Recent Tibetan adaptation for high altitude

From the New Scientist:

Mountain-dwelling Tibetans have genetically adapted to life at altitude in the past 3000 years – the fastest genetic change known to have occurred in humans.

Rasmus Nielsen at the University of California, Berkeley, and his colleagues looked at the DNA of people living in two villages at 4300 and 4600 metres above sea level in Tibet. At these heights, oxygen levels are about 40 per cent lower than at sea level and lowlanders experience hypoxia, which is associated with headaches, fatigue, smaller fetuses and more deaths in infancy.

Tibetans don't suffer from hypoxia, but it has been unclear why. Nielsen's team compared the DNA of 50 Tibetans with that of 40 Han Chinese people from Beijing and 200 people of European ancestry from Denmark, all of whom live at altitudes below 2000 metres.

By comparing the DNA of the three groups, the team identified the specific genetic differences between the Tibetan and Han populations, thought to have diverged around 2750 years ago.

Science Vol. 329. no. 5987, pp. 72 - 75
DOI: 10.1126/science.1189406

Genetic Evidence for High-Altitude Adaptation in Tibet

Tatum S. Simonson et al.

Abstract

Tibetans have lived at very high altitudes for thousands of years, and they have a distinctive suite of physiological traits that enable them to tolerate environmental hypoxia. These phenotypes are clearly the result of adaptation to this environment, but their genetic basis remains unknown. We report genome-wide scans that reveal positive selection in several regions that contain genes whose products are likely involved in high-altitude adaptation. Positively selected haplotypes of EGLN1 and PPARA were significantly associated with the decreased hemoglobin phenotype that is unique to this highland population. Identification of these genes provides support for previously hypothesized mechanisms of high-altitude adaptation and illuminates the complexity of hypoxia-response pathways in humans.

Link
Science Vol. 329. no. 5987, pp. 75 - 78
DOI: 10.1126/science.1190371

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

Xin Yi et al.

Abstract

Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPAS1 shows a 78% frequency difference between Tibetan and Han samples, representing the fastest allele frequency change observed at any human gene to date. This SNP’s association with erythrocyte abundance supports the role of EPAS1 in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus in genetic adaptation to high altitude.

Link

New England Centenarian study

(Last Update: Jul 8)

This project has a new paper in Science. It's a strange and fascinating achievement that a test purports to guess whether you'll live to be 100 with 77% accuracy.

Becoming a centenarian is rare, and guessing the occurrence of rare events is notoriously difficult. It will be interesting to see how these results generalize to a different study population.

UPDATE (Jul 8):

Well, as I mentioned above, guessing the occurrence of rare events is notoriously difficult, and scientists that have looked at this study cast doubt on its validity. If it's too good to be true, it probably ain't. The more interesting question: how did it slip into Science?

Science DOI: 10.1126/science.1190532

Genetic Signatures of Exceptional Longevity in Humans

Paola Sebastiani

Abstract

Healthy aging is thought to reflect the combined influence of environmental factors (lifestyle choices) and genetic factors. To explore the genetic contribution, we undertook a genome-wide association study of exceptional longevity (EL) in 1055 centenarians and 1267 controls. Using these data, we built a genetic model that includes 150 single-nucleotide polymorphisms (SNPs) and found that it could predict EL with 77% accuracy in an independent set of centenarians and controls. Further in silico analysis revealed that 90% of centenarians can be grouped into 19 clusters characterized by different combinations of SNP genotypes—or genetic signatures—of varying predictive value. The different signatures, which attest to the genetic complexity of EL, correlated with differences in the prevalence and age of onset of age-associated diseases (e.g., dementia, hypertension, and cardiovascular disease) and may help dissect this complex phenotype into subphenotypes of healthy aging.

Link

Parasites and Intelligence (Eppig et al. 2010)

This is as good an explanation for global differences in IQ as I have ever seen. It proposes that IQ differences between human groups are created during ontogeny due to an energetic trade-off between brain development and immune response to infectious disease. In regions of the world with a high parasite burden, there is an elevated amount of energy used up to fight disease, at the expense of brain development.

Notice that this is not an explanation requiring genetic adaptation. Parasite burden inhibits cognitive function development. Indeed, if one were to make an adaptive argument (and I will not!), it would be in the direction of greater brain development genetic potential in parasite-heavy locales to counteract the effects of disease, i.e., the selection of individuals that may withstand the rigors of fighting off infectious disease without compromising cognitive function.

The authors write:

Multiple regression shows that, of infectious disease, temperature, evolutionary novelty and AVED, infectious disease is the best predictor of intelligence by a large margin.

...

If the general pathway we propose is correct, there are two plausible mechanisms by which a trade-off in allocation of energy to immune function versus brain development and maintenance may occur. First, parasitic infection may intermittently cause the redirection of energy away from brain development. In this case, during periods of infection, the brain receives fewer energetic resources, but this allocation to brain function will return to pre-infection levels during healthy periods. During periods of infection, whatever aspects of the brain that are growing and developing will suffer reduced phenotypic quality. Second, exposure to infectious agents may cause a developmental pathway that permanently invests more energy into immune function at the expense of brain growth. In this scenario, large amounts of energy would be allocated into immune function during periods of health, as opposed to only redirecting energy during periods of infection. This could operate through a variety of mechanisms. A plausible mechanism is that higher investment in immune system is triggered by individual exposure to infectious disease at some point during ontogeny. This may include triggering from exposure to maternal antibodies while in utero.

