Measuring differentiation among populations at different levels of genetic integration

This (provisional PDF) looks interesting. The not-unexpected conclusion seems to be that deltas between populations are larger when considering multi-locus genotypes (as opposed to population gene frequencies).

This new approach to the analysis of genetic differentiation among populations demonstrates that the consideration of gene associations within populations adds a new quality to studies on population differentiation that is overlooked when viewing only gene-pools.

Northern Euros whiter than Southern Euros

More ASHG 2008:

Frequency distribution and selection in 4 pigmentation genes in Europe. M. P. Donnelly, W. C. Speed, J. R. Kidd, A. J. Pakstis, K. K. Kidd Dept Genetics, Yale Univ Sch Med.

Pigmentation is one of the more obvious forms of variation in humans, particularly in Europeans where one sees more within group variation in hair and eye pigmentation than in the rest of the world. We studied 4 genes (SLC24A5, SLC45A2, OCA2 and MC1R) that are believed to contribute to the pigment phenotypes in Europeans. SLC24A5 has a single functional variant that leads to lighter skin pigmentation. Data on 83 populations worldwide (including 55 from our lab) show the variant (at rs1426654) has almost reached fixation in Europe, Southwest Asia, and North Africa, has moderate to high frequencies (.2-.9) throughout Central Asia, and has frequencies of .1-.3 in East and South Africa. The variant is essentially absent elsewhere. SLC45A2 also has a single functional variant (at rs16891982) associated with light skin pigmentation in Europe. Data on 84 populations worldwide show the light skin allele is nearly fixed in Northern Europe but has lower frequencies in Southern Europe, the Middle East and Northern Africa. In Central Asia the frequency of the SLC45A2 variant declines more quickly than the SLC24A5 variant. It is absent in both East and South Africa. In OCA2 we typed 4 SNPs (rs4778138, rs4778241, rs7495174, rs12913832) with a haplotype associated with blue eyes in Europeans. This haplotype shows a Southeastern to Northwestern pattern in Europe with frequencies of .25 (.05 homozygous) in the Adygei to .85 (.75 homozygous) in the Danes. In MC1R we typed 5 SNPs (rs3212345, rs3212357, rs3212363, C_25958294_10, rs7191944) that cover the entire MC1R gene and found a predominantly European haplotype that ranges in frequency from .35 to .65 in Europe, reaching its highest levels in Southwest Asia and Northwestern Europe. Extended Haplotype Heterozygosity (EHH) and normalized Haplosimilarity (nHS) show evidence of selection at SLC24A5 in not only our European and Southwest Asian populations but also our East African populations. Neither SLC45A2 or OCA2 showed evidence of selection in either test. MC1R did not show evidence of selection for our European specific haplotype but we did see some evidence both upstream and downstream in our nHS test in Europe.

Genetic differentiation in the UK

An ASHG 2008 poster abstract on the People of the British Isles project:

The need for a well characterised UK Control Population. B. Winney, A. Boumertit, R. Bowden, D. Davison, S. Day, E. Echeta, I. Evseeva, K. Nicodemus, S. Tonks, X. Yang, P. Donnelly, W. Bodmer Dept. Clinical Pharmacology, University of Oxford, Oxford, OX3 7DQ, UK.

Until the recent advent of Whole Genome Association studies (WGAs), there were problems replicating significant associations between gene variation and complex diseases in studies that were generally underpowered. Population structure was widely considered to be the most significant reason. A powerful approach to this problem may be to characterise genetically both the cases and controls. Individuals from the controls can then be chosen to match the cases so as to minimise the stochastic differences between the two populations. Such a well-characterised control population would complement the current generation of WGAs. Importantly, the samples would be a resource that could be key to the search for rare variants that can be associated with disease susceptibility. We are assembling a UK control population as a resource for future studies. It will comprise 3,500 samples (3,200 collected so far), which will have been carefully selected from throughout the UK. Rural regions are targeted to avoid the admixture observed in large urban environments and volunteers are sought who were born in the same place as their parents and grandparents to ensure historical integrity. The collection will be genotyped for around 3,000 markers, with the aim of identifying about 200 ancestrally informative markers, which will then be used to match controls to cases. DNA from the samples will then be made available as a resource for future studies. An initial pilot project on about 400-500 samples, using a variety of markers, indicates that this approach is valid. MC1R data suggest structure differentiating the Celtic Fringe from Eastern England, whilst NRY data show evidence of Norse incursions into Orkney. Preliminary analyses of a larger pilot project, comprising about 700 samples and 400 markers, including HLA, provide further signals of population structure when all the samples are combined. There is also evidence of differentiation between some pairs of populations and simple admixture analyses suggest that there is an east-west gradient of Anglo-Saxon ancestry across England.

