April 28, 2007

Group-average correlations between traits do not imply individual correlations between traits

David B from Gene Expression has an interesting post on Correlation and Aggregation:
If data are aggregated and averaged, in some non-random way, the correlation between the resulting average values will often be higher than for the original disaggregated data, and may well increase with the level of aggregation.
David B is talking about a problem that I have talked about before in my post on Inference of between-individual differences from between-group differences.

The problem is the following:

Suppose that you have two traits, say TALLNESS and BLUENESS. You also have N populations of individuals. When you calculate the averages of these two traits in the N populations, you discover that TALL groups tend to be BLUER. Can you infer from this fact that TALL people tend to be BLUER within groups? Can you fact say anything about the relationship of TALLNESS and BLUENESS within groups?

The answer is no. In fact even a perfect positive correlation (+1.0) of TALLNESS with BLUENESS across groups may in fact mask a perfect negative correlation (-1.0) of TALLNESS and BLUENESS among individuals within groups.

The above claim can be proven by example. (b, t) represents the (BLUENESS, TALLNESS) pair of an individual:

Group A: (5,1), (4,2), (3,3), (2,4), (1,5)
Group B: (6,2), (5,3), (4,4), (3,5), (2,6)
Group C: (7,3), (6,4), (5,3), (4,6), (3,7)

Thus, within each of the three groups, there is a perfect negative correlation (-1.0) between BLUENESS and TALLNESS.

The averages of the groups are:

Group A: (3,3)
Group B: (4,4)
Group C: (5,5)

Thus, there is a perfect positive correlation (+1.0) between BLUENESS and TALLNESS across groups.

Of course, we could "pool" all individuals from the three different groups and calculate a single correlation coefficient. In the above example, this correlation coefficient turns out to be -0.5, which is again opposite to what we would expect by looking at the between-group correlation.

The conclusion to bear in mind is that whenever you hear that there is a correlation between two traits across groups (e.g., a party's tally in a state vs. average IQ in a state; a country' average skin color vs. a country's average IQ; a district's average cephalic index vs. a district's average income), then you should always ask: yes, but what about individuals? It may turn out that the correlations will point to the same direction, or that there are no significant correlations for individuals, or even that correlations for groups mask a completely different picture when it comes to individuals.

Prediction of Continent of Origin using randomly selected SNPs

A new article in BMC Genomics discusses the issue of predicting continental origin using randomly selected markers. The pdf is freely available.

One of the arguments of those who deny the existence of biological races is that their reality is subjective. Some extremists have argued that race is totally socially constructed; this is, however, disproven by the fact that socially constructed race is correlated with physical characteristics. Thus, rather than being separated from biology, the social phenomenon of race is rooted in biology.

A different argument holds that race is correlated with biology, but the differences are "skin-deep", i.e., involve only superficial, visible, (and by some strange logic unimportant) characteristics. According to the proponents of this view, the idea of biological race places an undue emphasis on a set of traits: it is a result of the subjective choice of a set of traits as race-defining. Thus, the commonly recognized races of traditional physical anthropology are discounted as subjective organizations of the biological data: we could just as simply speak of a "lactose-intolerant race" according to this view.

In forensic science and admixture analysis scientists often discover and use polymorphisms which exhibit large inter-population differences. Decoding DNA isn't free, thus, it makes sense to use the most informative, most "biased" markers when one is trying to discover the origin of a biological sample. For example, if Africans have 55% of gene version A and 45% of gene version B, and Europeans have 53% of A and 47% of B, it makes little sense to type this particular gene, since it cannot really tell us whether a sample is European or African. A gene where Africans have 90% of A while Europeans have 5% of A would be much more useful. Race skeptics claim, as with the physical anthropological data, that to privilege such carefully chosen genes is to stress the differences between groups; the implication is that in randomly chosen genes these differences are minor.

The new paper is one of many (you can click on the Clusters label to find more) recent papers that have discovered that no matter what genetic markers you choose: SNPs, STRs, no matter how you choose them: randomly or based on their "informativeness", it is relatively easy to classify DNA into the correct continental origin. Depending on the marker types (e.g., indel vs. microsatellite), and their informativeness (roughly the distribution differences between populations), one may require more or less markers to achieve a high degree of accuracy. But, the conclusion is the same: after a certain number of markers, you always succeed in classifying individuals according to continental origin.

Thus, the emergent pattern of variation is not at all subjectively constructed: it does not deal specifically with visible traits (randomly chosen markers could influence any trait, or none at all), nor does it privilege markers exhibiting large population differences. The structuring of humanity into more or less disjoint groups is not a subjective choice: it emerges naturally from the genomic composition of humans, irrespective of how you study this composition. Rather than proving that race is skin-deep, non-existent, or unimportant, modern genetic science is both proving that it is in fact existent, but also sets the foundation for the study of its true importance, which is probably somewhere in between the indifference of the sociologists and the hyperbole of the racists.

BMC Genetics

Geography and genography: prediction of continental origin using randomly selected single nucleotide polymorphisms

Dominic J Allocco et al.

