June 30, 2009

Uyghurs as an admixed not source population (Xu et al. 2009)

This paper is interesting not so much because it estimates admixture in Uyghurs (click on the post label for previous studies on the topic), but because it explicitly rejects the hypothesis that they are a source ("donor") population.

If a population has substantial genetic variation which overlaps with that of two other groups, then there are two possible interpretations:
  1. It represents the population from which the other two groups sprang, or at least contributed genes to both of them
  2. It represents a mixture of the two other groups
What this paper does, is to show that Uyghurs are best explained as a mixture of Caucasoids and Mongoloids (#2) rather than #1.

Molecular Biology and Evolution, doi:10.1093/molbev/msp130

Haplotype Sharing Analysis Showing Uyghurs Are Unlikely Genetic Donors

Shuhua Xu et al.


The Uyghur are a group of people primarily residing in Xinjiang of China which is geographically located in Central Asia, from where modern humans were presumably spread in all directions reaching Europe, east and northeast Asia about 40 kya. A recent study suggested that the Uyghur are ancestry donors of the East Asian gene pool. However, an alternative hypothesis, i.e. the Uyghur is an admixture population with both East Asian (EAS) and European (EUR) ancestries is also supported by our previous studies. To test the two competing hypotheses, here we conducted a haplotype sharing analysis based on empirical and simulated data of high density single nucleotide polymorphisms (SNPs). Our results showed that more than 95% of Uyghur (UIG) haplotypes could be found in either East Asian (EAS) or European (EUR) populations, which contradicts the expectation of the null models assuming that UIG are donors. Simulation studies further indicated that the proportion of UIG private haplotypes observed in empirical data is only expected in alternative models assuming that UIG is an admixture population. Interestingly, the estimated ancestry contribution of 44%:56% (EAS:EUR) based on haplotype sharing analysis is consistent with our previous estimation with STRUCTURE analysis. Although the history of Uyghurs could be complex, our method is explicit and conservative in rejecting the null hypothesis. We concluded that the gene pool of modern Uyghurs is more likely a sole recipient with contribution from both EAS and EUR.


June 28, 2009

Humans capable of (but not good at) assessing relatedness from faces

Proceedings of the Royal Society B doi: 10.1098/rspb.2009.0677

Human ability to detect kinship in strangers' faces: effects of the degree of relatedness

Gwenaël Kaminski et al.


The resemblance between human faces has been shown to be a possible cue in recognizing the relatedness between parents and children, and more recently, between siblings. However, the general inclusive fitness theory proposes that kin-selective behaviours are also relevant to more distant relatives, which requires the detection of larger kinship bonds. We conducted an experiment to explore the use of facial clues by ‘strangers’, i.e. evaluators from a different family, to associate humans of varying degrees of relatedness. We hypothesized that the visual capacity to detect relatedness should be weaker with lower degrees of relatedness. We showed that human adults are capable of (although not very efficient at) assessing the relatedness of unrelated individuals from photographs and that visible facial cues vary according to the degree of relatedness. This sensitivity exists even for kin pair members that are more than a generation apart and have never lived together. Collectively, our findings are in agreement with emerging knowledge on the role played by facial resemblance as a kinship cue. But we have progressed further to show how the capacity to distinguish between related and non-related pairs applies to situations relevant to indirect fitness.


June 27, 2009

A colorful view of the potency of skulls and the reality of race

(updated June 30)

I used distruct to create a graphical display of the clusters revealed by my 2004 model-based clustering of 2,504 human skulls on 57 metrical variates. As mentioned in the original article, these traits are enough to distinguish some human races (e.g., Caucasoids=Norse, Zalavar, Berg, Egyptian), or even individual populations (e.g., Eskimo, Buriat, or Bushmen).

Of course, some skulls don't fall in the right cluster, but this is to be expected both due to the state of the original collections (*) and due to the plasticity of the human skull that may create false associations.

But, on the whole, the clusters emerge as distinct and unmistakable entities; this level of resolution at a global scale is only possible -if at all- with hundreds of thousands of genetic markers, yet 57 linear measurements pretty much do the same trick.

One can only imagine what would be possible if someone takes a 3D scanner around the world to visit the same museum collections that Howells did several decades ago. But, perhaps, physical anthropologists have better things to do these days than discovering differences between human populations...

(*) For example, W.W. Howells noted in his work that one of the American skulls obviously belonged to a white settler.

UPDATE (June 30)

Please consult the original article for details on the populations and the methodology used. Note that K=14 is the number of clusters which maximizes the Bayes Information Criterion, but it is by no means the end of the story. For even higher K, some populations can be further separated, although some of them (e.g., Europeans) never split into fairly "clean" clusters with these 57 variables.

Below are all the results for K=2 to K=14. As with Rosenberg et al. (2002) and the work that followed it, the first split contrasts East Asians with Eurafricans. It is important to note that the pattern of successive splits should not be interpreted as a phylogeny of human populations, i.e., a history of human subdivisions.

June 26, 2009

Predomestication grain deposits in Jordan

See also: Crop domestication didn't happen overnight or in one place

Proc Natl Acad Sci U S A. 2009 Jun 22.

Evidence for food storage and predomestication granaries 11,000 years ago in the Jordan Valley.

Kuijt I, Finlayson B.

Food storage is a vital component in the economic and social package that comprises the Neolithic, contributing to plant domestication, increasingly sedentary lifestyles, and new social organizations. Recent excavations at Dhra' near the Dead Sea in Jordan provide strong evidence for sophisticated, purpose-built granaries in a predomestication context approximately 11,300-11,175 cal B.P., which support recent arguments for the deliberate cultivation of wild cereals at this time. Designed with suspended floors for air circulation and protection from rodents, they are located between residential structures that contain plant-processing instillations. The granaries represent a critical evolutionary shift in the relationship between people and plant foods, which precedes the emergence of domestication and large-scale sedentary communities by at least 1,000 years.


Quantifying the effect of different aspects of the Mediterranean diet: the EPIC study

BMJ. 2009 Jun 23;338:b2337. doi: 10.1136/bmj.b2337.

Anatomy of health effects of Mediterranean diet: Greek EPIC prospective cohort study.

Trichopoulou A, Bamia C, Trichopoulos D.

OBJECTIVE: To investigate the relative importance of the individual components of the Mediterranean diet in generating the inverse association of increased adherence to this diet and overall mortality. DESIGN: Prospective cohort study. SETTING: Greek segment of the European Prospective Investigation into Cancer and nutrition (EPIC). PARTICIPANTS: 23 349 men and women, not previously diagnosed with cancer, coronary heart disease, or diabetes, with documented survival status until June 2008 and complete information on nutritional variables and important covariates at enrolment. MAIN OUTCOME MEASURE: All cause mortality. RESULTS: After a mean follow-up of 8.5 years, 652 deaths from any cause had occurred among 12 694 participants with Mediterranean diet scores 0-4 and 423 among 10 655 participants with scores of 5 or more. Controlling for potential confounders, higher adherence to a Mediterranean diet was associated with a statistically significant reduction in total mortality (adjusted mortality ratio per two unit increase in score 0.864, 95% confidence interval 0.802 to 0.932). The contributions of the individual components of the Mediterranean diet to this association were moderate ethanol consumption 23.5%, low consumption of meat and meat products 16.6%, high vegetable consumption 16.2%, high fruit and nut consumption 11.2%, high monounsaturated to saturated lipid ratio 10.6%, and high legume consumption 9.7%. The contributions of high cereal consumption and low dairy consumption were minimal, whereas high fish and seafood consumption was associated with a non-significant increase in mortality ratio. CONCLUSION: The dominant components of the Mediterranean diet score as a predictor of lower mortality are moderate consumption of ethanol, low consumption of meat and meat products, and high consumption of vegetables, fruits and nuts, olive oil, and legumes. Minimal contributions were found for cereals and dairy products, possibly because they are heterogeneous categories of foods with differential health effects, and for fish and seafood, the intake of which is low in this population.


June 25, 2009

Relationship of cranial robusticity to cranial form, geography and climate

UPDATE (June 30)
This paper investigates the relationship between cranial robusticity and a number of factors said to underlie it, including cranial size and shape, climate, and neutral genetic variation. Genetic similarity between populations was assessed using the well-known Rosenberg et al. dataset from 2002.

