Updated Bayesian ancestry analysis software

Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations.

BMC Bioinformatics. 2008 Dec 16;9(1):539

Authors: Corander J, Marttinen P, Siren J, Tang J

ABSTRACT: BACKGROUND: During the most recent decade many Bayesian statistical models and software for answering questions related to the genetic structure underlying population samples have appeared in the scientific literature. Most of these methods utilize molecular markers for the inferences, while some are also capable of handling DNA sequence data. In a number of earlier works, we have introduced an array of statistical methods for population genetic inference that are implemented in the software BAPS. However, the complexity of biological problems related to genetic structure analysis keeps increasing such that in many cases the current methods may provide either inappropriate or insufficient solutions. RESULTS: We discuss the necessity of enhancing the statistical approaches to face the challenges posed by the ever-increasing amounts of molecular data generated by scientists over a wide range of research areas and introduce an array of new statistical tools implemented in the most recent version of BAPS. With these methods it is possible, e.g., to fit genetic mixture models using user-specified numbers of clusters and to estimate levels of admixture under a genetic linkage model. Also, alleles representing a different ancestry compared to the average observed genomic positions can be tracked for the sampled individuals, and a priori specified hypotheses about genetic population structure can be directly compared using Bayes' theorem. In general, we have improved further the computational characteristics of the algorithms behind the methods implemented in BAPS facilitating the analyses of large and complex datasets. In particular, analysis of a single dataset can now be spread over multiple computers using a script interface to the software. CONCLUSIONS: The Bayesian modelling methods introduced in this article represent an array of enhanced tools for learning the genetic structure of populations. Their implementations in the BAPS software are designed to meet the increasing need for analyzing large-scale population genetics data. The software is freely downloadable for Windows, Linux and Mac OS X systems at http://web.abo.fi/fak/mnf//mate/jc/software/baps.html.

PMID: 19087322 [PubMed - as supplied by publisher]


Sex, race, and selection for height

A few papers relating to a conversation I'm not particularly interested in. For the record, in the West:
Selection worked strongly in favor of very tall men, not just against short men. Since there were no hints of any evolutionary check on this selection, these findings suggest unconstrained directional selection for tallness in men. [Evidence of unconstrained directional selection for male tallness]
Height was weakly but significantly related to reproductive success [among women]. The relationship was U-shaped, with deficits at the extremes of height. This pattern was largely due to poor health among extremely tall and extremely short women. However, the maximum reproductive success was found below the mean height for women. Thus, selection appears to be sexually disruptive in this population, favouring tall men and short women. Over evolutionary time, such a situation tends to maintain sexual dimorphism. Men do not use stature as a positive mate-choice criterion as women do. It is argued that there is good evolutionary reason for this, because men are orientated towards cues of fertility, and female height, being positively related to age of sexual maturity, is not such a cue. [Women's height, reproductive success and the evolution of sexual dimorphism in modern humans]
Whereas, in Africa:
In Western societies, height is positively correlated with reproductive success (RS) for men but negatively correlated with RS for women. These relationships have been attributed to sexual selection: women prefer tall men, and men prefer short women. It is this success in the marriage market which leads to higher RS for tall men and short women. We have already shown that the relationship between height and RS for women is quite different in a non-Western context. In a subsistence farming community in rural Gambia, height is positively correlated with reproductive success for women, largely owing to the higher survival of the children of tall women. Here, the relationship between height and reproductive success is analyzed for men in the same community. For these Gambian men, there is no significant relationship between height and the number of children they produce, although tall men do contract more marriages than shorter men. We conclude that environmental context needs to be taken into account when analyzing human reproductive behavior. [Height and reproductive success: How a Gambian population compares with the west]

Society for Nordish Physical Anthropology: new URL

The SNPA website is now located at:


The domain also hosts a new forum, from the people who used to run The Nordish Portal.

Geographic population structure in Britain

This 2007 genome-wide SNP study provides some information on geographic population structure in Britain.
 Thirteen genomic regions showing strong geographical variation are listed in Table 1, and Supplementary Fig. 7 shows the way in which their allele frequencies vary geographically. The predominant pattern is variation along a NW/SE axis. The most likely cause for these marked geographical differences is natural selection, most plausibly in populations ancestral to those now in the UK. Variation due to selection has previously been implicated at LCT (lactase) and major histocompatibility complex(MHC)7–9, and within-UK differentiation at 4p14 has been found independently10, but others seem to be new findings. All but three of the regions contain known genes. Aside from evolutionary interest, genes showing evidence of natural selection are particularly interesting for the biology of traits such as infectious diseases; possible targets for selection include NADSYN1 (NAD synthetase 1) at 11q13, which could have a role in prevention of pellagra, as well as TLR1 (toll-like receptor 1) at 4p14, for which a role in the biology of tuberculosis and leprosy has been suggested10.

There may be important population structure that is not well captured by current geographical region of residence. Present implementations of strongly model-based approaches such as STRUCTURE11,12 are impracticable for data sets of this size, and we reverted to the classical method of principal components13,14, using a subset of 197,175 SNPs chosen to reduce inter-locus linkage disequilibrium. Nevertheless, four of the first six principal components clearly picked up effects attributable to local linkage disequilibrium rather than genome-wide structure. The remaining two components show the same predominant geographical trend from NW to SE but, perhaps unsurprisingly, London is set somewhat apart (Supplementary Fig. 8).

[The Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661-678 (7 June 2007) | doi:10.1038/nature05911]
A later study ("Investigation of the fine structure of European populations with applications to disease association studies") finds 11 of these 13 SNPs are also "involved in East–West and North–South gradients covering all of Europe".
I'd prefer to see Scotland broken down by region -- I'd expect Lowlanders to be more similar to northern English. Ignoring London and Scotland, we see a continuum with East Anglia on one end and Wales on the other, consistent with the major trend detected here being varying proportions of continental Germanic and indigenous British ancestry.

Related: Genetic differentiation in the UK

Balls and brains

That's The Economist's headline:
The quality of a man’s sperm depends on how intelligent he is, and vice versa

THERE are few better ways of upsetting a certain sort of politically correct person than to suggest that intelligence (or, rather, the variation in intelligence between individuals) is under genetic control. That, however, is one implication of a paper about to be published in Intelligence by Rosalind Arden of King’s College, London, and her colleagues. Another is that brainy people are intrinsically healthier than those less intellectually endowed. And the third, a consequence of the second, is that intelligence is sexy. The most surprising thing of all, though, is that these results have emerged from an unrelated study of the quality of men’s sperm.

[. . .]

Ms Arden found 425 cases where samples had been collected and analysed from unvasectomised men who had managed to avoid spilling their seed during the collection process and had answered all the necessary questions for her to test her hypothesis, namely that their g values would correlate with all three measures of their sperm quality.

They did. Moreover, neither age nor any obvious confounding variable that might have been a consequence of intelligent decisions about health (obesity, smoking, drinking and drug use) had any effect on the result. Brainy men, it seems, do have better sperm.

By implication, therefore, they have fitter bodies over all, at least in the Darwinian sense of fitness, namely the ability to survive, to attract mates and to produce offspring. That is an important finding. Hitherto, biologists have tended to disaggregate the idea of fitness into a series of adaptations that are more or less independent of each other. This work adds to the idea of a general fitness factor, f, that is similar in concept to g—and of which g is one manifestation. To him that hath, in other words, shall be given. Unfortunately for the politically correct, Dr Miller’s hypothesis looks stronger by the day.

Dienekes links to the study. While the result has no direct bearing on Rushton's cross-racial claims (which stand or fall on their own merits), it seems to contradict the broader theoretical underpinning of Race, Evolution, and Behavior, proving that intelligence and reproductive potential need not be inversely related in humans (at least in men).

