Archive for July, 2012

What is inbreeding?

By Razib Khan | July 22, 2012 10:23 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.

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CATEGORIZED UNDER: Population Genetics
MORE ABOUT: Inbreeding

Human behavioral ecology

By Razib Khan | July 22, 2012 8:55 pm

Jump to 3 minutes if you don’t have time.

MORE ABOUT: paternity

The Scots-Irish as indigenous people

By Razib Khan | July 22, 2012 5:04 pm

A fascinating comment below:

In traveling across America, the Scots Irish have consistently blown my mind as far and away the most persistent and unchanging regional subculture in the country. Their family structures, religion and politics, and social lives all remain unchanged compared to the wholesale abandonment of tradition that’s occurred nearly everywhere else.

Unfortunately, this has a lot to do with a powerful and long-running strand of paranoia and xenophobia. I’ve ridden trains through the rail towns of WV and KY and been regarded with more unprovoked hatred than anywhere else on Earth. On the other hand, when I’ve been introduced to their clan-based social structures by close friends, it is a uniquely close-knit and life-affirming culture that I’ve been honored to participate in.

What stuck me about this comment is that it is the sort of statement you regularly see from Western anthropologists or adventure tourists in relation to indigenous colored peoples the world over. That is, a parochial clannish folk trying to hold onto to their traditions, albeit with the downside of being inward looking and often regressive (downside from the perspective of Westerners that is). What these people lack in cosmopolitan openness, they make up for in adherence to authentic values which can’t but help earn some admiration. Substitute “Scots-Irish” for “Pashtun”, “Hmong” or “Berber” and you will see what I mean.

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MORE ABOUT: Scots-Irish

British class differences persisting down centuries?

By Razib Khan | July 22, 2012 11:01 am

People with Norman names wealthier than other Britons:

Research shows that the descendants of people who in 1858 had “rich” surnames such as Percy and Glanville, indicating they were descended from the French nobility, are still substantially wealthier in 2011 than those with traditionally “poor” or artisanal surnames. Artisans are defined as skilled manual workers.

As Steve Sailer observes strict adherence to surnames on a mass scale post-dates the Norman invasion by centuries. So the headline is pretty sensational. But I went and read the original working paper, and there is no mention of Norman or French names! The author of the piece in The Telegraph is probably right (i.e., a casual reading of history will show that Norman names are enriched in the English elite), but this is clearly another case of one having to be careful of the details when it comes to British media.

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CATEGORIZED UNDER: Anthroplogy, History
MORE ABOUT: Genetics, History

You can't scoop someone else's brain

By Razib Khan | July 21, 2012 11:07 pm

arXiving our papers:

I, and I’m sure other people, have worried about being scooped and beaten to publication due our arXived papers. But really this is silly as we’ve usually given talks, posters, etc on them at big conferences, so the idea that people somehow don’t know about our work before it appears in print is ridiculous. It is far better to get work out, once you consider it worthy of publication, so it can be read and cited by others.

This is in reference to the paper The Geography of Recent Genetic Ancestry across Europe. Go and read the materials and methods. I’m sure that a substantial minority of the readers of this weblog have used every single piece of software listed therein. Phasing and such requires a little bit of computational muscle, but that’s not an impossible hurdle. Additionally, many readers with academic affiliations could get their hands on the POPRES data set. But the generation of a paper, from methods to results to discussion, is not simply a robotic sequence of running data through software or algorithms. You need a first-rate statistical geneticist (e.g., the authors) to actually assemble the pieces together together coherently and with insight even granting the fundamental units of the whole.

Then there are sections of the methods with explication such as this:

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Are Jews white?

By Razib Khan | July 21, 2012 10:03 pm

A little over two years ago I put up some posts on Jewish genetics due to the publication of some really exciting research. Looking at the referrals I noticed two trends which together were relatively bizarre. People would look at the same PCA plot and conclude that:

  • Ashkenazi Jews are white
  • Ashkenazi Jews are non-white

First, some context. Most of these referrals were from websites with white nationalist or quasi-white nationalist sympathies. The non-Jews of this set tended toward the position that Jews were non-white, while the Jews felt that the genetic results vindicated the whiteness of Jews. In some cases the links were from Jews who were not necessarily white nationalists, but were also keen on making it clear that European Jews were not “schwartza”.

