October 28, 2006

mtDNA of island Southeast Asia

A new preprint has appeared in the American Journal of Human Genetics site about the mtDNA origins of island SE Asians.

American Journal of Human Genetics (preprint)

A mitochondrial stratigraphy for Island Southeast Asia

Catherine Hill et al.

Island Southeast Asia (ISEA) was first colonized by modern humans at least 45,000 years ago, but the extent to which the modern inhabitants trace their ancestry to the first settlers is a matter of debate. It is widely held in both archaeology and linguistics that they are largely descended from a second wave of dispersal, proto-Austronesian-speaking agriculturalists who originated in China and spread to Taiwan ~5,500 years ago. From there they are thought to have dispersed into Island Southeast Asia ~4,000 years ago, assimilating the indigenous populations. Here, we demonstrate that mtDNA diversity in the region is extremely high and includes a large number of indigenous clades. Only a fraction of these date back to the time of first settlement, and the majority appear to mark dispersals in the late Pleistocene or early
Holocene most likely triggered by post-glacial flooding. There are much closer genetic links to Taiwan than to the mainland, but most of these probably pre-dated the mid-Holocene ‘out of Taiwan’ event as traditionally envisioned. Only ~20% at most of modern mtDNAs in ISEA could be linked to such an event, suggesting that if an agriculturalist migration did take place it was demographically minor, at least as regards the involvement of women.

Link (pdf)

October 25, 2006

Blue-eyed men prefer blue-eyed women

Eye spy a cheat
BLUE-eyed men prefer blue-eyed women, apparently because eye colour can help reveal whether their partner has been faithful, researchers say.

"Before you request a paternity test, spend a few minutes looking at your child's eye colour," Bruno Laeng and colleagues at the University of Tromso in Norway said in the study.

Under the laws of genetics, two parents with blue eyes will always have blue-eyed children, it said. So a blue-eyed man can know his blue-eyed wife or partner has cheated on him if their child has brown eyes.

"Blue-eyed men may have unconsciously learned to value a physical trait that can facilitate recognition of own kin," the scientists said in the journal Behavioural Ecology and Sociobiology.

The scientists asked 88 students to rate the attractiveness of models based on pictures manipulated so that half of them had blue eyes and the other half had brown eyes.

The blue-eyed men in the group showed a preference for blue-eyed women.

But brown-eyed men, who cannot find any clues about paternity from a child's eye colour, had no preferences by eye colour.

Women showed no preference for brown or blue-eyed men, irrespective of their own eye colour.

A quarter of children born to two brown-eyed parents who have both brown and blue-eye genes among their ancestors will have blue eyes. The rest will be brown.

In a second study, 443 young adults of both sexes were asked about the eye colour of their partners – blue-eyed men were also the group with the highest proportion of partners with the same eye colour.
Behavioral Ecology and Sociobiology (online first)

Why do blue-eyed men prefer women with the same eye color?

Bruno Laeng et al.

Abstract The human eye color blue reflects a simple, predictable, and reliable genetic mechanism of inheritance. Blue-eyed individuals represent a unique condition, as in their case there is always direct concordance between the genotype and phenotype. On the other hand, heterozygous brown-eyed individuals carry an allele that is not concordant with the observed eye color. Hence, eye color can provide a highly visible and salient cue to the child’s heredity. If men choose women with characteristics that promote the assurance of paternity, then blue-eyed men should prefer and feel more attracted towards women with blue eyes. To test these predictions, close-up photos of young women and adult men with either blue or brown eyes were rated for their attractiveness by young women and men observers with either blue or brown eyes (N=88). The eye color in the photographs of each model was manipulated so that a same face would be shown with either the natural eye color (e.g., blue) or with the other color (e.g., brown). Both blue-eyed and brown-eyed female participants showed no difference in their attractiveness ratings for male models of either eye color. Similarly, brown-eyed men showed no preference for either blue-eyed or brown-eyed female models. However, blue-eyed men rated as more attractive the blue-eyed women than the brown-eyed ones. We interpret the latter preference in terms of specific mate selective choice of blue-eyed men, reflecting strategies for reducing paternity uncertainty. In a second study, a group of young adults (N=443) of both sexes and different eye colors (blue, brown, and green) were asked to report the eye and hair color of their romantic partners. Their responses indicated the presence of assortative mating by eye color as well as, to a less degree, for hair color. Most importantly, blue-eyed male respondents were the group with the largest proportion of partners of same eye color. These findings 1) indicate that blue-eyed men do prefer women with the same eye color and 2) specifically suggest the presence of a male adaptation for the detection of extra-pair paternity based on eye color, as a phenotypically based assurance of paternity (i.e., when the father’s and offspring’s phenotypes match) as well as a defense against cuckoldry (i.e., when the phenotypes do not match).


Korean mtDNA

Electrophoresis. 2006 Oct 23; [Epub ahead of print]

East Asian mtDNA haplogroup determination in Koreans: Haplogroup-level coding region SNP analysis and subhaplogroup-level control region sequence analysis.

Lee HY et al.

The present study analyzed 21 coding region SNP markers and one deletion motif for the determination of East Asian mitochondrial DNA (mtDNA) haplogroups by designing three multiplex systems which apply single base extension methods. Using two multiplex systems, all 593 Korean mtDNAs were allocated into 15 haplogroups: M, D, D4, D5, G, M7, M8, M9, M10, M11, R, R9, B, A, and N9. As the D4 haplotypes occurred most frequently in Koreans, the third multiplex system was used to further define D4 subhaplogroups: D4a, D4b, D4e, D4g, D4h, and D4j. This method allowed the complementation of coding region information with control region mutation motifs and the resultant findings also suggest reliable control region mutation motifs for the assignment of East Asian mtDNA haplogroups. These three multiplex systems produce good results in degraded samples as they contain small PCR products (101-154 bp) for single base extension reactions. SNP scoring was performed in 101 old skeletal remains using these three systems to prove their utility in degraded samples. The sequence analysis of mtDNA control region with high incidence of haplogroup-specific mutations and the selective scoring of highly informative coding region SNPs using the three multiplex systems are useful tools for most applications involving East Asian mtDNA haplogroup determination and haplogroup-directed stringent quality control.