Related: Physical correlates of cognitive ability

Implicit Association Test = leftwing pseudoscience

Researchers Disagree on Accuracy of Well-Known Bias Test (NYT):
“One can decrease racial bias scores on the I.A.T. by simply exposing people to pictures of African-Americans enjoying a picnic,” says Hart Blanton, a psychologist at Texas A&M. “Yet respondents who take this test on the Web are given feedback suggesting that some enduring quality is being assessed.” He says that even the scoring system itself has been changed arbitrarily in recent years. “People receiving feedback about their ‘strong’ racial biases,” Dr. Blanton says, “are encouraged in sensitivity workshops to confront these tendencies as some ugly reality that has meaning in their daily lives. But unbeknownst to respondents who take this test, the labels given to them were chosen by a small group of people who simply looked at a distribution of test scores and decided what terms seemed about right. This is not how science is done.”
Having just taken the "Race IAT" again, I'm told: "Your data suggest little to no automatic preference between African American and European American."

(The title of this post is slightly hyperbolic. I'm not sold either way on the general usefulness of IATs, but clearly Greenwald and Banaji are bent on social engineering.)

Brues on American physical types

Based on data collected on a large sample of U.S. soldiers in the middle of the last century, Alice Brues sees six broad physical types in America:
[. . .] table 10 [. . .] lists certain very broad categories of physical type (derived quite empirically from the data of tables 6 and 7, without retrospect on any special system of racial classification.) Under each physical type are listed the regions and national extractions characterized by it.

The first type, a tall thin-faced dolichocephal, is typical of Old Americans and British and of the Old American stronghold in the southern states east of the Mississippi. The second type, which is distinguished from the first by greater width of the face and head, is typical of Scandinavian extraction and of the West North Central and to a lesser extend the Mountain and Pacific states.

The third type, diametrically opposite from the first, is short, relatively brachycephalic, and broad-faced. It characterizes Germanic, Russian and Slavic extractions and the Middle Atlantic and East North Central states; i.e., the industrial north exclusive of New England. The fourth type, not too clearly marked, differs from the third in that the head breadth and bizygomatic are not high; this type is small all over. It characterizes Gallic and Mediterranean strains and the New England area.

The fifth type is peculiar to the West South Central states, and is not parallelled by any of the European extractions. It is characterized by a strong inverse relation of head breadth and bizygomatic (which otherwise show a very general correlation) the face breadth being disproportionately high. A clue to this may be seen in the 4% frequency of Latin American extraction in this are, though this alone could hardly account for the approximate 2.5 mm excess of face breadth relative to head breadth. Since this area, which includes Texas and Oklahoma, is not only the principal point of Mexican immigration, but also the area in which maximum infiltration of Indian blood into the general population has undoubtedly taken place, it appears probable that the excessive face breadth is the result of a tangible mongoloid admixture.

The sixth type is really no type at all; it comprises the Irish, who happen to be very close to the general averages of the total American melange, as well as very randomly distributed regionally.


The study includes 3075 white enlisted men measured by the Chemical Warfare Service, representing all sections of the United States. Stature and eight head and face measurements have been correlated with states of birth and national extraction. Cephalic index, head length and breadth, and nose breadth, afford the clearest differentiation both for nationality of origin and for place of birth within the United States. Regional differences are less marked than those associated with national extraction, but are statistically considerable. Residence in the United Sates appears to have effected and increase in stature, at least in the shorter European stocks, with a corresponding slight decrease in cephalic index : certainty on this point is prevented by ignorance of selective factors in immigration. Differences in national extraction between different areas of the United States are found to be considerable, reflecting the historical sequence of migrations. The physical differences of the various regions appear to be primarily determined by the distribution of the various European stocks which settled them. Traces of aboriginal population are indicated in only one area.

American "types" with regions and nationalities in which they predominate
  1. Stature and head length high
    Head breadth and bizygomatic low
    South Atlantic
    East South Central
    Old American

  2. Stature high, head length average or high
    Head breadth and bizygomatic not low
    West North Central
  3. Stature and head length low
    Head breadth and bizygomatic high
    Middle Atlantic
    East North Central

  4. Stature and head length low
    Head breadth and bizygomatic not high
    New England

  5. Head breadth low, bizygomatic high
    West South Central
  6. No marked deviation from U.S. average
[Alice M. Brues. Regional differences in the physical characteristics of an american population. American Journal of Physical Anthropology. 4:463-482, 1946.]
Based on Table 6, the "Germanic" group is intermediate between the British and Slavic in head length, head breadth, and bizygomatic. It's not obvious to me why Brues chose to include "Germanic" and Slavic in the same category. Considering "national extraction groups" individually:
the Slavic is most strongly differentiated from the total population [. . .] The significant differences are: plus in head breadth, bizygomatic, bigonial and nose breadth, and minus in head length.
After Slavic, the next most distinctive group is "Mediterranean, significantly less than average in stature and head length, and more than average in face length, nose length and nose breadth." Contra Boas:
The lowest cephalic index mean in the present series is 77.3 for Pure British. [. . .] The American "British" [. . .] appear to be fractionally more dolichocephalic than the British themselves. The highest cephalic index mean in the present series is 82.7 for Pure Slavic. [. . .] The general conclusion is nevertheless the same as in the case of the British group: the American "Slavics" are comparable to their European ancestors, with a suspicious tendency towards greater dolichocephaly, probably not more than one unit. [. . .] the difference appears to be that which might be expected from increase in height. It certainly appears that the European cephalic index differences, in the intermediate groups as well as in these two extremes, have been well preserved in their transplanted members, The long established position of the cephalic index as a critical and reasonably stable indicator of ancestry is well borne out by the present analysis. The probable decrease of the cephalic index in the presence of factors favoring greater physical size is small in relation to the hereditary differences.

Another nail in the coffin of the Iberian Irish myth

Within the last few months, the genetic genealogy community has placed a new SNP (L21 / rs11799226) on the Y chromosome phylogenetic tree downstream of the most frequent western European haplogroup (R1b). Preliminary results suggest the overwhelming majority of Irish R1b carry the mutation, while L21 is absent in the Iberian samples and subclades tested so far. R1b from England and continental northwestern Europe seem to be split between L21-derived and L21-ancestral. It's still early and I'd like to see more data, but I think L21 (and thus the direct male ancestor of the majority of the Irish) most likely originated in northwestern Europe. The supposed link between the Irish and Iberians was built on the high frequency of R1b Y-DNA in both regions. The autosomal and mtDNA data never supported any sort of special or close relationship between "Celts" and Basques; it's now clear that Y-DNA doesn't, either.

More ancient DNA from Germany (Corded Ware burials)

Via Dienekes:
Additionally, the Y chromosome haplogroup R1a of the boys corresponds with the man’s (ind. 3). It is noteworthy that in grave 99 the orientation of the adult individuals follows the established pattern of the CWC, whereas both children clearly deviate from it. It appears that the burial orientation pattern was overruled for each boy to face a parent to express a biological relationship.

[Haak et al. Ancient DNA, Strontium isotopes, and osteological analyses shed light on social and kinship organization of the Later Stone Age.
PNAS doi: 10.1073/pnas.0807592105.]

The R1a result is interesting, but I'd like to see Y-DNA results from many more samples before drawing any firm conclusions. Based on his analysis of physical remains, Roland Menk concluded:
The Corded Ware complex s.l. is biologically heterogeneous. The local groups of the core area (Central Germany, Czechoslovakia, Poland) form a very homogeneous block, issued from the local "Old Europe" substratum and persisting until Aunjetitz at least. This block shows no biological affinities to the Ukrainian Kurgan populations. There is no evidence for physical presence of Kurgan tribes in this area. Indo-Europeanization of Northern Europe could be explained by indirect Kurganization, i.e. by invasion of previously Kurganized neighbor groups.

[Roland Menk. A Synopsis of the Physical Anthropology of the Corded Ware Complex on the Background of the Expansion the Kurgan Cultures. Journal of Indo-European Studies, V. 8 361.]

On the other hand, Coon believed:
On the basis of the physical evidence as well, it is likely that the Corded people came from somewhere north or east of the Black Sea. The fully Neolithic crania from southern Russia which we have just studied include such a type, also seen in the midst of Sergi's Kurgan aggregation. Until better evidence is produced from elsewhere, we are entitled to consider southern Russia the most likely way station from which the Corded people moved westward.