...

Our findings suggest that the heritable variation in intelligence may come from two sources: brain structure and immune system quality. Thus, two individuals may possess identical genes for brain structure, but have different IQ owing to differences in immune system quality reflecting their personal allocation of energy into brain development versus immunity.

...

Our findings are consistent with a number of other findings in the literature. In particular, the Flynn effect (Flynn 1987) demands that any hypothesis regarding the worldwide variation and distribution of intelligence must be able to account for some factor that allows for large IQ gains over time spans seemingly too short to be attributed to evolution by natural selection. The parasite-stress hypothesis allows for such a factor in the form of reduced parasitic infection. As societies become modernized, decreased parasite stress may occur through multiple pathways. As national wealth increases, medicine, vaccinations and potable water can be purchased by both the government and by individuals. Moreover, there is cross-national evidence that, as democratization increases, there are corresponding increases in public health legislation and infrastructure. Democratization also increases levels of education, better allowing individuals to seek out and understand information that reduces parasitic infection (Thornhill et al. 2009). This source of endogeneity is not a flaw, but a prediction of our hypothesis.

Related:

• Pathogens and Collectivism
• Religious Diversity and pathogens

Proceedings of the Royal Society B doi:10.1098/rspb.2010.0973

Parasite prevalence and the worldwide distribution of cognitive ability

Christopher Eppig et al.

Abstract

In this study, we hypothesize that the worldwide distribution of cognitive ability is determined in part by variation in the intensity of infectious diseases. From an energetics standpoint, a developing human will have difficulty building a brain and fighting off infectious diseases at the same time, as both are very metabolically costly tasks. Using three measures of average national intelligence quotient (IQ), we found that the zero-order correlation between average IQ and parasite stress ranges from r = −0.76 to r = −0.82 (p less than 0.0001). These correlations are robust worldwide, as well as within five of six world regions. Infectious disease remains the most powerful predictor of average national IQ when temperature, distance from Africa, gross domestic product per capita and several measures of education are controlled for. These findings suggest that the Flynn effect may be caused in part by the decrease in the intensity of infectious diseases as nations develop.

Link

Brain structure and Personality Big Five

From the paper:

The associations of personality traits with volume in predicted brain regions were generally consistent with the hypothesis that larger brain tissue volume is associated with increased function (with the exception of the negative association of Agreeableness with volume in superior temporal sulcus). For example, Neuroticism was positively associated with volume in a region of the cingulate linked to the detection of error and response to pain, both of which increase with Neuroticism. Also, Neuroticism was negatively associated with volume in a region of PFC associated with emotional regulation, which decreases with Neuroticism. However, our findings do not provide definitive evidence to allow generalizations about the relation of volume to function, and further research should target this question directly.

Psychological Science doi:10.1177/0956797610370159

Testing Predictions From Personality Neuroscience
Brain Structure and the Big Five

Colin G. DeYoung et al.

Abstract

We used a new theory of the biological basis of the Big Five personality traits to generate hypotheses about the association of each trait with the volume of different brain regions. Controlling for age, sex, and whole-brain volume, results from structural magnetic resonance imaging of 116 healthy adults supported our hypotheses for four of the five traits: Extraversion, Neuroticism, Agreeableness, and Conscientiousness. Extraversion covaried with volume of medial orbitofrontal cortex, a brain region involved in processing reward information. Neuroticism covaried with volume of brain regions associated with threat, punishment, and negative affect. Agreeableness covaried with volume in regions that process information about the intentions and mental states of other individuals. Conscientiousness covaried with volume in lateral prefrontal cortex, a region involved in planning and the voluntary control of behavior. These findings support our biologically based, explanatory model of the Big Five and demonstrate the potential of personality neuroscience (i.e., the systematic study of individual differences in personality using neuroscience methods) as a discipline.

Link (pdf)

Earliest copper smelting from the Balkans

Journal of Archaeological Science doi:10.1016/j.jas.2010.06.012

On the Origins of Extractive Metallurgy: New evidence from Europe

Miljana Radivojević et al.

The beginnings of extractive metallurgy in Eurasia are contentious. The first cast copper objects in this region emerge c7000 years ago, and their production has been tentatively linked to centres in the Near East. This assumption, however, is not substantiated by evidence for copper smelting in those centres. Here, we present results from recent excavations from Belovode, a Vinča culture site in Eastern Serbia, which has provided the earliest direct evidence for copper smelting to date. The earliest copper smelting activities there took place c7000 years ago, contemporary with the emergence of the first cast copper objects. Through optical, chemical and provenance analyses of copper slag, minerals, ores and artefacts, we demonstrate the presence of an established metallurgical technology during this period, exploiting multiple sources for raw materials. These results extend the known record of copper smelting by more than half a millennium, with substantial implications. Extractive metallurgy occurs at a location far away from the Near East, challenging the traditional model of a single origin of metallurgy and reviving the possibility of multiple, independent inventions.