Background: Recent studies have shown that when individuals are grouped on the basis of genetic similarity, group membership corresponds closely to continental origin. There has been
considerable debate about the implications of these findings in the context of larger debates about race and the extent of genetic variation between groups. Some have argued that clustering according to continental origin demonstrates the existence of significant genetic differences between groups and that these differences may have important implications for differences in health and disease. Others argue that clustering according to continental origin requires the use oflarge amounts of genetic data or specifically chosen markers and is indicative only of very subtle genetic differences that are unlikely to have biomedical significance.
Results: We used small numbers of randomly selected single nucleotide polymorphisms (SNPs)
from the International HapMap Project to train naïve Bayes classifiers for prediction of ancestral
continent of origin. Predictive accuracy was tested on two independent data sets. Genetically
similar groups should be difficult to distinguish, especially if only a small number of genetic markers are used. The genetic differences between continentally defined groups are sufficiently large that one can accurately predict ancestral continent of origin using only a minute, randomly selected fraction of the genetic variation present in the human genome. Genotype data from only 50 random SNPs was sufficient to predict ancestral continent of origin in our primary test data set with an average accuracy of 95%. Genetic variations informative about ancestry were common and widely distributed throughout the genome.
Conclusion: Accurate characterization of ancestry is possible using small numbers of randomly
selected SNPs. The results presented here show how investigators conducting genetic association studies can use small numbers of arbitrarily chosen SNPs to identify stratification in study subjects and avoid false positive genotype-phenotype associations. Our findings also demonstrate the extent of variation between continentally defined groups and argue strongly against the contention that genetic differences between groups are too small to have biomedical significance.

Link (pdf)

April 26, 2007

Caucasoid mtDNA in Iron Age Central China

More on the Yu Hong tomb. From the second link:
Yu Hong (d. 592) was a high-ranking member of a community of Sogdians who had settled on the northern border of China at the beginning of the fourth century. While barely in his teens, Yu Hong began his career in the service of the most powerful nomadic tribe at the time, known as the Ruru, and was posted as an emissary to several countries, including Iran.
From a book on the subject:
The highlight of the excavation was the superbly-carved white marble sarcophagus which bears detailed scenes of daily life, hunting, mythology, banqueting and entertainment that have a strong Central Asian influence, including Sogdian and Sassanian. Many of the figures depicted are Caucasian.
Proc Biol Sci. 2007 Apr 24;

Evidence of ancient DNA reveals the first European lineage in Iron Age Central China.

By Xie CZ, Li CX, Cui YQ, Zhang QC, Fu YQ, Zhu H, Zhou H on Proc Biol Sci

Various studies on ancient DNA have attempted to reconstruct population movement in Asia, with much interest focused on determining the arrival of European lineages in ancient East Asia. Here, we discuss our analysis of the mitochondrial DNA of human remains excavated from the Yu Hong tomb in Taiyuan, China, dated 1400 years ago. The burial style of this tomb is characteristic of Central Asia at that time. Our analysis shows that Yu Hong belonged to the haplogroup U5, one of the oldest western Eurasian-specific haplogroups, while his wife can be classified as haplogroup G, the type prevalent in East Asia. Our findings show that this man with European lineage arrived in Taiyuan approximately 1400 years ago, and most probably married a local woman. Haplogroup U5 was the first west Eurasian-specific lineage to be found in the central part of ancient China, and Taiyuan may be the easternmost location of the discovered remains of European lineage in ancient China.


April 25, 2007

Dental analysis on spread of Neolithic in Italy

Am J Phys Anthropol. 2007 Apr 23; [Epub ahead of print]

Origins and spread of agriculture in Italy: A nonmetric dental analysis.

Coppa A, Cucina A, Lucci M, Mancinelli D, Vargiu R.

Dental morphological traits were employed in this study as direct indicators of biological affinities among the populations that inhabited the Italian peninsula from the Upper Paleolithic-Mesolithic to Medieval times. Our analysis aims at contributing to the ongoing debate regarding the origin and spread of agriculture in the peninsula by contrasting the dental evidence of archaeological and modern molecular samples. It is not possible to generalize given the complex and dynamic nature of these populations. However, the results from the principal component analysis, maximum likelihood, mean measure of divergence, and multidimensional scaling do indicate a net separation of the Paleo-Mesolithic sample from the other groups that is not related to dental reduction. This suggests that the shift in dental morphology was the product of Neolithic populations migrating into the peninsula from other areas. Nonetheless, the Paleo-Mesolithic populations share several discriminative traits with the Neolithic group. The biological relevance of such evidence suggests that, to some minor extent, the spread of agriculture did not occur by total population replacement. Because of regional small sample sizes, this hypothesis cannot be tested on a micro-regional scale. It is, however, feasible to depict a scenario where processes of genetic mixture or replacement probably took place at different rates on a macro-regional level.


Women's morning/evening orientation is related to their verbal IQ

Percept Mot Skills. 2007 Feb;104(1):335-8

Morningness-eveningness correlates with verbal ability in women but not men.

