December 31, 2006

Convergent skin color evolution in Caucasoids and Mongoloids

MBE Advance Access published online on December 20, 2006

Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians

Heather L. Norton et al.

Human skin pigmentation shows a strong positive correlation with ultraviolet radiation (UVR) intensity, suggesting that variation in skin color is, at least partially, due to adaptation via natural selection. We investigated the evolution of pigmentation variation by testing for the presence of positive directional selection in six pigmentation genes using an empirical FST approach, through an examination of global diversity patterns of these genes in the CEPH-Diversity Panel, and by exploring signatures of selection in data from the International HapMap project. Additionally, we demonstrated a role for MATP in determining normal skin pigmentation variation using admixture mapping methods. Taken together (with the results of previous admixture mapping studies), these results point to the importance of several genes in shaping the pigmentation phenotype and a complex evolutionary history involving strong selection. Polymorphisms in two genes, ASIP and OCA2, may play a shared role in shaping light and dark pigmentation across the globe while SLC24A5, MATP, and TYR have a predominant role in the evolution of light skin in Europeans but not in East Asians. These findings support a case for the recent convergent evolution of a lighter pigmentation phenotype in Europeans and East Asians.


Genetic components of Argentinean population

American Journal of Physical Anthropology (Early view)

Argentine population genetic structure: Large variance in Amerindian contribution

Michael F. Seldin et al.


Argentine population genetic structure was examined using a set of 78 ancestry informative markers (AIMs) to assess the contributions of European, Amerindian, and African ancestry in 94 individuals members of this population. Using the Bayesian clustering algorithm STRUCTURE, the mean European contribution was 78%, the Amerindian contribution was 19.4%, and the African contribution was 2.5%. Similar results were found using weighted least mean square method: European, 80.2%; Amerindian, 18.1%; and African, 1.7%. Consistent with previous studies the current results showed very few individuals (four of 94) with greater than 10% African admixture. Notably, when individual admixture was examined, the Amerindian and European admixture showed a very large variance and individual Amerindian contribution ranged from 1.5 to 84.5% in the 94 individual Argentine subjects. These results indicate that admixture must be considered when clinical epidemiology or case control genetic analyses are studied in this population. Moreover, the current study provides a set of informative SNPs that can be used to ascertain or control for this potentially hidden stratification. In addition, the large variance in admixture proportions in individual Argentine subjects shown by this study suggests that this population is appropriate for future admixture mapping studies.


December 30, 2006

New edition of YHRD database is online

From the curators of YHRD:
Hi Dienekes,

we have launched release 20 of the YHRD database, the largest update ever with 4,755 new haplotypes. See the news below and a geographical overview as an attachment.

December 28 YHRD update (Lutz Roewer, Sascha Willuweit)

The largest update since the database was started in 2000! Release 20 is out with 46,720 haplotypes in 386 populations. 44,863 haplotypes of these are completely typed for 9 and 17,824 for 11 loci. Twenty-nine populations were added today: from Ningxia in China (Han), from Qinghai in China (Salar), from Hungary including Romani speakers, from Germany (Bonn), from Sweden (Saami from Jokkmokk), from Norway (Bergen), from Libya (Tripolis), from Yemen (Sanaa), from Mexico (Chihuahua and Mexico City), from Serbia (Novi Sad), from Siberia (Stony Tunguska Evenks, Yakut speaking Evenks, Yakuts, Yukaghir, Tuva), from Western Russia (Belgorod, Kaluga, Mineralnye Vody, Nizhnii Novgorod, Orel, Pskov, Saratov, Tula, Vladimir, Volot, Yaroslavl) and from Southeastern Poland. Ten populations were updated: from Colombia (province Antioquia), from Ningxia in China (Hui), from Taiwan (Han), from Norway (Eastern, Central, Northern, Southern, Western parts and from Oslo) as well as from Russia (Novgorod). In two populations erroneous allele calls were corrected: Taraz (Kazakhstan) and Andalucia/Extremadura (Spain). We would like to thank the following colleagues for submissions, updates and corrections: Bofeng Zhu and his group (Shaanxi, P.R.China), Pamszav Horolma and her group (Budapest, Hungary), Anke Junge and her group (Bonn, Germany), Cheng-Hwai Tzeng and his group (Taipei, Taiwan), Andreas Karlsson and his group (Linkoeping, Sweden), Anibal Gaviria and his group (Medellin, Colombia), Thomas Rothaemel and his group (Hannover, Germany), Berit Myhre Dupuy and her group (Oslo, Norway), Uta Immel and her group (Halle, Germany), Hector Rangel-Villalobos and his group (Ocotlan, Mexico), Miljen Maletin and his group (Novi Sad, Serbia), Brigitte Pakendorf and her group (Leipzig, Germany), Marcin Wozniak and his group (Bydgoszcz, Poland), Grzegorz Kaczmarczyk and his group (Krakow, Poland) and Maria Jose Farfan and her group (Sevilla, Spain).

We wish you a happy new year !

Lutz Roewer, Sascha Willuweit
YHRD curators

December 29, 2006

Long Life and Good Mental Function Gene Identified

Single Gene Could Lead to Long Life, Better Mental Function
Barzilai and his colleagues examined 158 people of Ashkenazi, or Eastern European Jewish, descent who were 95 years of age or older. They chose Ashkenazi Jews since current generations stem from a relatively limited number of ancestors. This means they have a comparatively uniform genetic makeup, making it easier to identify important genetic differences.

The scientists gave these volunteers a common test of mental function, consisting of 30 questions. Correctly answering 25 of the questions meant a subject passed the test. Those centenarians who passed were two to three times more likely to have a common variant of a particular gene, called the CETP gene, than those who did not. When the researchers studied another 124 Ashkenazi Jews between 75 and 85 years of age, those subjects who passed the test of mental function were five times more likely to have this gene variant than their counterparts.

December 28, 2006

Kicking is more dangerous than fists or weapons

Feet, Not Fists, Cause More Severe Injuries, Report Says
Researchers at Cardiff University in Wales examined the medical records of nearly 25,000 people treated in a local hospital between 1999 and 2005 (related photos: the new Wales).

The researchers tallied the victims' injuries according to a five-point triage scale based on the urgency of treatment needed.

Reporting in a recent issue of the journal Injury Prevention, lead study author Jonathan Shepherd and colleagues found that while kicks were less common, such assaults caused greater damage than either punches or attacks with weapons.

Sexual practices and preferences in China

Arch Sex Behav. 2006 Dec 23; [Epub ahead of print]

Sexual Practices and Sexual Satisfaction: A Population Based Study of Chinese Urban Adults.

Parish WL, Luo Y, Stolzenberg R, Laumann EO, Farrer G, Pan S.

This study examined sexual satisfaction and its social and behavioral correlates among urbanites aged 20-64 in China, using data from a nationally representative sample of 1,194 women and 1,217 men with a spouse or other long-term sexual partner with whom they had sex during the last year. The results from structural equation models suggest a multiplex set of determinants of sexual satisfaction, including relationship characteristics, sexual knowledge and personal values, physical vitality, and environmental impediments. A large proportion of the effect of these background characteristics was mediated by frequent orgasms, varied sexual practices, and perceived partner affection. In particular, much of the effect of knowledge and beliefs was mediated through variety in sexual practices. While many of the observed patterns were shared among women and men, much of the effect of relationship characteristics was mediated through perceived partner affection for women. Men, in contrast, paid greater attention to his partner's physical attractiveness and to her extramarital sex. A sexual transition is well underway in urban China, even if more rapidly for men than for women. While knowledge and values are arguably more important in this transitional period, many antecedents of sexual well-being drawn from the literature on sexual behavior in developed Western countries are also applicable to urban China.


December 25, 2006

Handsome surgeons

According to this study, movie-surgeons are handsomer than real surgeons, who are handsomer than physicians. Famous surgeons in movies that come to mind are the Jack character in Lost and the Harrison Ford character in The Fugitive, plus many people in shows like Grey's Anatomy and ER which I haven't really watched. Any other famous surgeons in movies or TV, handsome or otherwise?

Surgeons are taller and better looking than other doctors
Phenotypic differences between male physicians, surgeons and film stars

Surgeons are taller and more handsome than physicians, finds a study in this week's Christmas issue of the BMJ.

Doctors at the University of Barcelona Hospital noticed that the tallest and most handsome male students were more likely to go for surgery, and the shortest (and perhaps not so good looking) ones were more likely to become physicians.

So they decided to test the theory that, on average, surgeons are taller and better looking than physicians.

They selected a random sample of 12 surgeons and 12 physicians from the hospital plus four external controls (well known film stars who played surgeons or physicians). All subjects were matched by age (52 +/- 7 years) and sex (all men), their height was recorded and they were asked to submit a digital picture.

Pictures of all subjects were then randomly organised and shown to an independent group of eight female observers (all in the same age group as the study subjects). Observers used the "good looking score" to classify each participant (ranging from 1, ugly to 7, very good looking).

The results show that, on average, senior male surgeons are significantly taller and better looking than senior male physicians. They also show that film stars who play doctors are significantly better looking than real surgeons and physicians.

There are several potential explanations for these findings, say the authors. For example, surgeons spend a lot of time in operating rooms, which are cleaner, cooler, and have a higher oxygen content than the average medical ward, where physicians spend most of their time. They also often wear clog-type shoes that adds 2-3 cm to their perceived height.

In contrast, physicians have a tendency to hang heavy stethoscopes around their necks, which bows their heads forward and reduces their perceived height.

Further studies are needed to assess if these findings also apply to junior male surgeons and physicians, as well as to senior and junior female staff, they add.

Happy Danes

Why are Danes the world's happiest nation?

Earlier this year, Denmark came top in a world map of happiness (the UK ranked 41st out of 178 nations). And for more than 30 years it has ranked first in European satisfaction surveys. So what makes Danes so content?

Researchers in this week's Christmas issue of the BMJ decided to find out why life satisfaction in Denmark substantially exceeds that in Sweden and Finland, the two countries most similar to Denmark.

Their hypotheses range from the unlikely (hair colour, genes, food and language) to the more plausible, such as family life, health and a prosperous economy.

However, their analysis points to two explanatory factors. Firstly, winning the 1992 European Football Championship put Danes in such a state of euphoria that the country has not been the same since. This may explain the high level of life satisfaction in Denmark after 1992, they write.

Secondly, while Danes are very satisfied, their expectations for the coming year are rather low. In contrast, Italy and Greece, which rank low on life satisfaction, rank high on expectations for the year to come, together with Swedes and Finns.