Link

Half of hidden heritability found (for height, at least)

This is a quite interesting paper, as it shows, by sampling a large number of individuals), that the heritability of height is not missing after all. The authors looked at a large number of individuals, and this allowed them to discover statitically significant associations between height and more SNPs than before.

This bears great promise as it may hint that genome-wide association studies, that have come under substantial criticism lately, may be failing not because of an inherent flaw, but rather because they are not sampling enough individuals.

The discovered SNPs account for 45% of the heritability of height. Where is the rest? The authors argue for two additional sources:

First, SNPs in current microarray chips sample the genome incompletely. Locations in-between discovered SNPs are in incomplete linkage disequilibrium with the discovered SNPs. So, there is undetected polymorphism, in the gaps between the hundreds of thousands of SNPs in current chips, that may explain a portion of the missing heritability.

Second, SNPs have different minor allele frequencies. For example, in one SNP the minor allele may occur at 10% of individuals, while in others at 30%. This is important, because it is more difficult to arrive at a statistically significant result in the former case.

Consider a SNP with a minor allele frequency of 2%. Then, if you sample 1,000 individuals, only about 20 of them are expected to have the minor allele. You cannot estimate the average height of the minor allele with a sample of 20 people as securely as you can with a sample of 500. Thus, if the SNP influences height in a small way, you will not be able to detect it.

A further complication, which I've written about before, is that some variation in the human genome is family-related, or at least occurs at fewer individuals than the allele frequency cutoff. If 99.9% of people have C at a given location and 0.1% of people have T, this variant is unlikely to be included in a microarray chp, because it is too rare to matter economically: you would only get a handful of individuals -if you're lucky- in a sample of 1,000 for such a variant. However, rarity does not mean that the variant is functionally unimportant, and the rare allele may play a substantial role in the height of the people who possess it.

The publication of this paper is a cause for optimism, as it shows that progress can be made by brute force: fuller genome coverage and more individuals. We'll have to wait and see whether or not the same approach will work for other complex traits, such as IQ or schizophrenia, that have been hitherto difficult to crack.

Obviously, the cost of sampling more individuals will become an issue in future studies, but the cost-per-individual is expected to drop. So, I'm guessing that more discoveries are in store for us in the next few years.

UPDATE (Jun 28):

Not the main point of the paper, but also included in the supplementary material (pdf) are some nice PCA results.

In the European-only PCA we see the familiar north-south gradient (anchored by Tuscans TSI and Netherlands NET on either side), and the orthogonal deviation of the Finns. Swedes (SWE) occupy a northern European end of the spectrum like the Dutch, but are spread towards Finns, reflecting low-level Finnish admixture in that population. Conversely, Finns are variable along the same axis, reflecting variable levels of admixture. Australians (AUS) and UK, on the other hand, are on the northern European edge of the main European gradient, with a number of individuals spread toward the Tuscan side.

The PCA with all populations is also quite interesting. East Eurasians (Chinese and Japanese) form a tight pole at the bottom right. Gujarati Indians (GIH) form a different pole, spread towards Europeans, reflecting variable levels of West Eurasian admixture in that population, probably corresponding to the ANI element recently discovered in Indian populations. Mexicans (MEX) are spread towards East Asians, reflecting their Amerindian admixture, but notice how they are not positioned exactly on the European-East Asian axis, probably reflecting the third, minority, Sub-Saharan element in their ancestry, as well as the fact that Amerindians are not perfectly represented by East Asians. Finns are tilted towards East Asians, as expected, reflecting the fact that their genetic specificity vis a vis Northern Europeans is due to low-level East Eurasian ancestry.

An interesting aspect of the first two PCs is the fact that the Maasai (MKK) and Luhya (LUW) from Kenya are not separated from Caucasoids, and neither are Yoruba from Nigeria (YRI). This is a good reminder of the fact that identity in the first two principal components may mask difference revealed in higher order components. This difference (at least for Maasai) is seen in the next two PCs.

Nature Genetics doi:10.1038/ng.608

Common SNPs explain a large proportion of the heritability for human height

Jian Yang et al.

Abstract

SNPs discovered by genome-wide association studies (GWASs) account for only a small fraction of the genetic variation of complex traits in human populations. Where is the remaining heritability? We estimated the proportion of variance for human height explained by 294,831 SNPs genotyped on 3,925 unrelated individuals using a linear model analysis, and validated the estimation method with simulations based on the observed genotype data. We show that 45% of variance can be explained by considering all SNPs simultaneously. Thus, most of the heritability is not missing but has not previously been detected because the individual effects are too small to pass stringent significance tests. We provide evidence that the remaining heritability is due to incomplete linkage disequilibrium between causal variants and genotyped SNPs, exacerbated by causal variants having lower minor allele frequency than the SNPs explored to date.