I don't think the place of origin of R1a or the timing of its expansion(s) has been pinned down tightly enough as of yet to allow an R1a lineage in a single family to contribute much to the debate on the biological origins of the Corded people.

Copernicus facial reconstruction

The identity of the skull was supposedly confirmed through DNA testing.
WARSAW, Poland – Researchers said Thursday they have identified the remains of Nicolaus Copernicus by comparing DNA from a skeleton and hair retrieved from one of the 16th-century astronomer's books. The findings could put an end to centuries of speculation about the exact resting spot of Copernicus, a priest and astronomer whose theories identified the Sun, not the Earth, as the center of the universe.

[. . .]

The reconstruction shows a broken nose and other features that resemble a self-portrait of Copernicus, and the skull bears a cut mark above the left eye that corresponds with a scar shown in the painting.

[. . .]

Swedish genetics expert Marie Allen analyzed DNA from a vertebrae, a tooth and femur bone and matched and compared it to that taken from two hairs retrieved from a book that the 16th-century Polish astronomer owned, which is kept at a library of Sweden's Uppsala University where Allen works.
If anyone has more details on the DNA analysis, please post them.

Related: Caroline Wilkinson's swarthy Bach reconstruction; more on Bach's skull.

New England political thought a century ago

The conclusion of a 1909 speech by Henry Cabot Lodge ("The Restriction of Immigration").
I have cited a witness of the highest authority and entire disinterestedness to support what I have said as to the fixed and determinate character of the English-speaking race. Now that I come to show what that race is by recounting its qualities and characteristics, I will not trust myself to speak, for I might be accused of prejudice, but I will quote again M. Le Bon, who is not of our race nor of our speech.

He says:—
Inability to foresee the remote consequences of actions and the tendency to be guided only by the instinct of the moment, condemn an individual as well as a race to remain always in a very inferior condition. It is only in proportion as they have been able to master their instincts—that is to say, as they have acquired strength of will and consequently empire over themselves—that nations have been able to understand the importance of discipline, the necessity of sacrificing themselves to an ideal and lifting themselves up to civilization. If it were necessary to determine by a single test the social level of races in history, I would take willingly as a standard the aptitude displayed by each in controlling their impulses. The Romans in antiquity, the Anglo-Americans in modern times, represent the people who have possessed this quality in the highest degree. It has powerfully contributed to assure their greatness.
Again he says, speaking now more in detail:—
Let us summarize, then, in a few words the characteristics of the Anglo-Saxon race, which has peopled the United States. There is not perhaps in the world one which is more homogeneous and whose mental constitution is more easy to define in its great outline. The dominant qualities of this mental constitution are, from the standpoint of character, a will power which scarcely any people except perhaps the Romans have possessed, an unconquerable energy, a very great initiative, an absolute empire over self, a sentiment of independence pushed even to excessive unsociability, a puissant activity, very keen religious sentiments, a very fixed morality, a very clear idea of duty.
Again he says:—
But, above all, it is in a new country like America that we must follow the astonishing progress due to the mental constitution of the English race. Transported to a wilderness inhabited only by savages and having only itself to count upon, we know what that race has done. Scarcely a century has been necessary to those people to place themselves in the first rank of the great powers of the world, and to-day there is hardly one who could struggle against them.

Such achievements as M. Le Bon credits us with are due to the qualities of the American people, whom he, as a man of science looking below the surface, rightly describes as homogeneous. Those qualities are moral far more than intellectual, and it is on the moral qualities of the English-speaking race that our history, our victories, and all our future rest. There is only one way in which you can lower those qualities or weaken those characteristics, and that is by breeding them out. If a lower race mixes whit a higher in sufficient numbers, history teaches us that the lower race will prevail. The lower race will absorb the higher, not the higher the lower, when the two strains approach equality in numbers. In other words, there is a limit to the capacity of any race for assimilating and elevating an inferior race; and when you begin to pour in unlimited numbers people of alien or lower races of less social efficiency and less moral force, you are running the most frightful risk that a people can run. The lowering of a great race means not only its own decline, but that of civilization. M. Le Bon sees no danger to us in immigration, and his reason for this view is one of the most interesting things he says. He declares that the people of the United States will never be injured by immigration, because the moment they see the peril the great race instinct will assert its itself and shut the immigration out. The reports of the Treasury for the last fifteen years show that the peril is at hand. I trust that the prediction of science is true, and that the unerring instinct of the race will shut the danger out, as it closed the door upon the coming of the Chinese.

That the peril is not imaginary or the offspring of race prejudice, I will prove by another disinterested witness, also a Frenchman. M. Paul Bourget, the distinguished novelist, visited this country a few years ago, and wrote a book containing his impressions of what he saw. He was not content, as many travelers are, to say that our cabs were high-priced, the streets of New York noisy, the cars hot, and then feel that he had disposed of the United States and the people thereof for time and for eternity. M. Bourget saw here a great country and a great people; in other words, a great fact in modern times. Our ways were not his ways, nor our thoughts his thoughts, and he probably like his own country and his own ways much better; but he none the less studied us carefully and sympathetically. What most interested him was to see whether the socialistic movements, which now occupy the alarmed attention of Europe, were equally threatening here. His conclusion, which I will state in a few words, is of profound interest. He expected to find signs of a coming war of classes, and he went home believing that if any danger threatened the United States it was not from a war of classes, but a war of races.

Mr. President, more precious even than forms of government are the mental and moral qualities which make what we call our race. While those stand unimpaired all is safe. When those decline all is imperiled. They are exposed to but a single danger, and that is by changing the quality of our race and citizenship through the wholesale infusion of races whose traditions and inheritances, whose thoughts and whose beliefs are wholly alien to ours, and with whom we have never assimilated or even been associated in the past. The danger has begun. It is small as yet, comparatively speaking, but it is large enough to warn us to act while there is yet time and while it can be done easily and efficiently. There lies the peril at the portals of our land; there is pressing the tide of unrestricted immigration. The time has certainly come, if not to stop, at least to check, to, sift, and to restrict those immigrants. In careless strength, with generous hand, we have kept our gates wide open to all the world. If we do not close them, we should at least place sentinels beside them to challenge those who would pass through. The gates which admit men to the United States and to citizenship in the great republic should no longer be left unguarded.
Restrictionist efforts, spearheaded by New Englanders like Lodge and New Yorkers like Madison Grant, culminated in the passage of the 1924 Immigration Act, which was rabidly opposed by and later overturned with aid from organized Jewry. Kevin MacDonald sees ethnic conflict. Moldbug claims to see an aracial minority aping New England Puritans in an attempt to win status points. I know which of these theories I find more convincing.

Moldbuggery Redux

More tiresome calumny against New England Puritans from self-described scion of communist Jews "Mencius Moldbug". Moldbug's libels typically take the form of absurdly-reasoned ten-thousand-word posts supported by links to whatever obscure, barely-relevant, centuries-old text he happens to be browsing on Google Books that day. My impression has been Moldbug prefers to dazzle his audience with pseudo-erudition and sheer volume of words, leaving it to his dumber commenters to try to state his world-view in direct and concise terms. Because when put simply moldbuggery makes claims about history which are blatantly counterfactual and easy to refute.

But MM has now surfaced in a desisite comment thread giving every bit as much indication as Jeff Williams of having failed high school-level American history. (Since, in light of MM's claimed educational credentials and implied obsessive reading habit, I find it unlikely simple ignorance is behind his lies, the question becomes what exactly is MM trying to accomplish? Some combination of deception and self-deception is clearly at play. Considering its author's ethnic background, it does seem slightly convenient that moldbuggery's central tenet holds "Dissenting British Protestantism caused All Leftism Ever" -- the corrollary being "The Juwes are the men That Will not be Blamed for nothing". Moldbug goes so far as to claim Jewish immigrants only transformed into communists through assimilating toward the culture of the descendants of New England Puritans.)

before the 1950s jews and catholics were allied as white ethnics against the protestant ascendancy. the new deal coalition was to some extent the culmination of this, though even as far back as the 19th century the two groups had to coordinate to defend themselves against protestant nativist groups. in the 1950s post-protestant intellectuals abandoned their nativism, and turned their guns on traditionalist religion, and secularized their anti-catholic rhetoric.