Killgore WD, Killgore DB

Individuals differ along a continuum of preference for diurnal activity level, known as Morningness-Eveningness. Some evidence suggests that an Eveningness orientation (i.e., preference for later rise and bed times) is weakly associated with higher cognitive ability, but no studies have examined this relationship using clinically accepted, psychometrically valid measures of cognitive ability. The present study examined the correlation between Morningness-Eveningness with scores on the Wechsler Abbreviated Scale of Intelligence (WASI) of 54 healthy volunteers. Lower Morningness (i.e., Greater Eveningness) orientation was correlated (r = -.23) with higher Verbal IQ for the entire sample. When the data were examined separately by sex, the correlation between Morningness-Eveningness and Verbal IQ was significant for women (r = -.44) but not for men (r = -.09).


April 24, 2007

Erik Trinkaus on Neanderthal admixture with early modern humans in Europe

Via Yann a link to a new article by Erik Trinkaus suggesting that early modern humans in Europe cannot be simply explained as the result of an expansion of African modern humans but exhibit features that are not found in earliest African modern humans.

According to Trinkaus, the early modern Europeans exhibit features that are consistent with Neanderthal admixture. This is certainly the case, but that does not mean that the case of admixture is clear-cut: the earliest modern Africans are represented by less than a handful of specimens; moreover these are separated by 100ky at least from the earliest modern Europeans. Thus, neither the African population of origin, neither its evolutionary history up to the time of the African Exodus are well characterized.

It is possible that modern Out-of-Africans (whom I have called elsewhere Afrasians) were already different from the earliest anatomically modern Africans. We simply do not know much about them skeletally. Their main features are usually inferred by either (a) looking at early modern humans in Africa and seeing how they differ from previous Africans, or (b) looking at early modern humans in Eurasia and seeing how they are different from previous Eurasians and similar to each other. Both these approaches have led to a rather minimalist definition of modern humans; consequently, features that cannot be explained well under this definition are attributed to admixture.

As the genomic study of Neanderthals progresses, we should be able to find direct evidence for the introgression of Neanderthal genetic material into Homo sapiens. I suspect that such positive evidence (or negative evidence, assuming enough Neanderthal DNA is retrieved) would finally decide the question one way or another.

PNAS (Published online)

European early modern humans and the fate of the Neandertals

Erik Trinkaus

Abstract: A consideration of the morphological aspects of the earliest modern humans in Europe (more than 33,000 B.P.) and the subsequent Gravettian human remains indicates that they possess an anatomical pattern congruent with the autapomorphic (derived) morphology of the earliest (Middle Paleolithic) African modern humans. However, they exhibit a variable suite of features that are either distinctive Neandertal traits and/or plesiomorphic (ancestral) aspects that had been lost among the African Middle Paleolithic modern humans. These features include aspects of neurocranial shape, basicranial external morphology, mandibular ramal and symphyseal form, dental morphology and size, and anteroposterior dental proportions, as well as aspects of the clavicles, scapulae, metacarpals, and appendicular proportions. The ubiquitous and variable presence of these morphological features in the European earlier modern human samples can only be parsimoniously explained as a product of modest levels of assimilation of Neandertals into early modern human populations as the latter dispersed across Europe. This interpretation is in agreement with current analyses of recent and past human molecular data.


April 23, 2007

Recent adaptive evolution in the human genome

PLoS Genetics (online early)

Localizing recent adaptive evolution in the human genome

Scott Williamson et al.

Identifying genomic locations that have experienced selective sweeps is an important first step toward understanding the molecular basis of adaptive evolution. Using statistical methods that account for the confounding effects of population demography, recombination rate variation, and SNP ascertainment, while also providing fine-scale estimates of the position of the selected site, we analyze a genomic data set of 1.2 million human SNPs genotyped in African-American, European-American, and Chinese samples. We identify 101 regions of the human genome with very strong evidence (P<10-5) of a recent selective sweep and where our estimate of the position of the selective sweep falls within 100 kb of a known gene. Within these regions, genes of biological interest include genes in pigmentation pathways, components of the dystrophin protein complex, clusters of olfactory receptors, genes involved in nervous system development and function, immune system genes, and heat shock genes. We also observe consistent evidence of selective sweeps in centromeric regions. In general we find that recent adaptation is strikingly pervasive in the human genome, with as much as 10% of the genome affected by linkage to a selective sweep.


April 21, 2007

mtDNA dispersal via Horn of Africa vs. Levantine corridor

Journal of Human Genetics (online early)

Mitochondrial DNA geneflow indicates preferred usage of the Levant Corridor over the Horn of Africa passageway

D. J. Rowold et al.

Abstract Both the Levantine Corridor and the Horn of Africa route have figured prominently in early hominid migrations from Africa to Eurasia. To gauge the importance of these two African–Asian thoroughfares in the demic movements of modern man, we surveyed the mtDNA control region variation and coding polymorphisms of 739 individuals representing ten African and Middle Eastern populations. Two of these collections, Egypt and Yemen, are geographically close to the Levant and Horn of Africa, respectively. In this analysis, we uncover genetic evidence for the preferential use of the Levantine Corridor in the Upper Paleolithic to Neolithic dispersals of haplogroups H, J*, N1b, and T1, in contrast to an overwhelming preference in favor of the Horn of Africa for the intercontinental expansion of M1 during the Middle to Upper Paleolithic. Furthermore, we also observed a higher frequency of sub-Saharan mtDNA compared to NRY lineages in the Middle Eastern collections, a pattern also seen in previous studies. In short, the results of this study suggest that several migratory episodes of maternal lineages occurred across the African–Asian corridors since the first African exodus of modern Homo sapiens sapiens.