To me the whole issue was bizarre, and it entailed that I monitor the comments of those posts pretty strictly. But I believe that a much milder version of the question crops up whenever people ask if European Jews are more European or Middle Eastern. The main conundrum in the whole framing of the question is that both European and Middle Eastern are highly heterogeneous constructions, and there isn’t a very good demarcation of which populations are which on the liminal margin. In contrast, the difference between East Asians or Sub-Saharan Africans and West Eurasians is more clear and distinct. “In-between” populations such as Uyghurs and Ethiopians seem to be relatively recent admixtures, suggesting that these three geographical races have had very low gene flow for long periods of time. Not so between Europeans and Middle Easterners.

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The nature of the media beast

By Razib Khan | July 21, 2012 5:26 pm

Interesting discussion on the nature of media today, and the tendency toward driving traffic via the information equivalent of Twinkies. Below are my top 10 posts since moving to Discover Magazine measured by visits. The numbers to the right is the ratio of visits of the post over the past 2 years to the rough number of visits in an average day on this weblog.

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Ashkenazi Jews are not inbred – 2

By Razib Khan | July 21, 2012 2:17 pm

I know I excoriate readers of this weblog for being stupid, ignorant, or lazy. But this constant badgering does result in genuinely insightful and important comments precisely and carefully stated on occasion. I put up my previous post in haste, and when I published it I wasn’t totally happy with the evidence from which the authors adduced that Ashkenazi Jews were not inbred. Here’s why, from the comments: Doesn’t identity-by-state permutations test reflect a counterbalance of admixture vs. inbredness + drift? Rather than just the degree of inbreeding? Since the population has strong admixture effects, a low IBS doesn’t exclude strong inbreeding, does it?

From my little personal experience IBS is not the best statistic from which to generalize widely, and can be highly misleading in admixed individuals, as implied by the commenter. First, since I’ve stated above that the Ashkenazi Jews are admixed, let me go into a tangent as to why Ashkenazi are admixed between a Middle Eastern and Western European population, as opposed to being a relatively unadmixed ancient Eastern Mediterranean group with affinities to both regions. The previous previous paper found evidence of linkage disequilibrium decay. This means that LD was high in admixed individuals in the past, and declined over time. Why?

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CATEGORIZED UNDER: Genetics, Genomics

Ashkenazi Jews are not inbred

By Razib Khan | July 20, 2012 9:59 am

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 test, which showed that average pairs of AJ individuals have significantly less genome-wide IBS sharing than pairs of EA or Euro individuals…Thus, our results show that the AJ population is more genetically diverse than Europeans. How could Ashkenazi Jews be more diverse? Look at what I wrote above, and what most people intuitively assume: Ashkenazi Jews are an admixed population, so they likely carry the alleles unique to both Western Europeans and Middle Eastern peoples! On the other hand, Ashkenazi Jews do have a lot of the genome identical by descent, as befits a population which has long been endogamous, and entered into a recent population expansion from a more modest base.

Image credit: Georges Beard.

The many Americas

By Razib Khan | July 20, 2012 1:25 am

One of my main hobbyhorses is that in the United States today the identities of race and religion get so much emphasis that it is easy forget the divisions among white Anglo-Protestants which persist, and to some extent serve as the scaffold for the rest of American culture. This is why I recommend Albion’s Seed and The Cousins’ Wars to anyone interested in American history. Often these realities of American “dark ethnicity,” the divisions between Yankees and Low Country Southerners, Scots-Irish and the people of the port cities of the Northeast, get conflated with issues of class. Class is a major dimension, but it is not the only one. For example, the people of Appalachia are poor, but they are not Appalachians because they are poor.

These issues of dark ethnicity rooted in “dark history” can crop up in the strangest places. For example, in The New York Times Magazine, Greg Ousley Is Sorry for Killing His Parents. Is That Enough?:

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The expanding crest of modern humanity

By Razib Khan | July 20, 2012 12:46 am

If you are interested in genomics and human evolution, a new review paper in PLoS Genetics is a must read, Genomic Data Reveal a Complex Making of Humans. A must read not because you need to agree with the thrust of the authors’ arguments, but because it provides a thorough bibliography for the last 2 to 3 years. Here is the abstract:

In the last few years, two paradigms underlying human evolution have crumbled. Modern humans have not totally replaced previous hominins without any admixture, and the expected signatures of adaptations to new environments are surprisingly lacking at the genomic level. Here we review current evidence about archaic admixture and lack of strong selective sweeps in humans. We underline the need to properly model differential admixture in various populations to correctly reconstruct past demography. We also stress the importance of taking into account the spatial dimension of human evolution, which proceeded by a series of range expansions that could have promoted both the introgression of archaic genes and background selection.