The causes of the stolid depth of Danish wellbeing are undoubtedly multifactorial, they say. The Danish football triumph of 1992 has had a lasting impact, but the satisfaction of the Danes began well before 1992, albeit at a more moderate level. The key factor that explains this, and that differentiates Danes from Swedes and Finns, seems to be that Danes have consistently low (and realistic) expectations for the year to come.

So the key to happiness may lie in the fact that if you lower your expectations enough you might feel a bit better next Christmas, they conclude.

Increase of weight in Greek schoolchildren in 20th century

Med Sci Monit. 2006 Dec 18;13(1):RA8-11 [Epub ahead of print]

The secular trend of body weight of Greek schoolchildren in the 20(th) century.

Papadimitriou A, Douros K, Fretzayas A, Nicolaidou P.

Background: Improvements in socioeconomic conditions in the 20(th) century had a dramatic impact on the growth and development of children, resulting in greater somatic growth and earlier pubertal maturation. Furthermore, in the last part of that century childhood obesity took on epidemic proportions in many countries The aim of the study was to present the secular trend of body weight of Greek schoolchildren in the 20(th) century. Material/Methods: The data were taken from growth studies the authors conducted themselves or were able to find in the Greek literature. All studies were cross-sectional and spanned the years from 1920 to 1995. The studies referred mainly to children living in Athens or other major cities of the country. Results: The data were taken from growth studies the authors conducted themselves or were able to find in the Greek literature. All studies were cross-sectional and spanned the years from 1920 to 1995. The studies referred mainly to children living in Athens or other major cities of the country. Conclusions: Improvement in the socioeconomic conditions in Greece resulted in an increase in body weight in Greek schoolchildren in the 20(th) century. However, this increase tended to stop in adolescent girls.


Haplogroups H and U and Alzheimer's

Cell Mol Neurobiol. 2006 Dec 21; [Epub ahead of print]

Do Haplogroups H and U Act to Increase the Penetrance of Alzheimer's Disease?

Fesahat F, Houshmand M, Panahi MS, Gharagozli K, Mirzajani F.

1. Alzheimer's disease (AD) is the most common form of dementia in the elderly in which interplay between genes and the environment is supposed to be involved. Mitochondrial DNA (mtDNA) has the only noncoding regions at the displacement loop (D-loop) region that contains two hypervariable segments (HVS-I and HVS-II) with high polymorphism. mtDNA has already been fully sequenced and many subsequent publications have shown polymorphic sites, haplogroups, and haplotypes. Haplogroups could have important implications to understand the association between mutability of the mitochondrial genome and the disease.2. To assess the relationship between mtDNA haplogroup and AD, we sequenced the mtDNA HVS-I in 30 AD patients and 100 control subjects. We could find that haplogroups H and U are significantly more abundant in AD patients (P = 0.016 for haplogroup H and P = 0.0003 for haplogroup U), Thus, these two haplogroups might act synergistically to increase the penetrance of AD disease.


Y chromosomes of Huichol tribe of Mexico

Leg Med (Tokyo). 2006 Jul;8(4):220-5. Epub 2006 Jun 21.

Y-linked haplotypes in Amerindian chromosomes from Mexican populations: genetic evidence to the dual origin of the Huichol tribe.

Paez-Riberos LA, Munoz-Valle JF, Figuera LE, Nuno-Arana I, Sandoval-Ramirez L, Gonzalez-Martin A, Ibarra B, Rangel-Villalobos H.

We studied six Y-linked short tandem repeats (Y-STRs) to describe the internal diversity of the Amerindian haplogroup Q-M3 in 129 males from eight Mexican populations. The low gene diversity in the Huichol tribe demonstrated the effects of genetic drift, attributable to geographic isolation and founder effect. The presence of two principal paternal lineages supported the historical and anthropometric records, which indicate that Huichols were formed by the fusion of two ancestral Mexican tribes. Moreover, genetic distances and close relationships of haplotypes between Huichols and Tarahumaras were in agreement with their linguistic affiliation. The high genetic diversity of the Purepechas and wide distribution of haplotypes along the constructed network-joining tree suggest that the present genetic composition was influenced by Purepecha dominance in western Mesoamerica. The Y-haplotypes shared between populations suggest that, among the Amerindian tribes studied herein, the paternal genetic pool of Nahuas could have contributed more importantly to the European-admixed population, the Mexican-Mestizos.


Y chromosomes of Zhuang Populations

Yi Chuan Xue Bao. 2006 Dec;33(12):1060-72.

Y-chromosome Genotyping and Genetic Structure of Zhuang Populations.

Jing C, Hui L, Zhen-Dong Q, Wen-Hong L, Wei-Xiong L, Rui-Xing Y, Li J, Shang-Ling P.

Zhuang, the largest ethnic minority population in China, is one of the descendant groups of the ancient Bai-Yue. Linguistically, Zhuang languages are grouped into northern and southern dialects. To characterize its genetic structure, 13 East Asian-specific Y-chromosome biallelic markers and 7 Y-chromosome short tandem repeat (STR) markers were used to infer the haplogroups of Zhuang populations. Our results showed that O*, O2a, and O1 are the predominant haplogroups in Zhuang. Frequency distribution and principal component analysis showed that Zhuang was closely related to groups of Bai-Yue origin and therefore was likely to be the descendant of Bai-Yue. The results of principal component analysis and hierarchical clustering analysis contradicted the linguistically derived north-south division. Interestingly, a west-east clinal trend of haplotype frequency changes was observed, which was supported by AMOVA analysis that showed that between-population variance of east-west division was larger than that of north-south division. O* network suggested that the Hongshuihe branch was the center of Zhuang. Our study suggests that there are three major components in Zhuang. The O* and O2a constituted the original component; later, O1 was brought into Zhuang, especially eastern Zhuang; and finally, northern Han population brought O3 into the Zhuang populations.


December 20, 2006

High IQ and vegetarianism

See also Meat eating men's armpits smell bad to women

BMJ. 2006 Dec 15; [Epub ahead of print]

IQ in childhood and vegetarianism in adulthood: 1970 British cohort study.

Gale CR, Deary IJ, Schoon I, Batty GD, Batty GD.

OBJECTIVE: To examine the relation between IQ in childhood and vegetarianism in adulthood. DESIGN: Prospective cohort study in which IQ was assessed by tests of mental ability at age 10 years and vegetarianism by self-report at age 30 years. SETTING: Great Britain. PARTICIPANTS: 8170 men and women aged 30 years participating in the 1970 British cohort study, a national birth cohort. MAIN OUTCOME MEASURES: Self-reported vegetarianism and type of diet followed. RESULTS: 366 (4.5%) participants said they were vegetarian, although 123 (33.6%) admitted eating fish or chicken. Vegetarians were more likely to be female, to be of higher social class (both in childhood and currently), and to have attained higher academic or vocational qualifications, although these socioeconomic advantages were not reflected in their income. Higher IQ at age 10 years was associated with an increased likelihood of being vegetarian at age 30 (odds ratio for one standard deviation increase in childhood IQ score 1.38, 95% confidence interval 1.24 to 1.53). IQ remained a statistically significant predictor of being vegetarian as an adult after adjustment for social class (both in childhood and currently), academic or vocational qualifications, and sex (1.20, 1.06 to 1.36). Exclusion of those who said they were vegetarian but ate fish or chicken had little effect on the strength of this association. CONCLUSION: Higher scores for IQ in childhood are associated with an increased likelihood of being a vegetarian as an adult.


The shape of beauty

J Cosmet Dermatol. 2006 Jun;5(2):190-4

The shape of beauty: determinants of female physical attractiveness.

Fisher ML, Voracek M.

Rarely has one research area gained as much attention as that which is observed for female physical attractiveness. The past decade has resulted in numerous, exciting developments, particularly with respect to three proposed determinants of beauty: waist to hip ratio (WHR), body mass index (BMI), and curvaceousness. The goal of our paper is to provide a highly necessary review of contemporary research on the female attractiveness, including an in-depth examination of these factors. In our review, we first discuss WHR, an index of fat deposition, which is calculated by measuring the circumference of the waist compared to the circumference of the hips. WHR is controlled by the sex hormones, and increases as women age, and hence, may influence perceptions of attractiveness. This factor has been hotly contested, as some researchers have claimed that a WHR of approximately 0.7 is universally most attractive, whereas others have found inconsistent findings, or suggest the importance of other factors, such as BMI. Body mass index (BMI), calculated by dividing the body weight (in kilograms) by height (in meters) squared, serves as a measure of body fat. Although WHR and BMI are correlated, they lead to different conclusions, and the importance of BMI as a measure of female attractiveness is debated in the literature. Similar to WHR research, BMI and its role in attractiveness is not cross-culturally consistent and is affected by the availability of resources within a given environment. It may be the case that both WHR and BMI influence female attractiveness. However, there has been little investigation of this possibility. We have explored this issue in our research, which revealed that both influence attractiveness, but in addition, we noticed that curvaceousness was also a factor. Curvaceousness is the degree of "hourglass" shape as determined, for example, by the size of the bust, relative to the circumference of the hips and waist, and the size of the buttocks. However, curvaceousness does not appear to be temporally stable as a marker of attractiveness, and it is not consistent across modes of presentation. For example, models in male-oriented magazines are more curvaceous than models in female-oriented magazines. In summary, faced with these recent findings, it is difficult to ascertain agreement among the various factors, especially when researchers investigate each determinant in isolation. We conclude that, although researchers have made many important initial steps in examining female attractiveness, there remains much to be discovered.


December 17, 2006

Gene Wars

A reader posted this article in the comments section. It covers quite a lot of material regarding the use of population genetics for political reasons. See also Indigenous Populations don't trust Genographic Project, and Genetic vs. Mythical Origins.

December 16, 2006

mtDNA haplogroups M1 and U6 originated in Eurasia

See also a related National Geographic story regarding this article.

15 December 2006:
Vol. 314. no. 5806, pp. 1767 - 1770

The mtDNA Legacy of the Levantine Early Upper Palaeolithic in Africa

Anna Olivieri et al.

Sequencing of 81 entire human mitochondrial DNAs (mtDNAs) belonging to haplogroups M1 and U6 reveals that these predominantly North African clades arose in southwestern Asia and moved together to Africa about 40,000 to 45,000 years ago. Their arrival temporally overlaps with the event(s) that led to the peopling of Europe by modern humans and was most likely the result of the same change in climate conditions that allowed humans to enter the Levant, opening the way to the colonization of both Europe and North Africa. Thus, the early Upper Palaeolithic population(s) carrying M1 and U6 did not return to Africa along the southern coastal route of the "out of Africa" exit, but from the Mediterranean area; and the North African Dabban and European Aurignacian industries derived from a common Levantine source.