This wording is a little misleading: it implies that the liberal, anti-nativist strain of the Puritan tradition is a post-WWII invention. Which, as I'm sure you know, is anything but the case.

Liberal mainline Protestantism shows an extremely clear continuity from the Second Great Awakening, through the abolitionists and Transcendentalists, to the Social Gospel, the settlement movement, the Progressive Era proper, Eleanor Roosevelt, etc, etc, etc. It has not always been politically dominant, but it has generally been socially dominant.

While I have little interest in tracing the intellectual development of Eleanor Roosevelt, in the interest of defending the descendants of New England Puritans, I'll point out that:
(1) Eleanor Roosevelt's ancestry was Dutch, Scottish, and Scotch-Irish. She had little or no New England Puritan blood.
(2) One of her grandparents was born in Georgia (or in Connecticuit to Georgian parents). Three were born in New York.
(3) She was an Episcopalian.
(4) She was an insecure child who (correctly) considered herself ugly.
(5) She was sent to a finishing school in England run by a French feminist, but I can't imagine that had any impact on her later politics.
(6) She campaigned in favor of Catholic Al Smith in 1928.

Moreover, this obscures a bit of geographical culture history: the "nativist," American-nationalist branch of mainline Protestantism (eg, Madison Grant) to which you refer, responsible for the Harding-Coolidge restoration and now pretty much extinct, has its roots in one branch of the Unionist coalition, namely the Midwestern (or as they said then, just "Western"). There were considerable tensions between the Westerners and the New Englanders - for example, the latter hated the South because it oppressed blacks, the former because it was full of blacks. The last remnants of Midwestern nativist politics are seen with the isolationists, Taft, etc.

This is just plain wrong, as others in the thread point out and as I've pointed out before. Rather than waste any more time than necessary reasserting reality, here are some links:

United States Presidential Election Results
Immigration Restriction League

And, while as someone with roots in the Midwest it might be nice to be able to claim Madison Grant, the idea that his thinking owes much in particular to that region is just bizarre. Grant was a New York progressive. Yankees such as Charles Davenport (born in CT), William Ripley and General Francis Walker (the latter two born in Massachusetts), on the other hand, undoubtedly did influence Grant.

The relationship with the Catholics is also more interesting than you describe. The Catholics were always Democrats. In 1932, someone had a bright idea: if the progressive wing of the Republican Party (which was the Northern Protestant party, containing both nativists and progressives) took over the Democrat name and the Democrat machine, they could wax fat on the votes of their enemies, the "hyphenated-American" inner-city white ethnics and the Solid South, for the next thirty years, before the suckers woke up. Done. Smooth move, gents.

[MM expands on the above claim in a later comment:]

Can you name names?

You mean, FDR? Or his advisers, like Louis Howe?

Of course, progressive takeover of the Democrats was nothing really new - see Wilson. But the level of cynicism was new. Wilsonians, for instance, aimed to smash the Democratic urban machines. Whereas the New Deal incorporated them, and raised vote-buying to an almost theological plane. (When you see Thomas Frank complaining that Kansans don't vote according to their "economic interests," basically what he's expressing is anger that they sold him their votes and didn't stay bought.)

Just bizarre. MM must be referring to some alternate universe, because these ravings bear little resemblance to actual history. As another commenter pointed out: "FDR was elected Democratic NY State Senator in 1910. Howe was an associate of FDR from around that time. The Democratic party in 1910 was not exactly an attractive vehicle for winning Presidential Elections, having held power for a grand total of 8 years in the previous 50. If either had previously been extreme progressive republicans, I don't know, but if they were - planning the New Deal coalition that arose out of the Great Depression 20 years before it happened - that would be some neat trick!" Moreover, Louis McHenry Howe hailed from Indianapolis, where he "began his journalism career at seventeen when he joined the staff of his father's Democratic-leaning weekly, The Sun". That sounds like one hell of a deep Yankee conspiracy.

Woodrow Wilson, of course, was of Scotch-Irish and Scottish ancestry. He was born in Virginia to Confederate loyalists. Thank god we have people like Jimmy Cantrell and Mencius Moldbug who can see past mundane facts and place the blame for Wilson where it's due: New England Puritans.

As for the Jews, being no suckers, they realized that they should assimilate into the most socially prestigious branch of the American tradition - the progressives. Again: done.

Brilliantly reasoned. This also helps explain why Jews in Russia assimilated so readily to local aristocratic norms.

"European Caucasian" unity

As manifested on the internet:
You say Europe is white? You are in dreamland and in denial. Spain white? the Greece white?, Italy white? They are by no means considered white. I am half Greek, half Dutch and my skin is olive color by the Greek side of my family. Italians and Spanish are along the same lines of that olive skin, dark eyes and hair from the majority of the populations. Europe is ready for an Obama of their own and the sooner the better to stop racism as soon as possible.

Posted by: sandra | November 12, 2008 2:26 AM
razib, yes,you are right it was not a good argument and I am probably a little bitter from certains types of discrimination. You are also right about being considered not white in the netherlands because of being half Greek, although that was while I was growing up, now things are starting to change, slowly. If you look at the Dutch and other Europeans today, you see a lot of mixes of different nationalities. I don't think that anyone is pure anything nowadays. I think that we should all be happy to be of the human race and not focuss so much on the color of ones hair, skin or eyes. What do you think?

Posted by: sandra | November 12, 2008 3:41 AM
Is this the sort of "change" we need more of?

ASHG "Ancestry Testing Statement"

The statement and press release (via GENEALOGY-DNA-L). I agree almost entirely with Blaine Bettinger's comments. The funniest part of the statement for me:
Knowledge about genetic ancestry – if undesirable and unexpected – can elicit a range of psychological responses including shock, disbelief, denial, anxiety, anger, fear and other well-known reactions to unwanted news. [. . .] The use of AIMs and admixture mapping techniques, in general, has brought about anxiety with regard to its apparent reification of race.
The earlier sentence ostensibly concerns the tender feelings of vulnerable consumers of genetic ancestry tests, but the sentence which begins the next paragraph reveals what seems to have been the primary concern that drove most of the committee members in drafting this trash.

The committee's first two recommendations are unobjectionable:
1. Because the science of ancestry determination has limitations, greater efforts are needed on the part of both industry and academia to make the limitations of ancestry estimation clearer to consumers, the scientific community, and the public at large. In turn, the public has the responsibility to avail themselves of information regarding ancestry testing and strive to better understand the implications and limitations of these assessments.

2. Additional research is required to further understand the extent to which the accuracy of genetic ancestry estimation is influenced by the individuals represented in existing databases, geographical patterns of human diversity, marker selection and statistical methods.

However, the committee negates any value their statement may have had with their subsequent advocacy of "counseling" "guidelines" for ancestry testing, full-employment for cultural Marxists, and government controls on ancestry testing.

Physical correlates of cognitive ability

General intelligence has been found to correlate with hair and eye color, among other physical characteristics:
Among these physical correlates of IQ are certain blood group and particularly the positive correlation of g with the number of homozygous genetic loci (i.e., the same alleles at each locus on both chromosomes) for various blood types, which indicates greater-than-usual genetic similarity of the individual's parents. This would ensure less immunological risk of antigenic incompatibility between mother and fetus, a prenatal factor that can have subtle deleterious effects on brain development in utero. The best-known antigenic incompatibility between mother and fetus with potentially harmful effects on fetal development is that for the Rh factor, which occurs in second-born (and later-born) children when the mother is Rh-negative and the fetus is Rh-positive (having received the RH+ allele from the father). Dizygotic (DZ) twins who are discordant for the RH factor (and certain other blood antigens as well) show greater IQ differences than DZ twins who are concordant. Another blood variable of interest is the amount of uric acid in the blood (serum urate level). Many studies have shown it to have only a slight positive correlation with IQ. But it is considerably more correlated with measures of ambition and achievement. Uric acid, which has a chemical structure similar to caffeine, seems to act as a brain stimulant, and its stimulating effect over the course of the individual's life span results in more notable achievements than are seen in persons of comparable IQ, social and cultural background, and general life-style, but who have a lower serum urate level. High school students with elevated serum urate levels, for example, obtain higher grades than their IQ-matched peers with an average or below-average serum urate level, and, amusingly, one study found a positive correlation between university professors' serum urate levels and their publication rates. The undesirable aspect of high serum urate levels is that it predisposes to gout. In fact, that is how the association was originally discovered. The English scientist Havelock Ellis, in studying the lives and accomplishments of the most famous Britishers, discovered that they had a much higher incidence of gout than occurs in the general populations.