From the paper:
If the robusticity traits are the subject of neutral evolutionary processes, then the distance matrix based on these characters will be strongly correlated with that based on the neutral genetic markers (microsatellite data) (e.g., Roseman, 2004).


A functional hypothesis that specifically implicates forces associated with mastication would be supported by a stronger correlation between cranial robusticity and the MLS rather than CLS as the former more directly captures morphology associated with mastication, although it is also possible that changes in overall
cranial shape may be related to mastication. A strong relationship between cranial robusticity and the climatic variables would support the influence of the local environment on the development of cranial robusticity.
Note: CLS/MLS=cranial/masticatory landmark set.

First of all, it turns out that Robusticity traits are closely correlated with each other, suggesting that they do indeed capture an overall factor of "Robusticity" rather than being independent from each other. A notable exception is occipital torus, which is not significantly related to other robusticity traits.

Next up, principal components analysis was performed:
In deciding how many PCs to evaluate, we applied the common Guttman-Kaiser criterion (keep all PCs with eigenvalues [1.0; Kaiser, 1961), which results in the retention of the first three components. However, a more conservative criterion, the Scree Plot (Cattell, 1966), suggests that only PC 1 should be retained. Although PC 1 accounted for a proportionally larger percentage of the total variance in cranial robusticity (27%), the second and third components each explain 11% of the variance and may indicate that there is more than one relevantpattern of cranial robusticity (Table 10).


The first PC reflects overall levels of robusticity as all 11 traits load positively (Table 10), although the occipital torus has a loading near zero. ... The groups with the highest median (and mean) scores are New Zealand, Australia/Tasmania, North
America, and South America, while the lowest scores belong to Mongolia, East Asia, Inuit, and Khoe-San (see Fig. 3).


Males score significantly higher than females on PC 1 within all groups except the East and West Europeans, East and West Africans, and Khoe-San (Table 11), but males scored higher on average than females even in those groups that did not reach statistical significance
Interestingly, in the test for sex differences in PC1, Europeans differed from each other. Southern Europeans (Peloponnesian Greeks and Italians) were most dimorphic, and West Europeans (Austrians and Germans) were least.

From the paper:
The second PC has both high positive (occipital torus, rounding of orbits) and high negative (sagittal keel, anterior mastoid, bregmatic eminence) loadings ... The highest scoring groups on PC 2 are East Asia, Mongolia, Australia/Tasmania, and the Khoe-San, while East Africa, West Africa, and Eastern Europe have low scores (Fig. 3a). Many of the pair-wise contrasts between the highest and lowest scoring groups are significant, particularly those that include East Africa, East Asia, and Mongolia (Table 10). It appears that while the East Asian populations are gracile overall (see above), they do display some characters typically considered as ‘‘robust’’ (e.g., the occipital torus).


The third PC also has a mixed pattern of positive and negative loadings. The traits with the highest loadings are sagittal keel, occipital torus, malar tubercle, bregmatic
eminence (all positive), infraglabellar notch and supraorbital torus (both negative). The North American and, to a lesser extent, New Zealand, groups score highest
on PC 3, in contrast to Australia/Tasmania, Southern Europe, Eastern Europe, and East Africa (Fig. 3b).
In PC1, sex and size differences contribute about 36% of the variation, but only 3 and 8% in PC2 an PC3 respectively.

The author calculated distances between populations for Robusticity, CLS, MLS, Climate, and microsatellites, and sees how the inter-population distance based on robusticity correlates with the other four potentially explanatory factors:
The correlation coefficients from the Mantel tests are weak, ranging from -0.115 to 0.387 (Table 12). The null hypothesis of neutral evolution was rejected as the robusticity distances were not significantly correlated with neutral genetic distances.

The strongest (and only significant) correlations are between cranial robusticity and cranial (CLS) or masticatory apparatus shape (MLS). Cranial robusticity in the combined male–female sample is significantly correlated with the masticatory shape, and its correlation with overall cranial shape approached significance (Table 12).
On the Southern European masticatory system:
Whereas South Europe is among the lowest scoring groups on both the shape and robusticity vectors, the highest scoring groups on the robusticity vector (e.g., South America and New Zealand) are not the highest scoring groups on the shape vector (specifically Australia/Tasmania). The more gracile groups (e.g., South European) have more anteriorly positioned zygomatic bones (as indicated by the inferior zygomaticotemporal suture and zygomaxillare), more laterally located postglenoid processes and frontotemporale, and relatively larger cheek teeth (in the anteroposterior direction) that are more superiorly positioned.
Finally, a bit on Australian aboriginals who often get singled out as being particularly robust. It turns out that they are, but their pattern of robusticity involves particular traits, while other human groups, such as Native Americans are robust in a different manner:
While Aboriginal Australians have long been the standard bearers for robust cranial morphology, this study reveals that human populations exhibit more than one pattern of cranial robusticity. The results of this study emphasize a primary trend of variability from gracile to robust (except in the occipital torus region), but also highlight secondary patterns of differential cranial trait expression within populations. For example, the Native American group from Grand Gulch, Utah is characterized by robust expression of the sagittal keel, bregmatic eminence, occipital torus, and malar tubercle, but a more gracile supraorbital region in contrast to the pattern seen in Aboriginal Australians.
All in all, this is an excellent data-driven paper, which combines data from skulls, genes, and climate to arrive at a comprehensive study of the phenomenon of modern human cranial robusticity and its etiology.

American Journal of Physical Anthropology doi:10.1002/ajpa.21120

Relationship of cranial robusticity to cranial form, geography and climate in Homo sapiens

Karen L. Baab et al.


Variation in cranial robusticity among modern human populations is widely acknowledged but not well-understood. While the use of robust cranial traits in hominin systematics and phylogeny suggests that these characters are strongly heritable, this hypothesis has not been tested. Alternatively, cranial robusticity may be a response to differences in diet/mastication or it may be an adaptation to cold, harsh environments. This study quantifies the distribution of cranial robusticity in 14 geographically widespread human populations, and correlates this variation with climatic variables, neutral genetic distances, cranial size, and cranial shape. With the exception of the occipital torus region, all traits were positively correlated with each other, suggesting that they should not be treated as individual characters. While males are more robust than females within each of the populations, among the independent variables (cranial shape, size, climate, and neutral genetic distances), only shape is significantly correlated with inter-population differences in robusticity. Two-block partial least-squares analysis was used to explore the relationship between cranial shape (captured by three-dimensional landmark data) and robusticity across individuals. Weak support was found for the hypothesis that robusticity was related to mastication as the shape associated with greater robusticity was similar to that described for groups that ate harder-to-process diets. Specifically, crania with more prognathic faces, expanded glabellar and occipital regions, and (slightly) longer skulls were more robust than those with rounder vaults and more orthognathic faces. However, groups with more mechanically demanding diets (hunter-gatherers) were not always more robust than groups practicing some form of agriculture.


More on the insanity that has dominated historical discourse in FYROM

I recently became aware of how insane some of the claims of the present-day FYROM government have become. It is hard to appreciate this for the Slav-less spectator who doesn't really have access to what is discussed in that country.

Thankfully, there are still rational voices in FYROM, and thanks to the efforts of brave citizens of that country such as Vasko Gligorjevic, we get to hear some of them.

Here are a couple of YouTube videos where the former Prime Minsiter of the country Ljubčo Georgievski describes the program of "antiquization" in the country, the adoption of fringe revisionist history as official, the denial of the Slavic element in modern Slavo-Paionians, and the extremely negative sentiments of proponents of "Ancient Macedonians" against those who emphasize the Slavic element in the country's history.

In the second clip, Mr. Georgievski asks why the proponents of "Ancient Macedonians" in FYROM seem so unconcerned with determining the Thracian, Illyrian, Dardanian, and Paeonian element in their ancestry, and are so hell-bent on discovering Macedonian ancestors. He also states -correctly- that Ancient Macedonia, including most of Upper Macedonia was in today's Greece, and all the rest (including FYROM) were conquered by the Macedonians, and not part of Macedonia itself.

June 24, 2009

Paleolithic Flutes from the early Aurignacian in Germany

The Hohle Fels site was in the news recently for the discovery of the "first depiction of the human form".

Nature doi:10.1038/nature08169

New flutes document the earliest musical tradition in southwestern Germany

Nicholas J. Conard et al.