April 20, 2007

Has ASPM been the target of recent selection?

Science Vol. 316. no. 5823, p. 370

Comment on "Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens"

Fuli Yu et al.

Mekel-Bobrov et al. (Reports, 9 September 2005, p. 1720) suggested that ASPM, a gene associated with microcephaly, underwent natural selection within the last 500 to 14,100 years. Their analyses based on comparison with computer simulations indicated that ASPM had an unusual pattern of variation. However, when we compare ASPM empirically to a large number of other loci, its variation is not unusual and does not support selection.


The effect of domestication of wheat on its genetic diversity

Molecular Biology and Evolution, doi:10.1093/molbev/msm077

Grinding up Wheat: a Massive Loss of Nucleotide Diversity Since Domestication

A Haudry et al.

Several demographic and selective events occurred during the domestication of wheat from the allotetraploid wild emmer (Triticum turgidum ssp. dicoccoides). Cultivated wheat has since been affected by other historical events. We analysed nucleotide diversity at 21 loci in a sample of 101 individuals representing four taxa corresponding to representative steps in the recent evolution of wheat (wild, domesticated, cultivated durum and bread wheats), to unravel the evolutionary history of cultivated wheats and to quantify its impact on genetic diversity. Sequence relationships are consistent with a single domestication event and identify two genetically different groups of bread wheat. The wild group is not highly polymorphic, with only 212 polymorphic sites among the 21,720 bp sequenced, and, during domestication, diversity was further reduced in cultivated forms — by 69% in bread wheat and 84% in durum wheat — with considerable differences between loci, some retaining no polymorphism at all. Coalescent simulations were performed and compared with our data, to estimate the intensity of the bottlenecks associated with domestication and subsequent selection. Based on our 21-locus analysis, the average intensity of domestication bottleneck was estimated at about 3 — giving a population size for the domesticated form about one third that of wild dicoccoides. The most severe bottleneck, with an intensity of about 6, occurred in the evolution of durum wheat. We investigated whether some of the genes departed from the empirical distribution of most loci, suggesting that they might have been selected during domestication or breeding. We detected a departure from the null model of demographic bottleneck for the hypothetical gene HgA. However, the atypical pattern of polymorphism at this locus might reveal selection on the linked locus Gsp1A, which may affect grain softness — an important trait for end-use quality in wheat.


April 17, 2007

Modern human origins in Australia

Homo (in press)

Modern human origins in Australasia: Testing the predictions of competing models

D. Curnoe


The evolutionary background to the emergence of modern humans remains controversial. Four models have been proposed to explain this process and each has clearly definable and testable predictions about the geographical origins of early Australians and their possible biological interaction with other Pleistocene populations. The present study considers the phenetic affinities of early Australians from Kow Swamp (KS 1 and KS 5) and Keilor to Pleistocene Africans and Asians from calvarial dimensions. The study includes analyses employing log-transformed and size-corrected (Mosimann variables) data. The strongest signals to emerge are as follows: (1) a phenetic pattern in which Australians are most like each other, (2) all three crania possess a mosaic of archaic and modern features, (3) Kow Swamp crania also show strong affinities to archaic remains, (4) Keilor is more modern than KS 1 and KS 5 and (5) Keilor shows affinities to Pleistocene East Asian modern crania (Liujiang and Upper Cave 101) providing evidence for a broad regional morphology. The results refute the predictions of multi-species replacement models for early Australians but are consistent with single-species models. Combined with published evidence from DNA, the present study indicates that the Assimilation model presently offers the best explanation for the origins of Pleistocene Australians.


Physical anthropology and ethnicity in Asia

J Physiol Anthropol. 2007 Mar;26(2):77-82.

Physical Anthropology and Ethnicity in Asia: The Transition from Anthropometry to Genome-based Studies.

Bittles H, Black ML, Wang W.

Initial physical anthropology studies into ethnic diversity were largely dependent on comparative whole body and craniometric measurements, and through time assessments of ethnic diversity based on these measures exhibited increasing statistical sophistication. Since the 1990s, in Asia as elsewhere in the world, human diversity studies have increasingly utilized DNA-based analyses, with Y-chromosome and mtDNA markers providing complementary perspectives on the origins and gene pool structures of different ethnic groups. This approach is illustrated in a study of population genetic structure in PR China, in which DNA samples from the Han majority and eight ethnic minorities were analyzed. The Y-chromosome and mtDNA data showed multiple paternal geographical and ethnic origins but restricted maternal ancestries. However, interpretive problems were apparent in the definition of a number of the ethnic study populations, which appear to reflect political as well as genetic influences. In all anthropological studies, whether based on anthropometry or genomic analysis, unambiguous and appropriate community identification is a prerequisite.