Going by the website, the project is now up to 3453 samples collected (out of 3500 sought). Looking forward to further results. Should shut some people up.

Admixture analysis: 23andMe vs. deCODEme

Customers of deCODE and 23andMe may have noticed that deCODE seems to overestimate non-European ancestry in European-descended people. A 23andMe employee explains:

Both companies will walk along each of this person's chromosomes, and will tend to find that each stretch is found in all three reference populations, but is most likely from Europe. This would be expressed by Decode as a high chance, maybe 80-90%, that the stretch comes from Europe, and a smaller chance, maybe more like 5-10% apiece, that the stretch comes from Africa or Asia. Adding up all the stretches, you'll tend to get 80-90% European ancestry, and 5-10% African and Asian ancestry, each, for the Northern European -- this is consistent with the Decode chromosomal ancestry analyses of Northern Europeans that I've seen. This is a reasonable way to show the data.

The reasoning behind 23and Me's Ancestry Painting is, while it's true that each stretch is found all over the world, we know or are willing to assume that the stretch can only have come from /one/ population, and it chooses the most likely population. For our example Northern European, for just about every stretch along their genome, the single most likely origin will almost always be European, and would be expressed in final ancestry proportion estimates of about 100% European, and about 0% African and Asian.

This is how Ancestry Painting and Decode can end up with different total ancestry estimates for the same person.

So, even leaving aside the question of data quality, deCODE's claims regarding James Watson's ancestry are revealed to be a hoax. Watson's alleged complement of 16% "black genes" was compared to a figure (originating with Kari Stefansson, I believe) of "no more than 1%" for "most people of European descent" -- a number clearly not arrived at using deCODE's platform. In fact, deCODE's technique can be expected to give most if not all Europeans implausibly high readings of non-European ancestry.

SNPs better than STRs for inferring population structure

Another ASHG 2008 abstract:

Inferring Human Population Structure: STR or SNP? S. Xu1, L. Jin1,2 1) Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China;; 2) Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.

Both microsatellites (STRs) and single nucleotide polymorphisms (SNPs) have played important roles in inferring population structure. With the availability of genome-wide STR and SNP data for the same collection of world-wide human population samples (HGDP-CEPH panel), we now have the opportunity to compare the usefulness of the two types of data in inferring population structure. We selected the same set of 940 unrelated HGDP individuals in which both 783 STRs and 650,000 SNPs were genotyped, and performed both classical (phylogenetic and principal component) analysis and STRUCTURE analysis. We found for all analyses, with the same allele number, SNP data perform better and generate more reasonable results than STR data. Notably, a) SNP data offer superior clustering of individuals and populations; b) the phylogenetic tree reconstructed using SNP data is consistent better with the geographical distribution of populations; c) SNP data reveals fine structures and reasonable admixture pattern in STRUCTURE analysis for both full samples and subset of samples, but STR can not.

Yes, Rienzi, if it wasn't already obvious, thousands of SNPs beat 32 STR loci. Why would anyone "agonize" over an inconsequential result?

Breeding sex ratio higher in Europe than sub-Saharan Africa

Another blow to Peter Frost's goofy-ass theories.

One interpretation of these results is that there is strong evidence for an unequal female and male Ne in at least three of our six populations, with estimates of the breeding sex ratio (i.e., the effective size of females to males) ranging from 2.1 in the San to 12.5 in the Basque.

[Hammer MF, Mendez FL, Cox MP, Woerner AE, Wall JD (2008) Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity. PLoS Genet 4(9): e1000202. doi:10.1371/journal.pgen.1000202]

Figure 2 shows Nx/Na is higher in Basques than in any of the sampled African populations (Mandenka, Biaka, and San).