Considerable debate surrounds claims for early evidence of music in the archaeological record. Researchers universally accept the existence of complex musical instruments as an indication of fully modern behaviour and advanced symbolic communication1 but, owing to the scarcity of finds, the archaeological record of the evolution and spread of music remains incomplete. Although arguments have been made for Neanderthal musical traditions and the presence of musical instruments in Middle Palaeolithic assemblages, concrete evidence to support these claims is lacking. Here we report the discovery of bone and ivory flutes from the early Aurignacian period of southwestern Germany. These finds demonstrate the presence of a well-established musical tradition at the time when modern humans colonized Europe, more than 35,000 calendar years ago. Other than the caves of the Swabian Jura, the earliest secure archaeological evidence for music comes from sites in France and Austria and post-date 30,000 years ago


mtDNA of Tyrolean Iceman using a multiplexed Single-Base-Extension assay

From the paper:
In addition, because the Iceman’s sequence matches the rCRS at nps 497, 498, and 5913 (diagnostic of K1a, K1c, and K1b, respectively), we can extend previous suggestions that the Iceman’s genotype does not belong to any of the three known clades of K1, and should be referred to a new (undefined) paraphyletic clade, of K1 [25] (Figure 1).


The likelihood of the current results representing the endogenous DNA of the Iceman is substantially increased by the haplotype falling outside of K1a/K1b/K1c, combined with the unique hg K transition C8137T, matching the results of [25].


The fallibility of independent replication

Given the absence of 16093C and 16362C amongst the replication results of Handt et al., the only plausible conclusion is that these derived from a second, entirely different, hg K source. These results, combined with a unique haplotype in [25] and the present study, strongly suggests that both laboratories in the original study suffered from hg K contamination. The mtDNA profiles of the staff in the primary laboratory of the first study were not provided [14]; although a subsequent publication of the replicated results [37] disclosed that a member of the secondary laboratory staff was hg K (16224C-16311C), substantially increasing the likelihood for contamination occurring.

[25] refers to Ermini et al. on the Tyrolean Iceman mtDNA sequence, [14] to Handt et al., and [37] to Richards et al.

BMC Genetics doi:10.1186/1471-2156-10-29

Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean Iceman

Phillip Endicott et al.

Abstract (provisional)


Progress in the field of human ancient DNA studies has been severely restricted due to the myriad sources of potential contamination, and because of the pronounced difficulty in identifying authentic results. Improving the robustness of human aDNA results is a necessary pre-requisite to vigorously testing hypotheses about human evolution in Europe, including possible admixture with Neanderthals. This study approaches the problem of distinguishing between authentic and contaminating sequences from common European mtDNA haplogroups by applying a multiplexed Single-Base-Extension assay, containing both control and coding region sites, to DNA extracted from the Tyrolean Iceman.


The multiplex assay developed for this study was able to test sufficient polymorphisms in one reaction to unequivocally demonstrate that the Iceman's mtDNA belongs to a new European mtDNA clade with a very limited distribution amongst modern data sets. Controlled contamination experiments show that the correct results are returned by the multiplex assay even in the presence of substantial amounts of exogenous DNA. The overall level of discrimination achieved by targeting both control and coding region polymorphisms in a single reaction provides a methodology capable of dealing with most cases of homoplasy prevalent in European haplogroups.


The new genotyping results for the Iceman confirm the extreme fallibility of human aDNA studies in general, even when authenticated by independent replication. The sensitivity and accuracy of the multiplex Single-Base-Extension methodology forms part of an emerging suite of alternative techniques for the accurate retrieval of ancient DNA sequences from both anatomically modern humans and Neanderthals. The contamination of laboratories remains a pressing concern in aDNA studies, both in the pre and post-PCR environments, and the adoption of a forensic style assessment of a priori risks would significantly improve the credibility of results.


June 23, 2009

Automatic writer identification of ancient greek inscriptions

IEEE Trans Pattern Anal Mach Intell. 2009 Aug;31(8):1404-14.

Automatic writer identification of ancient greek inscriptions

Panagopoulos M, Papaodysseus C, Rousopoulos P, Dafi D, Tracy S.

This paper introduces a novel methodology for the classification of ancient Greek inscriptions according to the writer who carved them. Inscription writer identification is crucial for dating the written content, which in turn is of fundamental importance in the sciences of history and archaeology. To achieve this, we first compute an ideal or "platonic" prototype for the letters of each inscription separately. Next, statistical criteria are introduced to reject the hypothesis that two inscriptions are carved by the same writer. In this way, we can determine the number of distinct writers who carved a given ensemble of inscriptions. Next, maximum likelihood considerations are employed to attribute all inscriptions in the collection to the respective writers. The method has been applied to 24 Ancient Athenian inscriptions and attributed these inscriptions to six different identified hands in full accordance with expert epigraphists' opinions.


Two letters on the origin of Y chromosome haplogroup N1b

published in the European Journal of Human Genetics, referring to this paper by Mirabal et al.

Both the original paper and the two letters use the "evolutionary" mutation rate, and hence the given dates should be divided by approximately 3 to obtain realistic dates.

Excerpts from the two letters:

On the origin of Y-chromosome haplogroup N1b

Boris Malyarchuk and Miroslava Derenko
Eur J Hum Genet advance online publication, June 17, 2009; doi:10.1038/ejhg.2009.100
A possible scenario explaining the phylogeographic pattern of hg N1b is that the subclusters N1b-A and N1b-E might have diverged from a common ancestor
anywhere in Siberia approximately 15 ky ago (with upper bound of divergence time, TD, between these subclusters estimated (according to Zhivotovsky9) as 14.7±5.9 ky). According to STR variation, expansion of Northwest Siberian/Uralic/Northeast European branch, N1b-E, may have occurred approximately 7 kya and the expansion of South Siberian branch N1b-A about 5 kya. Divergence time between South Siberian and Northwest Siberian/Uralic N1b-A haplotypes is 4 ky (TD¼4.0±1.0 ky), so this suggests that expansion of N1b-A lineages in Northwest Siberia and Urals
(about 3 kya) might have occurred right after their migrations from South Siberia. Future studies of Y-chromosome variation using a combined STR-SNP approach may enable a better definition of geographic origin of N1b-P43 mutation.

Reply to B Malyarchuk and M Derenko: a need for further investigation of Uralic and Siberian populations in the search for haplogroup N1b's origins

Sheyla Mirabal, Peter A Underhill and Rene J Herrera
Eur J Hum Genet advance online publication, June 17, 2009; doi:10.1038/ejhg.2009.101
The higher variance and age estimates (Tables 1 and 2) for both European and Uralic populations as compared to the Siberian groups lend support to our previous statement suggesting that N1b may have arisen in the Uralic range or in an area/region proximal to it; however, a much more exhaustive investigative effort must be conducted to trace the origins of N1b and its branches N1b-A and N1b-E.

June 20, 2009

Webcast of Opening of new Acropolis museum

The new Acropolis museum will have its official opening today (Saturday, June 20, 2009) at 8pm local time (7pm CEST, 1700 UTC, 1300 EDT, 1000 PDT, June 21 0300 EST)

June 19, 2009

HAPMIX for detection of chromosomal segments of distinct ancestry

The authors claim:
The three Middle Eastern populations (Bedouin, Palestinian, and Druze) all show a substantial African-related mixture (3%–9% African-related ancestry). The inferred dates of 60–90 generations correspond to about 2,000–4,000 years ago – contemporaneous with our estimate of the oldest admixture time for the North African Mozabite population – taking into account the fact that HAPMIX systematically underestimate mixture dates by up to 25% for mixtures this old (see simulations above). These results are historically interesting, allowing us to conclude that there is likely to be African ancestry in Middle Eastern populations today that dates to population mixture that occurred in Biblical times.
This is, however, contradicted, by the finding of virtually no "Yoruba" ancestry in the same Middle Eastern populations the best study to date.

It is not really difficult to see what went wrong. By using CEU and YRI populations as parentals, the authors were unable to discover the true ancestral components. Middle Eastern populations are composed primarily of Middle Eastern Caucasoids, not Northwestern Europeans; moreover, their African influences are mainly Northeastern, not West African.

As we know (see previous link), Caucasoids from Europe, Central/South Asia and the Near East are not uniform, but form separate clusters. Indeed, even Europeans themselves are not uniform.

Nor are Africans themselves uniform, according to the latest study of Tishkoff et al, and Middle Eastern populations (see Table S8) have no significant admixture from West Africa, but a noticeable "Cushitic" admixture.

