tunisian sample are Berbers. Southern and Northwest Spain are hard to differentiate. I wonder if this is due a lot of gene flow in the kingdom of Castile? I suspect that the gene flow from the Basques to northern Morocco has to do with Moriscos who arrived from Spain. The gene flow into the Spaniards, and Sardians, is Berber-like, not Middle Eastern.
Beauty matters a lot in our world. The entertainment and fashion industries are based on beauty. Obviously some aspect of beauty is socially constructed and contextual. Beauty standards can change. There was a time when many aspects of European physical appearance, from light hair and eyes, down to the lack of an epicanthic fold, were excluded from idealized canons in East Asia. Obviously that is not the case today, and one can give a very plausible explanation through recourse to recent history as to why those norms shifted. Similarly, there is even a possibility that something as central to evolutionary psychology as preference for a particular waist-to-hip ratio may vary as a function of material conditions. I is clear from the social historical scholarship that the ideal characteristics of a female mate are strongly conditioned on the resources of the male; lower status males put greater emphasis on the direct economic benefits which their partner may bring because they are more on the margin of survival. For much of history lower status males meant most males. That is, peasants.
And yet cross-culturally there does seem to be a certain set of preferences which one might argue are “cultural universals.” People from “small-scale” societies are still able to consistently rank photographs of people from WEIRD societies in facial attractiveness which correlation with results from participants in developed nations. This indicates that there is a strong innate basis. An element of taste deep in our bones, even if we may inflect it on the margins, or increase or decrease its weight in our calculations of what makes an optimal mate. There may be societies where Lena Dunham’s “thick” physique may be preferred to Bar Refaeli‘s svelte profile, but I am skeptical that there would be societies where the former’s facial features would strike individuals as preferable to those of the latter (one might have to correct for Refaeli’s species-atypical hair and eye color, but European norms are pretty widespread outside of small-scale societies now, so that shouldn’t be a major issue). So the question then becomes: is this adaptive?
Evolutionary psychologists have a panoply of ready explanations. They are often grounded in correlations, and then adaptationist logic. For example, women with lower waist to hip ratios (0.7 being the target) have more estrogen, and are more likely to be nubile, and so are more fertile, all things equal. Since being more fertile is going to be a target of selection, a lower waist to hip ratio is going to be a target of selection, because implicitly there is a genetic correlation between estrogen and waist to hip ratio. The problem is that genetic correlations have to be proved, not assumed. Correlations are not necessarily transitive. Just because A has a positive correlation with B and B has a positive correlation with C, does not entail (necessarily) that A has a positive correlation with C.
With that in mind, a new paper looks at facial attractiveness, averageness of facial features, and heritability of both these traits. They use a twin design, with an N of ~1,800. And, they relate it to a comprehensible causal mechanism: mutational load resulting in increased developmentally instability. Basically, the more mutations you have, the more likely you have to exhibit facial asymmetry, and therefore facial averageness is a good proxy for genetic quality. It is well known that average faces tend to be rated better looking than non-average faces. This is part of an argument that Geoffrey Miller put forth in The Mating Mind, a very fertile work. There is an elegance to it. Unfortunately follow up work over the past ten years is suggesting that this simple model is either wrong, or, everything is a whole lot more complicated.
Popular theory suggests that facial averageness is preferred in a partner for genetic benefits to offspring. However, whether facial averageness is associated with genetic quality is yet to be established. Here, we computed an objective measure of facial averageness for a large sample (N = 1,823) of identical and nonidentical twins and their siblings to test two predictions from the theory that facial averageness reflects genetic quality. First, we use biometrical modelling to estimate the heritability of facial averageness, which is necessary if it reflects genetic quality. We also test for a genetic association between facial averageness and facial attractiveness. Second, we assess whether paternal age at conception (a proxy of mutation load) is associated with facial averageness and facial attractiveness. Our findings are mixed with respect to our hypotheses. While we found that facial averageness does have a genetic component, and a significant phenotypic correlation exists between facial averageness and attractiveness, we did not find a genetic correlation between facial averageness and attractiveness (therefore, we cannot say that the genes that affect facial averageness also affect facial attractiveness) and paternal age at conception was not negatively associated with facial averageness. These findings support some of the previously untested assumptions of the ‘genetic benefits’ account of facial averageness, but cast doubt on others.
I’m going to reproduce some of the results from Table 4 below.
What you see is very modest heritability for averageness, and a decent one for attractiveness. But, there’s no statistically significant evidence that the genetic correlation is there (the confidence intervals are huge around 0.11, from 0 to 0.35). Though they state the environmental correlation passes statistical muster (so common environmental variables might be producing attractiveness and facial averageness). Please note that a heritability of 0.6 does no mean a correlation of 0.6. The heritability of height is 0.8 to 0.9, but correlation of the trait across siblings is ~0.5. Heritability is the proportion of variation of the trait explained by variation in genes, in the population.
If you just look at heritabilities, averageness seems to have been under stronger selection than attractiveness all things equal. Usually strong directional selection removes the heritable variation on a trait. The high heritability gives us a clue that there are a lot of ugly people around still, and some of that is just the way they are born. In contrast, there are fewer people with lop-sided faces. These are subjects from a Western society, so I bet the results are going to be different in a high pathogen load environment (my expectation is that heritability will decrease, but perhaps it will actually increase because as genetic factors which allow for one to be robust to disease will become more important in explaining variation in the trait).
Finally, in the near future there will be high coverage genomic sequences from many people. If you hit the same marker more than 30 times you can conclude with decent confidence if it’s a de novo mutation unique to the individual. You can actually check how well mutational load tracks with averageness and attractiveness (each human has <100 de novo mutations, so there’s a lot of inter-sibling variance presumably). At this point I’m moderately skeptical of a lot of the selectionist models, whereas five years ago I’d have thought there would be something there, and it would be easy to discover. And it may be that beauty, like many aspects of culture, is not about adaptation and function in any direct sense, but simply a cognitive side effect. Like what Steve Pinker has stated about music. I don’t really believe that, but we can’t dismiss that position out of hand anymore.
I just realized in the post below that I casually stated that pretty much all non-Basque people in Spain have significant ancestry from people who were Muslim at some point since the fall of the Visigothic kingdom. By significant I mean more than ~1%. So not just a genealogical line of descent, but genomic ancestry attributable to a specific historical event. But perhaps I should justify this a bit. The reason is two-fold. First, many people are not totally aware of what’s going on in genetics over the past five years or so. That’s important, because a lot of data has come online. Second, fleshing out the details matters. After all, one might contend that North African signals date to the Roman era, rather than the Moorish period.
This paper in PNAS, Gene flow from North Africa contributes to differential human genetic diversity in southern Europe, is the best survey I know. It establishes a few points. For example, the Basque differ from people from other regions of Spain in that they lack much evidence of North African admixture. The historical and social separation of the Basque country during the Moorish period, and also after the Reconquista, is a pretty good rationale for why this might be. Second, the paper establishes some regional variation in the admixture. There’s more in Andalusia. Roughly, it seems that areas closer to North Africa, but probably more significantly under Muslim rule longer, have more admixture from the Maghreb. Third, a lot of it is too recent to be Roman. Looking at segment length the authors estimate a lower bound of ~300 years. After reading the post from Saturday you should understand why this statistic needs to be handled with caution. Additionally, it is important to note that the gene-sharing between Spaniards and North Africans occurs in cases where the North African population of interest has no European ancestry at all. That is strongly indicative of gene flow from North Africa to Europe, rather than bidirectional dynamics. Finally, it looks to be that pretty much all the very low level Sub-Saharan admixture you can find in Spain is attributable to the Moorish period, because the Berbers and Arabs who arrived had that element in their ancestry due to the ubiquity of the trans-Saharan slave trade.