Realistic bust of Aristotle discovered

Aristotle as he really looked
A bust of Aristotle found beneath the Acropolis in Athens is the first to show the Greek philosopher with a hooked nose.

Archaeologists said that the 46cm (18in) marble bust, which dates from the 1st century AD, about 400 years after Aristotle lived, was “the best-preserved likeness ever found”. Alkestis Horemi, who supervises digs at the Acropolis, said: “This is the only bust portraying the philosopher with a hooked nose in line with ancient descriptions.” (AFP)

October 24, 2006

Horse domestication news from Kazakhstan

See also Botai and Horse Domestication.

New evidence of early horse domestication

Soil from a Copper Age site in northern Kazakhstan has yielded new evidence for domesticated horses up to 5,600 years ago. The discovery, consisting of phosphorus-enriched soils inside what appear to be the remains of horse corrals beside pit houses, matches what would be expected from Earth once enriched by horse manure. The Krasnyi Yar site was inhabited by people of the Botai culture of the Eurasian Steppe, who relied heavily on horses for food, tools, and transport.

"There's very little direct evidence of horse domestication," says Sandra Olsen, an archaeologist and horse domestication researcher at the Carnegie Museum of Natural History in Pittsburgh, PA. That's because 5,600 years ago there were no saddles or metal bits to leave behind. Equipment like bridles, leads, and hobbles would have been made from thongs of horse hide, and would have rotted away long ago. Likewise horses themselves have not changed much physically as a result of domestication, unlike dogs or cattle. So ancient horse bones don't easily reveal the secrets of domestication.

With research funding from the National Science Foundation, Olsen's team took a different tack. They looked for circumstantial evidence that people were keeping horses. One approach was to survey the Krasnyi Yar site with instruments to map out subtle electrical and magnetic irregularities in the soils. With this they were able to identify the locations of 54 pit houses and dozens of post moulds where vertical posts once stood. Some of the post moulds were arranged circularly, as would be most practical for a corral.

Next, geologist Michael Rosenmeier from the University of Pittsburgh collected soil samples from inside the fenced area and outside the settlement. The samples were analyzed for nitrogen, phosphorus, potassium, and sodium concentrations by Rosemary Capo, University of Pittsburgh geochemist, and her students. Modern horse manure is rich in phosphorous, potassium, and especially nitrogen, compared to undisturbed soils. But because nitrogen is mobile in soils, it can be lost to groundwater or transferred to the atmosphere by organic and inorganic processes. Phosphorus, on the other hand, can be locked into place by calcium and iron and is more likely to be preserved in the soils for millennia.

As it turned out, the soil from inside the alleged corral had up to ten times the phosphorus concentration as the soils from outside the settlement. Lots of phosphorus can also indicate a hearth, said Capo, but that phosphorus is usually accompanied by a lot of potassium, which is not the case in the corral at Krasnyi Yar.

The corral soils also had low nitrogen concentrations, says Capo, reducing the likelihood that the phosphorus came from more recent manure. "That's good, actually," she said of the recently completed nitrogen analyses. "It suggests we've got old stuff."

Even more compelling will be if we find long-lived molecules of fat, or lipids, directly attributed to horse manure in the soils, says Olsen.

The latest results from Krasnyi Yar site will be on display Monday morning, 23 October, at the Annual Meeting of the Geological Society of America in Philadelphia.

Early as the Botai were, they were probably not the first to domesticate horses, says Olsen. "The very first horse domestication was probably a bit earlier in Ukraine or western Russia," she said. "Then some horse-herders migrated east to Kazakhstan."

Horses allowed the Botai to build large perennial villages with, in one case, hundreds of homes. They did so without the benefit of agriculture, Olsen explained, as theirs was a horse economy.

The Botai were able to stay put year-round because horses are very well adapted to cold winters, she said. "Horses can survive ice storms and don't need heated barns or winter fodder," Olsen said. They are, in fact, some of the last remaining large, Ice Age, Pleistocene mammals living in one of the last places on Earth where Pleistocene vegetation survives.

Because they were domesticated, the horses supplied meat year-round and vitamin-rich mare's milk from spring through fall. "No one in their right mind would try to milk a wild mare," said Olsen.

There is also evidence that the Botai were carrying a lot of heavy material, like rocks and large skulls, over long distances. That is a lot more practical and explicable if they used pack horses.

Later people of the same region adopted shepherding and cattle raising, said Olsen. That created a more nomadic culture, since sheep and cattle are not well suited for sub-zero climates and therefore needed to be taken south in winter. The tradeoff, she says, was that cows and sheep give far fattier milk year round, which can be made into yogurt and cheese. Sheep also provide wool.

Kazakh people today still eat horsemeat. They were forced to abandon their nomadic lifestyle during the Soviet era and have returned to small village pastoralism, Olsen says.

October 22, 2006

IQ of Serbian Gypsies

Intelligence (Article in Press)

General mental ability in South Asians: Data from three Roma (Gypsy) communities in Serbia

J. Philippe Rushton et al.


To examine whether the Roma (Gypsy) population of Serbia, like other South Asian population groups, average lower than Europeans on g, the general factor of intelligence, we tested 323 16- to 66-year-olds (111 males; 212 females) in three different communities over a two-year-period on the Raven's Colored and/or Standard Progressive Matrices and four measures of executive function. Out of the total of 60 Matrices, the Roma solved an average of 29, placing them at the 3rd percentile on 1993 U.S. norms, yielding an IQ equivalent of 70. On the executive function tests, the Roma averaged at about the level of Serbian 10-year-olds. The Matrices showed a small mean sex difference favoring males. External validity was demonstrated by correlating the scores on Matrices with measures such as cranial capacity (r = 0.13, P < 0.01), spousal similarity (r = 0.17, P < 0.05), age at birth of first child (r = 0.26, P < 0.01), number of offspring (r = − 0.20, P < 0.01), and responsible social attitudes (r = 0.10, P < 0.05). Comparisons with extant data showed that items found difficult or easy by the Roma were those found difficult or easy by White, Indian, Colored, and Black South African 14- to 16-year-olds and by Black South African undergraduates (rs = 0.90). There was no evidence of any idiosyncratic cultural effect. Instead, Roma/non-Roma differences were found to be most pronounced on g. This was shown by item-total correlations (estimates of the item's g loading), which predicted the magnitude of Roma/non-Roma differences on those same items, regardless of from which sample the item-total correlations were calculated, and by confirmatory factor analysis. The results indicate the remarkable cross-cultural generalizability of item properties across South Asians, Europeans, and sub-Saharan Africans and that these reflect g more than culturally specific ways of thinking.