"Americans" are not homogeneous

Via Dienekes, another ASHG 2008 abstract. This research seems to reproduce earlier findings of separate, distinct clusters among "European Americans":

Ethnicity-Confirmed Genetic Structure in New Hampshire.

Genetic population structure is known to result from shared ancestry. Though there have been several studies of genetic structure within and among different geographic regions and ethnic groups, little is known of the genetic structure of highly admixed US populations or whether the structure is concordant with self-reported ancestry. In this study, 1529 single nucleotide polymorphisms (SNPs) from 864 healthy control individuals from New Hampshire were measured as part of a bladder cancer epidemiology study. The SNPs were from approximately 500 cancer susceptibility genes scattered throughout the genome. Of these, 960 Tag SNPs were used to cluster individuals using the Structure algorithm for between 2 and 5 subpopulations. Subtle genetic structure was found, suggesting the appropriate number of subpopulations to be either 4 or 5 (FSTs 4 populations: 0.0377, 0.0399, 0.0363, 0.0340; 5 populations: 0.0452, 0.0536, 0.0585, 0.0534, 0.0521). We coded the individuals self-reported ancestries in a genotype fashion (i.e. 0= not reporting that ancestry, 1= reporting part that ancestry, 2= reporting only that ancestry) and conducted a Spearmans rank correlation between each ancestry and the structure q value, which represents the proportion of an individual that originated from a certain genetic subpopulation. Those of Russian, Polish and Lithuanian ancestry most consistently clustered together. The ancestry results support either 4 or 5 subpopulations. In order to investigate linkage disequilibrium (LD), the complete set of SNPs from the 7 most densely genotyped genes were used to make haploview plots between the different groups. The results vary by gene, though for one gene in particular, GHR, the results are very different for 4 subpopulations. These results suggest that despite New Hampshires admixture and presumed homogeneity, there are 4 or 5 distinct genetic subgroups within the population that can be linked to self-reported ancestry and display differences in patterns of LD.

Previous research has identified at least three clusters among "European Americans", corresponding to Northern and Central European, Southern European, and Ashkenazi Jewish ancestry groups. I'm curious exactly which 4 or 5 subgroups have been identified here. From the context, it's not immediately clear whether the Russian/Polish/Lithuanian cluster consists of ethnic E. Euros or Ashkenazi Jews.

Greater genetic diversity in S. Europe due in part to African ancestry

Recent papers using genome-wide SNP data have indicated higher levels of haplotype diversity in Southern vs. Northern Europe. The authors have typically attributed this finding to south to north migrations within Europe. While such migrations no doubt must have occurred (at some remote date), it seems strange to me to ignore the subsequent extra-European gene flow into Southern Europe which also undoubtedly occurred. An ASHG 2008 abstract, after repeating the intra-European migration theory, includes some additional observations:

Interestingly, we find that within Europe there is a south-to-north gradient with decreasing levels of haplotype diversity moving north, consistent with south to north migrations. We also find that the southwestern European sample has higher haplotype diversity than the southeastern European sample. Additionally, a higher proportion of haplotypes are shared between the southwestern European sample and the Yoruba sample than between southeastern European sample and the Yoruba sample. These two patterns are consistent with recent admixture across the Mediterranean from Northern Africa.

(Inference of human demographic parameters using haplotype patterns from genome-wide SNP data.)

Increased genetic affinity between SW Euros and Yorubans is consistent with mtDNA data indicating sub-Saharan admixture in Iberia (Spain and particularly Portugal) at levels higher than typically observed elsewhere in Europe. My guess is a similar analysis would show an increased similarity between SE Euros and NE Africans -- as well as between SE Euros and Middle Easterners, obviously.

Digit ratio not a proxy for prenatal androgen exposure?