Of course we need to careful about over-interpreting this. It looks to be that on the order of ~10 percent of the ancestry is due to migration from North Africa. In my judgement this isn’t really that much, considering that most of Spain was ruled by Muslims for 400 years (Muslim power was in sharp recession by 1200, and the conquest of Granada nearly 300 years later was really just a mopping up expedition). This is likely due to two factors. First, Spain was one of the more populous regions of the Western Roman Empire, and the arrival of the Visigoths did not result in nearly the disruption as occurred elsewhere. Despite the Germanic character of the Visigoths, like southern France to my knowledge Roman culture exhibited some continuity in the peninsula. Second, the vast increase in the number of Muslims in the peninsula occurred as it did elsewhere, through conversion and intermarriage. Three of Caliph Abd-ar-Rahman III’s grandparents were born Christian (his paternal grandmother also gave rise to a prominent line of Christian princes through her second marriage). One source suggests that ~80 percent of population of the Iberian peninsula in 1100 was Muslim, after a massive wave of conversion over the previous two centuries (this sort of latency, where Islam is an elite religion for the first century or two, is actually typical). Combined with the genetic data, which suggests widespread admixture with a North African element throughout the population, it is highly likely that Spain is one area of the world where the vast majority of the population have many lineages which went from Christian to Muslim and then Christian again (as well as Jews who became Muslim and whose descendants became Christian!).
The point in rehashing all this is that in Michael Cook’s Ancient Religion, Modern Politics, he repeats a common belief that Islam in particular exhibits a tendency where cultures tend to have an irreversible transition. Once Muslim, always Muslim. He gives Morisco recalcitrance in Spain after the conquest of Granada as evidence, but that is misleading because these were a rump community, and even among Moriscos many converted in the century after the fall of the Muslim kingdom. Spain is one of the best examples that Islam is like any other religion, under concerted pressure and inducement individuals, and more importantly whole communities, switch identities.
Cook does grant that a substantial number of Muslims in China assimilated to a Han identity. This is well attested for elite lineages of Muslims and Jews (from Kaifeng), whose entrance into the mandarin class of scholar-bureaucrats almost always presaged total assimilation. But it is probably at least as true for the vast majority of non-elite Hui, many of whom also shifted toward the Han identity. In the 20th century it was a truism among the Hui, reported without much skepticism, that Han can become Hui (through conversion), but the converse is not true. The problem with this is that the social norms and mores as such that movement from Hui to Han is never going to be widely documented, while a shift in the other direction will be. As it happens, there is now ethnographic evidence from southern China and Taiwan of whole communities which shifted from Hui identity to a Han one, with their Muslim origins being preserved in oral memory, as well as the persistence of customs such as not offering pork on ancestral graves in deference to the religion of these forebears. Over the past few centuries Muslim communities in China proper have become reintegrated into the world-wide Ummah, and undergone several waves of reform which have resulted in conformity with world normative Islam. But before this it seems likely that there was a continuous flow of Hui into the Han population through assimilation, in particular because there are many documented beliefs of Hui in the 18th century which seem to suggest a convergence with Daoism and Pure Land Buddhism.
All this is not to say that Cook’s thesis, and the public perception, does not have an element of truth to it. It is simply that the reality is a little more complex and less supportive after you scratch below the surface.
Genetic addendum: I have my own data sets, and decided to double check the results above. Including in these data the 1000 Genomes IBS (Spain) samples. You can see from the PCA and TreeMix (all of them exhibited the same topology) that something is going on with non-Basque Spaniards. The Italian position is explained by the fact that these are southern Italian samples, and those tend to exhibit affinities to Eastern Mediterranean groups. Please note that I removed all markers with missing calls and outliers as well. There were 130,000 SNPs in the final data.
A week ago a friend was asking about my opinion on a long article that was shared on Facebook about ISIS and the nature of Islam. It came up that I don’t talk about religion too much on this blog in the same way I did before 2010 or so. The primary reason is that I don’t have too much to say. But, people who are not familiar with my oeuvre to that great an extent might not be conscious that I’ve written/thought/read a good amount on the topic. For example, someone on Twitter attempted to “educate” me on Christian theology, but I’ve read stuff as diverse as Aquinas and Plantiga. Just because I don’t talk about it all the time doesn’t mean I’m not familiar; I just happen to find theology as interesting and insightful as a Christian finds reading Sam Harris.
All this means that I am highly skeptical of a central assumption of Michael Cook’s Ancient Religions, Modern Politics: The Islamic Case in Comparative Perspective, that religions are concrete things which are constrained and defined by foundational premises and institutional structures. Cook’s work is detailed in fleshing out the thesis. But ultimately the acceptance of the chain of causality rests on prior plausibility of the assumption in your own mind. As I have read and accepted a wide range of individual level cognitive results which show that there is little logical constraint on interpretation of religious texts (see Theological Incorrectness). I do think Cook’s work is an impressive corrective to those who dismiss the importance of religious foundations and text. His scholarship makes a much better case than others, because he brings a wide range of material into contrasting relief.
And when you drilldown to the specifics it is easy to problematize. One of Cook’s contentions seems to be that Muslims in particular have very strong asabiyyah in relation to non-Muslims. An illustration of this idea is that once a society becomes Muslim it never switches to another state. Cook admits there are a few cases where this did occur, and in particular highlights the instance of the Moriscos of Spain. But, this actually proves the point of Muslim asabiyyah in the end, because the Moriscos were expelled in the early 17th century due to their indigestibility into the polity of Christian Castile.
There are two objections to this outline of Morisco indigestibility in relation to the Christian polity which became Spain. First, a fair number of Moriscos in fact did assimilate. Some of the most enthusiastic proponents of expulsion were descendants of Moriscos whose own loyalty and standing was threatened by the existence of a large crypto-Muslim population. There is an element of irony here, because the Moriscos were expelled as a people, and some believing Christians were exiled because of their ethnic affiliation as Muslims. Obviously deciding who was, and wasn’t, a Morisco was not cut & dried, though presumably interaction and integration into the community was key. Second, the focus on Moriscos misses the fact that the vast majority of the Muslims who lived in the Iberian peninsula became Christians over the centuries of the Reconquista.
In Victors and Vanquished: Christians and Muslims of Catalonia and Aragon, 1050-1300 the author outlines the process of initial toleration, and then assimilation, of the Muslims of northern Spain during the earlier phase of the Reconquista. Before the joint monarchy of Castile and Aragon finally conquered Granada, there had been a centuries long process of conversion, and over the longest time scale, re-conversion, of Muslim populations to Christianity. Focusing on the Morisco populations descended from groups which had had an Islamic identity the longest and most totally probably is not representative. The genetic data make it clear that outside of the far north of Spain there are low levels of admixture likely from people whose ancestry traces to North Africa all across the peninsula.
If there is a paper I read this week which blew my mind, it is The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds. Basically, the authors seem to argue that difficulties in resolving the phylogenetic origin of most birds right after the extinction of the dinosaurs. The issue seems to be that speciation occurred so rapidly in all directions from a large founding population that it is hard to resolve the genetic signals well into clean bifurcating speciation trees (ergo, the network). As someone who is more personally focused on a microevolutionary scale I wonder about the ubiquity of admixture, introgression, and hybridization, though that is not focused on too much in the paper.