Asthma and other allergies have a much-higher-than-average frequency in children wiht higher IQs (over 130), particularly those who are mathematically gifted, and this is an intrinsic relationship. [. . .]

Then there are also a number of odd and less-well-established physical correlates of IQ that have each shown up in only one or two studies, such as vital capacity (i.e., the amount of air that can be expelled from the lungs), handgrip strength, symmetrical facial features, light hair color, light eye color, above-average basic metabolic rate (all these are positively correlated with IQ), and being unable to taste the synthetic chemical phenylthiocarbamide (nontasters are higher both in g and in spatial ability than tasters; the two types do not differ in tests of clerical speed and accuracy). The correlations are small and it is not yet known whether any of them are within-family correlations. Therefore, no causal connection with g has been established.

Finally, there is substantial evidence of a positive relation between g and general health or physical well-being. In a very large national sample of high school students (about 10,000 of each sex) there was a correlation of +.381 between a forty-three-item health questionnaire and the composite score on a large number of diverse mental tests, which is virtually a measure of g. By comparison, the correlation between the health index and the students' socioeconomic status (SES) was only +.222. Partialing out g leaves a very small correlation between SES and healthy status.

[Arthur Jensen, The g factor, pp. 162-163]

I don't know if the relationship between IQ and light hair/eyes holds within ethnically homogeneous samples. Taking Europe as a whole, I would find the reported correlation unsurprising. Internationally, lighter skin correlates with greater intelligence:
We correlated mean IQ of 129 countries with per capita income, skin color, and winter and summer temperatures, conceptualizing skin color as a multigenerational reflection of climate. The highest correlations were − 0.92 (rho = − 0.91) for skin color, − 0.76 (rho = − 0.76) for mean high winter temperature, − 0.66 (rho = − 0.68) for mean low winter temperature, and 0.63 (rho = 0.74) for real gross domestic product per capita. The correlations with population of country controlled for are almost identical. Our findings provide strong support for the observation of Lynn and of Rushton that persons in colder climates tend to have higher IQs. These findings could also be viewed as congruent with, although not providing unequivocal evidence for, the contention that higher intelligence evolves in colder climates.

[Templer and Arikawa. Temperature, skin color, per capita income, and IQ: An international perspective. Intelligence. Volume 34, Issue 2, March-April 2006, Pages 121-139.]

Higher cognitive ability was found to be associated with sharper, more linear facial features in an ethnically British and Irish sample.

Facial shape covaried with cognitive performance in a sexually dimorphic manner. Among men, the regression model for time to complete Trail Making Test A was associated with one PC of facial shape, which explains 14% of the variance in completion time ( F = 6.21, d.f. = 1, P < 0.05); on visualization of this statistical model (Fig. 6), increasing spatial attention, visuomotor tracking and processing speed was associated primarily with a relative increase in anterior–posterior length and relative decrease in facial width. Time to complete Trail Making Test B, which places additional demands on attention and ‘set shifting’ relative to Test A, was associated with one PC of facial shape, which explains 22% of the variance in completion time ( F = 10.13, d.f. = 1, P < 0.005); on visualization of this statistical model (Fig. 6), increasing spatial attention, visuomotor tracking, processing speed and ‘set shifting’ was associated primarily with anterior displacement of chin, posterior displacement of mouth, narrowing of cheeks and anterior displacement of forehead. Conversely, verbal fluency was unrelated to any component of facial shape in men.

In women, times to complete Trail Making Tests A and B were not associated with any PC of facial shape. Conversely, the regression model for verbal fluency score was associated with two PCs of facial shape in women, which explain 16% of the variance in verbal fluency score ( F = 5.86, d.f. = 2, P < 0.005); on visualization of this statistical model (Fig. 6), increasing verbal fluency was associated primarily with anterior–inferior displacement of the nose, anterior–superior displacement of the chin, inferior displacement of the upper lip, inward displacement of the cheeks, posterior–superior displacement of the forehead and relative widening of the lateral face.

[Hennessy et al. Facial surface analysis by 3D laser scanning and geometric morphometrics in relation to sexual dimorphism in cerebral–craniofacial morphogenesis and cognitive function. Journal of Anatomy, Volume 207, Number 3, September 2005 , pp. 283-295(13).]

America as it might have been

What would America be like had it experienced no immigration after the colonial era? Ellsworth Huntington addresses this question in his study of the descendants of New England Puritans and concludes "that in many ways life would have been more satisfactory" [1].

  • Population size. Huntington projects that in the absence of immigration and other impediments, "the normal natural increase of these descendants of the early colonists would have given the United States approximately its present population." (And, even if America were left with a reduced population, Huntington argues, "there is no good reason to think that we are better off because of mere numbers. Quality counts for vastly more than quantity.")

  • Physical appearance. "Blue-eyed and fair haired people would be more numerous--as numerous as they are in eastern England north of London, or in southern Scotland. The average stature would also be greater than at present. Our cities would no longer contain great areas where a large share of the people are short and have black hair, dark brown eyes, and brunette skins." (Huntington notes: "Our studies seem to suggest that the blonder type is more prone to wander and to get on in the world than the darker types, but we do not attach great importance to this.")

  • Economic level. ". . . our sample of old New England suggest an average buying power about a quarter greater than that of the native whites of the country as a whole." The rate of home ownership is 50% higher in the Puritan sample. Huntington expects a reduction in "crime and pauperism" (see below) would save billions of dollars, and suggests individual savings, investments, "and general ability to withstand hard times would presumably be larger".

  • Crime. ". . . our New England sample shows less than half as great a criminal tendency as does the average population [. . .] Far more important than [the economic improvement], however, is the greater safety, freedom, and joy of life that would come under such circumstances. Think of the difference if we knew not only that kidnapping, racketeering, bootlegging, vice, graft, blackmail, murder, and theft were as rare as in England, but also that misrepresentation of investments, unfairly pyramided corporations, and all sorts of financial gold bricks were equally diminished in number."

  • Dependency. "Our study of old colonial names indicates that the descendants of the Puritans are only half as likely to be registered in the lists of social service exchanges as are the inhabitants of the country in general."

  • Government and politics: ". . . it seems to be clear that if this country had a larger percentage of people like the descendants of the old New Englanders, or of similar people derived from some other source, it would also have a larger percentage of the far more limited kind who take the lead in advancing the cause of true civilization. Moreover, the obstacles to putting new ideas into effect would be much diminished because the people as a whole would be more intelligent than is now the case. This would give the country greater wisdom politically and socially, as well as economically. It would diminish the power of the demagogue and political boss, for such men batten on ignorance. High minded, wise, disinterested men like Governor Cross of Connecticut, that former professor and dean of Yale, who stands so solidly for the good of all the people, would have a greater chance not only to get into high office, but to carry out their ideas. It is doubtful whether and institution like Tamanny Hall or the Republican machine of Philadelphia could have arisen in a community composed wholly of descendants of the old New Englanders, or of people derived from any one of a score of other equally good sources. Has not democracy failed among us mainly for lack of men who are both honest and able? There are indeed plenty of bad and stupid people among the old New England stock. There are also bad and clever ones who crop out sometimes in high places where they do untold damage. Nevertheless, the record set forth in these chapters seems to show that it would be much safer to entrust a country to men like those of early New England stock whom we have analysed in these pages than to the average of the country as a whole. It is certainly among them that we find the overwhelming majority of those who have led the march of progress. Thus it seems that if we had more such men, and fewer of the opposite kind, human progress would take place more evenly and effectively in all sorts of ways.