Selective Breeding for a Behavioral Trait Changes Digit Ratio:

The ratio of the length of the second digit (index finger) divided by the fourth digit (ring finger) tends to be lower in men than in women. This 2D:4D digit ratio is often used as a proxy for prenatal androgen exposure in studies of human health and behavior. For example, 2D:4D ratio is lower (i.e. more “masculinized”) in both men and women of greater physical fitness and/or sporting ability. Lab mice have also shown variation in 2D:4D as a function of uterine environment, and mouse digit ratios seem also to correlate with behavioral traits, including daily activity levels. Selective breeding for increased rates of voluntary exercise (wheel running) in four lines of mice has caused correlated increases in aerobic exercise capacity, circulating corticosterone level, and predatory aggression. Here, we show that this selection regime has also increased 2D:4D. This apparent “feminization” in mice is opposite to the relationship seen between 2D:4D and physical fitness in human beings. The present results are difficult to reconcile with the notion that 2D:4D is an effective proxy for prenatal androgen exposure; instead, it may more accurately reflect effects of glucocorticoids, or other factors that regulate any of many genes.

Yan RHY, Malisch JL, Hannon RM, Hurd PL, Garland T Jr (2008) Selective Breeding for a Behavioral Trait Changes Digit Ratio. PLoS ONE 3(9): e3216. doi:10.1371/journal.pone.0003216

State-level differences in personality

Update (9/14/08): Vanishing American comments; full text (pdf, final version).

The surprising results:

New York is home to the most neurotic and unfriendly people in American while North Dakota is where the nicest people live, according to a Cambridge University "personality map" of the USA.

[. . .]

Researchers created the first ever map of its kind is based on the results of a six year online survey of 620,000 people.

They claim it reveals how certain types of people are more likely to live and flourish in different parts of the country and showed links between personality traits and social phenomenon, like crime rates.

[. . .]

The report, "The Geography Of Personality; A Theory of the Emergence, Persistence and Expression of Geographic Variation in Basic Traits" is published in the journal, Perspectives On Psychological Science.

Key findings:

EXTRAVERSION
Personality traits: Sociable, energetic and enthusiastic

High-scoring states: North Dakota, Wisconsin, District of Columbia, Nebraska, Minnesota, Georgia, South Dakota, Utah, Illinois, Florida

Low-scoring states: Vermont, Washington, Alaska, New Hampshire, Maryland, Idaho, Virginia, Oregon, Montana, Massachusetts

AGREEABLENESS
Personality traits: Warm, compassionate, co-operative and friendly.

Highest-scoring states: North Dakota, Minnesota, Mississippi, Utah, Wisconsin, Tennessee, North Carolina, Georgia, Oklahoma, Nebraska.

Lowest-scoring states: New York, Nevada, Wyoming, District of Columbia, Alaska, Maine, Rhode Island, Virginia, Connecticut, Montana.

CONSCIENTIOUSNESS
Personality traits: Dutiful, responsible, self-disciplined.

Highest-scoring states: New Mexico, North Carolina, Georgia, Utah, Kansas, Oklahoma, Nebraska, Florida, Arizona, Missouri.

Lowest-scoring states: Wyoming, Rhode Island, Hawaii, Maine, Alaska, Connecticut, New Jersey, New Hampshire, Massachusetts, New York.

NEUROTICISM
Personality traits: Anxious, stressful and impulsive.

Highest-scoring states: West Virginia, Rhode Island, New York, Mississippi, New Jersey, Pennsylvania, Kentucky, Louisiana, Ohio, Arkansas.

Lowest-scoring states: Alaska, Oregon, South Dakota, Colorado, Utah, Washington, Arizona, Nebraska, North Dakota, Nevada.

OPENNESS
Personality traits: Curious, intellectual, creative.

Highest-scoring states: District of Columbia, New York, Oregon, Massachusetts, Washington, California, Vermont, Colorado, Nevada, Maryland.

Lowest-scoring states: Wisconsin, Alabama, Alaska, Wyoming, North Dakota, Hawaii, Kentucky, Nebraska, Iowa, Delaware.

Manuscript (pdf). Abstract.

Body type and perceived personality

The perceived associations of the participants in this study are reminiscent of--though not identical to--the associations argued for by Sheldon.

Through the use of many photographs and measurements of nude figures (mainly Ivy League students), Sheldon assigned people into three categories of body types in the 1940s: endomorphic, mesomorphic, and ectomorphic. He also assigned personality traits to the body types as well. Endomorphics had fat, soft, and round body types, and their personality was described as relaxed, fond of eating, and sociable. Mesomorphics were muscular, rectangular, strong, and personality-wise were filled with energy, courage, and assertive tendencies. Ectomorphics were thin, long, fragile, as well as brainy, artistic, and introverted; they would think about life, rather than consuming it or acting on it.