April 16, 2007

IQ and Wealth

Intelligence (Article in Press)

Do you have to be smart to be rich? The impact of IQ on wealth, income and financial distress

Jay L. Zagorskya et al.


How important is intelligence to financial success? Using the NLSY79, which tracks a large group of young U.S. baby boomers, this research shows that each point increase in IQ test scores raises income by between $234 and $616 per year after holding a variety of factors constant. Regression results suggest no statistically distinguishable relationship between IQ scores and wealth. Financial distress, such as problems paying bills, going bankrupt or reaching credit card limits, is related to IQ scores not linearly but instead in a quadratic relationship. This means higher IQ scores sometimes increase the probability of being in financial difficulty.


April 14, 2007

New YHRD release

The Y-chromosome Haplotype Reference Database (YHRD) has a new release:
Release 21 is out with 51,253 haplotypes in 447 populations. 49,396 haplotypes of these are completely typed for 9 and 23,075 for 11 loci. Fifty-nine populations were added today: from Macedonia, from three regions in Venezuela (Maracaibo, Isla Toas, San Jose Heras) and three Venezuelan Amerindian tribes (Bari, Wayuu, Yukpa), from 10 provinces at the Pacific and Caribbean coast in Colombia: Valle de Cauca, Cauca, Narino, Bolivar, Guajira, Magdalena, Cesar, Cordoba, Sucre and Atlantico, from Ecuador (Quito), from Germany (Stuttgart), from Southern Poland (Nowy Sacz, Nowy Targ, Limanowa, Zakopane), from the following districts of the Russian Federation: Archangelsk, Brjansk, Ivanowo, Lipezk, Novgorod, Orel, Pensa, Rjasan, Smolensk, Tambov, Tver and Vologda, from Sweden (updates of the already existing samples), from Rio de Janeiro (Brazilians of European and African ancestry), from Nicaragua, from Slovakia (Bratislava), from Belarus (Homiel, Hrodna, Mahiliou, Viciebsk), from the following prefectures in Japan: Tokyo, Aomori, Chiba, Ehime, Fukuoka, Gunma, Hiroshima, Hokkaido, Hyogo, Mie, Miyagi, Nagasaki, Nara, Okayama, Shizuoka, Toyama, Wakayama, Yamaguchi and Yamanashi, from the USA (European, African, Hispanic and Asian American). We would like to thank the following colleagues for submissions and updates: Zlatko Jakovski and his group (Macedonia), Lisbeth Borjas and Tatiana Pardo (Venezuela), Sandra Avila and Elena Romero (Colombia), Eduardo Arroyo and his group (Ecuador), Gerhard Baessler and his group (Stuttgart), Marcin Wozniak and his group (Poland), the groups in Berlin (Carmen Krueger, Lutz Roewer) and Leipzig (Ivan Nasidze) for the Russians, Gunilla Holmlund and her group (Sweden), Elizeu Fagundes de Carvalho and his group (Rio den Janeiro), Fabricio Gonzalez (Nicaragua), Krzysztof Rebala and his coworkers (Slovakia, Belarus), Natsuko Mizuno and her group (Japan) and Amy Decker and her group at NIST for the US data.

April 13, 2007

Y chromosomes of South Siberia

No abstract to this paper. An excerpt:
Archeological and paleontological evidence suggests that South Siberia is an area where the most ancient contacts occurred between the members of Caucasoid and Mongoloid peoples. These contacts have substantially affected the racial type of most populations of Eurasia. Analysis of mitochondrial DNA (mtDNA) inherited without recombination in the maternal line has shown that Southern Siberian populations have developed on a heterogeneous genetic basis. This is a result of not only the diversity of Mongoloid components that were either indigenous to the gene pools of Siberian populations since the Paleolithic Age or introduced in different periods of time from Central Europe and East Asia, but also the presence of the Caucasoid component expressed in different degrees in most populations that have contributed into this heterogeneity [1, 2]. The nonrecombining portion of the Y chromosome inherited in the paternal line is another genetic system widely used for studying the population genetic history. The Y chromosome polymorphism has been analyzed in a wide spectrum of Asian populations; nevertheless, the data on numerous aboriginal opulations of Southern Siberia are scanty with respect to both the number of populations and the set of loci studied. Therefore, there is no comprehensive idea as to how the gene pools of individual ethnic groups have been formed, taking into account the contributions of both paternal and maternal lineages [3, 4].


