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

July 22, 2012

What is inbreeding?

Filed under: Inbreeding,Population genetics — Razib Khan @ 9:23 pm

I’ve put up a bunch of posts relating to inbreeding recently (1, 2, 3, 4). But I haven’t really defined it. First, let’s stipulate what inbreeding is not: it is not the same as incest. Acts of incest can include individuals who have no blood relationship to each other (e.g., Hamlet). Additionally, there are instances of inbreeding which are not necessarily incestuous. If a population is highly inbred, then individuals who are not relations by social custom may still be so genetically similar to a point where the pairing can not credibly be stated as an outcross. But still, what do I mean? To refresh myself I re-read the section on inbreeding in Hartl & Clark. And I think that helped clarify one implicit assumption which I have which may not be clear to everyone, and I’ll get to that.

In any case, first, what’s the deal with inbreeding? The short answer is that inbreeding is a measure of the probability of identity by descent of two alleles at a given locus in a given individual. This concise definition itself is the problem. These are all abstract concepts, close to being ...

July 20, 2012

Ashkenazi Jews are not inbred

Jews, and Ashkenazi Jews in particular, are very genetically distinctive. A short and sweet way to think about this population is that they’re a moderately recent admixture between a Middle Eastern population, and Western Europeans, which has been relatively isolated due to sociocultural forces. As far as their inbreeding, well, here’s one recent paper, Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population: To explore the amount of genetic variation within the AJ and European populations, we first measured the mean heterozygosity. Surprisingly, we found a higher level of heterozygosity among AJ individuals compared with Europeans…confirming speculation made in one recent report and a trend seen in another…Although this difference may appear small, it is highly statistically significant because of the large number of individuals and markers analyzed, even after pruning SNPs that are in high LD. The higher diversity in the AJ population was paralleled by a lower inbreeding coefficient, F, indicating the AJ population is more outbred than Europeans, not inbred, as has long been assumed…The greater genetic variation among the AJ population was further confirmed using a pairwise identity-by-state (IBS) permutation ...

July 6, 2011

Marry far and breed tall strong sons

ResearchBlogging.orgThe Pith: When it comes to the final outcome of a largely biologically specified trait like human height it looks as if it isn’t just the genes your parents give you that matters. Rather, the relationship of their genes also counts. The more dissimilar they are genetically, the taller you are likely to be (all things equal).

Dienekes points me to an interesting new paper in the American Journal of Physical Anthropology, Isolation by distance between spouses and its effect on children’s growth in height. The results are rather straightforward: the greater the distance between the origin of one’s parents, the taller one is likely to be, especially in the case of males. These findings were robust even after controlling for confounds such as socioeconomic status. Their explanation? Heterosis, whether through heterozygote advantage or the masking of recessive deleterious alleles.

The paper is short and sweet, but first one has to keep in mind the long history of this sort of research in the murky domain of human quantitative genetics. This is not a straight-forward molecular genetic paper where there’s a laser-like focus on one locus, and the mechanistic issues are ...

May 30, 2011

’tis a far far better thing that they do….

Filed under: Inbreeding — Razib Khan @ 7:16 pm

Pakistani microcephalic

In response to my recent posts on inbreeding, a friend who is an academic human geneticist observed:

My sense from the papers I read is that the human genetics community owes much of its continued success to Muslim inbreeding. Inshallah, they’ll keep it up.

Who needs unethical breeding experiments? Pakistan Muslims will perform the experiments naturally and call them godly!

“Inbreeding” is Islamophobic?

Filed under: Genetics,Inbreeding,Incest — Razib Khan @ 12:21 pm

So apparently expressing thoughts which are the natural result of over a century of biological science is now prejudice:

Professor Steve Jones, from University College London, said the common practice in Islamic communities for cousins to marry each other increased the risk of birth defects.

‘There may be some evidence that cousins marrying one another can be harmful,’ he told an audience at the Hay Festival.

Studies have shown that 55 per cent of British Pakistanis are married to first cousins – and in Bradford, this rises to 75 per cent.

Mohammed Shafiq, chief executive of the Ramadhan Foundation, which promotes the image of Muslims in Britain, said: ‘I know many Muslims who have married their cousins and none of them have had a problem with their children.
‘Obviously, we don’t want any children to be born disabled who don’t need to be born disabled, so I would advise genetic screening before first cousins marry.