  • Technology and labor. Huntington argues: "If our population all had a degree of intelligence like that which their education records suggest among the descendants of the Puritans, people too incompetent for anything except common labor would be scarce. Therefore the conditions would be like those of many frontier communities where the scarcity of labor leads to high wages and this in turn attracts good men. [. . .] laborers would presumably be better organized, better paid, and more influential than now, as is the case in Australia. As time went on, however, the need for the less competent type of laborer as compared with the skilled workman would diminish. This is now happening, but it would be accelerated by the fact that according to our hypothesis inventions would be made even more rapidly that at present. We have see that inventiveness is a characteristic of the old Puritan stock. A larger proportion of this quality in the population as a whole would mean that labor saving machinery would be even more prevalent than now." Huntington sees a declining need for unskilled labor and "rapidly growing demand for competent people in new occupations". He concludes: "Our paramount need is for vastly more people with keen and highly trained minds that can contribute something to the great plans which must be worked out for the future. Without such minds civilization will break from its own weight like a giant dirigible. What we need most of all is a higher, better type of mentality. Thus it seems that even though the old New England stock may be very imperfect, it is at least better adapted to the requirements of the new social order than is our present population as it actually exists."
Unfortunately, even by the time the book was published in 1935, "the old New England stock [was] mingling with other types so fast that by the time any radical change in our racial outlook occurs its identity will almost have been lost." Thus: ". . . the lesson to be drawn [. . .] is not that we should try indiscriminately to increase the proportion of this old New England stock. [. . .] The lesson, as we see it, is that by proper selection the people of the United States as a whole, just as they are today, may give rise to descendants who possess unusually high qualities. Selection is the key word of this whole book" [2]. And: "If selection is to accomplish its full work it must be followed by segregation, or better still by continued selection from generation to generation." More on that later.

[1] Huntington, Ellsworth, and Martha Ragsdale. 1935. After three centuries; a typical New England family. Baltimore, Md: Williams & Wilkins Co. Chapter X ("What Might Have Been").

Kevin MacDonald briefly ponders a related question in Diaspora Peoples:

One wonders what might have happened if the British colonial authorities had allowed the colony complete sovereignty and if it had ultimately become a nation-state. Such a state, based on a clearly articulated exclusivist group strategy, might have been extremely successful. Composed of a highly intelligent, educated, and industrious citizenry, and with a proneness to high fertility and strong controls promoting high-investment parenting, it might have become a world power. One can imagine that as the 19th century wore on, Puritan intellectuals would have begun to see themselves as an ethnic-racial group and that Darwinism would have replaced Christianity as the ideological basis of the state, at least among the well-educated. The demise of Puritanism is likely a major event in the history of European peoples.
[2] I'm reminded a bit of Carleton Coon:
In the settlement of the United States the immigrants were not chose at random. Whole congregations migrated with their pastors to New England, and settled in sheltered coves and river mouths. [. . .] Middle-class artisans and skilled craftsmen predominated in early New England [. . .] Selection in migration operated from the beginning.

Pigmentation of old-stock Americans

Excerpts from a 1922 AJPA article by Ales Hrdlicka (full text free at Google books). Note: Czech immigrant Hrdlicka was on a mission to prove that "Old Americans" were not racially "Nordic". Semantics aside, he succeeded instead in demonstrating "Old Americans" were racially northwestern European, as expected.

By anthropology of the Old Americans is meant the status, physically, physiologically and demographically, of the oldest parts of the white population of the United States, as contrasted with the American population at large and with other units of the white race.

[. . .]

In order to supply as far as possible the need in these directions the writer undertook, in 1912, a systematic anthropological study of the oldest part of the "Old Americans." By "Old Americans" he designated all those who in their families had no mixture with more recent elements on either side for at least three generations. The study lasted until the present year. It was carried on in the anthropological laboratory of the U. S. National Museum, but eventually also in the field, and the utmost care was exercised throughout to assure the reliability of the data secured.

[. . .]


The above data on the eyes and hair permit the formulation of the following conclusions regarding pigmentation, and the other conditions here studied, in the Old Americans :

SKIN. 1. Two-thirds of the old stock males and three-fourths of the females show skin that may be classed as medium.

2. In only 5 per thousand in males, but in 52 per thousand in the females, is the skin plainly lighter than the medium. All of these cases are associated with pure light eyes and light or red hair.

3. In a little over one-fourth of the males and in one-sixth of the females the skin is perceptibly darker than medium. Such skin is generally associated with brown eyes and medium to dark hair.

HAIR. 1. Only 1 among 16 males and 1 among 14.5 females has real blond hair.

2. One-half of the males and over four-tenths of the females show medium (or "medium brown") hair.

3. In one-fourth of the males and three-tenths of the females the hair is dark ("dark brown"), to near black.

4. In approximately 1 percent in the males and but a little more in the females the hair is fully black.

5. In 2.6 per hundred of males and 4.9 per hundred in females the hair is red or near red.

6. The females show a slight to moderate excess of true blonds (especially golden and yellow), but also of darks, blacks and reds, over the males.

7. There are some areas in which hair pigmentation among the Old Americans, due to isolation and more thorough mixtures, differs from that of the group as a whole.

8. Differences between the "Yankees" and the "Southerners" in this respect are only moderate, the former showing somewhat more lights, less darks, few if any true blacks and less reds. But the southerners show almost identical conditions in regard to hair pigmentation as those of the central states and those of mixed-state ancestry.

EYES. 1. Approximately one-third of the eyes of the males and one-fourth of the eyes of the females of the Old Americans are pure lights.

2. One-sixth of the males and one-fifth of the females show eyes the iris of which is pure brown (light, medium or dark) .

3. Over one-half of the males as well as females have eyes that show plain traces of brown in light (mixed).

4. There are on the whole more light and less dark eyes than there is of light and dark hair.

5. Regional differences are less marked than with the hair, except in isolated localities.

6. There is a considerable but not a complete correlation between the pigmentation of the eyes and that of the hair. Light eyes may in some instances be associated with dark (though not black) hair; but medium to dark eyes are as a rule accompanied by medium, dark or black hair.

BLONDS AND BRUNETS. 1. The classification of the Old Americans on the basis of both the color of the eyes and hair brings a number of the conditions relating to pigmentation out with special clearness.

2. Over one-half of the males and nearly one-half of the females are " intermediates."

3. Blonds are scarce, as are also true brunets, but the latter are plainly more frequent, especially in the females.

4. The females show slightly more blondes, more brunettes and less intermediates than the males.

[. . .]

COMPARISONS. Suitable data for comparison are scarce. From what is available it appears that the pigmentation of both hair and eyes in the Old Americans is much like that of the present population of Great Britain, though the latter appears to show some excess of both dark eyes and dark hair.

As to changes with time, it seems probable that in both Great Britain and the United States there is taking place a slow progress towards a darker pigmentation of both eyes and hair, though the fact needs definite confirmation.

[Hrdlicka A. 1922. Physical Anthropology of the Old Americans. American Journal of Physical Anthropology 5(2):97-142.]


Technical details on 23andMe's improved global comparison feature

The feature. Dienekes' comments plus screenshots. A white paper from 23andMe:
White Paper 23-04: Global Similarity’s Genetic Similarity Map

Global Similarity: Genetic Similarity Map is a 23andMe feature that situates customers of unknown ancestry in the midst of a two-dimensional plot of reference individuals of known ancestry from around the world. The plot, or map, is constructed from the genetic distances between the reference individuals and the customers, such that the closer two individuals are related genetically, the nearer they appear in the map. The effect is that, when certain conditions are satisfied, customers appear nearest to the group of individuals to which they are most closely related. For example, a person with four Irish grandparents will tend to cluster amid Irish reference individuals, and be farther from French reference individuals, and further yet from Italian reference individuals.

This document is a technical description of the feature and the procedure used to produce the genetic similarity maps.