Graham Coop’s group has been exploring the implications of more complex models of spatial structured genetic variation and admixture for the last few years. I’ve already pointed Gideon Bradburd’s SpaceMix preprint, which attempts to differentiate genetic relatedness due to geographic proximity and therefore continuous gene flow, as opposed to an admixture event which is not congruous with spatial position (e.g., the Norwegian Sami have more Siberian than many groups to their east). Alisa Sedghifar now has a paper out in Genetics, The Spatial Mixing of Genomes in Secondary Contact Zones. Here’s the abstract:
Recent genomic studies have highlighted the important role of admixture in shaping genome-wide patterns of diversity. Past admixture leaves a population genomic signature of linkage disequilibrium (LD), reflecting the mixing of parental chromosomes by segregation and recombination. These patterns of LD can be used to infer the timing of admixture, but the results of inference can depend strongly on the assumed demographic model. Here, we introduce a theoretical framework for modeling patterns of LD in a geographic contact zone where two differentiated populations have come into contact and are mixing by diffusive local migration. Assuming that this secondary contact is recent enough that genetic drift can be ignored, we derive expressions for the expected LD and admixture tract lengths across geographic space as a function of the age of the contact zone and the dispersal distance of individuals. We develop an approach to infer age of contact zones using population genomic data from multiple spatially sampled populations by fitting our model to the decay of LD with recombination distance. To demonstrate an application of our model, we use our approach to explore the fit of a geographic contact zone model to three human genomic datasets from populations in Indonesia, Central Asia and India and compare our results to inference under different demographic models. We obtain substantially different results to the commonly used model of panmictic admixture, highlighting the sensitivity of admixture timing results to the choice of demographic model.
In a stylized fashion what’s going on here is that genome-wide data sets have allowed for the inference of admixture events which usually assume a single pulse of rapid random mating between two extremely diverse populations. This works in a controlled laboratory situation, but is less plausible for humans. There are cases which fit, such as the settlement of Pitcairn by the mutineers from the Bounty, but they’re exceptional (another case might be the admixture you see in some areas of Latin America from Amerindians, where the indigenous groups seem to have disappeared after a few generations, but it turns out that native women were assimilated into the European and African populations in a very short period of time). An alternative scenario is one where two populations come into contact, and admixture takes a longer period of time. In a spatial rendering there’d be a “contact zone” where gene flow might occur in fashion well modeled as a diffusion process. To give a concrete example of the latter case I will offer the Kalmyk people. The Estonian Biocentre has posted some data from this population, and all of them have varying levels of European admixture. As there is variance it is likely that this admixture did not happen all at once. Rather, once the Kalmyks migrated to Russia three hundred years ago there has been continuous gene flow into the community, as opposed to a frenzy of admixture, after which barriers might be thrown up. The latter scenario actually might be likely to occur in a case where only male Kalmyks migrated, but as it was the population it was a full folk wandering, where the tribes evacuated Dzungaria as a whole (I am aware that there were also back migrations, please don’t leave a comment explaining this to me!).
Citation: Moreno-Estrada, Andrés, et al. “Reconstructing the population genetic history of the Caribbean.” (2013): e1003925.
So what happens after an admixture event? As noted in this paper assuming a simple pulse admixture the distribution of ancestry tract lengths and LD decay is exponential. Is is a function of the fact that recombination is going to break apart ancestral allelic associations as a function of generation time. As a stylized example, the F1 offspring of two very different populations would have alternative ancestry tracts on their paternal and maternal chromosomes. Obviously LD would be very high as well. But as he F1 populations randomly mates the LD would be broken apart by recombination, as ancestry tracts would begin to alternate on chromosomal segments. You can see it when you perform ancestry deconvolution on groups such as Puerto Ricans. There are short segments due to old Native American ancestry which entered the population over a short period of time which has been chopped up by recombination. In contrast, the African segments have a wider range of block length in part because there has been more continuous admixture since the settlement of the island by the Spaniards.
Sedghifar et al. building an analytical framework to model to allow one to make inferences which are hopefully true to the more multi-textured manner in which populations actually admix than the single pulse. As the paper is open access I invite readers to peruse the formalism as well as the simulations which were performed to evaluate their framework. It strikes me that this is a definite first-pass, but a necessary one. As noted in the paper, but an well known for years, the single pulse admixture models tend to underestimate the dates of mixing (or, more charitably, they pick up the last “pulse”). So, often when I saw a paper giving an admixture estimate, I took that as a floor, and nothing more.
In the final section the framework is applied to realized data sets. There are two issues that jump out into the foreground. As noted by the authors, the HUGO Pan-Asian data set, which is what you need to use for many maritime Southeast Asian groups, has a thin marker set. At ~50,000 markers it’s really an animal grade data set, not human grade one (and even for animals they’re going beyond 60K SNP-chips). The second issue is geographical coverage. It strikes me that ideally they’d have transects that with more sampling by position. This obviously isn’t something that can be changed right now, so I assume that in the future the situation will improve on the data side and the methods can more robustly be applied.
They compared admixture in India, Southeast Asia, and Central Asia. It seems that their framework did not yield much in India, probably because the admixture patterns are complex and old, and could not be easily retrieved from the data with the few assumptions they had. This is really a situation where hopefully ancient DNA will allow researchers to fix some parameters. Additionally, I think (as implied in the paper) there are cases where compound pulse admixtures are actually a better model for reality than contact zones and diffusion gene flow across the borders. India may be a case. For example, the Tamil Brahmins seem to have some indigenous admixture, but very little variation of this admixture across individuals. That implies that once the admixture occurred, there was a long period where gene flow did not occur due to strict endogamy. In a world unencumbered by social constraints a contact zone would operate well, but South Asia may not be that world.
As expected the secondary contact zone model gave an older date of admixture for Southeast Asia, where Austronesians arrived over the lat 4,000 years. Perhaps even too old! They note: “Linguistic evidence suggests that the Austronesian expansion through Indonesia dates to ∼ 4000 years ago (Gray et al. 2009)…Our estimate of timing based on fitting a geographic contact zone (5800 years ago) is much older than dates estimated by single pulse models, but is also considerably older than the Austronesian expansion.” The citation for Gray et al. seems to be this paper, but I’m pretty sure it was meant to be Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement. In a inter-disciplinary field like this you need to rely on other researchers to complement your own understanding of specific domains. As it happens I am now more skeptical of linguistic phylogenetics than I was, so I don’t put too much stock that the date inferred was much older! Rather, I’d put more of an emphasis on material remains and archaeology, though dating and provenance can be hard to pin down on some occasions.
The last empirical illustration has to do with Central Asia, and I have a bit to say about this. The authors seem to be concerned that their signal of admixture is much older than the period of the Mongol invasions, ~700 years ago. Other studies, based on a pulse admixture model, pin this exact date, and others do not. The problem I have with this is that the real demographic history actually aligns well in my opinion with the dates that are given this paper. I don’t think they needed to take the Mongol model nearly as seriously as they did. But, I doubt that any Central Asianists peer reviewed this for Genetics, so a lot of weight was given probably to the older papers in genetics, where the Mongol angle is always played up. The reality is that there was a massive continuous movement of Turkic peoples from about 500 A.D. from greater Mongolia down into the Persianate world of Central Asia. While in India a contact zone model may not work well due to a history of endogamy, the situation is more amenable in Central Asia. I think further extensions of this framework in Inner Asia will be fruitful an necessary.
Though the authors here focus on human data sets, presumably because there was data and we know something about human demographic history, I think perhaps the secondary contact zone model formalized in this paper may be more useful with populations of animals and plants, where social constraints don’t exist to enforce endogamy (unless you count reinforcement!). Also, it probably will be useful in island situations, such as in Japan, where the migration patterns are probably defined by a single admixture followed by a wave of advance which likely had secondary contact zone dynamics (the Ainu have Yayoi ancestry).
Citation: Sedghifar, Alisa, et al. “The Spatial Mixing of Genomes in Secondary Contact Zones.” Genetics (2015).