Link

Genetic structure of Qatar (Hunter-Zinck et al. 2010)

(Last Update Jul 11)

On the left the position of the three groups on the global PCA (Supplementary Figure 1). What's interesting about this figure is that it is done on low-F_ST SNPs, which should make them more resilient to the effects of ascertainment bias, i.e., the fact that SNPs used in the Affymetrix chip were found to be polymorphic in different populations than those of Qatar, and, correspondingly, very informative Qatari SNPs may be missing from the chip. Nonetheless, the differentiation between the three groups follows closely what one gets from the full set that is in the paper.

UPDATE (Jul 11):

The split into three groups was verified by STRUCTURE analysis of the Qatari individuals. Qatar 1 (red), Qatar 2 (blue), Qatar 3 (green) are quite evident:

The authors then compared surnames with membership in the three Qatari clusters, uncovering that:

A Mantel test comparing Qatari subgroups and surname origins indicates highly significant (p = 0.0001) correlations across the three population groups in the frequency of these name classifications, with the Qatar1 population having mostly Arab surnames, the Qatar2 population having a large Persian component, and the Qatar3 population appearing to be the most diverse and having the largest African component (Figure 7).

I think that it is a good idea for future studies of national populations to perform similar analyses in order to determine their homogeneity or lack thereof. This is quite critical, as population-specific features in a heterogeneous population may be incorrectly inferred, depending on the exact "sample mix" of the tested individuals. In this study, for example, Qatar1 (Arab-dominated) individuals were the most consanguineous, but the level of their consanguinity would have been underestimated if they had not been identified as a distinct component of the Qatari population.

The American Journal of Human Genetics
doi:10.1016/j.ajhg.2010.05.018

Population Genetic Structure of the People of Qatar

Haley Hunter-Zinck et al.

People of the Qatar peninsula represent a relatively recent founding by a small number of families from three tribes of the Arabian Peninsula, Persia, and Oman, with indications of African admixture. To assess the roles of both this founding effect and the customary first-cousin marriages among the ancestral Islamic populations in Qatar's population genetic structure, we obtained and genotyped with Affymetrix 500k SNP arrays DNA samples from 168 self-reported Qatari nationals sampled from Doha, Qatar. Principal components analysis was performed along with samples from the Human Genetic Diversity Project data set, revealing three clear clusters of genotypes whose proximity to other human population samples is consistent with Arabian origin, a more eastern or Persian origin, and individuals with African admixture. The extent of linkage disequilibrium (LD) is greater than that of African populations, and runs of homozygosity in some individuals reflect substantial consanguinity. However, the variance in runs of homozygosity is exceptionally high, and the degree of identity-by-descent sharing generally appears to be lower than expected for a population in which nearly half of marriages are between first cousins. Despite the fact that the SNPs of the Affymetrix 500k chip were ascertained with a bias toward SNPs common in Europeans, the data strongly support the notion that the Qatari population could provide a valuable resource for the mapping of genes associated with complex disorders and that tests of pairwise interactions are particularly empowered by populations with elevated LD like the Qatari.

Link

Y chromosome haplogroup I and disease-based selection

There have been occasional studies about natural selection acting on Y chromosome haplogroups, but this seems to one be one of the most convincing ones.

From the paper:

In this study, we aimed to refine our understanding of AIDS susceptibility associated with hg-I. We first analyzed AIDS progression differences between hg-I subhaplogroups and the phylogenetically closest haplogroup, haplogroup J (hg-J). Previously, we reported faster progression to AIDS outcomes in hg-I compared to the most common European haplogroup R, but did not analyze hg-J. As hg-I and hg-J are sister clades with similar time depths, and likely to have relatively closely related sequence organizations, it is interesting to see if the disease susceptibility is unique to hg-I or common among the hg-IJ clades.

The authors did identify that the AIDS susceptibility was Hg-I specific and was not shared by its sister clade, haplogroup J. From the paper:

There were significant differences between the hg-I subhaplogroups and hg-J samples for AIDS progression, where hg-I subhaplogroups depleted CD4+ T cells and progressed to AIDS 1993 and AIDS 1987 faster (Table 1). However, the faster AIDS progression signal (compared to the hg-J samples) was not significant for every individual hg-I subhaplogroup, probably due to small sample sizes resulting in lack of statistical power. When all hg-I subhaplogroups were combined (representing hg-I) and compared against hg-J, the significant AIDS progression differences were more evident (Pp0.02 for each AIDS end point; Table 1).

In contrast, when the hg-I subhaplogroup samples were compared against each other, the Cox analyses did not show a significant AIDS progression differences between them (Table 1).

One of the most interesting things about haplogroup I is its paucity outside Europe, in either West Asia or Siberia. The very strong genetic patterning of its sub-haplogroups in Europe is also quite noteworthy.

So, I am very willing to entertain the possibility that haplogroup I's distribution was shaped by rather recent evolutionary events that time has not been able to smooth out, and directional selection on this haplogroup seems like a very likely proposition.

The predominance of this haplogroup in the Lichtenstein cave remains from Bronze Age Germany is certainly not conclusive, but it may hint at a shift in frequency of this haplogroup in Europe. Hopefully more studies in both extant and ancient populations may provide data on this haplogroup's history.