In general, our results suggest a significant genetic differentiation between the ethnic groups of Baikal and Altai–Sayan regions, which is mainly accounted for by
different contributions of the Central/East Asian and East European components into the gene pools of South Siberian ethnic groups.
Haplogroup distribution:

Doklady Biological Sciences, 2006, Vol. 411, pp. 466–470

The Diversity of Y-Chromosome Lineages in Indigenous Population of South Siberia

M. V. Derenko et al.

April 11, 2007

Y chromosome lineages in Sao Tome and Principe

Am J Hum Biol. 2007 Apr 9;19(3):422-428 [Epub ahead of print]

Y-chromosome lineages in Sao Tome e Principe islands: Evidence of European influence.

Goncalves R, Spinola H, Brehm A.

The Y-chromosome haplogroup composition of the population of Sao Tome e Principe (STP) archipelago was analyzed using 25 biallelic markers and compared with populations of different origins from Europe, Africa, and the Middle East. Two main Y-chromosome haplogroups were found: E3a, very common among sub-Saharans accounts for 84.2% of the paternal lineages and R1b, typical of West Eurasia, represents 8.7% of the overall male population. Nevertheless, we detected in the population of STP a significant heterogeneous distribution of R1b among the two main ethnic groups of the archipelago: Forros (10.3%) and Angolares (6.6%). Together, haplogroups known to be prevalent in West Eurasia reach 12.5% of the chromosomes analyzed unequally distributed among the two groups: Forros present 17.7% while Angolares display only 8.2% of west Eurasian haplogroups. Our findings suggest that, despite its sub-Saharan genetic background, a relevant contribution of European paternal lineages is present in nowadays STP population. This influence has shown to be stronger in Forros than in Angolares, which could be explained by the social isolation that these have last experienced through their history.


April 10, 2007

Genetic affinities of Uttar Pradesh populations

BMC Genet. 2007 Apr 7;8(1):12 [Epub ahead of print]

Genetic affinities between endogamous and inbreeding populations of Uttar Pradesh.

Khan F, Pandey AK, Tripathi M, Talwar S, Bisen PS, Borkar M, Agrawal S.

ABSTRACT: BACKGROUND: India has experienced several waves of migration since the Middle Paleolithic. It is believed that the initial demic movement into India was from Africa along the southern coastal route, approximately 60,000-85,000 years before present (ybp). It has also been reported that there were two other major colonizations which included eastward diffusion of Neolithic farmers (Elamo Dravidians) from Middle East sometime between 10,000 and 7,000 ybp and a southern dispersal of Indo Europeans from Central Asia 3,000 ybp. Mongol entry during the thirteenth century A.D. as well as some possible minor incursions from South China 50,000 to 60,000 ybp may have also contributed to cultural, linguistic and genetic diversity in India. Therefore, the genetic affinity and relationship of Indians with other world populations and also within India are often contested. In the present study, we have attempted to offer a fresh and immaculate interpretation on the genetic relationships of different North Indian populations with other Indian and other world populations. RESULTS: We have first genotyped 20 tetra-nucleotide STR markers among 1800 north Indian samples of nine endogamous populations belonging to three different socio-cultural strata. Genetic distances (Neis DA and Reynolds Fst) were calculated among the nine studied populations, Caucasians and East Asians. This analysis was based upon the allelic profile of 20 STR markers to assess the genetic similarity and differences of the north Indian populations. North Indians showed a stronger genetic relationship with the Europeans (DA 0.0341 and Fst 0.0119) as compared to the Asians (DA 0.1694 and Fst - 0.0718). The upper caste Brahmins and Muslims were closest to Caucasians while middle caste populations were closer to Asians. Finally, three phylogenetic assessments based on two different NJ and ML phylogenetic methods and PC plot analysis were carried out using the same panel of 20 STR markers and 20 geo-ethnic populations. The three phylogenetic assessments revealed that north Indians are clustering with Caucasians. CONCLUSIONS: The genetic affinities of Indians and that of different caste groups towards Caucasians or East Asians is distributed in a cline where geographically north Indians and socially both upper caste and Muslim populations are genetically closer to the Caucasians.


Nicholas Wade on human sexuality

Nicholas Wade has a very interesting article on recent advances in human sexuality in the New York Times. Some excerpts:
It is no surprise that the male and female versions of the human brain operate in distinct patterns, despite the heavy influence of culture. The male brain is sexually oriented toward women as an object of desire. The most direct evidence comes from a handful of cases, some of them circumcision accidents, in which boy babies have lost their penises and been reared as female. Despite every social inducement to the opposite, they grow up desiring women as partners, not men.


Presumably the masculinization of the brain shapes some neural circuit that makes women desirable. If so, this circuitry is wired differently in gay men. In experiments in which subjects are shown photographs of desirable men or women, straight men are aroused by women, gay men by men.

Such experiments do not show the same clear divide with women. Whether women describe themselves as straight or lesbian, “Their sexual arousal seems to be relatively indiscriminate — they get aroused by both male and female images,” Dr. Bailey said. “I’m not even sure females have a sexual orientation. But they have sexual preferences. Women are very picky, and most choose to have sex with men.”


Sexual orientation, at least for men, seems to be settled before birth. “I think most of the scientists working on these questions are convinced that the antecedents of sexual orientation in males are happening early in life, probably before birth,” Dr. Breedlove said, “whereas for females, some are probably born to become gay, but clearly some get there quite late in life.”