October 20, 2006

Skin tone and attractiveness

This study seems to echo the results of a different German study which I posted a few years ago. According to the older study:
Additional surveys showed that attractive female faces are narrower than unattractive ones, and that they possess a brown skin and full, well looked-after lips.
According to the new study:
Results show an overall main effect of skin tone, suggesting that light brown skin color is perceived by both Caucasian and African American models as more credible and attractive than models who are pale and dark skinned, F(2,71) = 14.7, p < .0001. Consistent with earlier theorizing, images of light brown models yielded more favorable responses than images featuring dark skinned or pale models, F = 18.70, p < .01. Consistent with the proposed relationships stated in hypothesis 1, when the participants were asked to evaluate an individual on the basis of physical attractiveness and credibility, participants in this study found light brown models more credible and more attractive than their counterparts with darker skin.
Facial plast Surg 2006; 22: 175-179

“Shades of Beauty”: Examining the Relationship of Skin Color to Perceptions of Physical Attractiveness

Cynthia M. Frisby


The purpose of this research project was to investigate the relationship between skin color and level of perceived physical attractiveness. Previous research suggested that skin color plays an important role in how we perceive an individual's physical attractiveness. The current study was conducted to determine how influential the role of race is on perceptions of physical attractiveness. In this study, 79 subjects were asked to evaluate images of potential endorsers to be used in an upcoming advertising campaign. The images were those of females of varying skin tones. Data were then collected and analyzed to determine whether skin tone and level of skin color can in fact influence the physical attractiveness stereotype.


October 19, 2006

Greek origins of some Pathans but not other Pakistanis

A new article in European Journal of Human Genetics investigates the Greek ancestry of Pakistani populations that sometimes claim descent from Alexander the Great's troops. In previous studies (use search on the right) it was demonstrated that these claims are mostly false, since modern Pakistanis mostly lack haplogroup E3b chromosomes that are found often in Greece.

The new study shows that among the Pakistani populations, only the Pathans seem to be closer to the Greeks, and not the pagan Kalash and the Burusho. Unfortunately, claims about the Hellenicity of the Kalash seem to persist despite the genetic evidence that has accumulated over the years.

Moreover, the similarity between the Pathans and the Greeks is not accidental. An argument for the real contribution of Greeks to the Pathan population is the discovery of specific haplotypes within haplogroup E3b1 that seem to be of Greek-Balkan origin and which are found only in the Pathans among the Pakistani populations.
Compelling evidence in support of the genetic relationship between the Pathan and Greek E3b1 Y chromosomes was provided by the median-joining network (Figure 4). One Pathan shared a Y-STR haplotype, that included a duplication of 10 and 13 repeat units for the DYS425 locus, with three Greek individuals and the other was separated from this cluster by a single mutation, which enabled us to estimate the TMRCA (mean+/-SD) using the Network software as between 2000+/-400 and 5000+/-1200 YBP depending upon the observed26 or inferred mutation rates,27 respectively. This coincides with the period of Alexander's invasion during 327–323 BC. This haplotype was not observed in any other E3b1-derived Pakistani Y chromosome but was highly specific for the Balkans – the highest frequency being in Macedonia.
European Journal of Human Genetics (advance online publication)

Y-chromosomal evidence for a limited Greek contribution to the Pathan population of Pakistan

Sadaf Firasat et al.

Three Pakistani populations residing in northern Pakistan, the Burusho, Kalash and Pathan claim descent from Greek soldiers associated with Alexander's invasion of southwest Asia. Earlier studies have excluded a substantial Greek genetic input into these populations, but left open the question of a smaller contribution. We have now typed 90 binary polymorphisms and 16 multiallelic, short-tandem-repeat (STR) loci mapping to the male-specific portion of the human Y chromosome in 952 males, including 77 Greeks in order to re-investigate this question. In pairwise comparisons between the Greeks and the three Pakistani populations using genetic distance measures sensitive to recent events, the lowest distances were observed between the Greeks and the Pathans. Clade E3b1 lineages, which were frequent in the Greeks but not in Pakistan, were nevertheless observed in two Pathan individuals, one of whom shared a 16 Y-STR haplotype with the Greeks. The worldwide distribution of a shortened (9 Y-STR) version of this haplotype, determined from database information, was concentrated in Macedonia and Greece, suggesting an origin there. Although based on only a few unrelated descendants, this provides strong evidence for a European origin for a small proportion of the Pathan Y chromosomes.


October 18, 2006

Human species 'may split in two'

BBC reports:
Humanity may split into two sub-species in 100,000 years' time as predicted by HG Wells, an expert has said.

Evolutionary theorist Oliver Curry of the London School of Economics expects a genetic upper class and a dim-witted underclass to emerge.

The human race would peak in the year 3000, he said - before a decline due to dependence on technology.

People would become choosier about their sexual partners, causing humanity to divide into sub-species, he added.
The idea that human evolution can be predicted across thousand-year time scales is pretty hard to swallow.

October 17, 2006

Hereditary facial expressions

Via the BBC and Scientific American and New Scientist. This idea makes sense:
Peleg speculates that genes might influence the muscle and nerve structure in the face. This, in turn, would create biological constraints that make facial expressions more similar among relatives.