Related:

• Y chromosome haplogroup I and rapid HIV progression
• mtDNA haplogroups and AIDS progression
• Male infertility induced by mtDNA/Y unfavorable combination? An association study on human mitochondrial DNA

J Hum Genet doi:10.1038/jhg.2010.77

Examination of disease-based selection, demographic history and population structure in European Y-chromosome haplogroup I.

Efe Sezgin et al.

Abstract

We attempted to refine the understanding of an association of Y-chromosomal haplogroup I (hg-I) with enhanced AIDS progression that had been previously reported. First, we compared the progression phenotype between hg-I and its phylogenetically closest haplogroup J. Then, we took a candidate gene approach resequencing DDX3Y, a crucial autoimmunity gene, in hg-I and other common European Y-chromosome haplogroups looking for functional variants. We extended the genetic analyses to CD24L4 and compared and contrasted the roles of disease-based selection, demographic history and population structure shaping the contemporary genetic landscape of hg-I chromosomes. Our results confirmed and refined the AIDS progression signal to hg-I, though no gene variant was identified that can explain the disease association. Molecular evolutionary and genetic analyses of the examined loci suggested a unique evolutionary history in hg-I, probably shaped by complex interactions of selection, demographic history and high geographical differentiation leading to the formation of distinct hg-I subhaplogroups that today are associated with HIV/AIDS onset. Clearly, further studies on Y-chromosome candidate loci sequencing to discover functional variants and discern the roles of evolutionary factors are warranted.

Link

Population structure in Ireland and Britain (O'Dushlaine et al. 2010)

From the paper:

Eigensoft PCA analysis across all seven of our European and European-ancestry populations broadly identified four sub-groups consisting of (i) Bulgarian, (ii) Portuguese, (iii) Swedish and (iv) Irish/British/Utah populations (see Figure 1a, Supplementary Figure S1). The first two principal components (PCs) separate out northern from southern, and western from eastern European ancestry, respectively. The Europe-wide PCA analysis positions the Scottish population (Aberdeen) intermediate between the Irish and English populations. We further explored this observation by restricting our PC analysis to residents of Ireland, Scotland (Aberdeen) and south/southeast England (Figure 1b, Supplementary Figure S1). This analysis confirms the observation that the Scottish population is intermediate between the Irish and English cohorts on the first principal component(this time dividing west from east). Although more subtle, the Scottish cohort is also shifted slightly from the other two on PC2.

The distinction between Britons and Swedes was also noted in an earlier study. It's nice to see Bulgarians and Portuguese sampled, as they have been rather neglected in genomic studies, but, unfortunately none of their neighbors or any other intermediate populations were included, which is understandable as the study focused on British Isles populations. Bulgarians and Portuguese served as "anchor points" to re-create the well-known correlation of the first two PCs of European genetic variation with longitude/latitude.

The intermediate position of Scottish populations relative to the Irish and English is not surprising, given the Gaelic connection between Scotland and Ireland.

The paper also has haplotype diversity data that can be compared with those recently published by Auton et al.

The authors observe:

In summary, our results illustrate a subtle genetic structure across Britain and Ireland in the context of the comparatively homogenous nature of the European genetic pool. We have observed slightly elevated levels of LD and genome-wide homozygosity in Ireland and Sweden compared with neighbouring British and European populations, although these levels do not approach those of traditional population isolates. Similarly, we have illustrated a decrease in HD in Britain and Ireland, more so in Scotland and Ireland than in England.

Finally, the authors present results of frappe analysis (Figure S2):


At K=2 we see a distinction between northern and southern Europeans.

At K=3 a distinction between British Isles and Sweden appears. The absence of the Western European component in Bulgarians is noteworthy and expected.

At K=4 the Bulgarian component is identified.

At K=5 a Portuguese component is identified.

British Isles populations are dominated by the "Northwestern" green component with variable "Scandinavian" white (which is higher in England as expected) and both "Iberian" and "Balkan" minority elements.

European Journal of Human Genetics doi: 10.1038/ejhg.2010.87

Population structure and genome-wide patterns of variation in Ireland and Britain

Colm T O'Dushlaine et al.

Abstract

Located off the northwestern coast of the European mainland, Britain and Ireland were among the last regions of Europe to be colonized by modern humans after the last glacial maximum. Further, the geographical location of Britain, and in particular of Ireland, is such that the impact of historical migration has been minimal. Genetic diversity studies applying the Y chromosome and mitochondrial systems have indicated reduced diversity and an increased population structure across Britain and Ireland relative to the European mainland. Such characteristics would have implications for genetic mapping studies of complex disease. We set out to further our understanding of the genetic architecture of the region from the perspective of (i) population structure, (ii) linkage disequilibrium (LD), (iii) homozygosity and (iv) haplotype diversity (HD). Analysis was conducted on 3654 individuals from Ireland, Britain (with regional sampling in Scotland), Bulgaria, Portugal, Sweden and the Utah HapMap collection. Our results indicate a subtle but clear genetic structure across Britain and Ireland, although levels of structure were reduced in comparison with average cross-European structure. We observed slightly elevated levels of LD and homozygosity in the Irish population compared with neighbouring European populations. We also report on a cline of HD across Europe with greatest levels in southern populations and lowest levels in Ireland and Scotland. These results are consistent with our understanding of the population history of Europe and promote Ireland and Scotland as relatively homogenous resources for genetic mapping of rare variants.