Two points in response to Dienekes:

(1) The plots are generated using multidimensional scaling, not PCA.
(2) The white paper points out that the feature "is not well-suited to individuals of mixed ancestry, and does not provide the precision that the feature does with people of homogeneous ancestry", and notes that "Ancestry Painting" is "well-suited to studying customers with mixed ancestry." I see little value in some of the additions Dienekes suggests. Instead, improved STRUCTURE-type analyses with more relevant reference populations might be more appropriate for Hispanic/Jewish/Afram customers.

Northern European population structure

As mentioned elsewhere by Tuuli Lappalainen, a new analysis of Northern European genome-wide SNP data is available today at PLoS One ("Genome-Wide Analysis of Single Nucleotide Polymorphisms Uncovers Population Structure in Northern Europe"). The results are broadly consistent with those of previous studies. British, German, and American samples are most similar to each other. Eastern Finns are most distinctive.
After genotyping on Affymetrix 250K Sty SNP arrays (see Methods and Table S1 for success rates and quality criteria), the data from 1003 European individuals were first compared without prior population assignment in the analyses of pairwise identities by state (IBS) and calculations with the Structure software. In multidimensional scaling of the IBS distances, there were four clusters: Eastern Finns, Western Finns, Swedes, and a group including the Germans, British and CEU (from now on called ”Central Europeans„; Fig. 2a,b, Fig. S1a). [. . .] The Structure analysis (Fig. 3, Fig. S2a,b) found most support for three or four clusters, one dominated by the Eastern Finns, one by the Swedes, and one by the Central Europeans; increasing the number of clusters did not bring out further differences. When only the Finnish samples were analysed with Structure, they formed two clusters (Fig. S2c), consisting of the Eastern and Western Finns, with only 1.8% of the samples associating more strongly to the cluster not corresponding to their geographic origin (data not shown). A Structure analysis of the three Central European populations combined found only one cluster.

[. . .]

Quantile-quantile plots of pairwise allele frequency differences (Fig. 5) and FST calculations (Table 1) showed a pattern of the largest differences being between Eastern Finland versus Great Britain, Germany and Sweden (FST = 0.0072–0.0094) and the smallest between the British and Germans (FST = 0.0005).
Incidentally, a different study reports an FST of 0.00054 between samples from north-east and southern Germany [1], suggesting the British and north Germans may be slightly more similar than some German subpopulations are to each other (although the data may not be strictly comparable).

The new paper touches on a couple items I've mentioned recently:
The differences between populations detected with FST and other measures accounted for such a small proportion of the total genetic variation that large numbers of SNPs are needed to observe them, once again illustrating how most of the human genetic variation is found between individuals instead of populations [39]. Even small differences between populations can be interesting regarding population history, but elucidating their phenotypic significance will require further studies.

The MDS plot of the European populations showed a pattern of population differences that was consistent with our other analyses and earlier observations of a greater degree of differentiation in the geographical extremes of Europe [3], [5], [7], [9]–[11]. Our German, British and CEU samples formed a single cluster, possibly due to a lack of neighbouring reference populations, and contrary to studies with a more comprehensive sampling from Central Europe [7], [9]. The Swedes showed a wider spreading than the other populations, but this was supported neither by diversity calculations nor by a more detailed comparison of the IBS and MDS distance matrices (results not shown). Thus, the differential spread was at least partly an artefact of the MDS, where the representation in a few dimensions likely fails to capture all aspects of complex data. Thus, as visually attractive as the MDS plots are, they must be interpreted with caution and, if sample sizes allow, be accompanied with analyses based on allele frequencies.
In fact, the differences between Eastern and Western Finns were of the same magnitude as the differences between Swedes and British, and much stronger than those between British and Germans. Thus, relevant units of genetic variation often do not correspond to preconceived political, linguistic or even cultural borders.

[1] Steffens et al. SNP-Based Analysis of Genetic Substructure in the German Population. Hum Hered. 2006;62(1):20-9. Epub 2006 Sep 21.

DNA analysis and small-scale admixture events

This paper ("Calculating expected DNA remnants from ancient founding events in human population genetics"; provisional PDF) concludes, based on a series of computer simulations:
while genetic data may be sensitive and powerful in large genetic studies, caution must be used when applying genetic information to small, recent admixture events. For some parameter sets, genetic data will not be adequate to detect historic admixture. In such cases, studies should consider anthropologic, archeological, and linguistic data where possible.
The authors point out that:
While genetic studies can provide considerable information, they are also accompanied by variation and stochasticity. Because of these limitations, even the most complete studies of human populations have been called “not unequivocal”[21] or “sobering”[22] by those conducting the research. Recent reports have also addressed the limited depth of current genetic studies[23], indicating that most studies make conclusions after sequencing less than 1% of subjects’ genomes, and sampling only small numbers of a population. Such methods can be especially problematic when dealing with historic admixture events that are very small. The difficulty is a function of the current architecture of genetic studies: researchers sample loci from a group of individuals and categorize individuals into groups based on which alleles they have at the loci tested[24, 25]. These categorizations are determined based on the most prevalent or probable genetic markers in an individual’s genome. The results of these studies, then, can overlook genetic markers that simply are not sampled, which is common in small admixture events. Additionally, stochastic events can lead to allele fixation and further complicate matters, particularly in small populations. It has been suggested that studies of even the largest migrations should couple genetic information with archeological, anthropological, and linguistic data[26].
The simulation results aren't too surprising:
The sizes of the migrant and native populations are fundamental for an understanding of expected allele frequency. With time since admixture as low as those we consider in our simulations, the most important factors are the sizes of the migrating and native populations. In our simulations, if the native population is large, changing the migrating population size results in a change of mean final allele frequency from .0243 to .0010. If the native population is small, those numbers change to .5016 and .0407. These are the most significant differences illustrated by our simulations and they attest to the important role of population sizes. Researchers should not expect to find many alleles from a small migratory group of 50 individuals in a large population today, even if sampling methods are exhaustive.

Sample size matters. Or, to kick a (hopefully) dead horse, why DNAprint is crap:
The average final allele frequency of the migrant allele in our population from the second simulation was 1.017%. We calculated the cumulative density function (CDF) for a genetic study that samples 50 loci for each individual and where the probability of detecting the migrant allele is equal to the probability found in our simulations. The CDF demonstrates that in 60% of individuals sequenced for 50 loci, we would not expect to find a single migrant allele (Figure 7a). Furthermore, we will only find more than one migrant allele in 9% of the subjects examined.

In the case of a large study with as many as 933 loci, based upon the expected migrant allele frequency of 1.017%, almost every subject would demonstrate at least one migrant allele (Figure 7b). In fact, most subjects would demonstrate more than 9 migrant alleles. However, while large studies would expect to succeed in finding more migrant alleles in today’s population, this alone cannot link the admixed population to the migrant population. The migrant alleles will still only represent, on average, 1% of every allele sequenced in the entire study. Therefore, although 9 migrant alleles may, on average, be found in each subject, it is hard to know if the migrant alleles will be redundant among loci and subjects or spread evenly throughout all the loci in the study. Additionally, these numbers could be considerably lower depending on the allele frequency in the migrating population.
As time increases, genetic drift causes the spread of final allele frequencies to increase, particularly when the population sizes are small. Thus, as the time since the admixture event increases, sample size for both loci and subjects becomes increasingly important.

In our second simulation, most of the migrant alleles are present in less than 2% of the population. In a study of a population where few subjects from many human populations are studied, alleles from a small-scale admixture will usually not be recovered at all. And these rare alleles could easily be ignored in favor of haplotypes that better categorize the population into clusters.
The authors conclude:
DNA data have been touted as a panacea for recovering information about the past, but their use depends so extensively on factors that are beyond our control that its applicability is not always appropriate. It is imperative, therefore, that researchers understand the implications of the variables we have presented and not rely solely on DNA sequence data when researching small, recent human migrations.