This paper could serve as a warning to the limitations of statistical inference. A good tool (and HAPMIX is indeed such), can lead to erroneous results (biblical-era admixture with Sub-Saharan Africans), if it is used with the wrong input data.

PLoS Genetics doi:10.1371/journal.pgen.1000519

Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations

Alkes L. Price et al.


Identifying the ancestry of chromosomal segments of distinct ancestry has a wide range of applications from disease mapping to learning about history. Most methods require the use of unlinked markers; but, using all markers from genome-wide scanning arrays, it should in principle be possible to infer the ancestry of even very small segments with exquisite accuracy. We describe a method, HAPMIX, which employs an explicit population genetic model to perform such local ancestry inference based on fine-scale variation data. We show that HAPMIX outperforms other methods, and we explore its utility for inferring ancestry, learning about ancestral populations, and inferring dates of admixture. We validate the method empirically by applying it to populations that have experienced recent and ancient admixture: 935 African Americans from the United States and 29 Mozabites from North Africa. HAPMIX will be of particular utility for mapping disease genes in recently admixed populations, as its accurate estimates of local ancestry permit admixture and case-control association signals to be combined, enabling more powerful tests of association than with either signal alone.


June 18, 2009

Origin of pig breeds

Molecular Biology and Evolution, doi:10.1093/molbev/msp118


O. Ramírez et al.


We have investigated the origin of swine breeds through the joint analysis of mitochondrial, microsatellite and Y-chromosome polymorphisms in a sample of pigs and wild boars with a worldwide distribution. Genetic differentiation between pigs and wild boars was remarkably weak, likely as a consequence of a sustained gene flow between both populations. The analysis of nuclear markers evidenced the existence of a close genetic relationship between Near Eastern and European wild boars making difficult to infer their relative contributions to the gene pool of modern European breeds. Moreover, we have shown that European and Far Eastern pig populations have contributed maternal and paternal lineages to the foundation of African and South American breeds. While West African pigs from Nigeria and Benin exclusively harboured European alleles, Far Eastern and European genetic signatures of similar intensity were detected in swine breeds from Eastern Africa. This region seems to have been a major point of entry of livestock species in the African continent as a result of the Indian Ocean trade. Finally, South American creole breeds had essentially a European ancestry although Asian Y-chromosome and mitochondrial haplotypes were found in a few Nicaraguan pigs. The existence of Spanish and Portuguese commercial routes linking Asia with America might have favoured the introduction of Far Eastern breeds into this continent.


Origin of Malagasy

Molecular Biology and Evolution doi:10.1093/molbev/msp120

On the origins and admixture of Malagasy: new evidence from high resolution analyses of paternal and maternal lineages

Sergio Tofanelli et al.


The Malagasy have been shown to be a genetically admixed population combining parental lineages with African and South East Asian ancestry. In the present paper we fit the Malagasy admixture history in a highly resolved phylogeographic framework by typing a large set of mtDNA and Y DNA markers in unrelated individuals from inland (Merina) and coastal (Antandroy, Antanosy, Antaisaka) ethnic groups. This allowed performance of a multi-level analysis in which the diversity among main ethnic divisions, lineage ancestries, and modes of inheritance could be concurrently evaluated. Admixture was confirmed to result from the encounter of African and South-East Asian people with minor recent male contributions from Europe. However, new scenarios are depicted about Malagasy admixture history. The distribution of ancestral components was ethnic- and sex-biased, with the Asian ancestry appearing more conserved in the female than in the male gene pool, and in inland than in coastal groups. A statistic based on haplotype sharing (DHS), showing low sampling error and time linearity over the last 200 generations, was here introduced for the first time and helped to integrate our results with linguistic and archeological data. The focus about the origin of Malagasy lineages was enlarged in space and pushed back in time. Homelands could not be pinpointed, but appeared to comprise two vast areas containing different populations from sub-Saharan Africa and South-East Asia. The pattern of diffusion of uni-parental lineages was compatible with at least two events: a primary admixture of proto-Malay people with Bantu-speakers bearing a western-like pool of haplotypes, followed by a secondary flow of Southeastern Bantu-speakers unpaired for gender (mainly male-driven) and geography (mainly coastal).


June 17, 2009

European admixture, diabetes incidence, and socioeconomic status in Latinos

Diabetologia. 2009 Jun 13. [Epub ahead of print]

Strong association of socioeconomic status with genetic ancestry in Latinos: implications for admixture studies of type 2 diabetes.

Florez JC et al.

AIMS/HYPOTHESIS: Type 2 diabetes is more prevalent in US American minority populations of African or Native American descent than it is in European Americans. However, the proportion of this epidemiological difference that can be ascribed to genetic or environmental factors is unknown. To determine whether genetic ancestry is correlated with diabetes risk in Latinos, we estimated the proportion of European ancestry in case-control samples from Mexico and Colombia in whom socioeconomic status had been carefully ascertained. METHODS: We genotyped 67 ancestry-informative markers in 499 participants with type 2 diabetes and 197 controls from Medellín (Colombia), as well as in 163 participants with type 2 diabetes and 72 controls from central Mexico. Each participant was assigned a socioeconomic status scale via various measures. RESULTS: Although European ancestry was associated with lower diabetes risk in Mexicans (OR [95% CI] 0.06 [0.02-0.21], p = 2.0 x 10(-5)) and Colombians (OR 0.26 [0.08-0.78], p = 0.02), adjustment for socioeconomic status eliminated the association in the Colombian sample (OR 0.64 [0.19-2.12], p = 0.46) and significantly attenuated it in the Mexican sample (OR 0.17 [0.04-0.71], p = 0.02). Adjustment for BMI did not change the results. CONCLUSIONS/INTERPRETATION: The proportion of non-European ancestry is associated with both type 2 diabetes and lower socioeconomic status in admixed Latino populations from North and South America. We conclude that ancestry-directed search for genetic markers associated with type 2 diabetes in Latinos may benefit from information involving social factors, as these factors have a quantitatively important effect on type 2 diabetes risk relative to ancestry effects.


June 16, 2009

Africans in Roman York, England

The authors used both anthroposcopy and FORDISC to assess ancestry. From the paper:
The results generated by the two different approaches for ancestral assessment were for the most part in accord. However, some individuals generated conflicting data (see Table 6). In these cases, it was the cranial vault rather than the facial characteristics that caused the discrepancy and this probably reflects a degree of intrapopulation variation, overlap, and genetic admixture (Howells, 1995). In addition, some crania showed little affinity with any of the FORDISC 3.0 reference populations (e.g., TDC472, TDC467, TDC317, and RE24, RE34, RE38) and may have originated from groups not represented in the dataset.


In the European groups, the crania showed the greatest affinity with the Northern European and American White reference samples. The diversity of the female crania from Trentholme Drive suggests a degree of heterogeneity, which contradicts Warwick’s (1962, p 110) assertion that the women from this site were indigenous. For the African groups, the crania demonstrated the greatest resemblance to the American Black reference samples of the nineteenth and twentieth centuries, perhaps reflecting a similar degree of genetic admixture in these populations. Individuals with a close affinity to the Egyptian skulls were also identified at both sites, and this is perhaps not surprising considering the Roman Empire included these areas of North Africa. What is also clear is that both males and females with affinities to African groups appear in both the high status Railway site and at Trentholme Drive.

American Journal of Physical Anthropology doi:10.1002/ajpa.21104 About DOI

Migration and diversity in Roman Britain: A multidisciplinary approach to the identification of immigrants in Roman York, England

Stephany Leach et al.


Previous anthropological investigations at Trentholme Drive, in Roman York identified an unusual amount of cranial variation amongst the inhabitants, with some individuals suggested as having originated from the Middle East or North Africa. The current study investigates the validity of this assessment using modern anthropological methods to assess cranial variation in two groups: The Railway and Trentholme Drive. Strontium and oxygen isotope evidence derived from the dentition of 43 of these individuals was combined with the craniometric data to provide information on possible levels of migration and the range of homelands that may be represented. The results of the craniometric analysis indicated that the majority of the York population had European origins, but that 11% of the Trentholme Drive and 12% of The Railway study samples were likely of African decent. Oxygen analysis identified four incomers, three from areas warmer than the UK and one from a cooler or more continental climate. Although based on a relatively small sample of the overall population at York, this multidisciplinary approach made it possible to identify incomers, both men and women, from across the Empire. Evidence for possible second generation migrants was also suggested. The results confirm the presence of a heterogeneous population resident in York and highlight the diversity, rather than the uniformity, of the population in Roman Britain.