Link

Genes predict village of origin in rural Europe (O'Dushlaine et al. 2010)

It is wonderful how fine-scale genetic analysis allows us to drill down to the village level. There was another paper on village-level differentiation in Sardinia, and the current report demonstrates that it was no fluke, but the phenomenon is broader. From the paper:

Using 300 000 SNPs and only unrelated, non-inbred individuals with all four grandparents from the same valley, village or isle, we here show the genomic differentiation across 8–30 km in three disparate areas of rural Europe, using genetic information alone (Figure 1). PCA of genomic sharing and model-based clustering (not shown) both allow separation of individuals with grandparents from each of three small Scottish isles, three alpine valleys in the north of Italy and two villages on one small island in Croatia. We used a supervised classification approach to predict subpopulation membership. Highly reliable levels of prediction were achieved with 100, 96 and 89% of individuals correctly classified on the basis of their genetic data for Italy, the Scottish Isles and Croatia, respectively.

Human population differentiation has many levels: continental populations, ethnic groups, regions, and now villages can be distinguished from each other. Even though most extant Europeans are not descended from a single village and -increasingly- from a single region within their countries of origin, it is a good guess that many of their ancestors were far less mobile than they were. Good genealogical records and modern genomics makes it -in principle- possible to reconstruct fine-scale genomic maps of Europe.

The only limiting factors are cost and interest. Even as fewer and fewer people live in isolated communities, intermixture has not yet proceeded to a degree that geographical distinctions will be lost forever. Of course, it's more difficult to infer village- or region-level genetic signatures from the jumbled genomes of modern Europeans, so it might be worthwhile to capture a snapshot of European genetic variation today than to puzzle it out in the future.

Related:

• Genetic differentiation at the village level in Sardinia

European Journal of Human Genetics doi: 10.1038/ejhg.2010.92

Genes predict village of origin in rural Europe

Colm O'Dushlaine et al.

Abstract

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

Link

Modern humans bite hard

From the paper:

Our findings offer an explanation for the apparently inconsistent presence of a dentition in H. sapiens that appears well adapted to resist high bite forces relative to other extant hominids, set in a cranium and mandible that are relatively gracile and characterized by less robust musculature. Thus, the teeth of humans need to be able to resist comparable bite reaction forces to those of other extant hominids, but, because considerably less muscle force is required to achieve any given bite reaction force in the human than in other hominids, less stress is produced.

...

We conclude that although humans are well adapted to produce high peak forces with the jaw moving in rotation, they may not be as well adapted to produce and maintain high bite forces with the jaw moving in translation. Thus, Homo sapiens may be comparable to other hominids in possessing an ability to access some relatively hard foods through the application of high transitory bite forces, however, our species may be less well adapted to consume tough or hard foods that require powerful, sustained chewing.

Proceedings of the Royal Society B doi: 10.1098/rspb.2010.0509

The craniomandibular mechanics of being human

Stephen Wroe et al.

Diminished bite force has been considered a defining feature of modern Homo sapiens, an interpretation inferred from the application of two-dimensional lever mechanics and the relative gracility of the human masticatory musculature and skull. This conclusion has various implications with regard to the evolution of human feeding behaviour. However, human dental anatomy suggests a capacity to withstand high loads and two-dimensional lever models greatly simplify muscle architecture, yielding less accurate results than three-dimensional modelling using multiple lines of action. Here, to our knowledge, in the most comprehensive three-dimensional finite element analysis performed to date for any taxon, we ask whether the traditional view that the bite of H. sapiens is weak and the skull too gracile to sustain high bite forces is supported. We further introduce a new method for reconstructing incomplete fossil material. Our findings show that the human masticatory apparatus is highly efficient, capable of producing a relatively powerful bite using low muscle forces. Thus, relative to other members of the superfamily Hominoidea, humans can achieve relatively high bite forces, while overall stresses are reduced. Our findings resolve apparently discordant lines of evidence, i.e. the presence of teeth well adapted to sustain high loads within a lightweight cranium and mandible.

Link

In search of Dionysos. Reassessing a Dionysian context in early Rome

This is the title of a recent dissertation by Carina Håkansson which can be downloaded here. The abstract:

In the present study the possibility of an early appearance of the god Dionysos and his sphere in archaic Rome, in the decades around 500 BC, will be examined.

In early scholarship, rooted in the 19th century, the phenomenon of Dionysian ecstatic rites, cults, and satyr-plays in Roman society was denied. According to that view and the subsequent tradition in religious studies, such cultic activities were not present in Rome. Furthermore, due to Christian presuppositions, religion could scarcely be connected with sexual activities and bawdy behaviour, and as this is one fundamental quality in Dionysian cultic activities, it was reason enough for neglect and rejection of the thought of Dionysian cult as religion proper, on the whole. These preconceptions have long prevailed and formed the foundation for research in Roman religious studies. Scholars in various disciplines now challenge these ideas.