This study looks at perceptions of six different body forms (three different body types, with and without abdominal obesity):

Physical characters were associated with the appropriate body forms as expected. The physical traits strong, rough and tough and physically aggressive were associated with the muscular non-obese [M−] figure. Lethargic was associated with F+. Disease prone was significantly associated with L− [lean, without central obesity] on the one hand and F+ [feminine, with central obesity] on the other indicating that people negatively associate both the extremes with health. The trait swift was also strongly associated with L−. The traits that are not obviously physical were also strongly associated with certain body forms. Brave, conscious about looks, influential, dominating, status conscious, modern and confident were associated with M−; physical risk avoider, money minded, political, rich, stupid, selfish and greedy were associated most strongly with F+; friendly, intelligent, methodical, business risk avoider, successful, loving, kind, and honest were associated with F− [feminine without central obesity]; and L− was the commonest choice for swift, physical risk avoider, talkative and the trait depressed was associated with L+ [table 1].

The abstract:

PLoS ONE 3(9): e3187. doi:10.1371/journal.pone.0003187

Obesity as a Perceived Social Signal

Manasee Mankar et al.

Fat accumulation has been classically considered as a means of energy storage. Obese people are theorized as metabolically ‘thrifty’, saving energy during times of food abundance. However, recent research has highlighted many neuro-behavioral and social aspects of obesity, with a suggestion that obesity, abdominal obesity in particular, may have evolved as a social signal. We tested here whether body proportions, and abdominal obesity in particular, are perceived as signals revealing personality traits. Faceless drawings of three male body forms namely lean, muscular and feminine, each with and without abdominal obesity were shown in a randomized order to a group of 222 respondents. A list of 30 different adjectives or short descriptions of personality traits was given to each respondent and they were asked to allocate the most appropriate figure to each of them independently. The traits included those directly related to physique, those related to nature, attitude and moral character and also those related to social status. For 29 out of the 30 adjectives people consistently attributed specific body forms. Based on common choices, the 30 traits could be clustered into distinct ‘personalities’ which were strongly associated with particular body forms. A centrally obese figure was perceived as “lethargic, greedy, political, money-minded, selfish and rich”. The results show that body proportions are perceived to reflect personality traits and this raises the possibility that in addition to energy storage, social selection may have played some role in shaping the biology of obesity.

23 and Me v2: new markers / major price reduction

I make no endorsement, but this may be of interest to some.

23andMe Democratizes Personal Genomics With New Analytical Platform

23andMe is proud to announce another step toward our goal of democratizing genetic information by giving as many people as much information as possible about their DNA.

With the introduction of v2, our next-generation analytical platform, 23andMe customers will have access to an even more powerful set of the SNPs we use to probe their unique genetic composition. And thanks to advances by Illumina, the provider of our genetic analysis technology, that information will now be available at the reduced price of $399. By making genetic data more affordable and accessible, we hope this development will spur the evolution of personal genomics as a potent force not just in science but also in medicine and everyday life.

Sexual imprinting in humans

BBC article:

Page last updated at 07:05 GMT, Wednesday, 3 September 2008 08:05 UK

Women pick men who look like dad

Women tend to choose husbands who look like their fathers, a study shows.

And it works both ways - the women in the Proceedings B study also resembled their partner's mother.

The latest work from the University of Pécs in Hungary provides yet more evidence for the phenomenon, known as sexual imprinting.

[. . .]

They found significant correlations between the young men and their fathers-in-law, especially on facial proportions belonging to the central area of face - nose and eyes.

Women also showed resemblance to their mothers-in-law in the facial characteristics of their lower face - lips and jaw.

Lead researcher Tamas Bereczkei said: "Our results support the sexual imprinting hypothesis which states that children shape a mental template of their opposite-sex parents and search for a partner who resembles that perceptual schema."

[. . .]

Experts say there may be an advantage to selecting a mate somewhat similar to themselves genetically.