‘But I find Steve Jones’s comments unworthy of a professor. Using language like “inbreeding” to describe cousins marrying is completely inappropriate and further demonises Muslims.’

First, Steve Jones’ pussyfooted. There isn’t any qualification about this. You can find straightforward calculations of the difference in recessive disease risk in terms of odds as a function of inbreeding and basal population risk (the rule of thumb is that the rarer a recessive disease is in the general population, the more it will be concentrated in inbred lineages). This isn’t speculation, but long established science, with a particular relevance to medical genetics and animal breeding.

Second, Mohammed Shafiq is probably lying. Yes, there have been some reports about diseases of inbreeding being problematic in the British Muslim community, but more importantly the Gulf Arab countries are funding a lot of biomedical research on helping infants who exhibit signs of these diseases. It isn’t as if Muslims aren’t unaware of these issues, and in places like the Gulf where there’s money they’re trying to alleviate some of the downsides. Many stupid Muslims assume that there is something to do with blood group incompatibilities, but unless the leaders are morons they have to know this is an issue (Shafiq acknowledges the problems by emphasizing the utility of genetic screening).

Third, the problem is not first cousin marriage, but repeated marriages within a lineage. In other words, a custom of first cousin marriage tends to foster the emergence of lineage networks which are highly inbred. Far beyond the level of relatedness typical for most first cousins (who share two grandparents in common).

Finally, there are probably many issues with being inbred which don’t show up on genetic screens. Doctors are focusing on diseases, but people who are inbred and don’t manifest a recessive disease, are probably “less fit” all things equal. First cousin marriage docks 5 I.Q. points from expectation last I checked.

April 29, 2011

The royal wedding and outbreeding

Filed under: Culture,Genetics,Inbreeding,Kate Middleton,Royals — Razib Khan @ 1:14 pm

In the wake of the post from earlier this week on the inbreeding within the House of Windsor (and current lack thereof), Luke Jostins, a subject of the British monarch, has a nice informative post up, Inbreeding, Genetic Disease and the Royal Wedding. This tidbit is of particular interest:

In fact, eleventh cousins is a pretty low degree of relatedness, by the standard of these things. A study of inbreeding in European populations found that couples from the UK are, on average, as genetically related as 6th cousins (the study looked at inbreeding in Scots, and in children of one Orkadian and one non-Orkadian. No English people, but I would be very suprised if we differed significantly). 6th cousins share about 0.006% of their DNA, and thus have about a 0.06% chance of developing a genetic disease via a common ancestor. Giving that the Royal Family are better than most at genealogy, we can probably conclude that the royal couple are less closely related than the average UK couple, and thus their children are less likely than most to suffer from a genetic disease. Good news for them, bad news for geneticists, perhaps?

That’s an interesting flip side of aristocratic ...

August 25, 2010

Inbreeding in the Persian Gulf

Filed under: Culture,Genetics,Inbreeding — Razib Khan @ 4:01 pm

On the heels of my post on cousin marriage, I thought readers might find this article on genetic screening in the United Arab Emirates of interest. One way to tackle the problem of genetic diseases which emerge out of consanguineous unions apparently isn’t to discourage the unions themselves, but dodge the outcomes. So pre-implantation screening of eggs as well as selective abortion of fetuses both seem to be options being evaluated. Aside from the costs, especially in the former case (though abortions are not without risk, and the initial stages of pregnancy are an investment of time as well), I still think there are long term problems with this. But first, Alan Bittles (who produced the map in the previous post) points to a major shortfall of a simple do-not-marry-cousins heuristic in this case:

People from the same tribe can also be highly genetically similar, he said.

“You can’t just compare the health of those children born of cousins but the comparison must be made within the tribes as well as between them, as some disorders are unique to particular tribes,” he said. “To stop consanguinity affecting health, you’d not only need to stop first cousin marriage but people in the same clan too, which is highly improbable and going against centuries of tradition.”

Another medical specialist opines:

Dr Anand Saggar, a clinical geneticist based in London, sees patients from the Gulf — who have been sponsored by their governments — at his clinic in Harley Street.

Western prejudice and health economics have led to the negative attitude towards cousin marriages, which are legal and accepted in many parts of the world, he said, pointing to Amish communities in the US.