The bar plot above shows the Kalash people in yellow as very distinctive group among a panoply of Eurasian populations. The figure is from a Rosenberg lab paper. There’s nothing aberrant about this result, you can generate this plot pretty easily by using any motley set of markers. The Kalash are distinctive. But it is important to keep the distinction in perspective. They’re not a relic population, remnants of an ancient race lost to time and memory. Rather, they happen to be a highly diverged northwest South Asian group. Their divergence is due to a small isolated breeding population which has been highly endogamous.
What this means is that the Kalash have a low long term effective population and have been more strongly impacted by drift in their allele frequency spectra. Small populations are subject to great allele frequency volatility generation to generation, and tend to lose a lot of their genetic diversity, and also fix many alleles. One consequence of this is genetic inbreeding and a higher recessive disease load. These populations with a lot of drift will have less efficacy of selection in removing deleterious alleles, and if a recessive expressing variant is fixed, then that’s that.
But another major consequence of strong drift on a population so that everyone is quasi-related for all practical purposes is that when you attempt some sort of clustering they naturally fall out as a very natural grouping. They’re low hanging fruit. When you plot populations on on a PCA you normally remove closely related individuals, because they will naturally form a tight cluster, and overwhelm the between population variation you’re looking for, hogging up all the highest dimension making them distinct from non-relatives. Inbred groups are like the Kalash do the same thing, if less boldly so. If you can keep this in mind it will allow for proper inferences about the natural history of a population. If you can’t, then you will be confused.
The Kalash and the Ari are extreme cases of this. But they illustrate the general principle that we should be cautious about making inferences when we don’t control for the vicissitudes of demographic history, which may skew the power of our methods to see in a fair and balanced manner.
* There’s an overlap of authors across the two publications, showing that scientists do and can overturn their own conclusions if new data or analysis can persuade them.
First, let’s put this in context. Canids area big deal. They’re big social mammals whose distribution and speciose character have undergone big changes across the Pleistocene. Sound familiar? Is it any surprise that one of their kind is our “best friend.” And, according to the anthropologist Pat Shipman the symbiotic relationship between dog and man is responsible for the victory of our lineage of hominins in the evolutionary war of all against all. About six months ago that thesis would seem a stretch, as the origin of dogs does not date until almost the Holocene according most scholarship. So tens of thousands of years after modern humans replaced other lineages. But ancient DNA suggests problems with calibration of earlier work, which may have dated their divergence from wolves too recently. That and the fact that the emergence of dogs as a distinct group of canids might be concurrent with the arrival of modern humans to Eurasia make Shipman’s thesis at least feasible, if not probable. And note that I stated divergence from wolves, not derivation. It turns out that dogs are a sister lineage to Palearctic wolves, not derived from them.
Where do jackals play into this? The golden jackal has a distribution which covers both Eurasia and Africa. The species’ was determined morphologically. In other words, they look similar. But sometimes you can’t judge a book by its cover. As an obvious example, most people would think that a hyrax on superficial inspection was a rodent. But a close examination of anatomical details indicated a relationship to elephants, which has been validated by DNA. But, as the paper above states plainly in the title the DNA here contradicts inferences made from morphology. Wolves and dogs, and African golden jackals, form a monophyletic lineage, to which Eurasian golden jackals are an outgroup! This determination was achieved through mtDNA analyses, as well as phylogenetic reconstruction from particular sequences, and, genome-wide comparisons on millions of polymorphisms.
But wait there’s more! One major difference between the example above of the hyrax vs. elephant and jackal vs. wolf is that the phylogenetic distance in the latter case is far smaller. That probably explains why morphological characters were not sufficient to discern the shared ancestry and derived characteristics of the wolf and the African jackal, as opposed to the Eurasian jackal. And, a corollary to this is that hybridization between these lineages is possible. In other words, this isn’t a phylogenetic tree, it’s a phylogenetic graph! Using D-statistics the authors show that there has been a fair amount of gene flow between Eurasian wolves and Eurasian jackals. And, in particular a lot of admixture from the Eurasian jackal to the dingo and basenji breeds.
Is this starting to sound a bit familiar? As population genomics has increased coverage of human populations, modern and ancient, as well as increase marker density and accuracy, first approximation coarse phylogenetic trees have given way to threads of gene flow edges tracing their away across the thick branches of the tree. The trees have given ways to myriad graphs which force us to make more subtle our understanding of the genetic background of our own lineage. I see no reason why the same will not be true for large mammals; I see why the same will not be true for many species.
In the near feature sequencing will be ubiquitous in ecological and systematic studies. At the coarsest big picture scale we’ll still see a confirmation of the tree of life as it’s classically envisioned, exploding outward from node to node, in subdivisions of clean monophyletic lineages. But as you focus in closely the bifurcations will turn in on themselves or thread together in tangle, as the branches begin produce gene flow. Look even closer and you’ll see that even within young species, like humans, our local geographic pedigrees also collapse in on themselves, and tangle and coalesce down to a set finite number of individuals, rather than the infinite space of genealogical possibilities.
Japan orange, Taiwan navy South Korea green, China light blue
Organized international Communism was responsible for on the order of tens of millions of deaths in a direct and concerted fashion, conservatively estimated. It also resulted in decades of repression for those who lived under it, but did not die under it. It fell with the Soviet Union, and today post-Communist (e.g., Russia) and quasi-Communist (e.g., China) nations are trying to move on beyond what was by and large a failed experiment in social engineering, with the failure resulting in massive levels of mortality and reduced life satisfaction on the part of those who lived under Communist regimes.
But can we move on? I have noted before that over the past generation in the aggregate Chinese economic development has resulted in the greatest reduction in poverty in the history of the world. With the economic crisis which is starting to afflict China, in all likelihood a deceleration from the very rapid growth phase induced by increased labor and capital inputs is upon us, and people are wondering about the long term trajectory of the nation. The problem is that China may grow old before it grows rich. The Chinese total labor force already peaked a few years ago. Over the next few decades its dependency ratio will shift in a direction similar to Japan’s. I am hopeful that the Chinese can meet their demographic challenges, and there are those who are optimistic. But we really don’t know.
And yet it has been brought to my attention that one could argue the Communist period in China is the cause of our current predicament. Compare the wealth trajectories of South Korea and Taiwan to the People’s Republic of China. It may be that for various reasons (e.g., Japanese investments in Korea and Taiwan, as well as differences between China’s Han population and the Fujianese preponderant in Taiwan) China under a non-communist regime would never have been as wealthy as South Korea or Taiwan are today. But does anyone doubt that China would be wealthier far earlier without the convulsions of the Great Leap Forward, Cultural Revolution, and grinding poverty of the 1970s? A billion people experienced deprivation due to the miscalculations of elite intellectuals in the mid-20th century, when Communism fused with nationalism was on the march. That’s behind us. But the late economic start for China is something we continue to live with today. We might have avoided this problem of China growing old before it grows rich, if it had a 30 year head start toward entrance into the modern economy. The world might have been a very different place…. (in fact, a best case scenario is that a dynamic China would have prodded India’s Permit Raj to liberalize earlier than the 1990s).
I remember very precisely that it was in the spring of 2008 that I finally transitioned toward being a total desktop Linux user. Basically I’d been in Linux for a few days…forgotten, and tried to watch something on Netflix streaming. I then realized I wasn’t in Windows! Now that Netflix works on Ubuntu I don’t really use Windows at all. I still have a dual-boot notebook, but I have two desktop computers than are Linux only machines.
Well, it looks like I’m somewhat of an outlier. I think the rise of Mac utilization among nerds over the past 10 years has really had an effect. Since you can go into the terminal on a Mac it removes a lot of the advantage of Ubuntu, which after all is still somewhat less “turn-key” that Windows or Mac OS.