The theoretical framework in this multidisciplinary study focuses on an intercontextual methodology and will have the approach of a case study. The starting point is thus to make a reassessment of the evidence at hand. The importance of the iconographic material is brought forward, beside the literary and epigraphic sources. Finds from the Greek and Etruscan areas supply a comparative perspective since Rome hardly can be seen as an isolated entity. It is suggested that ideas and values travelled rather freely in the area. Parallel Dionysian phenomena are known in the cultural spheres influencing Rome. Dionysos’ visual manifestations are in focus as well as Dionysos’ possible revelation in early Rome and plausible relation to the god Liber. Moreover, the diverse aspects of the satyrs as part of the Dionysian sphere are treated and an attempt is made to explain the satyr in a religious context. Liminality is a central feature when satyrs are concerned, and their function as a symbol of inversion of order is considered. Arguments are given for a strong connection between ritual and performance, thus indicating a cultic origin of performances in Rome, and for an early appearance of Dionysos and his thiasos.

Brown-eyed men perceived to be more dominant

(Last Update June 21)

The authors discovered that males with brown eyes were considered more dominant than males with blue eyes, but when they altered their pictures to turn brown eyes into blue, the effect persisted. Thus, it is not the color itself that creates the impression of dominance, but rather other factors correlated with the brown-eyed phenotype.

One of these "other factors" could be chin breadth, which is known to be perceived as dominant. From the paper:

The question arises: why are brown-eyed males rated as more dominant than blue-eyed? Some facial features such as square jaws, thick eyebrows and broad cheekbones are linked with higher perceived dominance; facial submissiveness, on the other hand, is characterized by a round face with large eyes, smallish nose, and high eyebrows (Berry, 1990; Berry & Mcarthur, 1986; Cunningham,Barbee, & Pike, 1990; Mazur, Halpern, & Udry, 1994; Mueller & Mazur,1997; Thornhill & Gangestad, 1994). The morphological differences between blue-eyed and brown-eyed males were visualized by deformation of thin-plate splines (Fig. 3). In contrast with blue-eyed males, brown-eyed males have statistically broader and rather massive chins, broader (laterally prolonged) mouths, larger noses, and eyes that are closer together with larger eyebrows. In contrast, blue-eyed males show smaller and sharper chins, mouths that are laterally narrower, noses smaller, and a greater span between the eyes. Especially the broader massive chin, bigger nose, and larger eyebrows of brown-eyed males may explain their higher perceived dominance.

The authors propose that true genetic linkage between eye color and these other facial features is unlikely, as eye color is determined by few loci, and these are unlikely to be the same ones that influence these other facial features. Thus, they propose a different explanation, namely that blue-eyed and brown-eyed children are treated differently by their parents as they grow up, and this "different treatment" manifests itself phenotypically. The argument in favor of different treatment stems from the fact that many people are born blue-eyed, but their eye color is set to a darker shade eventually. The authors write:

It is possible that subjects with blue eyes are treated as a small child for a longer period than brown-eyed children. Such early social experience may have been literally ‘‘inscribed” into their faces, preserved until adulthood, and finally bring on the perception of higher submissiveness. Rosenberg and Kagan (1987, 1989) investigated the association between eye color and behavioral inhibition, revealing that children with blue eyes are more inhibited. Coplan et al. (1998) found a significant interaction between eye color and social wariness within preschoolers. Blueeyed males were rated as more socially wary, i.e. being more temperamentally inhibited, displaying more reticent behavior and having more internalizing problems, than males with brown eyes, though there were no differences between blue- and brown-eyed females (Coplan et al., 1998).

There is an alternative explanation, that requires neither genetic linkage nor an environmental factor such as upbringing. That factor is latent population structure.

In a truly long-term random mating population, and assuming that eye color is not genetically linked with e.g. chin breadth, then all combinations of chin breadth and eye color would occur with a probability determined entirely by the frequency of their genetic determinants in the population.

However, consider the possibility that the population is an incomplete mixture of a blue-eyed "facially submissive" population element, and a brown-eyed "facially dominant" one. If that was the case, then brown-eyed folks would tend to have dominant facial features by reason of their ancestry rather than any genetic linkage between the two traits.

As an analogy, consider a hypothetical population made up of Europeans and East Asians. Initially, there would be a statistical association between straight hair and short stature in the total population that would be entirely due to population structure rather than either pleiotropic effects of genes affecting both characters or genetic linkage of hair/stature genes.

The Czech population is intermediate in its bigonial diameter between Germans and Slovaks (its immediate neighbors) [1], they are also genetically intermediate between Germans and Slavs. Procopius noted in early medieval times that Slavs had intermediate pigmentation. So, I wouldn't discount the possibility that population structure due to incomplete blending may account for eye color/facial structure associations in this population.

UPDATE:

Here are some values for German and Czech males from [1].

Bigonial (go-go): 97.6 / 109.5

Nasal height (n-sn): 52 / 54.0

Nasal breadth (al-al): 34.0 / 36.2

Mouth breadth (ch-ch): 50.9 / 53.8

Intercanthal distance (en-en): 31.2/30.9

Unfortunately there is no data for the eyebrows, but all of the above differences are in the expected direction under my theory: Germans have narrower jaws, smaller noses, narrower mouths, and eyes placed further apart than Czechs.