Several profound consequences follow from the fact that men have only one copy of the many X-related brain genes and women two. One is that many neurological diseases are more common in men because women are unlikely to suffer mutations in both copies of a gene.

Another is that men, as a group, “will have more variable brain phenotypes,” Dr. Arnold writes, because women’s second copy of every gene dampens the effects of mutations that arise in the other.

April 07, 2007

Neolithic Near Eastern Origin of domesticated cattle

Proc Biol Sci. 2007 Apr 3; [Epub ahead of print]

Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs.

Edwards CJ et al.

The extinct aurochs (Bos primigenius primigenius) was a large type of cattle that ranged over almost the whole Eurasian continent. The aurochs is the wild progenitor of modern cattle, but it is unclear whether European aurochs contributed to this process. To provide new insights into the demographic history of aurochs and domestic cattle, we have generated high-confidence mitochondrial DNA sequences from 59 archaeological skeletal finds, which were attributed to wild European cattle populations based on their chronological date and/or morphology. All pre-Neolithic aurochs belonged to the previously designated P haplogroup, indicating that this represents the Late Glacial Central European signature. We also report one new and highly divergent haplotype in a Neolithic aurochs sample from Germany, which points to greater variability during the Pleistocene. Furthermore, the Neolithic and Bronze Age samples that were classified with confidence as European aurochs using morphological criteria all carry P haplotype mitochondrial DNA, suggesting continuity of Late Glacial and Early Holocene aurochs populations in Europe. Bayesian analysis indicates that recent population growth gives a significantly better fit to our data than a constant-sized population, an observation consistent with a postglacial expansion scenario, possibly from a single European refugial population. Previous work has shown that most ancient and modern European domestic cattle carry haplotypes previously designated T. This, in combination with our new finding of a T haplotype in a very Early Neolithic site in Syria, lends persuasive support to a scenario whereby gracile Near Eastern domestic populations, carrying predominantly T haplotypes, replaced P haplotype-carrying robust autochthonous aurochs populations in Europe, from the Early Neolithic onward. During the period of coexistence, it appears that domestic cattle were kept separate from wild aurochs and introgression was extremely rare.


April 05, 2007

Y chromosomes across the Himalayas

American Journal of Human Genetics (online early)

The Himalayas as a Directional Barrier to Gene Flow

Tenzin Gayden et al.

High-resolution Y-chromosome haplogroup analyses coupled with Y–short tandem repeat (STR) haplotypes were used to (1) investigate the genetic affinities of three populations from Nepal—including Newar, Tamang, and people from cosmopolitan Kathmandu (referred to as "Kathmandu" subsequently)—as well as a collection from Tibet and (2) evaluate whether the Himalayan mountain range represents a geographic barrier for gene flow between the Tibetan plateau and the South Asian subcontinent. The results suggest that the Tibetans and Nepalese are in part descendants of Tibeto-Burman–speaking groups originating from Northeast Asia. All four populations are represented predominantly by haplogroup O3a5-M134–derived chromosomes, whose Y-STR–based age (±SE) was estimated at 8.1 ± 2.9 thousand years ago (KYA), more recent than its Southeast Asian counterpart. The most pronounced difference between the two regions is reflected in the opposing high-frequency distributions of haplogroups D in Tibet and R in Nepal. With the exception of Tamang, both Newar and Kathmandu exhibit considerable similarities to the Indian Y-haplogroup distribution, particularly in their haplogroup R and H composition. These results indicate gene flow from the Indian subcontinent and, in the case of haplogroup R, from Eurasia as well, a conclusion that is also supported by the admixture analysis. In contrast, whereas haplogroup D is completely absent in Nepal, it accounts for 50.6% of the Tibetan Y-chromosome gene pool. Coalescent analyses suggest that the expansion of haplogroup D derivatives—namely, D1-M15 and D3-P47 in Tibet—involved two different demographic events (5.1 ± 1.8 and 11.3 ± 3.7 KYA, respectively) that are more recent than those of D2-M55 representatives common in Japan. Low frequencies, relative to Nepal, of haplogroup J and R lineages in Tibet are also consistent with restricted gene flow from the subcontinent. Yet the presence of haplogroup O3a5-M134 representatives in Nepal indicates that the Himalayas have been permeable to dispersals from the east. These genetic patterns suggest that this cordillera has been a biased bidirectional barrier.


April 04, 2007

Nicholas Wade on Etruscan Origins

Nicholas Wade has an article in the New York Times summarizing the recent research ib Etruscan origins (click on the label below for more) and giving some interesting background on the dispute between 'indigenist' and 'migrationist' views of Etruscan origins:
“The overwhelming proportion of archaeologists would regard the evidence for eastern origins of the Etruscans as negligible,” said Anthony Tuck, an archaeologist at the University of Massachusetts Center for Etruscan Studies.