December 13, 2006

Sub-populations within haplogroups R1b3 and E3a

Article not on the journal website as of this writing.

Hum Mutat. 2006 Dec 8;28(1):97 [Epub ahead of print]

Sub-populations within the major European and African derived haplogroups R1b3 and E3a are differentiated by previously phylogenetically undefined Y-SNPs.

Sims LM, Garvey D, Ballantyne J.

Single nucleotide polymorphisms on the Y chromosome (Y-SNPs) have been widely used in the study of human migration patterns and evolution. Potential forensic applications of Y-SNPs include their use in predicting the ethnogeographic origin of the donor of a crime scene sample, or exclusion of suspects of sexual assaults (the evidence of which often comprises male/female mixtures and may involve multiple perpetrators), paternity testing, and identification of non- and half-siblings. In this study, we used a population of 118 African- and 125 European-Americans to evaluate 12 previously phylogenetically undefined Y-SNPs for their ability to further differentiate individuals who belong to the major African (E3a)- and European (R1b3, I)-derived haplogroups. Ten of these markers define seven new sub-clades (equivalent to E3a7a, E3a8, E3a8a, E3a8a1, R1b3h, R1b3i, and R1b3i1 using the Y Chromosome Consortium nomenclature) within haplogroups E and R. Interestingly, during the course of this study we evaluated M222, a sub-R1b3 marker rarely used, and found that this sub-haplogroup in effect defines the Y-STR Irish Modal Haplotype (IMH). The new bi-allelic markers described here are expected to find application in human evolutionary studies and forensic genetics.


Sexual preferences in China

Am J Hum Biol. 2006 Dec 7;19(1):88-95 [Epub ahead of print]

Studies of human physique and sexual attractiveness: Sexual preferences of men and women in China.

Dixson BJ, Dixson AF, Li B, Anderson MJ.

Men and women at Northwest University (n = 631), Xi'an, China, were asked to rate the attractiveness of male or female figures manipulated to vary somatotype, waist-to-hip ratio (WHR), secondary sexual traits, and other features. In study 1, women rated the average masculine somatotype as most attractive, followed by the mesomorphic (muscular), ectomorphic (slim), and endomorphic (heavily built) somatotypes, in descending order of preference. In study 2, the amount and distribution of masculine trunk (chest and abdominal) hair were altered progressively in a series of front-posed figures. Women rated figures with no or little trunk hair as most attractive. Study 3 assessed the attractiveness of front-posed male figures which varied only in length of their nonerect penis. Numerical ratings for this trait were low, but moderate lengthening of the penis (22% or 33% above average) resulted in a significant increase in scores for attractiveness. In study 4, Chinese men rated the attractiveness of back-posed female images varying in waist-to-hip ratio (WHR from 0.5-1.0). The 0.6 WHR figure was most preferred, followed by 0.7, while figures with higher ratios (0.9 or 1.0) were significantly less attractive. Study 5 rated the attractiveness of female skin color: men expressed a marked preference for images which were lighter in color, as compared to images of average or darker skin colors. These results, the first of their kind reported for a Chinese population, support the view that sexual selection has influenced the evolution of human physique and sexual attractiveness in men and women.


Physical strength in men correlates with attractiveness

Am J Hum Biol. 2006 Dec 7;19(1):82-87 [Epub ahead of print]

Male facial appearance signals physical strength to women.

Fink B, Neave N, Seydel H.

Previous studies showed that male faces with extreme features that are likely to be associated with testosterone (T) are perceived as dominant and masculine. Women were reported to prefer masculinized male faces, as they may consider T markers to be an "honest" indication of good health. However, it is also likely that female preferences for certain male faces arise from the fact that dominant- and masculine-looking males are signaling characteristics which may be beneficial in intrasexual conflict, and thereby also indicate potential achievers of high status, an important factor in female mate selection. Although numerous studies were built on this assumption, nothing is known about the relationship between perceived facial dominance and physical strength in men. We measured hand-grip strength, as a measure of overall physical strength, in a sample of 32 male students, and recorded age, body weight, and height. Seventy-nine women rated facial images of these men for dominance, masculinity, and attractiveness. After controlling for age and body weight, hand-grip strength was found to correlate significantly positively with all three measures. The present data thus support the supposition that a male's physical strength is also signaled via facial characteristics of dominance and masculinity, which are considered attractive by women


December 10, 2006

Indigenous populations don't trust Genographic Project

DNA Gatherers Hit a Snag: The Tribes Don’t Trust Them (NY Times)

SOUTH NAKNEK, Alaska — The National Geographic Society’s multimillion-dollar research project to collect DNA from indigenous groups around the world in the hopes of reconstructing humanity’s ancient migrations has come to a standstill on its home turf in North America.
From the article:
Geographic origin stories told by DNA can clash with long-held beliefs, threatening a world view some indigenous leaders see as vital to preserving their culture.
Related to the above read also Genetic vs. Mythical Origins. More from the article:
They argue that genetic ancestry information could also jeopardize land rights and other benefits that are based on the notion that their people have lived in a place since the beginning of time.
Does anyone's land rights really depend on living in a place since the beginning of time? If that was the criterion for possessing land rights, then 99.9% of the Earth's surface wouldn't belong to its current possessors. More:
In its first 18 months, the project’s scientists have had considerable success, persuading more than 18,000 people in off-the-grid places like the east African island of Pemba and the Tibesti Mountains of Chad to donate their DNA. When the North American team arrived in southwestern Alaska, they found volunteers offering cheek swabs and family histories for all sorts of reasons.
Glenn Fredericks, president of the Georgetown tribe, was eager for proof of an ancient unity between his people and American Indians elsewhere that might create greater political power. “They practice the same stuff, the lower-48 natives, as we do,” Mr. Fredericks said. “Did we exchange people? It would be good to know.”
The first large effort to collect indigenous DNA since federal financing was withdrawn from a similar proposal amid indigenous opposition in the mid-1990s, the Genographic Project has drawn quiet applause from many geneticists for resurrecting scientific ambitions that have grown more pressing. As indigenous groups intermarry and disperse at an ever-accelerating pace, many scientists believe the chance to capture human history is fast disappearing.

“Everyone else had given up,” said Mark Stoneking, a professor at the Max Planck Institute for Evolutionary Anthropology. “If they get even a fraction of what they are trying for, it will be very useful.”

I was wondering why the Genographic project has been slow to publish their research. If they had to contend with stuff like this, it all makes sense:
In May, project officials held a stormy meeting in New York with the indigenous rights group Cultural Survival while protestors carried signs reading “National Geographic Sucks Indigenous Blood.” Shortly after, the United Nations Permanent Forum on Indigenous Issues recommended suspending the project.
It is sad that stupid politics is keeping scientists from learning about humanity's past.
But among the 10 geneticists the society has given the task of collecting 10,000 samples each by the spring of 2010, Theodore G. Schurr, the project’s North American director, is in last place. Fewer than 100 vials of DNA occupy a small plastic box in his laboratory’s large freezer at the University of Pennsylvania, where he is an assistant professor of anthropology.
The reasons offered by Native American tribes are:
But almost every federally recognized tribe in North America has declined or ignored Dr. Schurr’s invitation to take part. “What the scientists are trying to prove is that we’re the same as the Pilgrims except we came over several thousand years before,” said Maurice Foxx, chairman of the Massachusetts Commission on Indian Affairs and a member of the Mashpee Wampanoag. “Why should we give them that openly?”
Someone should explain to them that scientists don't need to prove that. It has already been firmly established, indeed long before human genetics came into the picture. The point of research like that carried out by the Genographic Project is to determine how and when migrations into the Americas (and elsewhere) happened, not if they did.

Should scientists "respect" superstition for fear of offending indigenous tribes' feelings?
Some American Indians trace their suspicions to the experience of the Havasupai Tribe, whose members gave DNA for a diabetes study that University of Arizona researchers later used to link the tribe’s ancestors to Asia. To tribe members raised to believe the Grand Canyon is humanity’s birthplace, the suggestion that their own DNA says otherwise was deeply disturbing.

Division of Labor among Neanderthals and Modern Humans

CURRENT ANTHROPOLOGY Volume 47, Number 6, December 2006

What's a Mother to Do?
The Division of Labor among Neandertals and Modern Humans in Eurasia

by Steven L. Kuhn and Mary C. Stiner

Recent hunter-gatherers display much uniformity in the division of labor along the lines of gender and age. The complementary economic roles for men and women typical of ethnographically documented hunter-gatherers did not appear in Eurasia until the beginning of the Upper Paleolithic. The rich archaeological record of Middle Paleolithic cultures in Eurasia suggests that earlier hominins pursued more narrowly focused economies, with women's activities more closely aligned with those of men with respect to schedule and ranging patterns than in recent forager systems. More broadly based economies emerged first in the early Upper Paleolithic in the eastern Mediterranean region and later in the rest of Eurasia. The behavioral changes associated with the Upper Paleolithic record signal a wider range of economic and technological roles in forager societies, and these changes may have provided the expanding populations of Homo sapiens with a demographic advantage over other hominins in Eurasia.


December 08, 2006

Cranial morphology and population history

Cranial morphology has been used to determine patterns of population history, but it is not "neutral" but is correlated with climate. For example, equatorial populations in Africa and Oceania have rather wide noses and narrow skulls compared to more northerly populations; this is not due to any close family relationship, but rather because of adaptation in similar environments.

This new paper tries to determine how different parts of cranial morphology reflect climate vs. population history.

The Anatomical Record Part A: Discoveries in Molecular, Cellular, and Evolutionary Biology, Volume 288A, Issue 12 , Pages 1225 - 1233

Human cranial anatomy and the differential preservation of population history and climate signatures

Katerina Harvati, Timothy D. Weaver


Cranial morphology is widely used to reconstruct evolutionary relationships, but its reliability in reflecting phylogeny and population history has been questioned. Some cranial regions, particularly the face and neurocranium, are believed to be influenced by the environment and prone to convergence. Others, such as the temporal bone, are thought to reflect more accurately phylogenetic relationships. Direct testing of these hypotheses was not possible until the advent of large genetic data sets. The few relevant studies in human populations have had intriguing but possibly conflicting results, probably partly due to methodological differences and to the small numbers of populations used. Here we use three-dimensional (3D) geometric morphometrics methods to test explicitly the ability of cranial shape, size, and relative position/orientation of cranial regions to track population history and climate. Morphological distances among 13 recent human populations were calculated from four 3D landmark data sets, respectively reflecting facial, neurocranial, and temporal bone shape; shape and relative position; overall cranial shape; and centroid sizes. These distances were compared to neutral genetic and climatic distances among the same, or closely matched, populations. Results indicate that neurocranial and temporal bone shape track neutral genetic distances, while facial shape reflects climate; centroid size shows a weak association with climatic variables; and relative position/orientation of cranial regions does not appear correlated with any of these factors. Because different cranial regions preserve population history and climate signatures differentially, caution is suggested when using cranial anatomy for phylogenetic reconstruction.