Dr Lynda Boothroyd from the University of Durham, a psychologist who has carried out similar research, said: "There is an argument that a certain degree of similarity makes people more fertile and genetically compatible."

The abstract:

Facialmetric similarities mediate mate choice: sexual imprinting on opposite-sex paents
DOI 10.1098/rspb.2008.1021
Online Date Tuesday, September 02, 2008

Tamas Bereczkei, Gabor Hegedus, Gabor Hajnal

Former studies have suggested that imprinting-like processes influence the shaping of human mate preferences. In this study, we provide more direct evidence for assessing facial resemblance between subjects' partner and subjects' parents. Fourteen facial proportions were measured on 312 adults belonging to 52 families, and the correlations between family members were compared with those of pairs randomly selected from the population. Spouses proved to be assortatively mated in the majority of measured facial proportions. Significant correlations have been found between the young men and their partner's father (but not his mother), especially on facial proportions belonging to the central area of the face. Women also showed resemblance to their partner's mother (but not to their father) in the facial characteristics of their lower face. Replicating our previous studies, facial photographs of participants were also matched by independent judges who ascribed higher resemblance between partners, and subjects and their partners' opposite-sex parents, compared with controls. Our results support the sexual imprinting hypothesis which states that children shape a mental template of their opposite-sex parents and search for a partner who resembles that perceptual schema. The fact that only the facial metrics of opposite-sex parents showed resemblance to the partner's face tends to rule out the role of familiarity in shaping mating preferences. Our findings also reject several other rival hypotheses. The adaptive value of imprinting-related human mating is discussed, and a hypothesis is made of why different facial areas are involved in males' and females' search for resemblance.

Keywords
facial resemblance, sexual imprinting, homogamy

"Race" and European genetic substructure

The New Scientist article on the work of Novembre et al. asserts the following (my emphasis):

By reading single-letter DNA differences in the genomes of thousands of Europeans, researchers can tell a Finn from a Dane and a German from a Brit. In fact a visual genetic map mirrors the geopolitical map of the continent, right down to Italy's boot.

"It tells us that geography matters," says John Novembre, a population geneticist at the University of California, Los Angeles, who led one of the studies. Despite language, immigration and intermarriage, genetic differences between Europeans are almost entirely related to where they were born.

This, however, does not mean that the citizens of each European nation represent miniature races. "The genetic diversity in Europe is very low. There isn't really much," says Manfred Kayser, a geneticist at Erasmus University Rotterdam in the Netherlands, who led the other study.

The question of how genetic diversity in Europe relates to national borders is an empirical one. Finns probably constitute a local "race" or subrace (or two) distinict from other Europeans, while -- at the national level -- the Swiss apparently do not.

But I strongly take issue with the suggestion that "low" levels of genetic diversity are of no taxonomic significance. The paper under discussion (and many before it) pretty clearly demonstrate the opposite. One can imagine plenty of forensic, genealogical, preservationist, and other applications which may benefit from knowledge of these "small" genetic differences (and those which remain to be discovered). Precisely how one chooses to (sub-)classify Europeans will depend on one's objectives and the available statistical tools and data, but the existence of substructure is not in question. Choosing to call the resulting sub-European taxonomic units "miniature races", "subraces", "local types", or so on, is merely a matter of semantics.

Some relevant discussion of the race concept, from Anthropology A to Z [1]:

But race is, from the biological point of view, not a static, but a dynamic condition. Within the constantly changing movement of "life" it represents a breeding unit continously modifying itself, by infinitesimal degrees, through mtuations. This mobile condition was most aptly formulated by the American geneticist Dobzhansky, who said: "Race is a process." His statement at last fits the concept of race meaningfully into the history of life, and at the same time makes race understandable as the smallest ever-changing taxonomic unit (genetic population) by which we can interpret the total course of organic evolution.

To identify a race, it is theoretically sufficient to note the prevalence of a new gene and the consequent characteristic trait or traits that occur predominantly in a particular genetic population and distinguish it from neighboring populatins. But the one-trait basis of differentiation, considering the vast numbers of genes in mammals alone, would lead to an unjustifiable multiplicity of taxonomic units such as species and subspecies. Therefore, Fischer's early postulate -- of the gene groups in man which unite to produce certain characteristic patterns of traits, thus permitting a clear differentation of the various genetic poulations of a species within a large framework -- has been used as a basis for the determination and classification of races. [. . .]