Because Italians take pride in the Roman empire and the Etruscan state that preceded it, asserting a foreign origin for the Etruscans has long been politically controversial in Italy. Massimo Pallottino, the dean of modern Etruscan studies in Italy who died in 1995, held that because no one questioned that the French, say, developed in France, the same assumption should be made about the Etruscans. “Someone who had a different position didn’t get a job in archaeology,” said Antonio Torroni, a geneticist at the University of Pavia.


In Tuscany as a whole, part of the ancient Etruscan region of Etruria, the Torroni team found 11 minor mitochondrial DNA lineages that occur nowhere else in Europe and are shared only with Near Eastern people. These findings, the teams says, “support a direct and rather recent genetic input from the Near East, a scenario in agreement with the Lydian origin of the Etruscans.”

Dr. Torroni said he had data awaiting publication that are based on Y chromosomes and point to the same conclusion.

April 03, 2007

40,000 year old human from China

From EurekAlert:
Researchers at Washington University in St. Louis and the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) in Beijing have been studying a 40,000-year-old early modern human skeleton found in China and have determined that the "out of Africa" dispersal of modern humans may not have been as simple as once thought.

The research result will be published in the Proceedings of the U.S. National Academy of Sciences on April 3.

Erik Trinkaus, Professor of Anthropology at Washington University in St. Louis, his colleague Hong Shang, and others at the IVPP examined the skeleton, recovered in 2003 from the Tianyuan Cave, Zhoukoudian, near Beijing City.

The skeleton dates to 42,000 to 38,500 years ago, making it the oldest securely dated modern human skeleton in China and one of the oldest modern human fossils in eastern Eurasia.

The specimen is basically a modern human, but it does have a few archaic characteristics, particularly in the teeth and hand bone. This morphological pattern implies that a simple spread of modern humans from Africa is unlikely, especially since younger specimens have been found in Eastern Eurasia with similar feature patterns.

According to Trinkaus and Shang, "the discovery promises to provide relevant paleontological data for our understanding of the emergence of modern humans in eastern Asia."

April 02, 2007

Genetic genealogists gone wild

Amy Harmon has an interesting article in the New York Times about some extreme cases of genetic genealogists going to great lengths to fill in their family trees.

Derrell Teat, 63, a wastewater coordinator, recently found herself staking out a McDonald’s. The man she believed was the last male descendant of her great-great-great grandfather’s brother had refused to give her his DNA. So she decided to get it another way.

“I was going to take his coffee cup out of the garbage can,” said Ms. Teat, who traveled to the Georgia mountains from Tampa, Fla., with her test kit. “I was willing to do whatever it took.”


Since learning that she shares some markers with St. Luke the Evangelist, Kathy Johnston, 54, a dermatologist in Torrance, Calif., has been lobbying to have the saint’s remains more thoroughly analyzed.

She believes St. Luke’s mother was Celtic, as is her own lineage, not Syrian, as previous genetic tests on remains in Padua, Italy, have suggested. She is willing to pay for the test, but scientists at the University of Ferrara and the Roman Catholic Church have ignored her theories.


Bob Grieve, 55, stores a DNA kit in his refrigerator to use upon his father’s death.

After testing his own DNA at the request of a distant cousin, Mr. Grieve was shaken to discover that he did not match any of his extended family, including his first cousin, the son of his father’s brother.

That could only mean an occurrence of what genetic genealogists call a “nonpaternal event.” Either his father was not his father, or his grandfather was not his father’s father. But the elder Mr. Grieve has refused to surrender to the swab.

“I don’t put blame on anybody,” said Mr. Grieve, an engine design checker in Dearborn, Mich. “It would just be nice to know where I came from.”

Spencer Wells Interview

Via GNXP a link to an interview by Spencer Wells. The interesting bits:
The data are sent to a central database created by IBM. They supplied the server, which is sitting in the basement of National Geographic. They have given everybody laptops with biometric [i.e., fingerprint] recognition so that only the PIs can access to the database. We are working closely with their computational biology team on analyzing the data. So some of our first publications, which are starting to go into the journals now, are coming through that group.


We are expanding the survey of whole mitochondria genomes in Africa. We've doubled the size of that database and it's revealing interesting mitochondrial patterns. That effort has been spearheaded by Doron Behar in Haifa.

People tend to ignore what went on within Africa. There is this inherent bias in European and Asian scientists that we've “done” Africa and then things got interesting when we [humans] left, but of course there was still a lot going on within Africa. We're looking at routes people might have taken out of Africa and back migration into Africa. Information that is coming out, in part, from an expedition I organized in 2005 to the Tibesti mountains in Chad, up on the Libyan border.


We've gotten some fascinating results and a lot of e-mails. For example, a Hungarian woman wrote in and said, “You've got to redo my test. You told me I'm native American or Siberian, and I know my ancestors came from Hungary—I can tell you the village they were living in in the sixteenth century.” The Hungarian language, Magyar, is actually related to languages spoken in Siberia, and this is one of the first cases where we've actually seen Siberian lineages showing up in the Hungarian population. They are there at very low frequency. We now through this project have over 350 people who are of Hungarian descent and we see these [Siberian] lineages at four to five percent on both male and female sides.