European settlers of the Near East during the Crusades

American Journal of Physical Anthropology doi:10.1002/ajpa.21100

Migration to the Medieval Middle East with the crusades

Piers D. Mitchell, Andrew R. Millard


During the 12th and 13th centuries thousands of people moved from Europe to the Middle East to fight, undertake pilgrimage, or settle and make a new life. The aim of this research is to investigate two populations from the Crusader kingdom of Jerusalem, by determining who was born in Europe and who came from the Middle East. Oxygen and strontium stable isotope analyses were conducted on the enamel of teeth from skeletal remains excavated from Crusader contexts. Twenty individuals from the coastal city of Caesarea (10 high status and 10 low status), and two local Near Eastern Christian farmers from the village of Parvum Gerinum (Tel Jezreel) were analyzed as a control sample. Results were compared with known geographic values for oxygen and strontium isotopes. The population of the city of Caesarea appears to have been dominated by European-born individuals (probably 19/20, but at least 13/20), with few locals. This was surprising as a much higher proportion of locals were expected. Both controls from the farming village of Parvum Gerinum had spent their childhood in the area of the village, which matches our understanding of limited mobility among poor Medieval farmers. This is the first time that stable isotope analysis has been applied to the study of the migration of peoples between Medieval Europe and the Middle East at the time of the crusades. In view of these findings, we must now rethink past estimations of population social structure in Levantine coastal Medieval cities during the Crusader period.


June 13, 2009

Forensic reconstruction of Oberkassel female skull

There is also a NSFW-ish picture of the reconstruction in the paper. Not sure if this level of depigmentation is warranted for this time frame.

Related: a reconstruction of a Neolithic Italian from Quinzano culture by the same authors.


Marco Silvestri, Giancarlo Tomezzoli


Because our technique of facial reconstruction proved to be successful, we decided to apply it to a skull of an older female subject preserved at the Paläontologisches Museum in Munich (Germany). The skull was found in Oberkassel bei Bonn (Germany), its age is 10,500 years. It appears that the skull is well reconstructed, complete, not much deformed, without traces of severe illnesses. The subject was a woman aged probably 15-25 years. The causes of the death cannot be determined. Because, also in this case, the skull does not appear too dissimilar from the skulls of the present people, and because, as far as can be understood the subject was healthy, it is reasonable to assume that the thickness of the soft tissues on the different portions of the skull was not dissimilar from that of today’s young Central European women and/or young American women of Central European origins. For the pigmentation, according to current statistics, we assumed fair skin and light coloured eyebrows, hair, and eyes. The reconstructed female face looks not dissimilar from the faces of today’s central European female subjects. However, in the light of the well-reconstructed state of the skull and of our reasonable assumptions on pigmentation, we can say that the reconstructed 3D face model and its artistic representation are good approximations of the facial aspect of a girl who lived at the time of the Würm Ice Age.

Y chromosomes of Turks from Antalya

Of interest the presence of R1*(R1a, R1b) at a frequency of 6.6%. Unfortunately the presence of haplogroups likely to have been introduced to Turkey from Central Asia was not directly measured, although BR*(xD2,E,F) is a good candidate for a haplogroup C stand-in.

Rom J Leg Med 17 (1) 59 – 68 (2009)

Y-SNP haplogroups in the Antalya population in Turkish Republic

Timur Serdar, Demircin Sema


SNPs are known to be the most abundant source of sequence variation in the human
genome. The SNPs in the NRY (non-recombining Y-chromosome) region which passes from father to son as unchanged haplotype-blocks escaping recombination, provides important advantages in the investigations of sexual assault crimes, in the cases of parentage testing especially if the mother or alleged father is unavailable for testing and in the evolutionary studies. The aim of this study, was to determine the frequencies of Y SNP markers and the haplogroups, in order to define the Y-chromosome SNP markers which are polymorphic, have high discrimination power and can be used in forensic investigations in the Antalya population. For each of 75 unrelated males from Antalya, 35 different Y-SNP markers were amplified in a single reaction using multiplex minisequencing method. In the study, 18 markers of them were found to be polymorphic. The most frequent YSNP markers with mutations were M139 (100%), SRY10831/SRY1532 (92%), M89 (85.3%), M213 (85.3%), M9 (44%), 92R7 (30.6%), 12F2 (30.6%), M45 (29.3%), M172 (26.6%) and M173 (22.6%). The Y-chromosome haplogroups of Antalya population were defined by these 18 Y-SNP polymorphic loci and the frequencies and the distribution of haplogroups were determined. J2*(xJ2F2) (26.6%), K*(xN3,O,P) (13.3%), E3b (9.3%), F*(xH,I,J,K) (8%), R1a1*(xR1a1b) (8%), R1b*(xR1b1, R1b6, R1b8) (8%), P*(xQ3a,R1) (8%) haplogroups were identified as the most abundant in Antalya population. These haplogroups are reported as widespread also in European and neighboring Near Eastern populations.

Link (pdf)

June 12, 2009

Literature review of Sub-Saharan African IQ

Intelligence doi:10.1016/j.intell.2009.05.002

A systematic literature review of the average IQ of sub-Saharan Africans

Jelte M. Wicherts et al.


On the basis of several reviews of the literature, Lynn [Lynn, R., (2006). Race differences in intelligence: An evolutionary analysis. Augusta, GA: Washington Summit Publishers.] and Lynn and Vanhanen [Lynn, R., & Vanhanen, T., (2006). IQ and global inequality. Augusta, GA: Washington Summit Publishers.] concluded that the average IQ of the Black population of sub-Saharan Africa lies below 70. In this paper, the authors systematically review published empirical data on the performance of Africans on the following IQ tests: Draw-A-Man (DAM) test, Kaufman-Assessment Battery for Children (K-ABC), the Wechsler scales (WAIS & WISC), and several other IQ tests (but not the Raven's tests). Inclusion and exclusion criteria are explicitly discussed. Results show that average IQ of Africans on these tests is approximately 82 when compared to UK norms. We provide estimates of the average IQ per country and estimates on the basis of alternative inclusion criteria. Our estimate of average IQ converges with the finding that national IQs of sub-Saharan African countries as predicted from several international studies of student achievement are around 82. It is suggested that this estimate should be considered in light of the Flynn Effect. It is concluded that more psychometric studies are needed to address the issue of measurement bias of western IQ tests for Africans.


June 08, 2009

mtDNA of Native Mexicans

Human Genetics doi:10.1007/s00439-009-0693-y

Linguistic and maternal genetic diversity are not correlated in Native Mexicans

Karla Sandoval et al.


Mesoamerica, defined as the broad linguistic and cultural area from middle southern Mexico to Costa Rica, might have played a pivotal role during the colonization of the American continent. The Mesoamerican isthmus has constituted an important geographic barrier that has severely restricted gene flow between North and South America in pre-historical times. Although the Native American component has been already described in admixed Mexican populations, few studies have been carried out in native Mexican populations. In this study, we present mitochondrial DNA (mtDNA) sequence data for the first hypervariable region (HVR-I) in 477 unrelated individuals belonging to 11 different native populations from Mexico. Almost all of the Native Mexican mtDNAs could be classified into the four pan-Amerindian haplogroups (A2, B2, C1, and D1); only two of them could be allocated to the rare Native American lineage D4h3. Their haplogroup phylogenies are clearly star-like, as expected from relatively young populations that have experienced diverse episodes of genetic drift (e.g., extensive isolation, genetic drift, and founder effects) and posterior population expansions. In agreement with this observation, Native Mexican populations show a high degree of heterogeneity in their patterns of haplogroup frequencies. Haplogroup X2a was absent in our samples, supporting previous observations where this clade was only detected in the American northernmost areas. The search for identical sequences in the American continent shows that, although Native Mexican populations seem to show a closer relationship to North American populations, they cannot be related to a single geographical region within the continent. Finally, we did not find significant population structure in the maternal lineages when considering the four main and distinct linguistic groups represented in our Mexican samples (Oto-Manguean, Uto-Aztecan, Tarascan, and Mayan), suggesting that genetic divergence predates linguistic diversification in Mexico.