“We’ll never get rid of any old genetic diseases because our genetic code keeps on mutating. You just have to accept that genetic disease is part of our evolution. It is a foolish and erroneous assumption that to stop marrying cousins would eradicate genetic disease.”

The National is paper based out of the United Arab Emirates, a former British colony. Therefore, I won’t put it past them to quote mine or distort (rule: beware of British newspapers!)…but this is just kind of a dumb assertion. The problem with inbreeding isn’t that one has deleterious alleles, it’s that there are correlations of deleterious alleles at the same locus. So the Jewish community has sharply reduced the manifestation of Tay-Sachs disease through genetic screening. The Amish community is is also impacted by recessive genetic diseases. As I noted earlier, inbred communities should have lower aggregate genetic load, and yet the the fact that deleterious alleles are concentrated on specific loci mean that they have reduced physiological fitness.

I’m skeptical of Alan Bittles assumption that there’s something set in stone about current Arab practices. Apparently miniskirts and exposed hair were de rigueur among the Arab female smart set in the 1960s, but now veiling is all the rage. Times change. But, the logical conclusion of generations of genetic screening of particular Arab lineages is that the clans of the Persian Gulf will eventually transform themselves into clones with very low mutational load. Even if the power of screening shields these lineages from the ill effects of inbreeding (by literally yanking out all the deleterious alleles from the gene pool by discarding eggs with problematic genotypes every generation), biological uniformity is going to have problematic long term consequences when it comes to battling co-evolving pathogens. Monocultures aren’t built to last.

In any case, interesting idea for a science fiction short story. The formula would be to take a pre-modern custom (e.g., cousin marriage) and mix it with future technology, and iterate forward.

The individual & social risks of cousin marriage


The map above shows the distribution of consanguineous marriages. As you can see there’s a fair amount of cross-cultural variation. In the United States there’s a stereotype of cousin marriage being the practice of backward hillbillies or royalty. For typical middle class folk it’s relatively taboo, with different legal regimes by state. The history of cousin marriage in the West has been one of ups & downs. Marriage between close relatives was not unknown in antiquity. The pagan emperor Claudius married his niece Agrippina the Younger, while the Christian emperor Heraclius married his niece Martina. Marriage between cousins were presumably more common. With the rise in the West of the Roman Catholic Church marriages between cousins were officially more constrained. Adam Bellow argues in In Praise of Nepotism: A Natural History that there’s a material explanation for this: the Roman church used its power over the sacrament of marriage to control the aristocracy. Though the church required dispensations for marriages between cousins of even distant degrees of separation, they were routinely given, as was obviously the case among Roman Catholic royal families like the Hapsburgs. But once given the dispensation could be revoked, rendering the marriage null and void. A highly convenient power politically.

Henry-VIII-kingofengland_1491-1547But for much of European history the marriages of common folk were not of much concern to the church. Using ecclesiastical records L. L. Cavalli-Sforza documents very high levels of cousin marriage in Italy in the 19th century in Consanguinity, Inbreeding, and Genetic Drift in Italy. The rates dropped rapidly with economic development, especially better transportation networks in mountainous regions. I think this explains the patterns in the United States, extremely isolated communities are more inbred, while most Americans have traditionally been very mobile and not relied excessively on family networks. In northern Europe cousin marriage was not unknown in the 19th century, Charles Darwin famously married his cousin. With the Reformation official church sanctions against cousin marriage on the aristocracy and gentry were relaxed, and a few clusters of closely networked intermarried clans arose, such as the Darwin-Wedgewood family (the Catholic Church had also been a bulwark against forced marriages of aristocratic women, who always had life in a religious order as a possibility. The Reformation in Germany seems to have initially resulted in a sharp increase in the power of the patriarch over the marital fates of his daughters because of the removal of the religious safety valve as leverage). I think that the case of Charles Darwin and his social set speak to the attraction of cousin marriage: familiarity breeds affinity. In Victorian England a small group of closely related and affiliated elite gentry families, the Darwins, Keynes, Wedgewoods, Galtons, etc., created a subculture which spawned subsets such as the Bloomsbury Group.