Armand Leroi on Neo-Eugenics

Armand Leroi has a new article on neo-eugenics. Gene Expression summarizes its content. From the article:
Will neo-eugenics spread? Probably. At least it is hard to see what will stop it if, as I claim, it becomes possible to detect all known disease-causing mutations before birth or implantation, if the cost of IVF and PGD declines, and if eugenic screens have clear economic benefits. Some readers might find it peculiar that in this discussion of neo-eugenics, I have not considered the ethical or legal implications with which this subject is generally considered to be fraught. Although I do not doubt their importance, I simply have no particular knowledge of them. Peter Medawar put it best 40 years ago: "If the termination of a pregnancy is now in question, scientific evidence might tell us that the chances of a defective birth are 100 percent, 50 percent, 25 percent, or perhaps unascertainable. The evidence is highly relevant to the decision, but the decision itself is not a scientific one, and I see no reason why scientists as such should be specially well-qualified to make it" (Medawar, 1966).
What Leroi is saying is that it will be economical to test all known disease causing mutation on the cheap. Right now it is possible to test such mutations individually, but the cost and ease of testing for all of them is too steep.

Of course, this raises important issues for parents. Chances are that random recombination will result in embryos having at least some of the genetic susceptibilities of their parents. So, while parents will be able to choose which babies they don't want, they won't be able (at least easily) to custom-order "perfect" babies, i.e., those that score negatively for all disease-causing mutations.

EMBO reports 7, 12, 1184–1187 (2006)

The future of neo-eugenics. Now that many people approve the elimination of certain genetically defective fetuses, is society closer to screening all fetuses for all known mutations?

Armand Marie Leroi


December 07, 2006

Extreme Patterns of Variance in Small Populations

Ann Hum Genet. 2006 Nov 28; [Epub ahead of print]

Extreme Patterns of Variance in Small Populations: Placing Limits on Human Y-Chromosome Diversity through Time in the Vanuatu Archipelago.

Cox M.

Small populations are dominated by unique patterns of variance, largely characterized by rapid drift of allele frequencies. Although the variance components of genetic datasets have long been recognized, most population genetic studies still treat all sampling locations equally despite differences in sampling and effective population sizes. Because excluding the effects of variance can lead to significant biases in historical reconstruction, variance components should be incorporated explicitly into population genetic analyses. The possible magnitude of variance effects in small populations is illustrated here via a case study of Y-chromosome haplogroup diversity in the Vanuatu Archipelago. Deme-based modelling is used to simulate allele frequencies through time, and conservative confidence bounds are placed on the accumulation of stochastic variance effects, including diachronic genetic drift and contemporary sampling error. When the information content of the dataset has been ascertained, demographic models with parameters falling outside the confidence bounds of the variance components can then be accepted with some statistical confidence. Here I emphasize how aspects of the demographic history of a population can be disentangled from stochastic variance effects, and I illustrate the extreme roles of genetic drift and sampling error for many small human population datasets.


Cannibalistic Neanderthals

The BBC reports:
Starvation and cannibalism were part of everyday life for a population of Neanderthals living in northern Spain 43,000 years ago, a study suggests.

Bones and teeth from the underground cave system of El Sidron in Asturias bear the hallmarks of a tough struggle for survival, researchers say.

Analysis of teeth showed signs of starvation or malnutrition in childhood and human bones have cut marks on them.

Details appear in the Proceedings of the National Academy of Sciences.

December 06, 2006

Origin of Y chromosome haplogroup N in Asia

The haplogroup N/Tat-C "controversy" is finally over.

UPDATE: Also of interest:
Interestingly, 14 N2-individuals from Turkey, data from Cinnioglu et al6 (updated in this study), belong to the Asian subcluster N2-A, suggesting that the clade N2 might have geographically expanded from Siberia westward by at least two different flows: one northwest through the Volga-Ural region, giving rise to N2-E, probably mainly via the Finno-Ugric group, and the other, N2-A, southwest together with Turkic languages.

European Journal of Human Genetics advance online publication 6 December 2006; doi: 10.1038/sj.ejhg.5201748

A counter-clockwise northern route of the Y-chromosome haplogroup N from Southeast Asia towards Europe

Siiri Rootsi1,10, Lev A Zhivotovsky2,10, Marian Baldovic caron1,3, Manfred Kayser4, Ildus A Kutuev1,5, Rita Khusainova1,5, Marina A Bermisheva1,5, Marina Gubina1,6, Sardana A Fedorova1,7, Anne-Mai Ilumäe1, Elza K Khusnutdinova5, Mikhail I Voevoda6, Ludmila P Osipova6, Mark Stoneking8, Alice A Lin9, Vladimir Ferak3, Jüri Parik1, Toomas Kivisild1, Peter A Underhill9 and Richard Villems1


A large part of Y chromosome lineages in East European and East Asian human populations belong to haplogroup (hg) NO, which is composed of two sister clades N-M231 and O-M175. The O-clade is relatively old (around 30 thousand years (ky)) and encompasses the vast majority of east and Southeast Asian male lineages, as well as significant proportion of those in Oceanian males. On the other hand, our detailed analysis of hg N suggests that its high frequency in east Europe is due to its more recent expansion westward on a counter-clock northern route from inner Asia/southern Siberia, approximately 12–14 ky ago. The widespread presence of hg N in Siberia, together with its absence in Native Americans, implies its spread happened after the founder event for the Americas. The most frequent subclade N3, arose probably in the region of present day China, and subsequently experienced serial bottlenecks in Siberia and secondary expansions in eastern Europe. Another branch, N2, forms two distinctive subclusters of STR haplotypes, Asian (N2-A) and European (N2-E), the latter now mostly distributed in Finno-Ugric and related populations. These phylogeographic patterns provide evidence consistent with male-mediated counter-clockwise late Pleistocene–Holocene migratory trajectories toward Northwestern Europe from an ancestral East Asian source of Paleolithic heritage.


December 05, 2006

Pioneering study shows richest 2 percent own half world wealth

From the EurekAlert public release:
The richest 2% of adults in the world own more than half of global household wealth according to a path-breaking study released today by the Helsinki-based World Institute for Development Economics Research of the United Nations University (UNU-WIDER).

The most comprehensive study of personal wealth ever undertaken also reports that the richest 1% of adults alone owned 40% of global assets in the year 2000, and that the richest 10% of adults accounted for 85% of the world total. In contrast, the bottom half of the world adult population owned barely 1% of global wealth.

The research finds that assets of $2,200 per adult placed a household in the top half of the world wealth distribution in the year 2000. To be among the richest 10% of adults in the world required $61,000 in assets, and more than $500,000 was needed to belong to the richest 1%, a group which — with 37 million members worldwide — is far from an exclusive club.

And from the BBC:
The richest 2% of adults in the world own more than half of all household wealth, according to a new study by a United Nations research institute.

The report, from the World Institute of Development Economics Research at the UN University, says that the poorer half of the world's population own barely 1% of global wealth.

There have of course been many studies of worldwide inequality.

But what is new about this report, the authors say, is its coverage.

It deals with all countries in the world - either actual data or estimates based on statistical analysis - and it deals with wealth, where most previous research has looked at income.

What they mean by wealth in this study is what people own, less what they owe - their debts. The assets include land, buildings, animals and financial assets.

December 01, 2006

Sexual preferences for human physique in Cameroon

Arch Sex Behav. 2006 Nov 30; [Epub ahead of print]

Human Physique and Sexual Attractiveness: Sexual Preferences of Men and Women in Bakossiland, Cameroon.

Dixson BJ, Dixson AF, Morgan B, Anderson MJ.

Men and women living in a rural community in Bakossiland, Cameroon were asked to rate the attractiveness of images of male or female figures manipulated to vary in somatotype, waist-to-hip ratio (WHR), secondary sexual traits, and other features. In Study 1, women rated mesomorphic (muscular) and average male somatotypes as most attractive, followed by ectomorphic (slim) and endomorphic (heavily built) figures. In Study 2, amount and distribution of masculine trunk (chest and abdominal) hair was altered progressively in a series of front-posed male figures. A significant preference for one of these images was found, but the most hirsute figure was not judged as most attractive. Study 3 assessed attractiveness of front-posed male figures which varied only in length of the non-erect penis. Extremes of penile size (smallest and largest of five images) were rated as significantly less attractive than three intermediate sizes. In Study 4, Bakossi men rated the attractiveness of back-posed female images varying in WHR (from 0.5-1.0). The 0.8 WHR figure was rated markedly more attractive than others. Study 5 rated the attractiveness of female skin color. Men expressed no consistent preference for either lighter or darker female figures. These results are the first of their kind reported for a Central African community and provide a useful cross-cultural perspective to published accounts on sexual selection, human morphology and attractiveness in the U.S., Europe, and elsewhere.


November 30, 2006

Michael Crichton's Next

Michael Crichton, author of popular books such as Jurassic Park has written a new novel about genetic engineering, titled Next. I didn't much like his previous book which expressed unwarranted reservations about the reality of global warming, but this bit from a review of his book seems to me to be right on the money:
Slick, sanctimonious Dr. Robert Bellarmino at the National Institutes of Health touts future genetic cures he doubts will ever happen. Bellarmino knows that individual genes don't determine specific traits such as homosexuality, violence, high IQ, short stature or resistance to Alzheimer's disease; their interaction with other genes and with the environment is staggeringly complex. But it's good for the research business to pretend otherwise. When doctors bend the rules in long-odds attempts to provide the cures for inherited illnesses that the public demands, Bellarmino works to shield them from censure.

Nature article on Antikythera mechanism

From the BBC:
For example, the Moon sometimes moves slightly faster in the sky than at others because of the satellite's elliptic orbit.

To overcome this, the designer of the calculator used a "pin-and-slot" mechanism to connect two gear-wheels that introduced the necessary variations.