There is some disagreement concerning the numbers of races, even though the races are always differentiated in accordance with the same basic principles of genetics. The differences in the estimated numbers result mostly from differences in emphasis. Some writers tend to base their estimate on the number of observable regional genetic populations; others are concerned with more general considerations. Of course, the more local races that are subsumed under related super-regional entities, or "major races" (i.e., Caucasoid, Mongoloid, Congoid), the smaller the number of single traits withing each characteristic combination that can be taken into consideration. [n/a: Conversely, as we become technically able to measure very large numbers of traits (e.g., hundreds of thousands of SNPs using gene chips), we can refine classifications.] At at the same time, authors will differ in assigning local groups to one of the other major race, especially in the contact zones. These differences in taxonomy and in point of view do not militate, however, against the validity of the definition of race itself; they arise solely from the fact that various writers evaluate racial traits differently and assign a different significance to them. Such conceptual differences also underline the fact that in talk about races we are dealing with developing life, with processes not easily subsumed under the necessarily rigid schemes which our need for methodical classification demands.

[pp. 4-5]

A race is a group of individuals who belong to the same reproductive community, and are characterized by the possession of certain genes that differ from those corresponding populations of the same species. The original gene pool of a population is steadily, but very slowly, enriched through mutations, of which only a limited number will survive selection pressures over the long term. For the accumulation of favorable (partially new) genes within a population to an extent that might become characteristic, restriction of propagative activity for a certain time is necessary, so that the gene flow between it and neighboring genetic populations is stopped. This process is called isolation. Its result depends largely on the duration and the severity of the mating restrictions -- how long the gene flow in and out of the propagation circle is actually stoppped. This leads us to a prerequisite for the formation of a race. It is not possible for several new races to develop sympatrically -- that is, from the same original population and simultaneously in the same geographic space. The formation of a race can occur only allopatrically -- that is, in separate living areas, or isolates. The original population, just before splitting into daughter populations which in turn become isolated, was essentially uniform in the racial sense, and the daughter populations have come out of the same gene pool. Differentiation starts with the actual isolation. If differentiation continues for a certain span of time and a corresponding number of generations, the phylogenetic direction is established.

The isolation of populations is normally due to geographic barriers -- seas, deserts, dry prairies, obstructive forests or tropical-rain-forest zones, edge locations (peninsulas or continental tips).

[pp. 82-83]

Thus the foundations were laid for what seems almost self-evident to us today; namely, that races are groups of individuals with similar gene compositions, which were built from mutant alleles that combined in various ways and became differentiated in their geographic regions, but which may be disintegrated in the process of cross-breeding. Difference in race does not constitute a barrier to the production of offspring. It became possible to make the process of race formation increasingly understandable in terms of cause and effect. Genes go through mutation; then, through the mechanism of natural selection, they are either increased in frequency, becoming part of combinations in characteristic concentrations, or else they fail to perpetuate themselves.

[pp. 116-117]

[1] Heberer, Gerhard, Carleton S. Coon, Edward E. Hunt, Gottfried Kurth, and Ilse Schwidetzky-Roesing. 1963. Anthropology A to Z: Based on the work of Gerhard Heberer, Gottfried Kurth, and Ilse Schwidetzky-Roesing. New York: Grosset & Dunlap.

Jewish DNA

In Commentary:

In a class by itself is the mitochondrial DNA of Ashkenazi women. It does not correlate closely with the DNA of non-Jewish women in Western, Central, or Eastern Europe and it has a large Middle Eastern component. Yet in their maternal lineage, Ashkenazim, too, exhibit a strong “founder effect.” Over forty percent of them, a 2005 study showed, descend from just four “founding mothers” having Middle-Eastern-profile mitochondrial DNA. Since Ashkenazi Y-chromosome DNA does not exhibit so dramatic a founder’s effect, one can assume that Ashkenazi Jewry, too, began with the migration of a preponderantly male group of Jews to new territories. Because these territories, however, were more contiguous with the old ones than were far-flung regions like Bukhara or Yemen, the men were more able to import wives from existing Jewish communities and less dependent on marrying local Gentiles.