Estimating the IQ of states of the USA

From the paper:

Intelligence (article in press)

Estimating state IQ: Measurement challenges and preliminary correlates

Michael A. McDaniel


The purpose of this study is threefold. First, an estimate of state IQ is derived and its strengths and limitations are considered. To that end, an indicator of downward bias in estimating state IQ is provided. Two preliminary causal models are offered that predict state IQ. These models were found to be highly predictive of state IQ, yielding multiple R's of 0.83 and 0.89. Second, the extent to which state IQ predicts state outcome variables (e.g., gross state product, health, violent crime, and government effectiveness) is estimated. State IQ shows positive correlations with gross state product, health, and government effectiveness and negative correlations with violent crime. These results are consistent with the extent to which IQ predicts outcomes at the level of the individual. Third, a research agenda is provided for improving estimates of state IQ, identifying factors that cause differences in state IQ, and delineating the role of IQ in predicting important variables.


Brain size is not a good indicator of the evolution of human intelligence

Intelligence (Article in Press)

The evolution of human intelligence and the coefficient of additive genetic variance in human brain size

Geoffrey F. Millera and Lars Penke


Most theories of human mental evolution assume that selection favored higher intelligence and larger brains, which should have reduced genetic variance in both. However, adult human intelligence remains highly heritable, and is genetically correlated with brain size. This conflict might be resolved by estimating the coefficient of additive genetic variance (CVA) in human brain size, since CVAs are widely used in evolutionary genetics as indexes of recent selection. Here we calculate for the first time that this CVA is about 7.8, based on data from 19 recent MRI studies of adult human brain size in vivo: 11 studies on brain size means and standard deviations, and 8 studies on brain size heritabilities. This CVA appears lower than that for any other human organ volume or life-history trait, suggesting that the brain has been under strong stabilizing (average-is-better) selection. This result is hard to reconcile with most current theories of human mental evolution, which emphasize directional (more-is-better) selection for higher intelligence and larger brains. Either these theories are all wrong, or CVAs are not as evolutionarily informative as most evolutionary geneticists believe, or, as we suggest, brain size is not a very good index for understanding the evolutionary genetics of human intelligence.


October 15, 2006

Rio de Janeiro Y chromosomes

See also Brazilian Y chromosomes.

Am J Hum Biol. 2006 Oct 12;18(6):829-837 [Epub ahead of print]

Y-chromosome genetic variation in Rio De Janeiro population.

Silva DA, Carvalho E, Costa G, Tavares L, Amorim A, Gusmao L.

The present-day Brazilian gene pool is known to be the outcome of an admixture process of populations from different origins, mainly Amerindians, Europeans, and Africans. It is also known that in Brazil, a wide variation in the admixture process occurred in different regions of the country or even in different subpopulations from the same region. In the present study, we aimed to characterize the male lineages present in the Rio de Janeiro population, the second most populated of the 26 Brazilian states. A random sample of 127 unrelated males from Rio de Janeiro was typed for 28 Y-chromosome-specific biallelic markers. In total, 17 different haplogroups were defined within our sample, most of them of European ancestry (88.1%). Those of sub-Saharan African origin (E3a) amounted to 7.9%, while only 2 males carried Amerindian lineages (characterized by the presence of an M3 mutation: haplogroup Q3). Using both Y-STR haplotype and Y-SNP haplogroup information, genetic distances were calculated between the subgroup of Rio de Janeiro males carrying European haplogroups and the Portuguese population. Low, nonsignificant, values were obtained. Thus, in contrast with what is observed in their female counterparts, the vast majority of the present Rio de Janeiro male gene pool is of European extraction, while the original Amerindian lineages are residual and much less frequent than the sub-Saharan component resulting from the slave trade. These observations can be interpreted as the signature of the strong gender asymmetry of the admixture processes in colonial systems.


October 14, 2006

Discovering the ethnic roots of African Americans is difficult

It's great that scientists are beginning to critically examine the tall claims of many companies offering DNA tests for genealogy and ancestry. Over-interpretation of the results plagues the field, due both to individuals' confirmation bias or desire to get substantial information for the money spent, but also due to the willingness of companies to cater and re-inforce these desires.

Looking for roots in Africa? DNA search not easy
WASHINGTON (Reuters) - African-Americans hoping to use DNA to find their roots may have to look harder than previously thought, researchers said on Thursday in a study they said shows Africans are too genetically mixed to make tracing easy.

Several companies now offer to help Americans trace their African ancestry using mitochondrial DNA, which is passed from mother to daughter virtually unaltered.

"What's your tribe?" asks one. "Trace Your Roots Back in Time," offers another.

But biologist Bert Ely of the University of South Carolina and colleagues found that fewer than 10 percent of African-American mitochondrial DNA sequences that were analyzed can be matched to any single African ethnic group.

The news might disappoint people who cannot trace a long paper trail of ancestors. More than 11 million Africans were forcibly shipped to the Americas during the slave trade that peaked in the 17th and 18th centuries.

"The test that everybody does is the same test and it is all valid," Ely said in a telephone interview.

"It is just that some companies will over-interpret the data and give you the most likely result instead of all of the matches."

Working with colleagues at the University of Massachusetts and the University of Maryland, Ely looked at 3,700 mitochondrial DNA sequences from people in sub-Saharan Africa.
BMC Biology (open access)

African-American mitochondrial DNAs often match mtDNAs found in multiple African ethnic groups

Bert Ely et al.


Mitochondrial DNA (mtDNA) haplotypes have become popular tools for tracing maternal ancestry, and several companies offer this service to the general public. Numerous studies have demonstrated that human mtDNA haplotypes can be used with confidence to identify the continent where the haplotype originated. Ideally, mtDNA haplotypes could also be used to identify a particular country or ethnic group from which the maternal ancestor emanated. However, the geographic distribution of mtDNA haplotypes is greatly influenced by the movement of both individuals and population groups. Consequently, common mtDNA haplotypes are shared among multiple ethnic groups. We have studied the distribution of mtDNA haplotypes among West African ethnic groups to determine how often mtDNA haplotypes can be used to reconnect Americans of African descent to a country or ethnic group of a maternal African ancestor. The nucleotide sequence of the mtDNA hypervariable segment I (HVS-I) usually provides sufficient information to assign a particular mtDNA to the proper haplogroup, and it contains most of the variation that is available to distinguish a particular mtDNA haplotype from closely related haplotypes. In this study, samples of general African-American and specific Gullah/Geechee HVS-I haplotypes were compared with two databases of HVS-I haplotypes from sub-Saharan Africa, and the incidence of perfect matches recorded for each sample.