We can only hope to understand basic details of population history when quantifying genetic data and even valid results derived from genetic data may still be misleading if viewed unilaterally, as demonstrated by Harpending et. al.[46, 47]

Our results, however, are not completely ominous. Carefully designed studies should be able to draw specific and valid conclusions from genetic data. One area for major improvement is the number of individuals and loci sampled. Our results indicate that a large sample size and large number of loci are needed to obtain robust results. Studies that are unable to sample sufficiently do not have the power to draw appropriate conclusions and should be interpreted with caution.

[. . .]

The random nature of admixed genetic data seen in these simulations demonstrates that the utility of genetic data is dependent on the context of each individual study. Increasing the number of loci and the number of individuals sampled will increase the probability of detecting small traces of signal, but other sources of evidence should always be considered where possible.

DRD2*A1 and obesity

Frequencies of the DRD2*A1 allele are about twice as high in Africans and Asians as in Europeans.

The AP reports today:
WASHINGTON - Drink a milkshake and the pleasure center in your brain gets a hit of happy — unless you're overweight. It sounds counterintuitive. But scientists who watched young women savor milkshakes inside a brain scanner concluded that when the brain doesn't sense enough gratification from food, people may overeat to compensate.
[. . .]
A healthy diet and plenty of exercise are the main factors in whether someone is overweight. But scientists have long known that genetics also play a major role in obesity — and one big culprit is thought to be dopamine, the brain chemical that's key to sensing pleasure.
[. . .]
Yet that brain region was far less active in overweight people than in lean people, and in those who carry that A1 gene variant, the researchers reported. Moreover, women with that gene version were more likely to gain weight over the coming year.

It's a small study with few gene carriers, and thus must be verified, Volkow stressed.

Still, it could have important implications. Volkow, who heads NIH's National Institute of Drug Abuse, notes that "dopamine is not just about pleasure." It also plays a role in conditioning — dopamine levels affect drug addiction — and the ability to control impulses.

She wonders if instead of overeating to compensate for the lack of pleasure — Stice's conclusion — the study really might show that these people with malfunctioning dopamine in fact eat because they're impulsive.
The study covered in the above article:
Relation Between Obesity and Blunted Striatal Response to Food Is Moderated by TaqIA A1 Allele
E. Stice, S. Spoor, C. Bohon, and D. M. Small (17 October 2008)
Science 322 (5900), 449. [DOI: 10.1126/science.1161550]
Individuals whose reward centers of the brain respond sluggishly after eating prefer calorie-dense foods, which may account for their greater propensity to gain weight.
Podcast interview with Eric Stice.

Alcoholism, genetics, and race

Part-time GNXP houseboy / full-time mestizo failfuck "birch barlow" attributes his problems with alcohol and crack cocaine to "Anglo-Celtic" genes, while he raves about the quality genetics of small brown Asian women. It seems the self-proclaimed "cogelite" never bothered to actually check what genetic research suggests about relative group propensities for addictive behavior. So we're going to do it for him.

SNPedia lists several SNPs for which associations with Alcholism have been claimed, probably the most-studied of which is rs1800497:
rs1800497, a SNP also known as the TaqIA (or Taq1A) polymorphism of the dopamine D2 receptor DRD2 gene (even though it is actually located over 10,000bp downstream of the gene), gives rise to the DRD2*A1 allele. This allele (rs1800497(T)) is associated with a reduced number of dopamine binding sites in the brain [PMID 9672901], and has been postulated to play a role in alcoholism, smoking, and certain neuropsychiatric disorders.

The reduced number of dopamine binding sites may play a role in nicotine addiction by causing an "understimulated" state that can be relieved by smoking (and/or use of other drugs). [PMID 8873216]
The HapMap Phase III data indicates the following frequencies of the T/A (increased addiction risk) allele:
44% MEX (Mexican ancestry in Los Angeles, California)
44% CHB (Han Chinese in Beijing, China)
42% CHD (Chinese in Metroopolitan Denver, Colorado)
41% YRI (Yoruba in Ibadan, Nigeria)
40% ASW (African ancestry in Southwest USA)
40% JPT (Japanese in Tokyo, Japan)
28% GIH (Gujarati Indians in Houston, Texas)
21% CEU (Utah residents with Northern and Western European ancestry)
18% TSI (Toscans in Italy)

Not a good start for birch's imaginary mixed-race spawn. Let's look at another SNP:
rs1076560 is located in intron 6 of the dopamine receptor D2 gene.

In one study of Japanese males, rs1076560(A) alleles were 1.3 fold more associated with Alcoholism than the rs1076560(C) alleles. [PMID 17196743]

The DRD2 risk allele A was more prevalent in the alcoholic patients than in the healthy controls. These data identify rs1076560 as a potentially important variable in the development of alcoholism.
HapMap Phase III population frequencies for the A allele:
11% YRI (Yoruban)
12% TSI (Toscan)
14% ASW (Afram)
14% CEU (NW Euro)
27% GIH (Asian Indian)
36% MEX (Mexican)
40% JPT (Japanese)
45% CHB (Chinese)
46% CHD (Chinese)

Still not looking good. Next SNP:
The rs1799971(G) allele in exon 1 of the mu opiod receptor gene causes the normal amino acid at residue 40, asparagine, to be replaced by aspartic acid.

Carriers of at least one rs1799971(G) allele appear to have stronger cravings for alcohol than carriers of two rs1799971(A) alleles, and are thus hypothesized to be more at higher risk for alcoholism. [PMID 17207095]

Allele frequencies for rs1799971 (G):
4% ASW (Afram)
16% CEU (NW Euro)
18% TSI (Toscan)
20% MEX (Mexican)
33% CHB (Chinese)
42% GIH (Asian Indian)
46% JPT (Japanese)
47% CHD (Chinese)

By this point, birch should perhaps be thankful he's incapable of holding down a job long enough to buy that priced-to-sell Cambodian bride he has his eye on. Moving on:

Findings showed that SNP rs2232165 of the GHS-R1A gene was associated with heavy alcohol consumption (and therefore presumably alcohol dependence). SNP rs2948694 of the same gene as well as haplotypes of both the pro-ghrelin and the GHS-R1A genes were associated with an increased body mass in individuals consuming heavy amounts of alcohol.

Allele frequencies for rs2232165 (T):
8.3% YRI (Yoruban)
2.5% CEU (NW Euro)
0% CHB (Chinese)
0% JPT (Japanese)

Allele frequencies for rs2948694 (G):
33.8% JPT (Japanese)
32.4% CHB (Chinese)
9.6% YRI (Yoruban)
7.4% CEU (NW Euro)

But wait:
rs671 is a classic SNP, well known in a sense through the phenomena known as the "alcohol flush", also known as the "Asian Flush" or "Asian blush", in which certain individuals, often of Asian descent, have their face, neck and sometimes shoulders turn red after drinking alcohol.[PMID 6582480]

The rs671(A) allele of the ALDH2 gene is the culprit, in that it encodes a form of the aldehyde dehydrogenase 2 protein that is defective at metabolizing alcohol. This allele is known as the ALDH*2 form, and individuals possessing either one or two copies of it show alcohol-related sensitivity responses including facial flushing, and severe hangovers (and hence they are usually not regular drinkers). Perhaps not surprisingly they appear to suffer less from alcoholism and alcohol-related liver disease. [PMID 511165, PMID 16046871]
So much for "high executive function" saving Asians from the bottle. But only around a third of East Asians have genotypes associated with the flush reaction, and defective alcohol metabolism can't protect against opium (or cigarette) smoking. Unfortunately for birch:
"We have shown that Native Americans, who have a high rate of alcoholism, do not have these protective genes. The one that is particularly effective is a mutation of the gene for the enzyme aldehyde dehydrogenase, which plays a major role in metabolizing alcohol. The mutation is found very frequently in Chinese and Japanese populations but is less common among other Asian groups, including Koreans, the Malayo-Polynesian group, and others native to the Pacific Rim. "We've also looked at Euro-Americans, Native Americans, and Eskimos, and they don't have that gene mutation," says Li.
Amerindians also apparently have the world's highest frequencies of the DRD2 A1 allele, suggesting birch might be closer to the mark if he decided to blame his failure on his Amerindian ancestors.