Then of course there’s Android. So in a way Linux has won. Just not in the way people were imagining in the mid-2000s.
I get notifications for a lot of different things. Some of them are way off base (e.g., I think at some point a publicist sent me the contact information of a client who had written a book on homoepathy?). But some of them are spot on. I drink a lot of coffee. On the order of two to six large cups a day probably. So I was curious when I got a notification of a new KickStarter, Cultured Coffee: Reinventing Coffee. Of course for many people Folgers instant coffee will do, but that’s probably not most people who have the marginal income to engage in discretionary spending on coffee made from recently ground whole beans. Definitely curious where this will all go in the long run, though unlike the horrible “cupcake craze” it seems that coffee is here to stay.
The author of A New History of Western Philosophy admits a fondness for medieval thought, which he believes has been undervalued. There is something of a backlash to the Renaissance way of thinking about the “Middle Ages” recently, but it can get a little out of control. I have to be honest and admit that for whatever reason, many, though not all, medieval philosophers and their thoughts seem to be no more than hilarious language games. Much of this has to do with the fact that their metaphysics were different from what take for granted today. Or, perhaps more accurately they took metaphysics seriously, so their linguistic analyses of terms were a very serious affair for them.
The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population-genetic data analysis. Application of model-based clustering programs often entails a number of steps, in which the user considers different modelling assumptions, compares results across different predetermined values of the number of assumed clusters (a parameter typically denoted K), examines multiple independent runs for each fixed value of K, and distinguishes among runs belonging to substantially distinct clustering solutions. Here, we present clumpak (Cluster Markov Packager Across K), a method that automates the postprocessing of results of model-based population structure analyses. For analysing multiple independent runs at a single K value, clumpak identifies sets of highly similar runs, separating distinct groups of runs that represent distinct modes in the space of possible solutions. This procedure, which generates a consensus solution for each distinct mode, is performed by the use of a Markov clustering algorithm that relies on a similarity matrix between replicate runs, as computed by the software clumpp. Next, clumpak identifies an optimal alignment of inferred clusters across different values of K, extending a similar approach implemented for a fixed K in clumpp and simplifying the comparison of clustering results across different K values. clumpak incorporates additional features, such as implementations of methods for choosing K and comparing solutions obtained by different programs, models, or data subsets. clumpak, available at http://clumpak.tau.ac.il, simplifies the use of model-based analyses of population structure in population genetics and molecular ecology.
The website deploys the package as a web based application (kind of like Structure-harvester). I don’t do GUIs, but I thought I would mention it (the package is downloadable). I’ve shied away from posting admixture barplots not because I think they lack utility. Rather, over the years readers have had a hard time understanding their limitations, and tend to reify a little too much for my taste.
I was playing around with some data, and I saw a strange migration from Amerindians to Finns in one run. I looked through replicate runs the same pattern reoccurred. The weird thing is that I had a Siberian data set in there (Ngannassan, Koryak, and Chukchi). The Amerindians were a mix of Pima, Maya, and a few 1000 Genome Peruvians.
To explore this further I got ran TreeMix with progressively fewer populations. I got the Ancient North Eurasian genotype and also put it in there. Using various quality filters I got down to 112,000 SNPs. All of the plots are here, but representative ones are below.
As you can whatever I saw was an artifact. Probably due to merging the various Siberian populations together. Now there is a gene flow edge from at least near the Nganassans and Nenets toward the Finnic groups, or from the Finnic groups. The relationship of Mal’ta is complicated by the fact that it’s so old, and, the population structure of North-Central Eurasia seems to have changed several times over the past few tens of thousands of years.
About ten years ago David Reich and Nick Patterson were involved in a paper which posited “complex speciation” in the lineage that led to humans and chimpanzees. What that means is that there was some hybridization between the proto-chimp/bonobo lineage, and that leading to hominins. As the authors state: “These unexpected features [of the genome] would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently.” The primary result happens to be a disjunction between the patterns you see in the broader genome, the autosome, and the X chromosome. The divergence from the X chromosome is far less than it should be if you would set your expectation from the autosome, suggesting that it harbors signatures of recent gene flow across the two lineages.
The crux of the issue seems to be that the diversity on the X chromosome varies in a peculiar manner. In particular, incomplete lineage sorting, basically the overlap of variation across two species due to common ancestral alleles, seems to exhibit a bimodal distribution on the X chromosome (the bottom panel above). Going beyond just a chromosome-wide summary or average, the authors found that there were huge deserts where variation was gone, in contrast with broad swaths of the X chromosome genome where the variation is totally in light with roughly neutral assumptions (i.e., the effective population of the X chromosome is ~3/4 of the autosome, so that increases the power of drift, etc.).
Why this pattern? One explanation could be background selection. This is basically the removal of deleterious alleles as they arise, often resulting in reduced variation across a genomic region because of linkage. The X chromosome has a peculiar dynamic because in males normally recessive alleles, whether favored or disfavored, are subject to the full force of selection (since most recessive mutations are deleterious, they’d be purged more effectively). But background selection is a relatively gentle and continuous process. The width of the flanking regions impacted by selection against a focal mutant should be modest. What they found was that there were huge genomic blocks without any segments of incomplete lineage sorting in humans and chimpanzees. That is, variation was removed in some portions of the genome and not others. One process that can cause this are positive selective sweeps. The authors posit there were many of these to explain how many regions of the X chromosome seem to have been affected.
What was driving these sweeps? At this point they’re really tentative. But they suggest meiotic drive. Meiotic drive is pretty famous from the deleterious t haplotype in mice, but there might be a major bias in when we see drive, because if it doesn’t have a deleterious drag it might result in such rapid sweeps to fixation that we won’t ever catch it in the act. It could be pervasive as a phenomenon, but we might have a skewed perspective of its basic nature.
Finally, they also report that these regions of reduced ILS correlate with regions of the X chromosome where there is very little Neanderthal admixture. So this might be part of a broader evolutionary dynamic among apes. Mailund promises more, and I’ll be waiting….
14 – And Moses was wroth with the officers of the host, with the captains over thousands, and captains over hundreds, which came from the battle.
15 – And Moses said unto them, Have ye saved all the women alive?
16 – Behold, these caused the children of Israel, through the counsel of Balaam, to commit trespass against the Lord in the matter of Peor, and there was a plague among the congregation of the Lord.
17 – Now therefore kill every male among the little ones, and kill every woman that hath known man by lying with him.
18 – But all the women children, that have not known a man by lying with him, keep alive for yourselves.
- King James Bible, Numbers 31
In the 20th century the Lithuanian archaeologist Marija Gimbutas posited that the emergence of pre-Christian European culture went through two phases after the Mesolithic. First, there were the Neolithic Old Europeans who brought agriculture. Then there were the Kurgan people from the steppe, who brought Indo-European languages and warlike patriarchal values to the continent.By the 1990s many archaeologists had turned against the Kurgan model of Indo-Europeanization, leaning rather toward the proposition that the Old Europeans themselves were Indo-Europeans. I believe that the latest work in genetics, utilizing powerful statistical inference techniques leveraging genomics and computational biology, and ancient DNA, suggest that Gimbutas was right in terms of the role of the Kurgan people as promoters of Indo-European culture in Northern Europe. Even those who supported the Kurgan hypothesis, such as David Anthony, were apparently shocked at the magnitude of the genetic turnover.
But Gimbutas probably went very wrong is the idea that Old Europeans were a peaceful and matriarchal society. First, though there are matrilineal societies, and matrifocal societies, to my knowledge there are no matriachal societies which are analogs to the patriarchies you might find in the modern Arab world or ancient Athens (and frankly, most agricultural and post-agricultural societies). Certainly there were societies where powerful women were shaping the course of events. This influence may even be institutionalized (I’m thinking of the Iroquois as an instance of a case). But there were no societies where rulers were exclusively women and men were forced into roles of total passivity in matters of war and politics, and property as a class.