When two independent African-American samples were analyzed, more than half of the sampled HVS-I mtDNA haplotypes exactly matched common haplotypes that were shared among multiple African ethnic groups. Another 40% did not match any sequence in the database, and fewer than 10% were an exact match to a sequence from a single African ethnic group. Differences in the regional distribution of haplotypes were observed in the African database, and the African-American haplotypes were more likely to match haplotypes found in ethnic groups from West or West Central Africa than those found in eastern or southern Africa. Fewer than 14% of the African-American mtDNA sequences matched sequences from only West Africa or only West Central Africa.


Our database of sub-Saharan mtDNA sequences includes the most common haplotypes that are shared among ethnic groups from multiple regions of Africa. These common haplotypes have been found in half of all sub-Saharan Africans. More than 60% of the remaining haplotypes differ from the common haplotypes at a single nucleotide position in the HVS-I region, and they are likely to occur at varying frequencies within sub-Saharan Africa. However, the finding that 40% of the African-American mtDNAs analyzed had no match in the database indicates that only a small fraction of the total number of African haplotypes has been identified. In addition, the finding that fewer than 14% of African-American mtDNAs matched mtDNA sequences from a single African region suggests that few African Americans might be able to trace their mtDNA lineages to a particular region of Africa, and even fewer will be able to trace their mtDNA to a single ethnic group. However, no firm conclusions should be made until a much larger database is available. It is clear, however, that when identical mtDNA haplotypes are shared among many ethnic groups from different parts of Africa, it is impossible to determine which single ethnic group was the source of a particular maternal ancestor based on the mtDNA sequence.


October 12, 2006

Neolithic goats

Goats Key to Spread of Farming, Gene Study Suggests
Goats accompanied the earliest farmers into Europe some 7,500 years ago, helping to revolutionize Stone Age society, a new study suggests.

The trailblazing farm animals were hardy and highly mobile traveling companions to ancient pioneers from the Middle East who introduced agriculture to Europe and elsewhere, researchers say.

The onset of farming ushered in the so-called Neolithic Revolution, when settled communities gradually replaced nomadic tribes and their hunter-gatherer lifestyles between 8000 and 6000 B.C.

A team of archaeologists and biologists has traced the origins of domesticated goats in Western Europe to the Middle East at the beginnings of the Neolithic period.

The study is based on DNA analysis of goat bones from a Stone Age cave in France and suggests the animals spread across Europe quickly after their introduction. (Get goat photos, facts, and more.)

Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0602753103

Divergent mtDNA lineages of goats in an Early Neolithic site, far from the initial domestication areas

Helena Fernández et al.

Goats were among the first farm animals domesticated, 10,500 years ago, contributing to the rise of the "Neolithic revolution." Previous genetic studies have revealed that contemporary domestic goats (Capra hircus) show far weaker intercontinental population structuring than other livestock species, suggesting that goats have been transported more extensively. However, the timing of these extensive movements in goats remains unknown. To address this question, we analyzed mtDNA sequences from 19 ancient goat bones (7,300-6,900 years old) from one of the earliest Neolithic sites in southwestern Europe. Phylogenetic analysis revealed that two highly divergent goat lineages coexisted in each of the two Early Neolithic layers of this site. This finding indicates that high mtDNA diversity was already present >7,000 years ago in European goats, far from their areas of initial domestication in the Near East. These results argue for substantial gene flow among goat populations dating back to the early neolithisation of Europe and for a dual domestication scenario in the Near East, with two independent but essentially contemporary origins (of both A and C domestic lineages) and several more remote and/or later origins.


October 10, 2006

Study paints bleak picture of ethnic diversity

By John Lloyd in London
Published: October 8 2006 22:08 | Last updated: October 8 2006 22:08

A bleak picture of the corrosive effects of ethnic diversity has been revealed in research by Harvard University’s Robert Putnam, one of the world’s most influential political scientists.

His research shows that the more diverse a community is, the less likely its inhabitants are to trust anyone – from their next-door neighbour to the mayor.

This is a contentious finding in the current climate of concern about the benefits of immigration. Professor Putnam told the Financial Times he had delayed publishing his research until he could develop proposals to compensate for the negative effects of diversity, saying it “would have been irresponsible to publish without that”.

The core message of the research was that, “in the presence of diversity, we hunker down”, he said. “We act like turtles. The effect of diversity is worse than had been imagined. And it’s not just that we don’t trust people who are not like us. In diverse communities, we don’t trust people who do look like us.”

Prof Putnam found trust was lowest in Los Angeles, “the most diverse human habitation in human history”, but his findings also held for rural South Dakota, where “diversity means inviting Swedes to a Norwegians’ picnic”.

When the data were adjusted for class, income and other factors, they showed that the more people of different races lived in the same community, the greater the loss of trust. “They don’t trust the local mayor, they don’t trust the local paper, they don’t trust other people and they don’t trust institutions,” said Prof Putnam. “The only thing there’s more of is protest marches and TV watching.”

British Home Office research has pointed in the same direction and Prof Putnam, now working with social scientists at Manchester University, said other European countries would be likely to have similar trends.

His 2000 book, Bowling Alone, on the increasing atomisation of contemporary society, made him an academic celebrity. Though some scholars questioned how well its findings applied outside the US, policymakers were impressed and he was invited to speak at Camp David, Downing Street and Buckingham Palace.

Prof Putnam stressed, however, that immigration materially benefited both the “importing” and “exporting” societies, and that trends “have been socially constructed, and can be socially reconstructed”.

In an oblique criticism of Jack Straw, leader of the House of Commons, who revealed last week he prefers Muslim women not to wear a full veil, Prof Putnam said: “What we shouldn’t do is to say that they [immigrants] should be more like us. We should construct a new us.”