With a more fluid and harshly meritocratic global elite the attraction of cousin marriage seems to have diminished in the Western world. Consider the tycoon Rupert Murdoch. He is an American citizen born in Australia married to a Cantonese woman with grandchildren who are 1/4 Ghanaian, 1/4 Dutch, 1/4 ethnic Scotch (Australian) & 1/4 ethnic Estonian (Australian) . As for the common people, geographical and social isolation is sharply mitigated by modern transportation networks, as well as larger scale non-kin institutions such as the Christian church. The same dynamics do not necessarily apply outside of the developed world. A friend whose father is Arab once explained that cousin marriage was so pervasive in that culture in part because you marry who you meet, and it is difficult in Arab societies for men to meet women who were not their cousins. In less individualistic societies where zero sum power dynamics are still operative it may also be beneficial for a wife to be related to the family into which she is marrying. Anthropologists in South Asia attribute the more equitable power dynamics between the genders in Hindu South India as opposed to more patriarchal Hindu North India to the fact that in the South cousin (and uncle-niece) marriage is practiced, while in the north exogamy is the norm. In the latter case a young woman leaves her family and becomes a “stranger” in her husband’s home. In the former case one of the new in-laws is a blood aunt or uncle.

But that’s the cultural anthropology. What may be fit for a cultural kin-unit may not be biological fit for individual lineages. What are the risks of cousin marriage? Most obviously there are recessive diseases. Those illnesses which are expressed when you carry two malfunctional copies of a gene. Cystic fibrosis, tay sachs, various forms of deafness. Why is it that cousins have a higher risk of this occurring? Because two cousins are much more likely than two random individuals to share the same distinct gene from a common ancestor, because their common ancestors are so much more recent. More precisely the coefficient of kinship between two first cousins is 1/8. That means that at any given locus there’s a 1 out of 8 chance that the two individuals will have alleles which are identical by descent, which means that the genetic variant comes down from the same person in the family line.

If the allele is “good,” that is, totally normal/wild type, not associated with any pathology, then we’re in the clear. That’s why most first cousin marriages don’t produce children who are monsters. What a first cousin marriage does is change the odds. How you present these odds matters a great deal in how scary they sound. If I told you than the chance of first cousins having children with a birth defect is 4-7%, vs. 3-4% for a non-consanguineous couple, it might not sound that bad. But if I told you that the odds of having a birth defect is ~50% greater, then it sounds worse. Additionally, the costs of congenital illness are born by the offspring, and society through health insurance premiums. If you compared a society which had a tradition of universal first cousin marriages vs. one which didn’t, you’d see 50% more birth defects in the former society in the aggregate, all things equal.

But that’s the not the only issue there. There are two opposing forces which diminish the problems of common cousin marriage and make it worst. The first is the purging of genetic load which occurs when you expose deleterious recessive alleles. Remember that low frequency recessively expressed alleles aren’t exposed to natural selection because they’re mostly found in heterozygotes. This means they get to float around in the gene pool for very long periods of time. In plant breeding you can just “self” the plants, which will expose the alleles rather quickly, since selfing is an extreme form of inbreeding, purging heterozygosity. The deleterious alleles then are removed from the gene pool through the death of individuals who carry them in homozygote state. The theory is that some human populations which practice cousin marriage at higher frequencies may have a lower frequency of deleterious recessive alleles. Alan Templeton reports this for South Indian Hindus in Population Genetics and Microevolutionary Theory, and L. L. Cavalli-Sforza does the same for the Japanese in the aforementioned monograph. In the proximate sense this purging of the genetic load occurs through human misery. The early death of individuals, or their sterility, or sharply reduced fertility because of illness. In the ultimate sense it’s somewhat speculative, and many geneticists are skeptical that complex mammals are easy to analogize with plants which do occasionally self in the wild.

777px-Carlos_segundo80That’s the positive genetically. What’s the negative? Pedigree collapse. I’ve been talking about marriages between first cousins throughout this post, but that’s really a small issue next to this. Even first cousin marriages produce individuals with a fair amount of inbreeding. I ran a test for runs of homozygosity in my 23andMe genetic profile and I got 3 hits, while a friend whose parents are first cousins got ~70 (the parameters for the test aren’t important, just giving a relative sense). For inbred clans it gets much worse because people are related in many different ways, and genetically are far closer than first cousins. That is what happened to the Spanish Hapsburgs. As you can see from the pedigree of Charles II his parents were closer than typical first cousins. The Samaritans of Israel are a religious sect which seems to be going through pedigree collapse. Some of them are proactively marrying outsiders to prevent their extinction through high infant mortality rates. Others, “traditionalists,” oppose exogamy because intermarriage within the group is the custom, and diseases are God’s will.