That’s the truism as informed by what we know from surveying cultures in the historical record and extant today. But there is a spectrum of empirical phenomena in terms of magnitude. During the Roman Empire the women of the Latin West continued to have liberties and freedoms that were customary for them during antiquity (the power of the Julio-Claudian women and Theodora seem less shocking when considering the public prominence of elite women during the Republicanperiod, which some ascribe to the role of Etruscan women in their society). When the focus of Roman power shifted toward Constantinople in the 4th century, one visible marker distinguishing elite women of western cultural affiliation, as opposed to those who were of the Greek nobility, is that the latter were often veiled, perhaps echoing the seclusion of ancient Athenian women of good family.
Similarly, though Japanese civilization is influenced, perhaps even derived, in large part from Chinese civilization, one major distinction between the two is that the in the ideal and often in practice the Chinese have subordinated military values to civilian ones to an exceptional extent for a pre-modern society. In contrast, the Japanese developed a military aristocracy which eventually superseded the civilian nobility. This results in the anachronistic romanticization of a martial ethos such as in bushido, which has no clear analogy in the Chinese world view. Obviously here I am not saying that the Chinese were a purely pacific people. And there were ages when martial values were ascendant, for example the early Tang. But the fact that the founder of the Song dynasty, a general, encouraged a demilitarization of his ruling class makes much more sense in light of the ethos of Chinese elite culture going back to the end of the Warring States period. In contrast, the Western aristocracy, often directly descended from Germanic warlords, have retained an ethos where physical violence and competition is more meritorious. The emergence of firearms necessitated a shift away from direct front-line combat to minimize casualties, and a channeling of energies into patronage of high culture and foppish self-cultivation. But even today the princes of the House of Windsor continue to serve in military professions, putting the role of the soldier in Western society in stark relief as one of esteem.
I bring this up to reiterate that though we see the past through a dark mirror, we must filter its probabilities through what we know of societies today, and those that are historically attested. Human phenomena is not infinitely flexible, but exhibits modal peaks across the distribution of possibilities. Our expectations should not be uniform and agnostic. The Old Europeans may have been gynocentric pacifists, but if they were then they were sui generis among human societies. As time machines are not feasible we will never truly know in a direct sense what they were like. Rather, we must look to aligning material remains with theoretical expectations given what we know about the nature of human societies. Interpretation will always occur. The key is to obtain the proper framework to generate true inferences. In Lawrence Keeley’s War Before Civilization the author observes how the objects which might be useful as weapons in graves have often been interpreted as “ritual” markers of status, as if conspicuous consumption was always the primary form of status competition. Written in the 1990 War Before Civilization was a seminal work taking on the neo-Rousseauan model head-on, that war was somehow a contingent invention of civilization. A terrible mistake.
The Early Neolithic massacre-related mass grave of Schöneck-Kilianstädten presented here provides new data and insights for the ongoing discussions of prehistoric warfare in Central Europe. Although several characteristics gleaned from the analysis of the human skeletal remains support and strengthen previous hypotheses based on the few known massacre sites of this time, a pattern of intentional mutilation of violence victims identified here is of special significance. Adding another key site to the evidence for Early Neolithic warfare generally allows more robust and reliable reconstructions of the possible reasons for the extent and frequency of outbreaks of lethal mass violence and the general impact these events had on shaping the further development of the Central European Neolithic.
The body of of the text engages in a deep osteological analysis, but in the language of the street, “they fucked these people up.” In particular, the victims seem to have had their lower extremities maimed or crushed. If they were still alive when this occurred then it was clearly a form of torture. If they were dead, then it was clearly a spiteful mutilation of the dead, and the valence has to be symbolic rather than utilitarian. The victims in the assemblage exhibited a curious demographic pattern. There were infants below one year of age, as well as young children, but no older children or adolescents. The only two adult women were over the age of forty. The rest of the adults killed were men.
We can’t know what happened with certainty. These were preliterate people. But with what we know about the nature of human culture it seems that an obvious narrative presents itself. As noted in the paper this was an LBK site. But, it seems that the community was on the border of two LBK trade networks (as inferred from the distribution and character of material remains). On the frontier of agricultural production, when land is in surplus, one can imagine that there was little inter-group conflict between LBK coalitions. What we would probably term “tribes.” Additionally, there was almost certainly a “meta-ethnic frontier” which Mesolithic hunter-gatherers, who we now know were genetically and physically very distinct from the LBK people (naively projecting genetic variance statistics, their difference was in the ballpark as that between modern Chinese and Northern Europeans, Fst ~ 0.10).
But what happens when Malthusian constraints begin to close in? In the Moral Consequences of Economic Growth Benjamin Friedman suggests that in American history economic stagnation and stress lead to greater xenophobia, and reduced openness. And one doesn’t need a deep history lesson to observe what occurred in Europe during the 1930s. Retrenchment invariably leads to turning back to collective units of organization and protection. Once the LBK reached a stationary state, which reduced marginal returns to labor input, and likely produced increased sensitivity to environmental perturbations, then it is entirely expected that “inter-group competition” would emerge as one of the ways in which the carrying capacity would maintain a “check” on numbers. Sedentary agriculturalists must scramble for scarce resources. There’s no running off, at least at this stage of social complexity.
The fact that the LBK turned on each other should condition our understanding of how the transition to the Corded War may have occurred. The Y chromosomes of the LBK period are very different from what we find in Bronze Age Europe. The most reasonable model I believe is that these lineages did not go silently into the night. As they did to each other, so was done unto them. In J. R. R. Tolkien’s work there are allusions to the coming Third Age of Middle Earth, an age of men. The rise of agricultural mass society was the age of men in our world. Hunter-gatherer societies were no idyll, but due to their small scale, and complementarity in economic production, the relationship between the sexes was not one of male domination, where women were property to be traded as chattel. But concentrated and sedentary units of economic production that arose with village life became an inevitable target of extraction from collective groups of males, who translated their significant superior upper body strength into a reign of coercive terror. That coercion was translated into reproductive success, which is evident in the explosion of a finite set of Y chromosomal lineages on the order of ~5,000 years ago. The common R1a1a ancestor of Daniel MacArthur and myself was the original O G thug.
In evolutionary genetics R. A. Fisher introduced the idea that when selection pressures come to bear upon a population, large effect mutations may increase rapidly in frequency to increase population mean fitness. But, these mutations are not without cost, one reason that they were likely at low frequency in the first place. For example, one of the most well known adaptations to malaria famously has a very large segregation load in terms of a recessive disease. Evolutionary theory predicts over time that the adaptation will be less genetically disruptive. New mutations which allow for adaptation without the costs may emerge, or, other mutations may arise to “mask” and “modify” the deleterious effect of the initially favored allele.
When John Maynard Keynes purchased the papers of Isaac Newton he was shocked at the proportion of the great physicists writings devoted to matters occult and esoteric. Keynes declared that Newton was the ” last of the magicians, the last of the Babylonians and Sumerians, the last great mind which looked out on the visible and intellectual world with the same eyes as those who began to build our intellectual inheritance rather less than 10,000 years ago.” In opening the new age with his beautiful system of rational science, Newton nevertheless reflected an ancient ethos which persisted down into the modern period.