From the Financial Times

New Anatomical Record on Flores hominid

On the heels of the recent paper on PNAS about the Flores hominid (aka "Hobbit"), a new paper in the Anatomical Record also questions the validity of Homo floresiensis. Here is the press release from the Field Museum:
CHICAGO -- What may well turn out to be the definitive work in a debate that has been raging in palaeoanthropology for two years will be published in the November 2006 issue of Anatomical Record.

The new research comprehensively and convincingly makes the case that the small skull discovered in Flores, Indonesia, in 2003 does not represent a new species of hominid, as was claimed in a study published in Nature in 2004. Instead, the skull is most likely that of a small-bodied modern human who suffered from a genetic condition known as microcephaly, which is characterized by a small head.

"It's no accident that this supposedly new species of hominid was dubbed the 'Hobbit;'" said Robert R. Martin, PhD, Curator of Biological Anthropology at the Field Museum and lead author of the paper. "It is simply fanciful to imagine that this fossil represents anything other than a modern human." The new study is the most wide-ranging, multidisciplinary assessment of the problems associated with the interpretation of the 18,000-year-old Flores hominid yet to be published. The authors include experts on:

* scaling effects of body size, notably with respect to the brain: Dr. Martin and Ann M. MacLarnon, PhD, School of Human & Life Sciences, Roehampton University in London;
* clinical and genetic aspects of human microcephaly: William B. Dobyns, PhD, Department of Human Genetics, University of Chicago; and
* stone tools: James Phillips, PhD, Departments of Anthropology at the University of Illinois at Chicago and the Field Museum.

This is just one of four separate research teams that have recently published evidence indicating concluding that the Flores hominid is far more likely to be a small-bodied modern human suffering from a microcephaly than a new species derived from Homo erectus, as was claimed in the original Nature paper.

Significantly, the second most recent publication to conclude that the "Hobbit" was microcephalic--another multidimensional study that was published in the September 5, 2006, issue of Proceedings of the National Academy of Sciences--includes a co-author who was also a co-author of the original publication in Nature. That scientist, R.P. Soejono of the National Archaeological Research Center in Jakarta, Indonesia, now writes that the Flores hominid was microcephalic rather than a new hominid species.

The Anatomical Record Part A Published Online: 9 Oct 2006

Flores hominid: New species or microcephalic dwarf?

Robert D. Martin et al.


The proposed new hominid "Homo floresiensis" is based on specimens from cave deposits on the Indonesian island Flores. The primary evidence, dated at ~18,000 y, is a skull and partial skeleton of a very small but dentally adult individual (LB1). Incomplete specimens are attributed to eight additional individuals. Stone tools at the site are also attributed to H. floresiensis. The discoverers interpreted H. floresiensis as an insular dwarf derived from Homo erectus, but others see LB1 as a small-bodied microcephalic Homo sapiens. Study of virtual endocasts, including LB1 and a European microcephalic, purportedly excluded microcephaly, but reconsideration reveals several problems. The cranial capacity of LB1 ( ~400 cc) is smaller than in any other known hominid


October 08, 2006

Jensen's default hypothesis rejected

A new article in Intelligence presents strong evidence against Jensen's default hypothesis that "group differences in IQ have the same genetic and environmental bases, in the same ratio, that underlie individual differences within a racial group." According to the authors, IQ scores are due both to intelligence, but also to the provisioning of information. Whites and Blacks do not differ in intelligence, but rather in the information that they have acquired. Whites and Blacks are able to answer questions correctness at the same rate when they both possess the same information: this indicates that their brains' processing efficiency is not worse than Whites'. It is in the test items for which Blacks do not possess the same information as Whites that they underperform. Moreover, Whites and Blacks both have the same ability to acquire new information, so it is rather a lack of stimulation rather than lack of any skill of acquiring new information that is the root of Black underperformance. From the paper:
In what ways are African-Americans deprived of access to information? Differences in exposure to information on the parts of African-Americans and Whites are an empirical fact. As noted by Fagan (2000), Hart and Risley (1995) conducted a longitudinal study on the frequency of verbal stimulation and the resulting language development of children from 1 to 3 years of age. They found that amount of exposure to language predicted the vocabulary development and the IQ scores of the children at three years. They also found that the children of professionals (typically, Whites) were exposed to five times the amount of words than were children of parents on welfare (typically, African-Americans). The Hart and Risley results tell us that the child's exposure to words in their homes during their first few years influences their later IQ. Whites and African-Americans differ in IQ by as early as 3 years (Montie and Fagan, 1988 and Peoples et al., 1995). Numerous studies (e.g. see reviews by Bjorklund, 2005 and Courage and Howe, 2002) have focused on the knowledge gained by infants through the infants' ability to process information and how that processing ability during the first year of life is predictive of later IQ (Fagan, 1992). All of these findings tell us that the search for racial differences in the kind of knowledge required to solve items on conventional IQ tests must begin in the first months and years of life.
Intelligence (online early)

Joseph F. Fagan, and Cynthia R. Holland


African-Americans and Whites were asked to solve problems typical of those administered on standard tests of intelligence. Half of the problems were solvable on the basis of information generally available to either race and/or on the basis of information newly learned. Such knowledge did not vary with race. Other problems were only solvable on the basis of specific previous knowledge, knowledge such as that tested on conventional IQ tests. Such specific knowledge did vary with race and was shown to be subject to test bias. Differences in knowledge within a race and differences in knowledge between races were found to have different determinants. Race was unrelated to the g factor. Cultural differences in the provision of information account for racial differences in IQ.


October 07, 2006

Head circumference and height in autism

According to this article, autistic individuals have a greater head circumference than normal people, but not greater than that of their parents. Their head circumference is also larger relative to their height.

I wish someone would give a standard battery of psychometric and anthropometric tests to a large sample of normal individuals. We so often get an impression of a person's character and competence from a quick glance, that I would be very surprised if there was no correlation between appearance and psychology that could be quantified.

Am J Med Genet A. 2006 Oct 4

Head circumference and height in autism: A study by the collaborative program of excellence in autism

Lainhart JE et al.