Iraq,_Saddam_Hussein_(222)The Samaritans are an extreme case. But we may be seeing a thousand Samaritan flowers blooming across the Middle East. From what I know cousin marriage in the Middle East is not limited to Muslims, Christians and Jews practice it as well. But among many Muslims it has some cachet because of particular hadiths which point to this practice as preferred. Setting religion aside, there are also social reasons why this practice is common. As I noted above sex segregation means that you may not know women outside of your family well, and in some societies where veiling is practiced it may be that you do not see many women you are not related to (even if veiling occurs at puberty, you may have seen your cousin at a younger age). Marriages are bonds which may tie a family into one operational social unit, and so produce a powerful inbred clan. This illustrates the cross-purposes of a cultural unit of selection vs. the individual unit of selection. In a society where clan vs. clan competitions are critical sorting mechanisms consanguineous marriages may serve as beneficial cross-linkages. Balanced against this of course are marriages across clans. On an individual level a first cousin marriage reduces the reproductive fitness, but higher potential reproductive fitness of two individuals who have no social support because of ostracism may be a moot point.

From my cursory reading of the literature consanguineous marriage is not declining in much of the Muslim, especially Arab, world. Why? I can think of two superficial reasons obvious to someone like me, who is no anthropologist or sociologist with area knowledge. First, high fertility rates and lower infant mortality means that the sample space of possible matches increases. One way you can remove the option of cousin marriage is by shrinking the pool of potential cousins you may marry. In a Malthusian world the average family has only two children who manage to survive to adulthood and reproduce. The variance around this expectation means that many families will disappear within two or three generations simply due to stochastic forces. This is why Augustus attempted to use moral suasion and coercion to have the Roman Senatorial class reproduce at a higher rate. The aristocracy was going extinct as clans which were defined by a legitimate male line succession would routinely have a generation without a male heir (this explains the popularity of adoption in Roman society, with adoptees often being younger sons of related lineages). Later in imperial history Marcus Aurelius and his maternal cousin, Faustina the Younger, had thirteen children, but only four survived to adulthood. The modern world is very different, and great clans can rise in just a few generations if one has the will. A second reason I believe that cousin marriage is popular in the Arab world is economics. Specifically, commodity/resource driven economic growth doesn’t require great median human capital investment, so there isn’t an incentive to shift toward a less familial social structure. In plain English going to university, moving regularly for your career, etc., are going to weaken the bonds of affinity you may have with your family. This is not necessary for many Gulf Arabs, who have a guaranteed a minimum income because of resource revenue. Not only has this allowed them to preserve a relatively archaic set of social norms, but I believe it’s also allowed for the baroque elaboration of their customary traditions. I don’t find the second explanation persuasive for most Muslim nations though, as they aren’t as reliant on resource driven revenue, and have had to make more accommodations with the exigencies of the modern world. I believe that in all likelihood large families are probably responsible for the resurgence or persistence of the practice in societies where it has been the preferred pairing.

inbreeding-1-400x499This post was inspired by a recent Channel 4 special, When Cousins Marry: Reporter Feature. If you live in Britain you can probably watch it online (I can not). But it highlights that the issue is going to be salient in the United Kingdom for a generation or so at a minimum. As I said, in the United States inbreeding is a way to make fun of poor, uneducated, and isolated whites. The photo to the right is from a blog entry mocking anti-Obama activists who were protesting his address to the children of the nation as “racist, inbred hicks.” The American perception of inbred people is not particularly positive, and the accusations of being inbred are used to mock and humiliate. But when it comes to the issue in Britain it is different, because consanguineous marriage is a feature of the Muslim community, and there are issues of race, religion and class which are operative. It isn’t just custom and tradition which are driving people to marry their cousins in Britain (perhaps more accurately, parents are demanding their children marry their cousins). Marrying one’s cousin is a rather convenient way in which to allow more of your relatives to immigrate. In a subculture where arranged marriage is the norm the marrying a cousin abroad seems eminently rational for the clan’s prospects. But there are other forces at work in the community which perpetuate and encourage it as well, and those forces can not be frankly addressed because of the tensions which are normal in many multicultural societies. From the summary of the program:

‘An attack on Pakistani culture’

However I also spoke to some people in cousin marriages who felt there were great benefits and questioned if it was yet another aspect of their culture that was coming under attack.