The main problem I have at this point is the general mode of range expansions, whereby population A expands as a demographic wave across a substrate of population B. These sorts of models seem to assume a sort of continuous dynamic process. In contrast, I am beginning to suspect that much of the human demographic past was characterized by discrete events. The closer to the present the more I’m convinced of this, though honestly I am now pushing back my own timing for the origins of many of the human distinctive traits, such as culture, well before behaviorally modern humans.

MORE ABOUT: Human Evolution

Cousin marriage can reduce I.Q. a lot

By Razib Khan | July 20, 2012 12:33 am

In light of the previous post I was curious about the literature on inbreeding depression of IQ. A literature search led me to conclude two things:

- This is not a sexy field. A lot of the results are old.

- The range in depression for first cousin marriages seems to be on the order of 2.5 to 10 IQ points. In other words ~0.15 to ~0.65 standard deviation units of decline in intelligence.

The most extreme case was this paper from 1993, Inbreeding depression and intelligence quotient among north Indian children. The authors compared the children of first cousin marriages, and non-bred in individuals, from a sample of Muslims in Uttar Pradesh of comparable socioeconomic status (though the authors note that inbreeding has a positive correlation with socioeconomic status in this community). A table with results speaks for itself:

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Inbred shorter people

By Razib Khan | July 20, 2012 12:10 am

Evidence of Inbreeding Depression on Human Height, a paper with over 1,000 authors! (I exaggerate) It’s interesting because it seems to establish that inbreeding does have a deleterious effect on traits whose genetic architecture is presumably polygenic and additive. Why is this theoretically important? Because inbreeding depression is often assumed to be driven by the exposure of rare recessive larger effect alleles, which recombine in near relations. Using tens of thousands of individuals from across a dozen European nations the authors found that there is a consistent relationship between inbreeding and reduction in height.

As the authors note height is a convenient trait to explore. First, it’s highly heritable. 80 to 90 percent of the variation in the population is explained by variation in genes. Second, it’s easy to measure. Also, implicit in the paper is the fact that in Europe today there is far less of a environmental effect on height (that’s why the heritability value is high). Even in poor European nations most people have enough to eat, so height is highly heritable, allowing for appropriate cross-national comparison.

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CATEGORIZED UNDER: Genetics, Genomics
MORE ABOUT: Genomics, Height

Iranian religious distinctiveness is not primal

By Razib Khan | July 19, 2012 2:03 pm

Dienekes has a discussion up of a new paper on Iranian Y-chromosome variation. My post isn’t prompted by the genetics here, but rather a minor historical note within the text which I want to correct, again, because it isn’t totally minor in light of contemporary models of the uniqueness of Iranian (specifically Persian) identity in the Middle East:

Persian identity refers to the Indo-European Aryans who arrived in Iran about 4 thousand years ago (kya). Originally they were nomadic, pastoral people inhabiting the western Iranian plateau. From the province of Fars they spread their language and culture to the other parts of the Iranian plateau absorbing local Iranian and non-Iranian groups. This process of assimilation continued also during the Greek, Mongol, Turkish and Arab invasions. Ancient Persian people were firstly characterized by the Zoroastrianism. After the Islamization, Shi’a became the main doctrine of all Iranian people.

As Dienekes observes I’ve objected to this confusion before:

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MORE ABOUT: History, Iran, Shia

Women wanted more children in 2000s, but had fewer

By Razib Khan | July 17, 2012 11:04 pm

As someone with mild concerns about dysgenic (albeit, with a normative lens that high intelligence and good looks are positive heritable traits) trends, I’m quite heartened that Marissa Mayer is pregnant. Of course she’s batting well below the average of some of her sisters, but you take what you can get in the game of social statistics. Quality over quantitative thanks to assortative mating.

This brings me to a follow up of my post from yesterday, People wanted more children in 2000s, but had fewer. A reader was curious about limiting the data set to females. Therefore, I did. The same general pattern seems to apply (the limitations/constraints were the same). The only thing I’ll note is that there were only ~40 women in the data set with graduate degrees in the 1970s who were also asked these particular questions, so take this with a grain of salt.