Data from 10 sites of the NICHD/NIDCD Collaborative Programs of Excellence in Autism were combined to study the distribution of head circumference and relationship to demographic and clinical variables. Three hundred thirty-eight probands with autism-spectrum disorder (ASD) including 208 probands with autism were studied along with 147 parents, 149 siblings, and typically developing controls. ASDs were diagnosed, and head circumference and clinical variables measured in a standardized manner across all sites. All subjects with autism met ADI-R, ADOS-G, DSM-IV, and ICD-10 criteria. The results show the distribution of standardized head circumference in autism is normal in shape, and the mean, variance, and rate of macrocephaly but not microcephaly are increased. Head circumference tends to be large relative to height in autism. No site, gender, age, SES, verbal, or non-verbal IQ effects were present in the autism sample. In addition to autism itself, standardized height and average parental head circumference were the most important factors predicting head circumference in individuals with autism. Mean standardized head circumference and rates of macrocephaly were similar in probands with autism and their parents. Increased head circumference was associated with a higher (more severe) ADI-R social algorithm score. Macrocephaly is associated with delayed onset of language. Although mean head circumference and rates of macrocephaly are increased in autism, a high degree of variability is present, underscoring the complex clinical heterogeneity of the disorder. The wide distribution of head circumference in autism has major implications for genetic, neuroimaging, and other neurobiological research.


October 06, 2006

What makes us different

Time has a nice long article about what differentiates humans from other animals. An interesting tidbit:
And sometime in the next few weeks, a team led by molecular geneticist Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology, in Leipzig, Germany, will announce an even more stunning achievement: the sequencing of a significant fraction of the genome of Neanderthals--the human-like species we picture when we hear the word caveman--who are far closer to us genetically than chimps are. And though Neanderthals became extinct tens of thousands of years ago, Pääbo is convinced he's on the way to reconstructing the entire genome of that long-lost relative, using DNA extracted, against all odds, from a 38,000-year-old bone.

Breast feeding doesn't make babies smarter

A new study in the British Medical Journal suggests that breast feeding does not have an effect on children's intelligence once you account for mother's IQ.

BMJ, doi:10.1136/bmj.38978.699583.55 (published 4 October 2006)

Effect of breast feeding on intelligence in children: prospective study, sibling pairs analysis, and meta-analysis

Geoff Der et al.

Objective To assess the importance of maternal intelligence, and the effect of controlling for it and other important confounders, in the link between breast feeding and children's intelligence.

Design Examination of the effect of breast feeding on cognitive ability and the impact of a range of potential confounders, in particular maternal IQ, within a national database. Additional analyses compared pairs of siblings from the sample who were and were not breast fed. The results are considered in the context of other studies that have also controlled for parental intelligence via meta-analysis.

Setting 1979 US national longitudinal survey of youth.

Subjects Data on 5475 children, the offspring of 3161 mothers in the longitudinal survey.

Main outcome measure IQ in children measured by Peabody individual achievement test.

Results The mother's IQ was more highly predictive of breastfeeding status than were her race, education, age, poverty status, smoking, the home environment, or the child's birth weight or birth order. One standard deviation advantage in maternal IQ more than doubled the odds of breast feeding. Before adjustment, breast feeding was associated with an increase of around 4 points in mental ability. Adjustment for maternal intelligence accounted for most of this effect. When fully adjusted for a range of relevant confounders, the effect was small (0.52) and non-significant (95% confidence interval -0.19 to 1.23). The results of the sibling comparisons and meta-analysis corroborated these findings.

Conclusions Breast feeding has little or no effect on intelligence in children. While breast feeding has many advantages for the child and mother, enhancement of the child's intelligence is unlikely to be among them.


October 05, 2006

Height changes in Greece in the 20th century

Hormones (Athens). 2002 Oct-Dec;1(4):245-50.

Secular growth changes in the Hellenic population in the twentieth century.

Papadimitriou A, Chiotis D, Tsiftis G, Hatzisimeon M, Maniati M, Krikos X, Tzonou A, Dacou-Voutetakis C.

Statural growth is dependent on hereditary and environmental factors, i.e disease, nutrition. The improvement of socioeconomic conditions that took place during the 20th century resulted in a secular trend towards greater height and earlier sexual maturation. Greek society has changed dramatically from a mainly agricultural society at the beginning of the 20th century to a mainly urban one in the second half of the century, and during this period Greece became a developed country. The various studies examining the height of children living in Athens during this period show a gradual increase in the height of children, the difference of the mean height between 2001 and 1928 being 11.8 cm and 7.3 cm for 17 year old boys and girls, respectively. The difference in mean height was present at all ages. The difference in final height was mainly due to prepubertal growth. Girls at the age of 10 and boys at 11 years were about 8 cm taller in 2001 than in 1928. A growth study carried out on conscripts in 1990 found no significant difference in the height of males coming from urban or rural areas of the country, whereas such a difference was detected in 1968, rural men being significantly shorter than urban ones in 1968. There are only a few studies on the sexual maturation of Greek children. The available data suggest a secular trend towards earlier puberty in females; however, this can not be substantiated for males. Menarcheal age in Greek girls showed a positive secular change that is in agreement with the observed trend for earlier pubertal maturation in girls. In conclusion, Greek children in the 20th century experienced a positive secular trend in stature which also includes final height. A secular trend for earlier sexual maturation can be shown only for girls.


October 04, 2006

Stability of personality from elementary school to midlife

J Pers Soc Psychol. 2006 Oct;91(4):763-79.

A first large cohort study of personality trait stability over the 40 years between elementary school and midlife.

Hampson SE, Goldberg LR.

This report provides some initial findings from an investigation of the relations between childhood Big Five personality traits assessed by elementary school teachers and similar traits assessed 40 years later by self-reports at midlife (N = 799). Short-term (1-3 years) test-retest reliabilities were lower (.22-.53) in childhood when personality was developing than they were in adulthood (.70-.79) when personality stability should be at its peak. Stability coefficients across the 40-year interval between the childhood assessment and the 2 measures of adulthood personality were higher for Extraversion (e.g., .29) and Conscientiousness (e.g., .25) than for Openness (e.g., .16), Agreeableness (e.g., .08), and Neuroticism (e.g., .00). Construct continuity between childhood and adulthood was evaluated by canonical analysis and by structural equation modeling and indicated continuity at both a broad, two-dimensional level and at the level of the Big Five. The findings are discussed in relation to A. Caspi, B. W. Roberts, and R. L. Shiner's (2005) principles of rank-order personality stability.