June 07, 2009

Craniofacial norms of Malays

Singapore Med J. 2009 May;50(5):525-8.

Craniofacial anthropometric norms of Malays

Ngeow WC, Aljunid ST.

INTRODUCTION: This study was undertaken to establish the craniofacial anthropometric norms of young adult Malaysian Malays. METHODS: The study group consisted of convenient samples of 100 healthy volunteers (aged 18-25 years), with an equal number of female and male subjects who had no history of mixed racial parentage. 22 linear measurements were taken twice from 22 landmarks over six craniofacial regions. RESULTS: The Malays shared many similar sizes of measurements with the Singaporean Chinese. Their left eye fissure length and mouth width (ch-ch) were almost identical for both genders. However, Malay females had an upper lip height (sn-sto) (left) and ear width (pra-pa) similar to Singaporean Chinese females. Six other measurements, viz. the head width (eu-eu), head circumference (on-op), face height (n-gn), lower face height (sn-gn), (left) eye fissure height (ps-pi), cutaneous upper lip height (sn-ls) and cutaneous upper lip height (ls-sto), were 0.4-4.3 mm less in the Malays. Measurements for another four parameters, viz. the length of the head (g-op), biocular width (ex-ex), lower vermillion height (sto-li) and (left) ear length (sa-sba), were 0.5-3.6 mm higher in the Malays. Only three measurements were obviously different; the height of the head (v-n) and intercanthal width (en-en), were lower, and the protrusion of the nasal tip (sn-prn) was higher in the Malays. CONCLUSION: These findings suggest that three features, i.e. the height of the head (v-n), intercanthal width (en-en) and protrusion of the nasal tip (sn-prn) may be useful in differentiating a Malay face from a Singaporean Chinese one.


Lactase persistence in Greece and Italy

From the paper:
Furthermore, they indicate the existence of a genetic heterogeneity in Italy, in accordance with previous studies on classical markers (Piazza et al., 1988) and Y-chromosome (Capelli et al., 2007; see also Francalacci and Sanna, 2008). On the contrary, a substantial homogeneity was detected among Greek groups (Supporting Information Table S3), which is congruent with the only previous genetic study conducted in Greece on a multiregional scale (Di Giacomo et al., 2003).
The occurrence of lactase persistence in Greece and Southern Italy is virtually the same, which is not very surprising given the origins of the latter population.

American Journal of Human Biology
Volume 21 Issue 2, Pages 217 - 219, doi:10.1002/ajhb.20851

Tracing the distribution and evolution of lactase persistence in Southern Europe through the study of the T-13910 variant

Paolo Anagnostou et al.


We investigated the occurrence and intra-allelic variability of the T-13910 variant located upstream of the lactase gene in 965 individuals from 20 different locations of Italy and Greece. The T-13910 frequency ranges from 0.072 (Sardinia) to 0.237 (North-East Italy), with a statistically significant difference between North-East Italians and other Italian populations. The comparison of the lactose tolerance predicted by T-13910 and that assessed by other studies using physiological tests shows a one-way statistically significant discrepancy that could be due to sampling differences. However, the possible role of other genetic factors underlying lactase persistence is worth exploring. The time of the most recent common ancestor and departures from neutrality of the T-13910 allele were assessed using three microsatellite loci. Time estimates were found to be congruent with the appearance of dairy farming in Southern Europe and the occurrence of a single introgression event. Robust signals of selection can be observed in North-East Italy only. We discuss the possible role of cultural traits and genetic history in determining these observed micro-evolutionary patterns.


June 06, 2009

MAOA and gang membership/weapon use

Comprehensive Psychiatry doi:10.1016/j.comppsych.2009.03.010

Monoamine oxidase A genotype is associated with gang membership and weapon use

Kevin M. Beaver et al.



A functional polymorphism in the promoter region of the monoamine oxidase A (MAOA) gene has been found to be associated with a broad range of antisocial phenotypes, including physical violence. At the same time, it is well known that gang members represent some of the most serious violent offenders. Even so, no research has ever examined the association between MAOA and gang membership.


The aim of this study is to examine the association between MAOA and gang membership and between MAOA and weapon use.


We examined the effects of MAOA by using a molecular genetic association research design.


A nonclinical sample was used in this study.


Participants were drawn from the National Longitudinal Study of Adolescent Health (1155 females, 1041 males).

Main Outcome Measures

The outcome measures of this study are gang membership and weapon use.


The low MAOA activity alleles conferred an increased risk of joining a gang and using a weapon in a fight for males but not for females. Moreover, among male gang members, those who used weapons in a fight were more likely to have a low MAOA activity allele when compared with male gang members who do not use weapons in a fight.


Male carriers of low MAOA activity alleles are at risk for becoming a gang member and, once a gang member, are at risk for using weapons in a fight.


YHRD updated germline mutation rates

YHRD has updated with new mutation rates for Y-STR loci. This is an invaluable resource, as it pools mutation rates from all published studies to produce an overall rate based on a large sample. 

As I have argued elsewhere, uncertainty about the mutation rate is one of the major sources of uncertainty about age estimates of Y-chromosome common ancestors. Hopefully more researchers will start using these rates (as e.g., Di Gaetano et al. did) rather than those picked from single papers of the literature, especially "evolutionary" ones.

June 05, 2009

Geography and human adaptation (Coop et al. 2009)

From the paper:
More generally, alleles that strongly differentiate the French from both the Han and Yoruba (Figure 3D) are typically present at high frequency across all of Europe, the Middle East and South Asia (an area defined here as “west Eurasia”), and at low frequency elsewhere. This pattern of sharing across the west Eurasian populations is highly consistent with observations from random markers showing that the populations in west Eurasia form a single cluster in some analyses of worldwide population structure [40]. Allele frequencies at high- FST SNPs in two central Asian populations, the Uygur and Hazara, tend to be intermediate between west Eurasia and east Asia, consistent with observations that these populations have recent mixed ancestry between west Eurasia and east Asia [38],[40],[66].

From Figure 3: "frequency distributions for 50 of the most extreme SNPs genome-wide in the following pairs of comparisons: (A, B): SNPs for which Yoruba are highly differentiated from both Han and French; (C, D): French are differentiated from Yoruba and Han; (E, F): Han are differentiated from Yoruba and French."

From the paper:
Our results therefore suggest that local adaptation is tightly constrained by the ancestral relationships and migration rates among populations. It seems likely that selection in humans is generally not divergent enough to generate large frequency differences at individual loci between population pairs that are either recently separated, or regularly exchange migrants [53],[54]. Furthermore, populations may be too mobile, or their identities too fluid, to experience very localized pressures consistently over the several thousand years that may be required for large allele frequency changes.

However in contrast, it seems that selected alleles may not spread effectively between broad geographic regions (see Figure 3, Supplementary Figure 15 in Text S1 and [21]). Perhaps this is because populations usually adapt to similar selection pressures by parallel mutation [18],[23],[25] rather than by the spread of migrants between regions [72],[73].

UPDATE (June 5)

From the public release:
In recent years, geneticists have identified a handful of genes that have helped human populations adapt to new environments within just a few thousand years—a strikingly short timescale in evolutionary terms. However, the team found that for most genes, it can take at least 50,000-100,000 years for natural selection to spread favorable traits through a human population. According to their analysis, gene variants tend to be distributed throughout the world in patterns that reflect ancient population movements and other aspects of population history. "We don't think that selection has been strong enough to completely fine-tune the adaptation of individual human populations to their local environments," says co-author Jonathan Pritchard. "In addition to selection, demographic history -- how populations have moved around -- has exerted a strong effect on the distribution of variants."

To determine whether the frequency of a particular variant resulted from natural selection, Pritchard and his colleagues compared the distribution of variants in parts of the genome that affect the structure and regulation of proteins to the distribution of variants in parts of the genome that do not affect proteins. Since these neutral parts of the genome are less likely to be affected by natural selection, they reasoned that studying variants in these regions should reflect the demographic history of populations.

The researchers found that many previously identified genetic signals of selection may have been created by historical and demographic factors rather than by selection. When the team compared closely related populations they found few large genetic differences. If the individual populations' environments were exerting strong selective pressure, such differences should have been apparent.