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Identity by descent & the Völkerwanderung

By Razib Khan | July 17, 2012 9:07 pm

Early this year I received an email from Dr. Peter Ralph, inquiring if I might discuss some interesting statistical genetic results from analyses of the POPRES data set which might have historical relevance. I’ve been excitingly waiting for the preprint to be made public so it could trigger some wider discussion. I believe that the methods outlined in the paper perhaps show us a path into the near future, where we might gain a much sharper perspective upon the recent past. So it’s finally out, and you can read it in full. Ralph and Dr. Graham Coop have posted put it up at arXiv, The geography of recent genetic ancestry across Europe. The paper uses ~500,000 SNPs from the POPRES data set individuals, and looks at patterns of identity by descent as a function of geography. By identity by descent, we’re talking about segments of the genome which are derived from a common ancestor. Because of recombination the length of the segments can give us a sense of the date of the last common ancestor; long segments indicate more recent ancestry because fewer recombination events have chopped up sequence.

Here’s the big takeaway of the paper: …There is substantial regional variation in the number of shared genetic ancestors: especially high numbers of common ancestors between many eastern populations likely date to the Slavic and/or Hunnic expansions, while much lower levels of common ancestry in the Italian and Iberian peninsulas may indicate weaker demographic effects of Germanic expansions into these areas and/or more stably structured populations. Recent shared ancestry in modern Europeans is ubiquitous, and clearly shows the impact of both small-scale migration and large historical events….

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CATEGORIZED UNDER: Demographics, History

Just a simple caveman

By Razib Khan | July 17, 2012 12:01 pm

Apropos of the discussion below, Classic SNL Clip Of The Day: Unfrozen Caveman Lawyer. Probably one of the best arguments against resurrecting Neandertals.


Is resurrecting Neandertals unethical?

By Razib Khan | July 17, 2012 9:34 am

An interview with paleoanthropologist Chris Stringer:

This raises one more question: Could we ever clone these extinct people?

Science is moving on so fast. The first bit of Neanderthal mitochondrial DNA was recovered in 1997. No one then could have believed that 10 years later we might have most of the genome. And a few years after that, we’d have whole Denisovan and Neanderthal genomes available. So no one would have thought cloning was a possibility. Now, at least theoretically, if someone had enough money, and I’d say stupidity, to do it, you could cut and paste those Denisovan mutations into a modern human genome, and then implant that into an egg and then grow a Denisovan.

I think it would be completely unethical to do anything like that, but unfortunately someone with enough money, and vanity and arrogance, might attempt it one day. These creatures lived in the past in their own environments, in their own social groups. Bringing isolated individuals back, for our own curiosity or arrogant purposes, would be completely wrong.


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People wanted more children in 2000s, but had fewer

By Razib Khan | July 16, 2012 7:19 pm

The readers of this weblog are relatively non-fecund, at least going by reader surveys. But I was curious nonetheless about the attitudes toward number of children, and realized goals of number of children, in the General Social Survey. I decided to look at two variables:



The former asks the respondent how many children they had, the latter how many they’d like to have. I restricted the sample to whites ages 45-65 for every survey year. I then combined all the years of a particular decade, so you have 1970s, 1980s, 1990s, and 2000s. For demographics I looked at highest educational attainment, and household income indexed to 1986 real value dollars (so they are comparable across decades).

Two major takeaways:

1) Education matters more than income in terms of number of children. Having lots of education tends to reduce family size. No great surprise.

2) Ideal number of children increased in the 2000s, but the decline in average number of children continued.

There is often talk in the literature on the disjunction between ideal family size in Third World nations and the realized family size, with a larger number of children than women may want. What is less discussed is the inverse discussion. It seems that Americans want larger families than they manage to have. Of course, there is the distinction between avowed and realized preferences here.

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MORE ABOUT: Demographics

Minding the trend: Bain Capital

By Razib Khan | July 16, 2012 9:19 am

Long time readers know that I like to use analytics like Google Trends to put up short posts. Why? I was prompted by the fact that the mainstream often likes to write meandering “trend” pieces which are basically spiffed-up versions of the type of think-pieces essays you’d pen in 10th grade. Basically the modus operandi is to start with a novel or counter-intuitive proposition, and then assemble a number of individuals or data points supporting your theses. For example, It’s Hip to Be Round, which argued 3 summers ago that male New York New York hipsters were now sporting potbellies fashionably. The problem with these sorts of pieces is that it’s not 10th grade in the pre-internet era, where you have a fine number of resources and time. Using above system you can construct a trend piece around any thesis. Just dive through the Google stack, or ask enough people and just cull the ones willing to be quoted. The modern trend piece in fact is a perfect exemplar of the sort of non-fiction which someone with a deconstructive mindset might argue is actually form of fiction. Trend pieces which reflect genuine social truths are then rather like historical novels, narrative elaborations upon factual events or dynamics.

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