Ancient Greco-Roman hair dyes used nanotechnology

Ancient hair dye used nanotechnology
A 2000-year-old recipe for hair dye shows Ancient Greeks and Romans used nanotechnology to permanently colour grey hair black, say experts.

Dr Philippe Walter of the French state museum agency's Centre for Research and Restoration and colleagues report their findings online in the journal Nano Letters.

The researchers made up a batch of dye according to a recipe used since Greco-Roman times, which includes a mixture of lead oxide and slaked lime.

They soaked 50 milligrams of blond human hair in the dye for three days, then studied the hair closely.

The hair turned progressively black and when the researchers took cross-sections of hair and studied it under the microscope they found nanocrystals of lead sulfide inside the hair shaft.

The lead in the lead oxide had reacted with sulfur from the amino acids found in hair keratins, the scientists say, giving the black colour.

They say the 5 nanometre lead sulfide crystals look very much like lead sulfide quantum dots that are made today by advanced materials science methods.

The researchers say their discovery might help develop new mineral-based nanomaterials.

Dr Ivan Kempson, a materials scientist and research fellow at the University of South Australia, is impressed with the research.

"It's the highest resolution and most detailed study of the incorporation of a metal like lead into hair," he says.

Kempson says the findings are interesting for his own work, which looks at how hair takes up metals from the environment.

But he says it is not yet clear how the sulfur in the keratin is made available to interact with the lead in the hair.

Kempson says the research is also of interest to the cosmetics industry in developing hair dyes.

"If you know how they penetrate the hair and how they react within the hair then you can develop better cosmetic products," he says.

The research team includes a member from L'Oréal cosmetics company.

Nano Lett., ASAP Article 10.1021/nl061493u S1530-6984(06)01493-7

Early Use of PbS Nanotechnology for an Ancient Hair Dyeing Formula

Philippe Walter et al.

Lead-based chemistry was initiated in ancient Egypt for cosmetic preparation more than 4000 years ago. Here, we study a hair-dyeing recipe using lead salts described in text since Greco-Roman times. We report direct evidence about the shape and distribution of PbS nanocrystals that form within the hair during blackening. It is remarkable that the composition and supramolecular organization of keratins can control PbS nanocrystal growth inside a hair.


October 03, 2006

Adaptive evolution in Myostatin a muscle growth regulator

A pre-print in AJHG discusses Myostatin, a negative regulator of muscle growth. Loss of function mutations in Myostatin cause organisms to grow bigger muscles. According to this study, two variants of this gene have been under recent positive selection, reaching relatively high frequencies in sub-Saharan Africans but being rare elsewhere.

American Journal of Human Genetics (preprint)

Human adaptive evolution at Myostatin, a regulator of muscle growth

Matthew A. Saunders et al.

Myostatin (GDF8) is a negative regulator of muscle growth in mammals and loss of-function mutations are associated with increased skeletal muscle mass in mice, cattle and humans. Here we show that positive natural selection has acted on human nucleotide variation at GDF8 as the observed ratio of non-synonymous to synonymous changes among humans is significantly greater than expected under the neutral model and is strikingly different from patterns observed across mammalian orders. Furthermore, extended haplotypes around GDF8 suggest that two amino acid variants have been subject to recent positive selection. Both mutations are rare among non-Africans yet are at frequencies of up to 31% in sub-Saharan Africans. These signatures of selection at the molecular level suggest that human variation at GDF8 is associated with functional

Link (preprint pdf)

October 02, 2006

DNA to be extracted from Kent's cavern tooth

According to the Scotsman:
SCIENTISTS are attempting to extract DNA for the first time from the fossilised bones thought to be of a Neanderthal man who roamed Britain 35,000 years ago.

Experts plan to use a tooth from an upper jaw to establish whether the closest relative of modern humans lived on the British Isles later than it was once thought.

The fragment of an upper jaw, which was found in 1926 at Kent's Cavern in Devon, was originally thought to be human, but experts now think it could date back even further.

Chris Stringer, research leader in Human Origins at the Natural History Museum in London, said it was a critical test that could have historic results. The only late Neanderthal fossils on the British Isles were found on the Channel Islands around 1910.

However, Stringer said the teeth discovered at the site date back to a time when the island was joined to France around 50,000 years ago.

The director of the Ancient Human Occupation of Britain (AHOB) project said: "Neanderthal DNA is very distinct and would show up clearly in tests. It is a critical test as this could be the first late Neanderthal fossil on mainline Britain.

"But it is also historic if there is modern human DNA as this would prove they were here earlier than previously thought.

"Neanderthals are so close to us in time, living 30,000 to 40,000 years ago, and a closely related species. We have lots of Neanderthal tools but no fossils. The team is excited about the tests, but we need a bit of luck as the DNA may not have survived."

The roots, crown, size and shape of the tooth, which is thought to date back 35,000 years, would also be studied.

Torquay Museum in Devon, which looks after the piece of jaw bone, has agreed in principle to the DNA and carbon dating tests, Stringer said.

The group, which found evidence which dated the arrival of primitive ancestors in Britain to 700,000 years ago, 200,000 years earlier than previous findings, includes archaeologists, paleontologists and geologists from the Natural History Museum, the British Museum, Royal Holloway, University of London, and the University of Durham.

AHOB was set up in 2001 and funded for five years with £1.2m from the Leverhulme Trust which provides grants for education and research.

The second phase of research, which is called AHOB2 and runs until 2010, starts today after the Leverhulme Trust provided a £999,000 grant.

The next phase will include comparative studies in continental Europe.

The new project will also test the theory that there were no humans in Britain between 180,000 and 60,000 years ago due to the creation of the English Channel, making access to Britain more difficult.