This sentiment has been echoed several times during the making of this Dispatches programme. It’s a subject that has provoked a defensive and sometimes hostile reaction every time we’ve touched upon it. We spoke to dozens of families who refused to talk about it on camera and we were told frequently that even to discuss the issue was an attack on Pakistani culture or worse still, Islam.

Since Britain has the NHS this is a going to be a major public health issue. On the one hand, there is individual freedom of choice. This is a core Western value. On the other hand, there is the fact that health care costs are a long term structural issue for the fiscal health of any society. Ethnic Pakistanis are only a few percent of Britain’s population, so it is manageable right now, but their proportion will slowly rise because of higher fertility and continued immigration. If cousin marriage continues to remain popular in the community the later generations are going to have even greater health problems because of higher inbreeding coefficients (due to repeated cousin marriages across the generations within the family).

But why should we limited these sorts of social utilitarian considerations to cousin marriage? How about the increased debilities associated with the children of older mothers? Mothers who make recourse to assisted reproductive technology such as in vitro fertilization? Lines have to be drawn. Costs and benefits have to be evaluated. With the passage of health care reform in the United States in 2010 the issue is now explicitly socialized in all developed nations. I began the post with a social-cultural narrative, and I end it with a reiteration of the importance of a social-cultural context.


Image Credits: Wikimedia, Consang.net, youoffendmeyouoffendmyfamily

July 15, 2010

Really fine grained genetic maps of Europe

Filed under: European genetics,European Genomics,Genomics,History,Inbreeding — Razib Khan @ 12:41 am

genmap1A few years ago you started seeing the crest of studies which basically took several hundred individuals (or thousands) from a range of locations, and then extracted out the two largest components of genetic variation from the hundreds of thousands of  variants. The clusters which fell out of the genetic data, with each point being an individual’s position, were transposed onto a geographical map. The figure to the left (from this paper)   has been widely circulated. You don’t have to be a deep thinker to understand why things shake out this way; people are more closely related to those near than those far because gene flow ties populations together, and its power decreases as a function of distance.

Of course the world isn’t flat, and history perturbs regularities. Jews for example often don’t shake out where they “should” geographically, because of their historical mobility contingent upon random and often capricious geopolitical or social pressures. The Hazara of Afghanistan have their ethnogenesis in the melange of peoples who were thrown together after the Mongol conquest of Central Asia and Iran in the 13th century, and the subsequent collapse of the Ilkhan dynasty. Though the Hazara have mixed with their Persian, Tajik and Pashtun neighbors, they still retain a strong stamp of Mongolian ancestry which means that they are at some remove on the “genetic map” from their geographical neighbors.

So when interpreting these sorts of results you have two extreme dynamics operative. On the one hand you have an equilibrium state where gene flow is mediated through continuous but small flows of migration; women moving between villages, younger sons venturing out of the village in search of better opportunities. Then you have the random (or perhaps modeled as a poisson distribution) “shocks” which are attributed to world-historical (or region-historical) events which leave an outsized and often perplexing stamp and distort the genetic map from the geographic one. Sometimes the two are not in balance. In much of the New World and Australasia the native populations were genetically replaced by settlers from the outside. Thousands of years of genetic variation accumulated and shaped by localized gene flow events were wiped clean off the map by the demographic tsunami.

Obviously that’s an extreme scenario. The macroscale does not always render the microscale irrelevant in such a fashion. A new short paper in The European Journal of Human Genetics gives us an example. Genes predict village of origin in rural Europe:

The genetic structure of human populations is important in population genetics, forensics and medicine. Using genome-wide scans and individuals with all four grandparents born in the same settlement, we here demonstrate remarkable geographical structure across 8–30 km in three different parts of rural Europe. After excluding close kin and inbreeding, village of origin could still be predicted correctly on the basis of genetic data for 89–100% of individuals.