But where did Ashkenazi Jewry, male and female alike, derive from if not from the Rhineland? One possibility that is more consistent with the linguistic data is that it entered southern Germany from northern Italy and pushed further north from there into the Slavic-speaking areas of Europe. Another is that Jews migrated to Slavic lands from the Byzantine Empire. These hypotheses, which are not mutually exclusive, can now claim a measure of scientific support, since the Y chromosomes of Ashkenazi Jews have more in common with those of Italians and Greeks than with those of West Europeans.

[. . .]

As far as much of the rest of the world is concerned, biological Jewishness has always been an embarrassing anachronism—at least ever since the time of the Roman Empire and early Christianity. For the most part, Jews have nevertheless managed to go their own unembarrassed way. The genetic record shows that they have on the whole succeeded.

[Hillel Halkin, "Jews and Their DNA", September 2008]

Novembre working on admixture analysis

The lead author of the recent European genetic structure paper comments in Technology Review:

Even so, Novembre says that he plans to extend this sort of research to cover larger parts of the world and individuals of mixed ancestry. "At the moment, if you have mixed grandparent ancestry you appear between the set of countries where the grandparents come from," he says. "So if they are part Italian and part British, they would appear in Switzerland. But we are working on algorithms that will be able to infer grandparent ancestry and get around this."

Eventually, this sort of research is likely to be picked up by the growing number of companies offering DNA home tests over the Internet to people wishing to trace their genealogy. At the moment, these services tend to offer fairly rough pictures of one's origins. But as the microarray technology becomes cheaper and the statistical software used to map it becomes more sophisticated, these kinds of services should greatly improve, Novembre says.

Exactly what I've been saying for years.

Another European genetic structure paper

I was alerted to this study through a post by one of gnxp's competent (i.e., most likely white) posters, and I haven't yet read it. The findings appear to be similar to those of the study released earlier this month (I would guess--based on another recent paper by some of the same authors--they even use some of the same samples). But there are a few new data points: samples from Latvia, Russia, Ukraine, Cyprus, and Turkey show up in the plot. Contrary to the speculation of some, Balts and Russians appear to be even more distant than Finns on PC2, rather than intermediate between Finns and other Europeans.

Update: Per the supplementary material, the sample sizes for Finland, Slovakia, and Ukraine are only 1 each, and 6 for Russia.

Nature advance online publication 31 August 2008 | doi:10.1038/nature07331; Received 30 May 2008; Accepted 12 August 2008; Published online 31 August 2008

Genes mirror geography within Europe

John Novembre et al.

Understanding the genetic structure of human populations is of fundamental interest to medical, forensic and anthropological sciences. Advances in high-throughput genotyping technology have markedly improved our understanding of global patterns of human genetic variation and suggest the potential to use large samples to uncover variation among closely spaced populations1, 2, 3, 4, 5. Here we characterize genetic variation in a sample of 3,000 European individuals genotyped at over half a million variable DNA sites in the human genome. Despite low average levels of genetic differentiation among Europeans, we find a close correspondence between genetic and geographic distances; indeed, a geographical map of Europe arises naturally as an efficient two-dimensional summary of genetic variation in Europeans. The results emphasize that when mapping the genetic basis of a disease phenotype, spurious associations can arise if genetic structure is not properly accounted for. In addition, the results are relevant to the prospects of genetic ancestry testing6; an individual's DNA can be used to infer their geographic origin with surprising accuracy—often to within a few hundred kilometres.

Also of interest, from the gnxp post:

These authors also develop a model that does reasonably well at predicting the country of origin of an individual based on genetics alone.
[ . . .]
The method the authors develop for predicting an individual's country of origin from genetics are only a beginning for this kind of application of genetic data. They note that the SNP chip used in the study only includes common variation, while rare variants are likely to be much more geographically restricted (and thus more informative in this kind of analysis). The limits to the resolution of these sorts of methods are likely to be very fine indeed; the authors note that, even with this panel, they're able to distinguish with some confidence individuals that are from the German, Italian, and French-speaking parts of Switzerland. With full resequencing data, it's likely that even the precise village of origin of an individual will be predictable from genetics alone.