Selection may still be occurring in many regions of the genome, says Pritchard. But if so, it is exerting a moderate effect on many genes that together influence a biological characteristic. "We don't know enough yet about the genetics of most human traits to be able to pick out all of the relevant variation," says Pritchard. "As functional studies go forward, people will start figuring out the phenotypes that are associated with selective signals," says lead author Graham Coop. "That will be very important, because then we can figure out what selection pressures underlie these episodes of natural selection."
Gene Expression has a long post on this study.

PLoS Genetics doi:10.1371/journal.pgen.1000500

The Role of Geography in Human Adaptation

Graham Coop et al.


Various observations argue for a role of adaptation in recent human evolution, including results from genome-wide studies and analyses of selection signals at candidate genes. Here, we use genome-wide SNP data from the HapMap and CEPH-Human Genome Diversity Panel samples to study the geographic distributions of putatively selected alleles at a range of geographic scales. We find that the average allele frequency divergence is highly predictive of the most extreme FST values across the whole genome. On a broad scale, the geographic distribution of putatively selected alleles almost invariably conforms to population clusters identified using randomly chosen genetic markers. Given this structure, there are surprisingly few fixed or nearly fixed differences between human populations. Among the nearly fixed differences that do exist, nearly all are due to fixation events that occurred outside of Africa, and most appear in East Asia. These patterns suggest that selection is often weak enough that neutral processes—especially population history, migration, and drift—exert powerful influences over the fate and geographic distribution of selected alleles.


Regional population structure in Iceland (Price et al. 2009)

In 2008 Ethnicity Struck Back, but in 2009, it already seems we're well on our way to finding the structure within ethnic groups themselves, as was possible in Sardinia and Estonia.

A new paper shows that such structure exists in Iceland, a population often used for association studies, because of its presumed homogeneity.

Individuals with most of their ancestry from one of several regions tend to cluster together in the PCA plot (top), but "random" individuals with ancestry from many regions tend to be all over the map. 

From the paper:
The ancestry predictions were correct for 47% of samples, correct to within a distance of one region for 74% of samples, and correct to within a distance of two regions for 93% of samples. The accuracy increased to 58% (87% to within one region, 97% to within two regions) when restricting to the 98 (of 250) samples with at least 16 of 32 ancestors from a single region.
Figure 3 shows the Icelandic populations in the context of Scotland and Norway. From the paper:
Based on the available data, the optimal linear combination yielded an estimate of 64% Norse and 36% Scottish ancestry, with a standard error of less than 2%.  [...] For each region, the estimate of Norse ancestry was between 62% and 65%, with a standard error of less than 2% (except region 1, for which we obtained 61% with a standard error of less than 3%).
Admixture took place so long ago, that it has spread evenly across Iceland, with no regions being particularly "Norse" or "Scottish" in ancestry. But, while the ancestral components are regionally the same, it is clear from the accuracy of region estimates that the various populations of Icelanders have not been panmictic, and thus some barriers to gene flow even in this very homogeneous population has allowed for the emergence of regional structure.

A consequence of the recent origin of the genetic differences between Icelandic subpopulations is that allele frequency differences follow the null distribution predicted by neutral drift. Thus, there is little risk of false positive associations due to population stratification in disease association studies, despite the fact that there are genuine differences between regions.

PLoS Genetics doi:10.1371/journal.pgen.1000505

The Impact of Divergence Time on the Nature of Population Structure: An Example from Iceland

Alkes Price et al.


The Icelandic population has been sampled in many disease association studies, providing a strong motivation to understand the structure of this population and its ramifications for disease gene mapping. Previous work using 40 microsatellites showed that the Icelandic population is relatively homogeneous, but exhibits subtle population structure that can bias disease association statistics. Here, we show that regional geographic ancestries of individuals from Iceland can be distinguished using 292,289 autosomal single-nucleotide polymorphisms (SNPs). We further show that subpopulation differences are due to genetic drift since the settlement of Iceland 1100 years ago, and not to varying contributions from different ancestral populations. A consequence of the recent origin of Icelandic population structure is that allele frequency differences follow a null distribution devoid of outliers, so that the risk of false positive associations due to stratification is minimal. Our results highlight an important distinction between population differences attributable to recent drift and those arising from more ancient divergence, which has implications both for association studies and for efforts to detect natural selection using population differentiation.


Population density and cultural complexity (Powell et al. 2009)

From ScienceDaily:
High population density leads to greater exchange of ideas and skills and prevents the loss of new innovations. It is this skill maintenance, combined with a greater probability of useful innovations, that led to modern human behaviour appearing at different times in different parts of the world.

In the study, the UCL team found that complex skills learnt across generations can only be maintained when there is a critical level of interaction between people. Using computer simulations of social learning, they showed that high and low-skilled groups could coexist over long periods of time and that the degree of skill they maintained depended on local population density or the degree of migration between them. Using genetic estimates of population size in the past, the team went on to show that density was similar in sub-Saharan Africa, Europe and the Middle-East when modern behaviour first appeared in each of these regions. The paper also points to evidence that population density would have dropped for climatic reasons at the time when modern human behaviour temporarily disappeared in sub-Saharan Africa.
Science doi:10.1126/science.1170165

Late Pleistocene Demography and the Appearance of Modern Human Behavior

Adam Powell et al.


The origins of modern human behavior are marked by increased symbolic and technological complexity in the archaeological record. In western Eurasia this transition, the Upper Paleolithic, occurred about 45,000 years ago, but many of its features appear transiently in southern Africa about 45,000 years earlier. We show that demography is a major determinant in the maintenance of cultural complexity and that variation in regional subpopulation density and/or migratory activity results in spatial structuring of cultural skill accumulation. Genetic estimates of regional population size over time show that densities in early Upper Paleolithic Europe were similar to those in sub-Saharan Africa when modern behavior first appeared. Demographic factors can thus explain geographic variation in the timing of the first appearance of modern behavior without invoking increased cognitive capacity.


June 04, 2009

mtDNA haplogroup U5b3 (Pala et al. 2009)

As always, time estimates depend on the mutation rate used:
Because the mutation rate of Mishmar et al.37 is probably an overestimate, mainly caused by partial saturation of some synonymous mutations,40 and that of Kivisild et al.39 represents an underestimate,41 we used the intermediate global coalescence time of modern human mtDNA recently proposed by Perego et al.42 as a reference point for the internal calibration of both approaches. Accordingly, we converted the haplogroup sequence divergences into time estimates by using averaged time calibrations corresponding to 4610 years per coding-region substitution and 7650 years per synonymous transition (Table 1). With this approach, the coalescence time estimates for the entire U5b3 are between 10.1 ky and 8.1 ky.
See Time dependency of the human mtDNA evolutionary mutation rate for some discussion of mutation rates and archaeological correlations, and the newer paper on Purifying selection and the mtDNA clock.

American Journal of Human Genetics doi:10.1016/j.ajhg.2009.05.004

Mitochondrial Haplogroup U5b3: A Distant Echo of the Epipaleolithic in Italy and the Legacy of the Early Sardinians

Maria Pala et al.


There are extensive data indicating that some glacial refuge zones of southern Europe (Franco-Cantabria, Balkans, and Ukraine) were major genetic sources for the human recolonization of the continent at the beginning of the Holocene. Intriguingly, there is no genetic evidence that the refuge area located in the Italian Peninsula contributed to this process. Here we show, through phylogeographic analyses of mitochondrial DNA (mtDNA) variation performed at the highest level of molecular resolution (52 entire mitochondrial genomes), that the most likely homeland for U5b3a haplogroup present at a very low frequency across Europewas the Italian Peninsula. In contrast to mtDNA haplogroups that expanded from other refugia, the Holocene expansion of haplogroup U5b3 toward the North was restricted by the Alps and occurred only along the Mediterranean coasts, mainly toward nearby Provence (southern France). From there, 7,0009,000 years ago, a subclade of this haplogroup moved to Sardinia, possibly as a result of the obsidian trade that linked the two regions, leaving a distinctive signature in the modern people of the island. This scenario strikingly matches the age, distribution, and postulated geographic source of a Sardinian Y chromosome haplogroup (I2a2-M26), a paradigmatic case in the European context of a founder event marking both female and male lineages.


Purifying selection and the mtDNA clock (Soares et al. 2009)

This paper deals with the problem of a time-varying mutation rate due to purifying selection, i.e., the removal of harmful variation from the mtDNA gene pool.