So, I think it is quite likely that the blue-eyed facially submissive type found in this sample may have a German origin.

PS: I did an average of the blue- and brown-eyed averages for reference:

[1] International anthropometric study of facial morphology in various ethnic groups/races, Leslie G Farkas, J Craniofac Surg 16:615-46

Personality and Individual Differences
Volume 49, Issue 1, July 2010, Pages 59-64

Eye color predicts but does not directly influence perceived dominance in men

Karel Kleisner et al.

This study focuses on the relationship between eye color, gender, and psychological characteristics perceived from the human face. Photographs of 40 male and 40 female students were rated for perceived dominance and attractiveness. Attractiveness showed no relation with eye color. In contrast, eye color had a significant effect on perceived dominance in males: brown-eyed men were rated as more dominant than men with blue eyes. To control for the effect of eye color, we studied perceived dominance on the same photographs of models after changing the iris color. The eye color had no effect on perceived dominance. This suggests that some other facial features associated with eye color affect the perception of dominance in males. Geometric morphometrics have been applied to reveal features responsible for the differences in facial morphospace of blue-eyed and brown-eyed males.

Link

Radiocarbon based chronology for ancient Egypt (Ramsey et al. 2010)

Science Vol. 328. no. 5985, pp. 1554 - 1557
DOI: 10.1126/science.1189395

Radiocarbon-Based Chronology for Dynastic Egypt

Christopher Bronk Ramsey et al.

The historical chronologies for dynastic Egypt are based on reign lengths inferred from written and archaeological evidence. These floating chronologies are linked to the absolute calendar by a few ancient astronomical observations, which remain a source of debate. We used 211 radiocarbon measurements made on samples from short-lived plants, together with a Bayesian model incorporating historical information on reign lengths, to produce a chronology for dynastic Egypt. A small offset (19 radiocarbon years older) in radiocarbon levels in the Nile Valley is probably a growing-season effect. Our radiocarbon data indicate that the New Kingdom started between 1570 and 1544 B.C.E., and the reign of Djoser in the Old Kingdom started between 2691 and 2625 B.C.E.; both cases are earlier than some previous historical estimates.

Link

Wealth and people and the invasion of alien species

This is an open access paper.

PNAS doi:10.1073/pnas.1002314107

Disentangling the role of environmental and human pressures on biological invasions across Europe

Petr Pyšek et al.

The accelerating rates of international trade, travel, and transport in the latter half of the twentieth century have led to the progressive mixing of biota from across the world and the number of species introduced to new regions continues to increase. The importance of biogeographic, climatic, economic, and demographic factors as drivers of this trend is increasingly being realized but as yet there is no consensus regarding their relative importance. Whereas little may be done to mitigate the effects of geography and climate on invasions, a wider range of options may exist to moderate the impacts of economic and demographic drivers. Here we use the most recent data available from Europe to partition between macroecological, economic, and demographic variables the variation in alien species richness of bryophytes, fungi, vascular plants, terrestrial insects, aquatic invertebrates, fish, amphibians, reptiles, birds, and mammals. Only national wealth and human population density were statistically significant predictors in the majority of models when analyzed jointly with climate, geography, and land cover. The economic and demographic variables reflect the intensity of human activities and integrate the effect of factors that directly determine the outcome of invasion such as propagule pressure, pathways of introduction, eutrophication, and the intensity of anthropogenic disturbance. The strong influence of economic and demographic variables on the levels of invasion by alien species demonstrates that future solutions to the problem of biological invasions at a national scale lie in mitigating the negative environmental consequences of human activities that generate wealth and by promoting more sustainable population growth.

Link

Mediterranean diet improves autonomic heart function among middle-aged men

Circulation: Cardiovascular Quality and Outcomes doi: 10.1161/CIRCOUTCOMES.109.905810

Mediterranean Dietary Pattern Is Associated With Improved Cardiac Autonomic Function Among Middle-Aged Men

A Twin Study

Jun Dai et al.

Background Reduced heart rate variability (HRV), a measure of cardiac autonomic dysfunction, is a risk factor for coronary artery disease. Diet can influence HRV, but this association may be confounded by genetic and environmental factors.

Methods and Results We administered the Willett Food Frequency Questionnaire to 276 middle-aged male twins. We derived a score measuring the extent to which an individual's diet conformed to the Mediterranean diet following a published algorithm. The higher the score, the greater the similarity to the Mediterranean diet. All twins underwent 24-hour ambulatory ECG recording. Time and frequency domain measures of HRV were calculated. Mixed-effects regression was used to partition the association into between- and within-twin pair differences. After adjusting for energy intake, other nutritional factors, shared genes, and common environment, a 1-unit higher score was significantly associated with 3.9% to 13% higher time and frequency domain HRV parameters. Further controlling for known cardiovascular risk factors and use of fish oil supplements and medications did not substantially change the estimates.

Conclusions The Mediterranean dietary pattern is associated with higher HRV.

Link