Here’s the ubiquitous PC chart, except on the scale of villages:


As noted above they excluded close relatives, out to second cousins. They judge the genetic time depth is about ~120 years into the past back to the common ancestry. Remember that if their grandparents are from this village they obviously are going to be somewhat inbred, from the perspective of an American whose ancestors are from different nations. But for most of history the European case was the typical one, not the American one where people from different continents mingled.

Here’s part of the discussion which I think needs highlighting:

To explore how many markers are required to recover these fine scale patterns of structure, we ranked SNPs by FST among villages and repeated the PCA for the most differentiated subsets of 30 000, 10 000, 3000 and 300 SNPs in each population. In all three populations, 10 000 or more high FST SNPs recovered an essentially identical picture to that using the full data set, and even 3000 SNPs preserved considerable separation between the villages (not shown). Using only the most discriminating 300 SNPs, little structure could be observed between the two Croatian villages; however, in Scotland and Italy one of the three settlements included in each location remained completely differentiated from the other two (not shown). We note that these results are only indicative of the minimum number of SNPs required to separate these populations, as by necessity SNPs have been selected intrinsically on the basis of FST within the same data set, rather than extrinsically from other data.

The slightly lower differentiation of the Croatian villages is not surprising given the fact that they are physically the closest of those considered here, being 8 km apart, with only low hills separating them. In contrast, the settlements in the Scottish Isles and Italy are separated by 15–30 km of sea in the former case, and of 3000 m mountains in the latter, although there are deep connecting valleys.

First, we get a sense of the range of informative markers necessary to discern population structure well in much of the Old World. For continental races (e.g., Europeans vs. East Asians) you need on the order of 10-100 markers to distinguish them with a high degree of confidence (closer to the low bound than the high). It looks like in the case of village vs. village differences, it will be on the order of 100-1000 markers. I suspect in Iraq or the Caucasus you’ll need less than 300 markers, because genetic differentiation is higher over a shorter distance due to inbreeding, ethnic diversity, and geography (more the former in Iraq, more the latter in the Caucasus). In contrast, in regions where geography is conducive to transport and local norms enforce exogamy  I wouldn’t be surprised if you need more like a thousand markers.

Second, observe the importance of topographical detail. I have observed before than Sardinia is a genetic outlier in Europe. That’s not because Sardinians interbred with native elves of that island. Rather, a water barrier serves as a major check on continuous gene flow mediated by banal contacts (e.g., going to the market and meeting a person from the neighboring village). Islands become worlds unto themselves. Though they are effected by the exogenous shocks, they are less subject to the continuous gene flow at the equilibrium because the water serves as a barrier. Similarly mountains can produce genetic barriers as well, because they make travel rather difficult. In Consanguinity, Inbreeding, and Genetic Drift in Italy L. L. Cavalli-Sforza documents in detail through Roman Catholic Church records what a big impact modern roads had on inbreeding coefficients, which plunged in the 19th century. Distortions of the genetic map tells about variations in elevation in the third dimension on the geographic map!

The utility of this sort of data collection and analysis in the modern world is an empirical question. On the one hand many Europeans are relatively less inclined to move in comparison to Americans. And yet the breaking down of borders with the European Union and the likely need for a more productive economic sector on that continent because of changing demographics point to greater mobility, migration and mixing, which would make these sorts of studies of only near-term use. Of more interest to me are going to be fine-grained analyses of social groups. For example the Indian caste system. Last fall in the Reich et al. paper the authors seemed to be indicating the likelihood of a lot of between population variance groups these groups. It doesn’t matter if a particular Bania sub-caste from Gujarat is scattered across the world, from Kenya to England to the United States. They may all still marry amongst a set of individuals who hale from the same original few villages.

Good times.

Citation: O’Dushlaine, C., McQuillan, R., Weale, M., Crouch, D., Johansson, Aulchenko, Y., Franklin, C., Polašek, O., Fuchsberger, C., Corvin, A., Hicks, A., Vitart, V., Hayward, C., Wild, S., Meitinger, T., van Duijn, C., Gyllensten, U., Wright, A., Campbell, H., Pramstaller, P., Rudan, I., & Wilson, J. (2010). Genes predict village of origin in rural Europe European Journal of Human Genetics DOI: 10.1038/ejhg.2010.92

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