"When you see it your jaw just drops and you think: 'bloody hell, that's clever'. It's a brilliant technical design," said Professor Mike Edmunds.

The New York Times:
The mechanism, presumably used in preparing calendars for seasons of planting and harvesting and fixing religious festivals, had at least 30, possibly 37, hand-cut bronze gear-wheels, the researchers reported. An ingenious pin-and-slot device connecting two gear-wheels induced variations in the representation of lunar motions according to the Hipparchos model of the Moon’s elliptical orbit around Earth.

The functions of the mechanism were determined by the numbers of teeth in the gears. The 53-tooth count of certain gears, the researchers said, was “powerful confirmation of our proposed model of Hipparchos’ lunar theory.”

Jo Marchant writing in Nature:
The researchers realized that the ratios of the gear-wheels involved produce a motion that closely mimics the varying motion of the Moon around Earth, as described by Hipparchus. When the Moon is close to us it seems to move faster. And the closest part of the Moon's orbit itself makes a full rotation around the Earth about every nine years. Hipparchus was the first to describe this motion mathematically, working on the idea that the Moon's orbit, although circular, was centred on a point offset from the centre of Earth that described a nine-year circle. In the Antikythera Mechanism, this theory is beautifully translated into mechanical form. "It's an unbelievably sophisticated idea," says Tony Freeth, a mathematician who worked out most of the mechanics for Edmunds' team. "I don't know how they thought of it."


Charette also hopes the new Antikythera reconstruction will encourage scholars to take the device more seriously, and serve as a reminder of the messy nature of history. "It's still a popular notion among the public, and among scientists thinking about the history of their disciplines, that technological development is a simple progression," he says. "But history is full of surprises."

François Charette in Nature:

From the paper:
The Antikythera Mechanism shows great economy and ingenuity of design. It stands as a witness to the extraordinary technological potential of Ancient Greece, apparently lost within the Roman Empire.

Nature 444, 587-591 (30 November 2006)

T. Freeth et al.

The Antikythera Mechanism is a unique Greek geared device, constructed around the end of the second century bc. It is known1, 2, 3, 4, 5, 6, 7, 8, 9 that it calculated and displayed celestial information, particularly cycles such as the phases of the moon and a luni-solar calendar. Calendars were important to ancient societies10 for timing agricultural activity and fixing religious festivals. Eclipses and planetary motions were often interpreted as omens, while the calm regularity of the astronomical cycles must have been philosophically attractive in an uncertain and violent world. Named after its place of discovery in 1901 in a Roman shipwreck, the Antikythera Mechanism is technically more complex than any known device for at least a millennium afterwards. Its specific functions have remained controversial11, 12, 13, 14 because its gears and the inscriptions upon its faces are only fragmentary. Here we report surface imaging and high-resolution X-ray tomography of the surviving fragments, enabling us to reconstruct the gear function and double the number of deciphered inscriptions. The mechanism predicted lunar and solar eclipses on the basis of Babylonian arithmetic-progression cycles. The inscriptions support suggestions of mechanical display of planetary positions9, 14, 15, now lost. In the second century bc, Hipparchos developed a theory to explain the irregularities of the Moon's motion across the sky caused by its elliptic orbit. We find a mechanical realization of this theory in the gearing of the mechanism, revealing an unexpected degree of technical sophistication for the period.


November 29, 2006

The Gagauz of Moldova

Annals of Human Genetics (Online Early)

The Gagauz, a Linguistic Enclave, are not a Genetic Isolate

Ivan Nasidze et al.


The Gagauz are a Turkic-speaking group that migrated from Turkey to their present location in the southern part of the Republic of Moldova about 150 years ago. Surrounded by Indo-European-speaking populations, they thus form a linguistic enclave, which raises the following question: to what extent have they remained in genetic isolation from their geographic neighbours? Analyses of mtDNA and Y chromosome variation indicate that despite their linguistic differences, the Gagauz have admixed extensively with neighbouring groups. Our data suggest that there has been more mtDNA than Y chromosome admixture, in keeping with the patrilocal nature of these groups. Moreover, when compared with another linguistic enclave, the Kalmyks there appears to be a correlation between the amount of genetic admixture and the amount of linguistic influence that these two linguistic enclaves have experienced from neighbouring groups.


November 23, 2006

Copy number variation in humans

From the paper:
We obtained the optimal clustering with the assumption of three ancestral populations, with the African, European and Asian populations clearly differentiated

Nature 444, 444-454 (23 November 2006)

Global variation in copy number in the human genome

Richard Redon et al.

Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.

Link (Free access)

November 17, 2006

Phylogeography of mtDNA haplogroup L1c

Mol Phylogenet Evol. 2006 Oct 5; [Epub ahead of print]

Phylogeography of the human mitochondrial L1c haplogroup: Genetic signatures of the prehistory of Central Africa.

Batini C, Coia V, Battaggia C, Rocha J, Pilkington MM, Spedini G, Comas D, Destro-Bisol G, Calafell F.


Interindividual variation of human mitochondrial DNA has been extensively studied over the last two decades, and its usefulness for reconstructing evolutionary relationships of extant populations has been proved. However, some mitochondrial lineages still need to be studied using a combination of larger and tailored datasets and increased level of resolution in order to shed light on their origin and on the processes underlying their present distribution. In this study, we analyze the phylogeny of the L1c haplogroup of human mitochondrial DNA using sequence data from hypervariable regions 1 and 2 obtained from 455 individuals (extracted from a total sampling of 2542 individuals) belonging to sub-Saharan African and African-American populations. We propose a substantial revision of L1c phylogeny, by introducing one new sub-haplogroup (L1c4), two new L1c1 clades (L1c1b and L1c1c), and by reassigning the previous L1c1a1 sequences to a clade which we termed L1c5. The new phylogeny encompasses distinct lineages with different evolutionary histories. In fact, based on population frequency, internal variation and mismatch distribution, we propose that L1c1b, L1c1c and L1c2 originated in Bantu ancestors, whereas L1c1a, L1c4 and L1c5 evolved among Western Pygmies. The population structure of L1c is not comparable to any known mitochondrial or, even, Y-chromosomal haplogroup, and challenges the current view that most of mtDNA variation in Pygmies might reflect admixture with Bantu or a persistence of plesiomorphic characters. In fact, the unique feature of the L1c is that it retains a signature of a phase common to the ancestors of the Bantu and Western Pygmies, while encompassing some specific sub-clades which can indicate their divergence. This allowed us to attempt a phylogenetically based assessment of the evolutionary relationships between the two groups. Taking into consideration estimates of the time to the most recent common ancestor of L1c and its clades together with archaeological and paleoclimatological evidence, we propose that the ancestors of Bantu and Western Pygmies separated between 60 and 30kya.


Human eye color explained by a three-SNP haplotype

A very exciting new preprint in AJHG describes how a haplotype defined by three SNPs, i.e., single-letter changes in the genetic code, describes most variation in human eye color. I am sure that this paper will make the news once its edited version appears, but this is very exciting development for many different reasons.
  • First, it shows that a very striking observable difference among humans can be explained by minute differences in the genetic code. This should be a reminder to those who engage in grocery-style genetics. Quantity matters not.
  • Second, eye color is an important phenotypical character that people actually care about. Genetics becomes exciting when it's about stuff that people are interested in (intelligence, eye color, the chance of getting cancer before 40, etc.).
  • Third, we are finally getting to the point where genetics can be used to infer characteristics of organisms that are not preserved in bones. This will doubtlessly lead to applications in ancient DNA research (see also here).

American Journal of Human Genetics (preprint)

A three-SNP haplotype in the first intron of OCA2 explains most human eye color variation

David L. Duffy, Grant W. Montgomery, Wei Chen, Zhen Zhen Zhao, Lien Le, Michael R. James, Nicholas K. Hayward, Nicholas G. Martin, Richard A. Sturm


We have previously shown that a QTL linked to the OCA2 region of 15q accounts for 74% of variation in human eye color. We conducted additional genotyping to clarify the role of the OCA2 locus in the inheritance of eye color and other pigmentary traits associated with skin cancer risk in white populations. Fifty eight synonymous and non-synonymous exonic SNPs and tagging SNPs were typed in a collection of 3839 adolescent twins, their sibs, and parents. The highest association for blue:non-blue eye color was found with three OCA2 SNPs; rs7495174 T/C, rs6497268 G/T and rs11855019 T/C (P-values of 1.02x10-61, 1.57x10-96, and 4.45x10-54 respectively) in intron 1. These three SNPs are in one major haplotype block with TGT representing 78.4% of alleles. The TGT/TGT diplotype found in 62.2% of samples was the major genotype seen to modify eye color, with a frequency of 0.905 in blue or green compared with only 0.095 in brown eye color. This genotype was also at highest frequency in subjects with light brown hair and was more frequent in fair and medium skin types, consistent with the TGT haplotype acting as a recessive modifier of lighter pigmentary phenotypes. Homozygotes for rs11855019 C/C were predominantly without freckles and had decreased mole counts. The minor population impact of the nonsynonymous coding region polymorphisms Arg305Trp and Arg419Gln associated with non-blue eyes, and the tight linkage of the major TGT haplotype within the first intron of OCA2 with blue eye color and lighter hair and skin tones, suggest that differences within the 5’ proximal regulatory control region of OCA2 gene alter expression or mRNA transcript levels and may be responsible for these associations.


November 16, 2006

Personality traits of voters for US presidential elections

Personality and Individual Differences (Article in Press)

Voters’ personality traits in presidential elections

Claudio Barbaranelli et al.


Personality measures of more than 6000 US electors on the Big Five Factors have been collected on the Web through a Web site designed to assess their personality. By means of structural equation modeling the impact of personality factors as well as of demographic variables, such as age and sex, on voting intentions on the forthcoming US presidential elections was investigated. Personality variables accounted for 16% of variance of voting intentions, while gender and age accounted for no more than 3%. High Agreeableness and Openness were predictive of intention to vote for Kerry, while all high Energy, Conscientiousness and Emotional Stability were predictive of intention to vote for Bush. Results are consistent with previous research conducted in a different country, using a different language.


Being rich lowers mens' attractiveness to women

Personality and Individual Differences (Article in Press)

Too good to be ‘true’? The handicap of high socio-economic status in attractive males

Simon Chu et al.