The Jewish people have been critical in the development of a universal ethical monotheism in the West, part of the broader evolution away from the supernatural systems of the Bronze Age that occurred across the Axial Age. But the Hebrew Bible preserves within it a world far removed from the divine Logos, a God of law and morality. The angry and jealous sky god of the Hebrews also enjoins upon them genocide of other tribes. Though the Hebrew Bible is pregnant with the possibilities of religious ethical universalism, the voice of the prophets’ righteous indignation raw with rage alive in our age, and channeled through the gentler voices of Hillel and Jesus, it also is a record of a parochial and peculiar people, who wash their hands of their atrocity by attributing it to the capricious and vindictive will of their god. If Moses and Joshua did exist, they almost certainly would have more in common with the war-chiefs of early Neolithic Europe, 4,000 years before their time, than men such as Constantine, who 1,300 years later promulgated a universal religion for a universal empire.
Ancient Egypt, with its autocratic god-kings, was arguably one of the end-points of the Neolithic experiment with mass culture and ideology. So were Shang China and Mycenaean Greece, with their human sacrifices to propitiate the gods. Increasing primary productivity by an order of magnitude, which farming did, resulted in the emergence of huge amalgamations of humanity, and we as a species are culturally creative enough to have come up with adaptations. Literacy, cities, and social stratification, were all responses to the stresses and pressures that the opportunity of mass society presented. The emergence of powerful menacing and extortionate patrilineages was another. This was a world of gangs, thugs, and the question was not whether you would become a thug, it was whether you would be a thug or a victim of a thug. They were necessary, inevitable, cultural mutations against the background pressures that agricultural imposed upon humanity.
But as per Fisher’s model, mutants with deleterious consequences invite their own response. They are tamed and civilized by a scaffold of modifiers. The brutal gods which were but reflections of human vice and caprice were drafted in the service of primal human psychological impulses forged during the Paleolithic, reciprocity and egalitarianism arose against the background of brutality beyond imagining unleashed by the social dislocation that was a consequence of agricultural society. The men and women shaped by the Hebrew prophets and Christian Church Fathers, the rishis of the Upanishads and the Chinese sages, they are all closer to us 2,000 years later, then they were to their own forebears only a few hundred years earlier in their own past.
These models operate in the world between one of naive innate cognitive reflexes and pure cultural inventions generated without reference to the functional constraints of our minds and environments. The independent experiment of the Aztec Mesoamerican society suggests that the same stage of brutal social order that had occurred during the Neolithic was playing out in the New World. The Aztecs were engaging in ritual cannibalism and human sacrifice in a manner not seen in Old World civilizations since the Bronze Age. Some inventions are inevitable, emergent properties of the intersection of our biobehavioral toolkit and our species’ incredible cultural flexibility. Though we may believe ourselves to be far beyond the LBK people, the Nazi gas chambers or the more recent events in Rwanda suggest that the same mental reflexes of coalition-building and competition can be co-opted toward organized violent ends even today. Peace is possible, but violence is always imaginable.
Addendum: This Azar Gat article argues for the reality of war among hunter-gatherers, extensively citing what we know about Australian Aboriginal culture on the eve of European settlement. It would indicate that the only thing separating our Pleistocene ancestors from ourselves in terms of violence would be scale and organization, with ideology a novel handmaid.
If population genetics is “study of the distributions and changes of allele frequency in a population,” then the understanding of the maintenance of variation (or lack thereof) is one of the major topics of focus. In the first half of the 20th century when there was a lot more theory than data there were arguments about whether polymoprhism (in this era they’re talking about classical markers) was maintained through balancing selection or whether it was just a transient phenomena, and that at any given moment you’re just getting a snapshot of alleles sweeping up to fixation, or being purged out of the gene pool. In the second half of the 20th century it was all about neutral theory, and its discontents. Then the post-genomic era showed up, and geneticists had access to a lot of data and computational power to analyze it. Rather than relying on older molecular tests which were geared toward detecting inter-specific selection events population geneticists began scouring haplotype structure.
But even now there’s a lot of mystery. First, you might be able to adduce that selection is highly likely in a given region, but you may have no clue what that region does functionally (in some cases the region may not even be genic, in which case it has be a mysterious regulatory element). There are some good case studies where the mystery has cleared. Lactase persistence. The ways you can fight malaria. But over the past day I’ve been having to admit that it sure looks like the regions of the genome around pigmentation function are the targets of selection. But we don’t really know what selection is selecting for. And this is actually a set of selection events that I can imagine some day reaching a resolution into their probable cause. But we’re far from that.
A few years ago Eimear Kenney and company solved the mystery of why some Melanesian populations had very dark skins but blonde hair. I blogged about it, but didn’t read the paper too closely. Looking at the publication date, May 2012, I realize I was busy studying for some really big end of first year exams at that time, so that explains my lack of attention. In any case they found that a mutation, rs13289810 in TYRP1, results in blonde hair when it’s a homozygote. They didn’t find strong evidence for recent selection. That is there wasn’t a long haplotype block indicating a sweep in the past 10,000 years. The allele frequency difference across populations as well as long range LD was suggestive of past selection.
This was in the Solomon Islands. Today I decided to see if there was any follow up on this work. Well, Heather Norton’s group published a paper, Distribution of an allele associated with blond hair color across Northern Island Melanesia. It’s on a different set of islands, but the same results pretty much hold. The allele has a recessive effect on hair color, not much on skin color (there was a small effect in the original paper, so it seems it’s not wholly tissue specific in expression). But I just kept staring at this map and the frequencies. Look at the derived proportions…they don’t get above 0.50. But in most of the populations they’re around in appreciable proportions. I had a hard time not thinking there wasn’t balancing selection going on here. That this was something old that was persisting, but not fixing.
I asked Carlos Bustamante, and he got back me on Twitter:
I also had an exchange with the first author, and she pointed out in the supplements that the frequencies in the Solomons were quite curious too:
Frequency of 93C
When they looked in the HGDP data set it’s ancestral everywhere else. The derived variant isn’t floating around at low frequencies. One might naively think that it’s overdominance, but I suspect we’re looking at some negative frequency dependent selection. In the 2014 paper by Norton et al. it’s pretty clear that this is distributed across rather disparate populations. It is unlikely in my opinion to be purely due to population structure, as diverse islands have been sampled. It looks to be an old variant that’s persisted, so it dates to the Pleistocene settlement of Near Oceania. It’s also found in Australia, though we don’t know the genetic basis.
Ten years ago I would have been super excited to know the genetic basis of an interesting trait like this. But now I’m left with why? Why? We’ll be grappling with a lot of why’s in the next few decades.
Whenever I post about Indian genetics there are really weird comments that pop up which go like this: “this guy doesn’t know anything about genetics, he totally ignores the research [usually published in the late 2000s and utilizing mtDNA haplgroups] of [Indian researcher that I don't really know] which has proven [something which has been superseded long ago].” Usually these are at my Facebook account, though they also pop-up on Twitter. Often I’ll indulge this people, but usually I just ignore them. If your world-view needs to be supported by mtDNA haplogroup analyses published in Human Biology, more power to you! Or 8 autosomal microsatellite studies from 2005.
As it is today in a few hours you can really resolve what’s going on with questions about Indian genetics, or whether the Chinese are genetically differentiated, as long as you don’t have too strong of an agenda and don’t go sniffing for particular results. A few weeks ago a friend who is from a Tamil Brahmin background asked me if I knew anything about the genetics of this group. Well, a bit. Above and to the left is a bar plot with admixture fractions from Harappa DNA Project . You can see that the Tamil Brahmins are homogeneous. This suggests that they’re an endogamous community with genetic coherency.