From the paper:
Thus, it estimates the coalescence time of the mtDNA tree overall at ~160,000 kya, L3 (the clade that evolved within Africa and gave rise to the three major non-African haplogroups—sometimes termed ‘‘macrohaplogroups’’— M, N, and R) at 65 kya, and M, N, and R themselves at 40–50 kya.


In any event, L3 probably expanded ~70 kya, possibly associated with an improvement of the climatic conditions around that time after a long period of drought.103 There are no ‘‘pre-M’’ or ‘‘pre-N’’ clades extant either within or outside Africa, so the out-of-Africa event could be as early as the coalescence time of L3. These data render an outof- Africa dispersal prior to the Toba eruption in Sumatra at ~74 kya less likely.


the age of haplogroup M in India, at 49.4 (39.0; 60.2) kya, is significantly lower than in East Asia, at 60.6 (47.3; 74.3) kya (both are lower in r but the proportional
difference is similar; see Table 3).


Europe was first settled by modern humans ~45 kya, and it is believed that one of the branches of U, U5 or a genetically close ancestor to U5, arose among the first settlers. The ML estimate of haplogroup U5 is 36.0 (25.3; 47.2) kya, and lower with r at 30.7 (21.4; 40.5) kya and 33.0 (13.3; 52.8) with our synonymous rate. [...] The closest link in the tree with the Near East is the root of haplogroup U, placing any early migration into Europe involving U5 or its ancestors between ~55 kya and ~30 kya.
The new chronology of human mtDNA. As you can see, about 2/3 of the age of mtDNA represents within-Africa variation. L3 Africans and Eurasians are much closer related (matrilineally) than they are with any other Africans. The next closest relation is with L2 Africans, separated by L3's by ~43ky.

American Journal of Human Genetics

Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock

Pedro Soares et al.


There is currently no calibration available for the whole human mtDNA genome, incorporating both coding and control regions. Furthermore, as several authors have pointed out recently, linear molecular clocks that incorporate selectable characters are in any case problematic. We here confirm a modest effect of purifying selection on the mtDNA coding region and propose an improved molecular clock for dating human mtDNA, based on a worldwide phylogeny of > 2000 complete mtDNA genomes and calibrating against recent evidence for the divergence time of humans and chimpanzees. We focus on a time-dependent mutation rate based on the entire mtDNA genome and supported by a neutral clock based on synonymous mutations alone. We show that the corrected rate is further corroborated by archaeological dating for the settlement of the Canary Islands and Remote Oceania and also, given certain phylogeographic assumptions, by the timing of the first modern human settlement of Europe and resettlement after the Last Glacial Maximum. The corrected rate yields an age of modern human expansion in the Americas at 15 kya that - unlike the uncorrected clock - matches the archaeological evidence, but continues to indicate an out-of-Africa dispersal at around 5570 kya, 520 ky before any clear archaeological record, suggesting the need for archaeological research efforts focusing on this time window. We also present improved rates for the mtDNA control region, and the first comprehensive estimates of positional mutation rates for human mtDNA, which are essential for defining mutation models in phylogenetic analyses.


Y chromosome haplogroup G phylogeny updated (Sims et al. 2009)

Figure 1 has the updated phylogeny with the new SNPs.

PLoS ONE doi:10.1371/journal.pone.0005792.g001

Improved Resolution Haplogroup G Phylogeny in the Y Chromosome, Revealed by a Set of Newly Characterized SNPs

Lynn M. Sims et al.



Y-SNP haplogroup G (hgG), defined by Y-SNP marker M201, is relatively uncommon in the United States general population, with only 8 additional sub-markers characterized. Many of the previously described eight sub-markers are either very rare (2–4%) or do not distinguish between major populations within this hg. In fact, prior to the current study, only 2% of our reference Caucasian population belonged to hgG and all of these individuals were in sub-haplogroup G2a, defined by P15. Additional Y-SNPs are needed in order to differentiate between individuals within this haplogroup.

Principal Findings

In this work we have investigated whether we could differentiate between a population of 63 hgG individuals using previously uncharacterized Y-SNPs. We have designed assays to test these individuals using all known hgG SNPs (n = 9) and an additional 16 unreported/undefined Y-SNPS. Using a combination of DNA sequence and genetic genealogy databases, we have uncovered a total of 15 new hgG SNPs that had been previously reported but not phylogenetically characterized. Ten of the new Y-SNPs are phylogenetically equivalent to M201, one is equivalent to P15 and, interestingly, four create new, separate haplogroups. Three of the latter are more common than many of the previously defined Y-SNPs. Y-STR data from these individuals show that DYS385*12 is present in (70%) of G2a3b1-U13 individuals while only 4% of non-G2a3b1-U13 individuals posses the DYS385*12 allele.


This study uncovered several previously undefined Y-SNPs by using data from several database sources. The new Y-SNPs revealed in this paper will be of importance to those with research interests in population biology and human evolution.


June 03, 2009

Birth size and IQ in Asian children

2.19 IQ points for an extra kg of birth weight seems quite meager.

Pediatrics. 2009 Jun;123(6):e1011-e1016.

The Influence of Birth Size on Intelligence in Healthy Children.

Broekman BF, Chan YH, Chong YS, Quek SC, Fung D, Low YL, Ooi YP, Gluckman PD, Meaney MJ, Wong TY, Saw SM.

OBJECTIVE. Birth parameters have been hypothesized to have an influence on IQ. However, studies within the range of normal birth size have been sparse. With this study we examined the associations between birth length, birth weight, head circumference, and gestational age within the normal birth size range in relation to childhood IQ in Asian children. METHODS. A cohort of 1979 of 2913 Asian children aged 7 to 9 years, recruited from 3 schools in Singapore, were followed yearly from 1999 onward. Birth parameters were recorded by health personnel. Childhood IQ was measured with the Raven's Standard Progressive Matrices at ages 8 to 12. RESULTS. The mean IQ score across the sample (n = 1645) was 114.2. After controlling for multiple confounders for every 1-cm increment in birth length, 1 kg in birth weight, or 1 cm in head circumference, there was a corresponding increase in IQ of 0.49 points (P for trend less than .001), 2.19 points (P for trend = .007) and .62 points (P for trend = .003), respectively. These associations persisted even after exclusion of premature children and children with extreme weights and head circumferences. CONCLUSIONS. Longer birth length, higher birth weight, or larger head circumferences within the normal birth size range are associated with higher IQ scores in Asian children. Our results suggest that antenatal factors reflected in altered rates of growth but within the normative range of pregnancy experiences play a role in generating cognitive potential. This has implications for targeting early intervention and preventative programs.


June 02, 2009

Patterns of natural selection and phenotype convergence in FUT2

This paper shows an example of convergent evolution in humans, in which similarity in an observable trait is explained by different underlying gene variants. Another example of this phenomenon is convergent evolution of skin color with depigmentation of Caucasoids and Mongoloids relative to the African ancestral form occurred due to different mutations, or lactase persistence where the ability to digest milk evolved independently in Europe and Africa.

Molecular Biology and Evolution doi:10.1093/molbev/msp108

A natural history of FUT2 polymorphism in humans

Anna Ferrer-Admetlla et al.


Because pathogens are powerful selective agents, host cell surface molecules used by pathogens as identification signals can reveal the signature of selection. Most of them are oligosaccharides, synthesized by glycosyltransferases. One known example is balancing selection shaping ABO evolution as a consequence of both, A and B antigens being recognized as receptors by some pathogens, and anti-A and/or anti-B natural antibodies produced by hosts conferring protection against the numerous infectious agents expressing A and B motifs. These antigens can also be found in tissues other than blood if there is activity of another enzyme, FUT2, a fucosyltransferase responsible for ABO biosynthesis in body fluids. Homozygotes for null variants at this locus present the non-secretor phenotype (se), since they can not express ABO antigens in secretions. Multiple independent mutations have been shown to be responsible for the non-secretor phenotype, which is coexisting with the secretor phenotype in most populations. In this study, we have resequenced the coding region of FUT2 in 732 individuals from 39 worldwide human populations. We report a complex pattern of natural selection acting on the gene. While frequencies of secretor and non-secretor phenotypes are similar in different populations, the point mutations at the base of the phenotypes are different, with some variants showing a long history of balancing selection among Eurasian and African populations, and one recent variant showing a fast spread in East Asia, likely due to positive selection. Thus a convergent phenotype composition has been achieved through different mutations with different evolutionary histories.