Empirical evidence concerning human mate-choice preferences suggests that females should select partners on the basis of cues to genetic quality and/or ability to contribute resources to childcare. Paradoxically, while high levels of both factors should be an attractive combination to females, they might also dissuade females from entering into a relationship with such males since, by definition, they are likely to be highly attractive to other females, and therefore might increase the likelihood that such a male may cheat or desert the relationship. If so, females should be wary of entering into long-term relationships with physically attractive, high status males as compared with males of lower physical attractiveness or status. We asked females to rate a number of different males in terms of attractiveness as a long-term partner. Females were presented with attractive, average and unattractive male faces paired with lonely-hearts advertisements implying high, medium or low socio-economic status. Highest ratings were consistently given to attractive males of medium status rather than high status. We suggest that females see physically attractive, high status males as being more likely to pursue a mating strategy rather than parenting strategy. Under particular circumstances, high socio-economic status in males can be subtly counter-productive in terms of attractiveness as a long-term partner.


November 13, 2006

Culture and ratings of attractiveness of different body shapes

Evolution and Human Behavior
Volume 27, Issue 6 , November 2006, Pages 443-456

Changing perceptions of attractiveness as observers are exposed to a different culture

Martin J. Tovée et al.


It has been suggested that certain physical cues can be used to predict mate quality and that sensitivity to these cues would therefore be adaptive. From this, it follows that in environments where the optimal values for these features differ, the attractiveness preferences should also be different. In this study, we show that there are striking differences in attractiveness preferences for female bodies between United Kingdom (UK) Caucasian and South African Zulu observers. These differences can be explained by different local optima for survival and reproduction in the two environments. In the UK, a high body mass is correlated with low health and low fertility, and the converse is true in rural South Africa. We also report significant changes in the attractiveness preferences of Zulus who have moved to the UK. This suggests that these preferences are malleable and can change with exposure to different environments and conditions. Additionally, we show that Britons of African origin, who were born and who grew up in the UK, have exactly the same preferences as our UK Caucasian observers. These results suggest that humans have mechanisms for acquiring norms of attractiveness that are highly plastic, which allow them to track different ecological conditions through learning.


Even facial color is attractive in women

The study I had posted about earlier.

Evolution and Human Behavior
Volume 27, Issue 6 , November 2006, Pages 433-442

Visible skin color distribution plays a role in the perception of age, attractiveness, and health in female faces

Bernhard Fink et al.


Evolutionary psychologists have proposed that preferences for facial characteristics, such as symmetry, averageness, and sexual dimorphism, may reflect adaptations for mate choice because they signal aspects of mate quality. Here, we show that facial skin color distribution significantly influences the perception of age and attractiveness of female faces, independent of facial form and skin surface topography. A set of three-dimensional shape-standardized stimulus faces—varying only in terms of skin color distribution due to variation in biological age and cumulative photodamage—was rated by a panel of naive judges for a variety of perceptual endpoints relating to age, health, and beauty. Shape- and topography-standardized stimulus faces with the homogeneous skin color distribution of young people were perceived as younger and received significantly higher ratings for attractiveness and health than analogous stimuli with the relatively inhomogeneous skin color distribution of more elderly people. Thus, skin color distribution, independent of facial form and skin surface topography, seems to have a major influence on the perception of female facial age and judgments of attractiveness and health as they may signal aspects of underlying physiological condition of an individual relevant for mate choice. We suggest that studies on human physical attractiveness and its perception need to consider the influence of visible skin condition driven by color distribution and differentiate between such effects and beauty-related traits due to facial shape and skin topography.


Female advantage in recognizing emotional facial expressions

Evolution and Human Behavior
Volume 27, Issue 6 , November 2006, Pages 401-416

A female advantage in the recognition of emotional facial expressions: test of an evolutionary hypothesis

Elizabeth Hampson et al.


A set of computerized tasks was used to investigate sex differences in the speed and accuracy of emotion recognition in 62 men and women of reproductive age. Evolutionary theories have posited that female superiority in the perception of emotion might arise from women's near-universal responsibility for child-rearing. Two variants of the child-rearing hypothesis predict either across-the-board female superiority in the discrimination of emotional expressions (“attachment promotion” hypothesis) or a female superiority that is restricted to expressions of negative emotion (“fitness threat” hypothesis). Therefore, we sought to evaluate whether the expression of the sex difference is influenced by the valence of the emotional signal (Positive or Negative). The results showed that women were faster than men at recognizing both positive and negative emotions from facial cues, supporting the attachment promotion hypothesis. Support for the fitness threat hypothesis also was found, in that the sex difference was accentuated for negative emotions. There was no evidence that the female superiority was learned through previous childcare experience or that it was derived from a sex difference in simple perceptual speed. The results suggest that evolved mechanisms, not domain-general learning, underlie the sex difference in recognition of facial emotions.


November 10, 2006

Origin of mtDNA haplogroup H

Molecular Biology and Evolution (Advance Access published online on November 10, 2006)

Origin and Expansion of Haplogroup H, the Dominant Human Mitochondrial DNA Lineage in West Eurasia: the Near Eastern and Caucasian Perspective

U. Roostalu et al.


More than a third of the European pool of human mitochondrial DNA (mtDNA) is fragmented into a number of subclades of haplogroup (hg) H, the most frequent hg throughout western Eurasia. While there has been considerable recent progress in studying mitochondrial genome variation in Europe at the complete sequence resolution, little data of comparable resolution is so far available for regions like the Caucasus and the Near and Middle East - areas where most of European genetic lineages, including hg H, have likely emerged. This gap in our knowledge causes a serious hindrance for progress in understanding the demographic pre-history of Europe and western Eurasia in general. Here we describe the phylogeography of hg H in the populations of the Near East and the Caucasus. We have analyzed 545 samples of hg H at high resolution, including 15 novel complete mtDNA sequences. As in Europe, most of the present-day Near Eastern - Caucasus area variants of hg H started to expand after the Last Glacial Maximum (LGM) and presumably before the Holocene. Yet importantly, several hg H sub-clades in Near East and Southern Caucasus region coalesce to the pre-LGM period. Furthermore, irrespective of their common origin, significant differences between the distribution of hg H sub-hgs in Europe and in the Near East and South Caucasus imply limited post-LGM maternal gene flow between these regions. In a contrast, the North Caucasus mitochondrial gene pool has received an influx of hg H variants, arriving from the Pontocaspian/East European area.


The Perfect comedy face

Anthony Little has created a facial composite of comedians. From the BBC:
Scientists have used computer software to come up with what they say is the perfect comedy face.

The University of Stirling team blended together 179 different facial aspects of 20 top comedians.

They said soft and feminine features, typified by Ricky Gervais, were more likely to make people laugh.

The researchers also concluded that Conservative leader David Cameron, unlike Tony Blair or Gordon Brown, has features prone to make people laugh.

However, they said it was questionable whether a funny face was an electoral asset.

Researcher Dr Anthony Little, a psychologist, whose work was commissioned by Jongleurs comedy clubs, showed faces with a range of different features to volunteers, and asked them to rate how funny they thought the person was.

He said: "The features most likely to mark male comedians out for success are predominantly soft and feminine.

"The face is a strong indication of character, and today's study appears to explain why comedians of a certain appearance would have been drawn to their career.

"The characteristics of a feminine face imply that the person may be agreeable and co-operative, which can be causal in our first impressions of comedians as being friendly and funny."

Dr Little said Mr Cameron's round and wide facial shape, large eyes and soft features meant he had the right natural physical attributes for comedy.

November 08, 2006

Switch to Blogger beta

I have switched the blog to Google's blogger beta. Everything seems to work fine so far, but the site feed has a new address. You might want to update it in your news reader, since I'm not sure whether the old feed will continue to be updated (I will know after posting this).

UPDATE: Yep, the old feed still works.

UPDATE: The gmail-like system of search+label rocks! I just labeled all 911 posts of the blog in a few minutes right from the dashboard. Another great feature: no more waiting on the "publishing 34%" whenever you change your template or republish a post.

Intelligence and socioeconomic success

Intelligence (in press)

Intelligence and socioeconomic success: A meta-analytic review of longitudinal research

Tarmo Strenze


The relationship between intelligence and socioeconomic success has been the source of numerous controversies. The present paper conducted a meta-analysis of the longitudinal studies that have investigated intelligence as a predictor of success (as measured by education, occupation, and income). In order to better evaluate the predictive power of intelligence, the paper also includes meta-analyses of parental socioeconomic status (SES) and academic performance (school grades) as predictors of success. The results demonstrate that intelligence is a powerful predictor of success but, on the whole, not an overwhelmingly better predictor than parental SES or grades. Moderator analyses showed that the relationship between intelligence and success is dependent on the age of the sample but there is little evidence of any historical trend in the relationship.


Microcephalin haplotype from Neanderthals

Bruce Lahn continues his work on the Microcephalin haplogroup D. In a new paper in PNAS he and his team suggest that this brain gene may have introgressed into the modern human gene pool ~37kya from a separate Homo lineage, possibly the Neanderthals. Note that this is an open access article.

UPDATE (May 15, 2010): Neandertals had ancestral MCPH1 allele; hence this paper's inference is essentially falsified.

Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0606966103

Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage

Patrick D. Evans et al.

At the center of the debate on the emergence of modern humans and their spread throughout the globe is the question of whether archaic Homo lineages contributed to the modern human gene pool, and more importantly, whether such contributions impacted the evolutionary adaptation of our species. A major obstacle to answering this question is that low levels of admixture with archaic lineages are not expected to leave extensive traces in the modern human gene pool because of genetic drift. Loci that have undergone strong positive selection, however, offer a unique opportunity to identify low-level admixture with archaic lineages, provided that the introgressed archaic allele has risen to high frequency under positive selection. The gene microcephalin (MCPH1) regulates brain size during development and has experienced positive selection in the lineage leading to Homo sapiens. Within modern humans, a group of closely related haplotypes at this locus, known as haplogroup D, rose from a single copy {approx}37,000 years ago and swept to exceptionally high frequency ({approx}70% worldwide today) because of positive selection. Here, we examine the origin of haplogroup D. By using the interhaplogroup divergence test, we show that haplogroup D likely originated from a lineage separated from modern humans {approx}1.1 million years ago and introgressed into humans by {approx}37,000 years ago. This finding supports the possibility of admixture between modern humans and archaic Homo populations (Neanderthals being one possibility). Furthermore, it buttresses the important notion that, through such adminture, our species has benefited evolutionarily by gaining new advantageous alleles. The interhaplogroup divergence test developed here may be broadly applicable to the detection of introgression at other loci in the human genome or in genomes of other species.