But how do they relate to other South Indians and other Brahmins? This is a question that is politically fraught. I really don’t care though, because I’m not Indian, and even if I was, I still wouldn’t care. I don’t have Zack’s data set, but I do have three Tamil Brahmin genotypes. You can see them on the PCA plot above. The North Indian data set is all Punjabi, while the South Indians are a mix of non-Brahmin Tamils and Telugus, from the 1000 Genomes. The rest is from the Estonian Biocentre data. The results are clear, you can see that Tamil Brahmins are strongly shifted toward the North Indian cluster but in comparison to Uttar Pradesh Brahmins they are South Indian skewed. The most parsimonious explanation taking into account their generally agreed upon communal history of migration from northern India is that they are predominantly a northern origin caste with some admixture from the local substrate. This seems entirely reasonable with how we know demographic processes work.
Using TreeMix I ran 20 plots each of two different data sets with Tamil Brahmins. All the plots are here (tar.gz). But below are two representative plots.
In the first set of plots the Tamil Brahmins tend to be near the positions of the North Indian groups, but have a consistent migration edge from near the Velamas. From what I can tell the Velamas are not a marginal group, but somewhat elite. It seems entirely reasonable that native gene flow into Brahmins coming from the north would be from local high status populations, since the Brahmins themselves were coming into the region as a priestly elite to serve the rulers of South India and sanctify their domains. Usually I read something about the assimilation of local religious elites, so that’s probably what happened. Also, note that Uttar Pradesh Brahmins consistently receive gene flow from Chamars, a Dalit caste in Uttar Pradesh. I suspect what’s going on her is that the Chamars are representative of the pre-Indo-Aryan population, and the Indo-Aryans amalgamated with local elites as they pushed the Aryavarta beyond the Punjab. There are allusions which can be interpreted this way in the older Hindu texts.
The second set of plots is a little more confused. The positioning of the various groups is a little schizophrenic, and you can see gene flow edges back and forth attempting to make the “fit” of the topology better. The position of the Tamil Brahmins is next to the Chamar here, but they are getting a lot of gene flow (nearly 50%) from the Uttar Pradesh Kshatriya, again indicates that the group is a composite. The Chamar make direct contributions to both Uttar Pradesh high castes.
A major shortcoming of these analyses is a paucity of good source populations for these gene flow edges. A lot of the public data is from obscure tribal groups who are somewhat inbred, and so often drift into long branches. The 1000 Genomes data has no ethnic label, so you are pooling a lot of different groups together. For whatever reason we know a lot more about the genetics of the Tharu people or the Kol than we do about the Brahmins of Tamil Nadu or Uttar Pradesh, or the Kayastha of West Bengali.
Finally, I was curious about runs of homozygosity. If the South Indian Brahmins went through a bottleneck of some sort, and have been endogamous, they’d have built up some of these. I have three 23andMe South Indian Brahmin samples, along with a Kayastha from Uttar Pradesh, and myself. I took the HapMap populations and intersected SNPs so that I got 750,000. Below is a density plot of total kb of runs of homozygosity of HapMap populations, as well as vertical lines which show where some individuals come out. I was struck that the South Indian Brahmins had 24, 25, and 26, runs respectively using default cut offs. The Kayastha from UP had 19. And I had 11. I think my relative lack is due to two factors. First, the last few generations above me in my pedigree have seen a lot of intermarriage between what in different parts of India would be different jatis (it doesn’t map totally to Muslims, but I do have a fair number of Hindu ancestors in the last few hundred years and sort of know their caste by the surname). Second, I’m Bengali, with a lot of East Asian ancestry, so without inbreeding that’s going to break apart a lot of blocs which might otherwise exist in the genome because of population admixture. If you are curious about the GIH, Gujarati population, there are a lot of Patels in that sample. They’re skewing the distribution up.
People routinely mistake the action of adaptive evolutionary process as occurring on the level of the species. Not only is this a misunderstanding that crops up in the general public, but I’ve talked to biologists who make the same mistake. The reality is that the mainstream tradition in modern evolutionary biology is very skeptical of “for the good of the species” arguments. For me one simple reason is that I don’t think species are necessarily a clear and distinct taxonomic class. But the major factor is the reality that altruism of this sort is vulnerable to being superseded by an invading selfish free-riding strategy. As a matter of pervasive phenomena much of the “struggle for survival” that an organism experiences won’t be due to exigencies of environment or the threat from other lineages, but rather within one’s own species. Though this can be conceptualized in terms of violence, more often one can chalk it up to competition for finite resources in a Malthusian world at carrying capacity.
The logical conclusion leads to the sort of individual-level focus that is at the heart of The Selfish Gene, though Richard Dawkins’ book is to a large extent an exposition of a Neo-Darwinian tradition which goes back to R. A. Fisher, and matured with W. D. Hamilton and George Williams. But over the past few decades there has been a small group of biologists who have rebelled from the focus on individuals and genes, and made the case for selection operating at multiple levels or biological organization, from the intra-genomic all the way to “super-organisms” such as ant colonies. Rather than old-style species/group selection, the new theorists refer to “multi-level selection.” The primary force behind this movement has been David Sloan Wilson. I like David personally and he’s a great scientist (I did a BloggingHeads with him 6 years ago). But he has a tendency in my opinion of declaring unilateral victory when most people would argue that there’s still a lot to hash out, and the war continues. His new book, Does Altruism Exist?, is in my Kindle “to-read” stack, but from what I’ve seen of the reviews he does do this again! (no worries, the rest of the book looks interesting anyway)
My own views have evolved…over the years I have realized I am not entirely satisfied with models of human cultural variation that are individual level or entirely non-adaptive. I have long been broadly sympathetic to the project of Peter Richerson and Richard Boyd of using the frameworks developed in evolutionary biology to understand cultural processes. Additionally, I’m a big fan of Joe Henrich’s research, to the point of pre-ordering his book The Secret of Our Success: How Culture Is Driving Human Evolution, Domesticating Our Species, and Making Us Smarter six months ahead of time. There are good reasons why above-the-individual level selection would be able to operate in humans. The reduction in a verbal sense is that human cultural phenomena are such that between group variation can dwarf within group variation. The canonical example of this is language, where differences between groups are very large, and rather smaller within groups. This is simply a function of how culture, and language in particular, spreads in a population: it can be asymmetric in terms of vertical transmission. This is in contrast to genes, where you have equal contributions from both parents. One can imagine a population expanding into another where it absorbs individuals from hostile groups, changes its own genetic makeup, but by and large maintains its cultural integrity. To give a concrete example, the Xhosa people of South Africa are approximately ~25 percent Khoisan in genetic ancestry. But their culture is not “25% Khoisan.” There are influences, such as click sounds in their language, but those are accents on the basic Bantu cultural substrate which is preserved, and ties them with populations in Central and Eastern Africa.
It is a rather different matter with biological processes because of the enforced symmetry in transmission. Maintaining between group variance requires ingenious processes, which some find implausible. But ultimately it’s an empirical matter on a species-by-species basis. I would commend readers to look through first half of Wilson’s Unto Others to get a sense of how inter-demic selection processes might be ubiquitous. My position on the role that biological above-the-level-of-individual selection plays in evolution is to be skeptical in the generality but open-minded in the specifics. After all, bdelloid rotifers show that there are cases where complex asexual species can persist, even if the general rule about asexual lineages is that they are prone to extinction.
For whatever reason arguments about multi-level selection get rather heated among evolutionary biologists. It’s often closely related to the debate about kin selection (see this post from Jerry Coyne, and follow the links). I suppose David Sloan Wilson would suggest that it’s an illustration of inter-group competition, as individuals conform to particular positions due to their identity as members of a coalition.
I’m not an evolutionary theorist, so I’m not going to take sides (though to be honest I always find Goodnight to be a little too vociferous for my taste, but perhaps that’s just how it comes across in print). Rather, I’m chewing through some of the ideas, and find that these papers are excellent starting points to explore the literature. It’s also nice that they’re open access, as there are people who are not in academia who might have some things to say about these topics, or, who might pursue research as a career after stumbling upon these sorts of papers.