November 07, 2006

Mongoloid components in Eastern Europe

Slavs and other eastern Europeans are typically Caucasoid although one does not seldom find among them individuals with certain attenuated Mongoloid influences. The extent of Mongoloid admixture in eastern Europe will eventually be determined by autosomal admixture studies which sample the relevant source populations of the Mongoloid component in Europe, namely the Uralic and Altaic speakers of Siberia and Central Asia.

At present, the only study which studied the genomic study of a Slavic sample of Russians (Science 20 December 2002: Vol. 298. no. 5602, pp. 2381 - 2385) determined a 93% membership coefficient in the main Caucasoid cluster, with a 3% membership in the main (East Asian) Mongoloid cluster. Unfortunately Central Asian Turkic and Finno-Ugrian populations from Europe and Asia were not sampled.

The presence of Mongoloid mtDNA types in East Europe is well established, but it should be remembered that movements from the east did not usually involve large numbers of women (*). Therefore, one expects that inference from mtDNA will underestimate the total number of immigrants.

Moreover, as I have pointed out before, Turkic speakers of Central Asia were likely to possess majority components of Caucasoid Y chromosomes associated with Mongoloid mtDNA components. Today, haplogroup C chromosomes make up a large component of Y-chromosome variation in Central Asia (including the famous "Genghis Khan" line), but these were probably added (from the east), late in history, since the Mongol expansion is at the end of the great period of Altaic migrations to the west (Huns, Seljuks, Ottomans, Bulgars, etc.)

As a result a proportion of the eastern immigrants into Europe would be undetectable with Y-chromosome markers, namely the substantial fraction with Caucasoid Y chromosomes and Mongoloid mtDNA. The male immigrants of this type would impart their Y chromosomes in the regions they invaded, but not their maternal mtDNA. In the Altai-Kizhi group, for example, 71% Caucasoid Y chromosomes are associated with 76% non-Caucasoid mtDNA.

Consider a population with 3/4 Caucasoid Y chromosomes and 3/4 Mongoloid mtDNA. Consider that the migrant group consists of 3/4 men and 1/4 women. Under such circumstances we would expect approximately the same rate of Mongoloid mtDNA and Y chromosomes in the recipient population. Moreover, the inferred admixture proportion from the frequencies of Mongoloid mtDNA and Y chromosomes would underestimate the true rate of Mongoloid admixture by a factor of 2.

Unfortunately, the presence of Mongoloid Y chromosomes has not been properly studied until now. In the recent Y chromosome study of the Czech Republic for example, the main Mongoloid Y-haplogroups (C, Q, O) likely to have accompanied the women bearing the 3% Mongoloid mtDNA were not examined and could be part of the Y*, P*, and K* paragroups. Similarly, none of these haplogroups were studied in a recent study on Poland and Germany.

In conclusion:
  • The mtDNA evidence suggests a very low-level introgression of Mongoloid components into Eastern Europe.
  • The extent of this admixture is likely to be underestimated by the genetic profile of the source population and the excess of male migrants.
  • The best estimate of the admixture rate will be determined by autosomal studies that sample relevant Uralic-Altaic source populations, but is probably unlikely to amount to more than a few percentage points.
(*) Except in folk migrations such as those of the Kalmyks.

November 06, 2006

ASHG 2006 abstracts

The meeting of the American Society of Human Genetics took place this October and the abstracts of the meeting are online in a big pdf file. A few items of interest:

The genetic variation and population history in the Baltic Sea region
Sharp genetic borders within a geographically restricted region are known to exist among the populations around the northern Baltic Sea on the northern edge of Europe. We studied the population history of this area in greater detail from paternal and maternal perspectives with Y chromosomal and mitochondrial DNA markers. Over 1700 DNA samples from Finland, Karelia, Estonia, Latvia, Lithuania and Sweden were genotyped for 18 Y-chromosomal biallelic polymorphisms and 8 microsatellite loci, together with 18 polymorphisms from the coding area of mtDNA and sequencing of the HVR1. Y chromosomal haplogroups from the biallelic data indicate both various phases of gene flow and existence of genetic barriers within the Baltic region. Haplogroup N3, being abundant on the eastern side of the Baltic, differentiates between eastern and western sides of the Baltic Sea, just like R1b that has a reverse frequency pattern to N3. The typically Scandinavian haplogroup Ia1 has a high frequency of up to 40%, separating not only Sweden but also Western Finland from the other populations. The frequency of haplogroup R1a1, most characteristic to Slavic peoples, varied substantially across the populations. In addition to biallelic markers, Y-chromosomal microsatellite loci were analyzed for a more detailed approach to the history of the paternal lineages in the region. We also analyzed mtDNA markers with special interest for sub-haplogroups of H and U, that among other haplogroups, show substantial variation between the populations (e.g. haplogroups H1, H2, T and J1). In conclusion, our current Y-chromosomal and mtDNA data suggest various incidents of gene flow from different sources, each reaching partly different areas of the Baltic region, which can be thus seen as a meeting point of a not only culturally but also genetically diverse set of populations.
Asian Nomads traces in the mitochondrial gene pool of Slavs.
Mitochondrial DNA (mtDNA) variability was studied in a sample of 179 individuals representing Czech population from west Bohemia. MtDNA analysis revealed that the majority of Czech mtDNAs belongs to the common West Eurasian mitochondrial haplogroups. However, about 3 per cent of Czech mtDNAs encompass East Eurasian lineages (A, N9a, D4, M*). Comparative analysis of published data has shown that different Slavonic populations contain small but marked amount of East Eurasian mtDNAs (e.g. 1.3 per cent in Eastern Slavs, 1.8 per cent in Western Slavs, and 1.2 per cent in Southern Slavs). It is noteworthy that Baltic populations (Latvians, Lithuanians and Estonians) have avoided a marked influence of maternal lineages of East Eurasian origin (0.3-0.6 per cent). The two East Eurasian mtDNA haplogroups, Z1 and D5, are present in gene pools of North European Finnic populations (Saami, Finns, and Karelians). Unlike them, Slavonic populations in general are characterized by heterogeneous mtDNA structure, defined, in addition to Z1 and D5, by haplogroups A, C, D4, G2a, M*, N9a, F and Y. Therefore, different scenarios of female-mediated East Eurasian genetic influence on Northern and Eastern Europeans should be highlighted: (1) the most ancient, probably originated in the early Holocene, influx of Asian tribes, which brought a few selected East Asian mtDNA haplotypes (like Z and D5) to Fennoscandia (Tambets et al. 2004), and (2) gradual gene flows of historic times occurred mostly in the Middle Ages due to migrations of nomadic peoples (such as the Huns, Avars, Bulgars, Mongols) to Eastern and Central European territories inhabited mainly by Slavonic tribes. We suggest that the presence of East Eurasian mtDNA haplotypes is not original feature of gene pool of the proto-Slavs, but mostly is a consequence of admixture with Central Asian nomadic tribes, who migrated into Central and Eastern Europe in the early middle Ages.
Use of Forensic Markers in the Assessment of Population Stratification.
Assignment of individuals to population groups is important to genetic case control association studies, admixture mapping, medical risk assessment, genealogy, and forensic studies. Polymorphic sequences can be used to infer ancestry but their utility for such an application is related to the number of alleles and relative frequency differences of these alleles between the population groups under study. Multiple study designs differing in numbers and types of polymorphic markers with differing levels of informativeness make comparison of studies difficult. The use of commercially-available highly-informative markers that are used internationally in forensic applications could provide a universal first tier analysis for assignment of individuals to population groups prior to inclusion in association and admixture studies. We evaluated the utility of the PowerPlex kit of 16 markers from Promega for this purpose. Multiple population groups including African, Bengalis, Chinese, Japanese, Koreans, Crypto Jews, Sephardic Jews, and Dutch were genotyped using the PowerPlex kit. The data were analyzed with STRUCTURE (Pritchard et al.) using an admixture model, correlated alleles and 3 clusters. Africans, Asians (Bengalis, Koreans, Chinese and Japanese), and Caucasians (Dutch, Sephardic Jews, and Crypto Jews) were clearly delineated. Individuals showing admixture were detectable and their removal resulted in more discrete clustering. An independently collected and genotyped set of Dutch individuals was indistinguishable from the original Dutch group providing reproducibility across data sets. The sensitivity conferred by the number of markers used in the analysis was assessed by removing markers. Delineation of population groups was apparent when 14 markers were used, although clusters were noisier; however it was not possible to delineate population groups when only 8 markers were used. The use of forensic markers is a promising strategy for clustering individuals into population groups and will be an inevitable outcome of their forensic use.
Evaluation of Ancestry and Linkage Disequilibrium Sharing in Admixed Population in Mexico
National Institute of Genomic Medicine, Mexico. More than 80% of the Mexican population is considered Mestizo, resulting from the admixture of ethnic groups with Spaniards. To generate an initial estimate of ancestral contribution (AC) of populations from Europe, Africa and Asia to the Mexican Mestizos, we genotyped 104 samples from the states of Sonora (n=20), Yucatan (n=17), Guerrero (n=21), Zacatecas (n=19), Veracruz (n=18) and Guanajuato (n=8) using the 100K Affymetrix SNP array, and used data from the International HapMap Project as the parental population information. From 3,055 ancestry informative SNPs reported by Smith et al. and Choudhry et al., we identified 105 present in the 100K array and used them to calculate AC from each population to our sample. To infer AC we used Structure software under the admixture model. Based on this analysis, the average AC in our samples is 58.96% European, 10.03% African and 31.05% Asian. Sonora shows the highest European contribution (70.63%) and Guerrero the lowest (51.98%) where we also observe the highest Asian contribution (37.17%). African contribution ranges from 7.8% in Sonora to 11.13% in Veracruz. Based on these data, we grouped our population according to European AC (<50%,>70%). We used the Carlson algorithm to derive European tagSNPs from the 100K marker set. To explore Linkage Disequlibrium Sharing (LDS) between Mestizos and Europeans, we calculated the proportion of tagSNP-marker pairs that maintained an r2≥0.8 in each evaluated population. In general, comparison of LDS between European and Asian population is ~73%, whereas comparison with African population is ~40%. Mestizos from Guerrero show the lowest LDS (74%), whereas those from Sonora show the highest (77%). Similar results are seen in the group of lower (<50%)>70%) European ancestry. Our results suggest that the Mexican Mestizo population shows ancestry-based stratification that will requiere the appropriate corrections to avoid spurius results in association studies. Our results show that admixed populations have unique patterns of LD depending on levels of ancestral contribution.
European mitochondrial haplogroups exhibit differential risk of developing presbycusis.
The genetic basis of human presbycusis (age-related hearing loss) is unknown. This common disorder is characterized by difficulty understanding conversation, particularly in noisy backgrounds. Audiograms of presbycusics show sloping hearing loss, with greatest deficiencies at the highest frequencies, and over time an individual’s hearing loss progresses into the lower frequencies that are more important for understanding speech. We investigated the hypothesis that the mitochondrial (mt) genome plays a role in presbycusis. Subjects of European ancestry, all over age 58, were tested using both classical and advanced audiometric measures and then genotyped to determine mt haplogroups. We found that subjects belonging to haplogroup H (N=93) had better hearing than other Europeans (N=80), with the greatest differences observed in the right ear at 3 kHz (p=0.017) and 10-14 kHz (p=0.016). The difference at 3 kHz correlates with the common noise notch location, and thus may indicate a difference in susceptibility to noise damage. Distortion product otoacoustic emissions also indicated better hair cell health in haplogroup H subjects, at higher frequencies and in the right ear (average DPOAEfor 4-6 kHz, p= 0.010). These results support the hypothesis that a mitochondrial factor influences susceptibility to the development of presbycusis. We are currently investigating the mt genome for causative mutations linked to the haplogroups.

Estimating the split time of Human and Neanderthal populations
Previous genetic studies of Neanderthal ancestry have used mtDNA and thus have been limited in their conclusions on the relationship of humans and Neanderthals. We present here the first use of Neanderthal genomic DNA to assess the joint history of human and Neanderthal populations. Our data consist of 37kb of short fragments of genomic DNA sequenced in Neanderthal. By studying the degree to which modern human diversity is shared with Neanderthal we can assess the time at which the human and Neanderthal populations split. We use a flexible simulation based approach that demonstrates the power of using human variation data in such analyses. We find that the two populations split ~400,000 years, predating the emergence of modern humans. Our best fitting model predicts that the Neanderthal lineage will be outgroup to the human population ~52% of the time.
The Genetic Structure of Human Populations in Africa.
Africa contains the greatest levels of human genetic variation and is the source of the worldwide range expansion of all modern humans. Knowledge of the genetic population boundaries within Africa has important implications for the design and implementation of genetic epidemiologic studies of Africans and African Americans, and for reconstructing modern human origins. A dataset consisting of ~3.7 million genotypes has been generated from the Marshfield panel of 773 microsatellites and 392 in-del polymorphic genetic markers. These markers were genotyped in ~3,200 individuals from >100 diverse ethnic populations across Africa as well as in 118 African Americans and in the CEPH Human Genome Diversity Panel, consisting of 1048 individuals from 51 globally diverse populations. Preliminary analysis of population structure using the program STRUCTURE1 indicates considerably more substructure amongst global populations (estimate for the number of genetic clusters, K, is 12) and amongst African populations (K = 9) than had previously been recognized2. Population clusters are correlated with self-described ethnicity and shared cultural and/or linguistic properties (e.g. Pygmies, Khoisan-speakers, Bantu-speakers, etc). African Americans have predominantly West African Bantu (~80%) and European (~17%) ancestry, although individual admixture levels vary considerably. These results justify the need to include a broad range of geographically and ethnically diverse African populations in studies of human genetic variation. 1Pritchard JK, et al. Genetics 155:945-59 (2000) 2Rosenberg NA, et al. Science 298:2381- 5 (2002).
Patterns of admixture in Latino populations
We examined the diversity of 13 Latino populations from seven countries (Mexico, Guatemala, Costa Rica, Colombia, Chile, Argentina and Brazil) typing 745 autosomal microsatellite markers in 250 individuals. Estimates of genetic ancestry for these populations varied substantially. Native American ancestry varied between 19.6% and 70.3%, European ancestry between 26.9% and 70.6%, and African ancestry between 1.1% and 9.8%. Genetic structure analysis provides evidence of a genetic continuity between pre- and post-Columbian populations for specific geographic regions. For instance, a Chibchan-Paezan ancestry is detectable in Latinos from lower Central America and northwest South America. Individual admixture estimates vary considerably between populations. Some Latinos (e.g. Mexico City) show marked variation in individual admixture, whereas others (e.g. Antioquia and Costa Rica) show little variation. This variation is likely to reflect the history of admixture of each geographic region examined: some Latino populations are still undergoing substantial admixture whereas others underwent admixture mostly in early colonial times. These results have important implications for admixture mapping and association mapping studies in Latino populations.

Genomic diversity and population structure of Native Americans
We examined 745 autosomal microsatellite markers in 432 individuals sampled from 24 indigenous populations in the Americas. These data were analyzed jointly with similar data available in 54 other indigenous populations from across the world (including an additional 5 Native American groups). The populations from the Americas show lower diversity and more differentiation than populations from other continental regions (global Fst=0.08). Signals of long-range linkage disequilibrium are detectable to a greater extent in Native Americans than in other populations, as are signals of recent bottlenecks followed by population growth. A negative correlation is observed between population diversity and geographic distance from the Bering Strait, an observation consistent with the north-to-south dispersal of humans upon initial entry into the continent. A higher diversity is observed in western vs. eastern South American populations, potentially reflecting differences in long-term effective population size or in colonization routes within South America. Phylogenetic trees relating Native American populations show a marked differentiation between Canadian and other Native populations. Canadian natives also show a detectable shared ancestry with contemporary Siberian populations, which is less visible for more southerly Americans. A substantial agreement is observed between phylogenetic relatedness and population affiliation according to the linguistic classification of Greenberg.

The rare nonsynonymous SCN5A-S1103Y variant in Caucasians is due to recent African Admixture as revealed by 100k SNP genotyping.
The SCN5A-S1103Y variant is an established and confirmed risk factor conferring an odds ratio up to 8.5 for cardiac ventricular arrhythmias and sudden cardiac death (Splawski et al, Science, 2002, Burke et al., Circulation, 2005, Plant et al., J. Clin. Invest. 2006). In Africans it is a common nonsynonymous SNP (MAF=8%), but it is rarely observed in Caucasians (Chen et al, J. Med. Genet. 2002). In a Bavarian family appearing of entirely Caucasian descent and affected with long QT Syndrome we have detected this variant in heterozygote state as the only causal nonsynonymous variation upon diagnostic ion channel resequencing. To resolve the question, whether in the family the variant was (a) of ancient African descent, (b) due to recent African admixture or (c) a de novo mutation, we analyzed the genetic segment it resided on. Dense SNP genotyping in admixed individuals allows to infer the ethnicity of chromosomal regions if allele frequencies are known in the original populations. Ethnicity inference for any given locus can be carried out by applying the product rule to a sliding window of neighboring SNPs or via modeling ancestry by hidden Markov Chain Monte Carlo Methods (Tang et al. Am. J. Hum. Genet, 2006). By 100k SNP genotyping of the Bavarian family, we demonstate that the S1103 variant is due to recent African admixture (b) and could rule out possibilities (a) and (c). This application demonstrates that inferring ethnicity of chromosomal regions by high density SNP genotyping is a powerful approach with prospects also to admixture mapping of disease loci and population stratification correction of genomewide association mapping of complex disease loci.

Allele frequency estimates from DNA pools for 317,000 SNPs for multiple European and worldwide populations and discovery of Ancestry Informative Markers for Europe.
The identification of Ancestry Informative Markers (AIMs) and inference of individual genetic history is useful in many applications, including studies of geography and evolution of human populations, forensic sciences, pharmacogenomics, admixture mapping and association studies of complex diseases. While many AIMs have been reported that define strong genetic differences between major continents, it is more difficult to identify markers that reflect subtle, within-continent diversity, such as the heterogeneous ancestry of European Americans contributed by different populations within Europe. We have analyzed DNA pools, each for a different population, on Illumina HumanHap300 BeadArrays to estimate allele frequencies for ~317,000 Single Nucleotide Polymorphisms for 9 European, 6 African, and 2 Amerindian populations in the Human Genome Diversity Project collection. We have also evaluated the performance of this method by analyzing three HapMap pools (YRI, CHB, and JPT), for which the true allele frequencies are already known from the International HapMap Project. We found that the allele frequency estimates differed between replicate chips by less than +/-5% for 95% of the SNPs, and that the estimated frequencies and the true frequencies differed by +/-5-10% for 90% of the SNPs. The data for nine European populations, from western Caucasus, Scotland, Tuscany, Sardinia, France, Iberia, Russia, Northern Italy, and a Basque region, showed a clear excess of SNPs having large allele frequency differences (e.g. >30%) between most pairs of populations, compared to what would be expected given the sample sizes. These results provide a valuable resource of European AIMs for monitoring within-continent stratification in association studies. We are currently validating the most informative SNPs by individually genotyping samples that formed the pools as well as those from additional European populations.

Mitochondrial haplogroups are associated with asthma and total serum IgE levels
Maternal history of asthma and/or atopy is a major risk factor for the subsequent development of asthma and allergy in childhood. Although mitochondrial mutations have been implicated in several maternally inherited monogenic disorders, no studies of mitochondrial polymorphisms and asthma have been reported.Weevaluated whether common mitochondrial haplogroups are associated with asthma and total serum IgE levels. 8 common mitochondrial single nucleotide polymorphisms (mtSNP) were genotyped in two cohorts of European ancestry: 512 adult women with incident asthma and 517 matching controls participating in the Nurses’ Health Study (NHS) and 654 children ages 5-12 years with mild to moderate asthma participating in the Childhood Asthma Management Program (CAMP). Genotyping was performed using TaqMan® probe hybridization assays. 93 random NHS samples were run in duplicate for all assays and demonstrated 100% concordance. In the CAMP Study, genotype data from probands’ mothers was also 100% concordant across all assays. Completion rates in both cohorts were > 95% for all markers. mtSNP 9055 was seen at higher frequency in NHS asthma cases (frequency 11.1%) than controls (8.0%, p = 0.02). Association analysis using haplo.score identified two haplogroups associated with asthma: one haplogroup at a frequency of 3.83% among cases compared to 1.27% among controls (p=0.0002) and another at a frequency of 9.97% among cases and 11.3% among controls (p=0.04). The CAMP Study is a case-only (family-based) cohort, thus precluding evaluation of mitochondrial SNP associations with asthma status. However, quantitative analysis of mitochondrial haplogroups identified two haplogroups of 11.0% and 1.87% frequency that were associated with log-transformed total serum IgE levels, an important intermediate phenotype in asthma and atopy (p=0.006 and 0.01, respectively). These data suggest that common mitochondrial haplogroups influence asthma diathesis.