A fascinating new paper from the June issue of Current Anthropology explores ancient multiple graves and raises the possibility that hunter gatherers in what is now Europe may have practiced ritual human sacrifice. This practice – well-known in large, stratified societies – supports data emerging from different lines of research that the level of social complexity reached in the distant past by groups of hunter gatherers was well beyond that of many more recent small bands of modern foragers.
Due to their number, state of preservation, richness, and variety of associated grave goods, burials from the Upper Paleolithic (26,000-8,000 BC) represent an important source of information on ideological beliefs that may have influenced funerary behavior. In an analysis of the European record, Vincenzo Formicola (University of Pisa, Italy) points to a high frequency of multiple burials, commonly attributed to simultaneous death due to natural disaster or disease.
However, a look at grave composition reveals that some of the multiple burials may have been selective. Not only do the skeletons in these graves vary by sex and age, but the most spectacular sites also include a severely deformed individual with a pathological condition that would have been apparent since birth, for example, dwarfism or congenital bowing of the bones.
These multiple graves are also richly ornamented and in choice locales. For example, the remains of an adolescent dwarf in Romito Cave (Calabria, Italy) lie next to a female skeleton under an elaborate engraving of a bull. In the Sunghir double burial (Russia), the skeletons of a pre-teen boy and girl are surrounded by ivory objects including about 5,000 beads, each of which may have taken an hour to make.
"These findings point to the possibility that human sacrifices were part of the ritual activity of these populations and provide clues on the complexity and symbolism pervading Upper Paleolithic societies as well as on the perception of "diversity" and its links to magical-religious beliefs," Formicola writes. "These individuals may have been feared, hated, or revered . . . we do not know whether this adolescent received special burial treatment in spite of being a dwarf or precisely because he was a dwarf."
Eurekalert
May 30, 2007
Health status of Greek centenarians
Arch Gerontol Geriatr. 2007 May 16; [Epub ahead of print]
Assessment of the health status of Greek centenarians.
Darviri C, Demakakos P, Charizani F, Tigani X, Tsiou C, Chalamandaris AG, Tsagkari C, Chliaoutakis J.
The present study aims at describing the health status of a sample of relatively functional and healthy Greek centenarians and at exploring the potential gender differences in health in this sample. Its objectives are to add to the accumulation of knowledge about the health status of centenarians and therefore to contribute to the exploration of the mechanisms of healthy longevity. The study employs a non-representative community sample of Greek centenarians of both sexes (N=47). It uses descriptive statistics in order to outline the health status of the participants and non-parametric tests to assess the statistical significance of the observed sex-differences. The study shows that the centenarians of our sample are relatively healthy and functional (15% of the sample was free of any major chronic disease). It also suggests, that the sex-difference in survival is statistical significant (p less or equal 0.013), and that the morbidity and co-morbidity rates of the Greek centenarians are relatively low (mean value of co-morbidity=1.4+/-0.97, S.D.). Moreover, it provides valuable information on the anthropometric characteristics of the sample, and on health services utilization. These results indicate that exceptional longevity is not necessarily accompanied by disability, disease and total dependence on others.
Link
Assessment of the health status of Greek centenarians.
Darviri C, Demakakos P, Charizani F, Tigani X, Tsiou C, Chalamandaris AG, Tsagkari C, Chliaoutakis J.
The present study aims at describing the health status of a sample of relatively functional and healthy Greek centenarians and at exploring the potential gender differences in health in this sample. Its objectives are to add to the accumulation of knowledge about the health status of centenarians and therefore to contribute to the exploration of the mechanisms of healthy longevity. The study employs a non-representative community sample of Greek centenarians of both sexes (N=47). It uses descriptive statistics in order to outline the health status of the participants and non-parametric tests to assess the statistical significance of the observed sex-differences. The study shows that the centenarians of our sample are relatively healthy and functional (15% of the sample was free of any major chronic disease). It also suggests, that the sex-difference in survival is statistical significant (p less or equal 0.013), and that the morbidity and co-morbidity rates of the Greek centenarians are relatively low (mean value of co-morbidity=1.4+/-0.97, S.D.). Moreover, it provides valuable information on the anthropometric characteristics of the sample, and on health services utilization. These results indicate that exceptional longevity is not necessarily accompanied by disability, disease and total dependence on others.
Link
Migration routes in Romania
Ann Hum Genet. 2007 May 28; [Epub ahead of print]
Migration Rates and Genetic Structure of two Hungarian Ethnic Groups in Transylvania, Romania.
Brandstatter A, Egyed B, Zimmermann B, Duftner N, Padar Z, Parson W.
Institute of Legal Medicine, Innsbruck Medical University, Austria.
Transylvania's ethnic mosaic is composed of Romanians, German Saxons and Hungarians. The ethnic groups of the Hungarian minority that settled in Romania show differences in dialects, customs and religious affiliations. In this study entire mtDNA control region sequences from 360 individuals of Hungarian ethnicity from two populations (the Csango and the Szekely), settled in the historical region of Transylvania in Romania, were generated and analyzed following high quality sequencing standards. Phylogenetic analyses were used for haplogroup determination, quasi-median network analyses were applied for the visualization of character conflicts, and median joining reconstructions were used for depicting haplotype structures. Affiliation of haplotypes to major west Eurasian haplogroups was confirmed using coding region SNPs. Gene flow between the two populations was low and biased towards a higher migration rate from the Csango to the Szekely than vice versa. Phylogeographic analyses revealed effects of genetic isolation within the Csango population, which is, in its genetic structure, clearly different from the Szekely population. The pronounced genetic divergence between the two populations is in sharp contrast to the expectation of high genetic similarity due to the close geographic proximity of their native homelands. The population data will be incorporated in the EMPOP database (http://www.empop.org).
Link
Migration Rates and Genetic Structure of two Hungarian Ethnic Groups in Transylvania, Romania.
Brandstatter A, Egyed B, Zimmermann B, Duftner N, Padar Z, Parson W.
Institute of Legal Medicine, Innsbruck Medical University, Austria.
Transylvania's ethnic mosaic is composed of Romanians, German Saxons and Hungarians. The ethnic groups of the Hungarian minority that settled in Romania show differences in dialects, customs and religious affiliations. In this study entire mtDNA control region sequences from 360 individuals of Hungarian ethnicity from two populations (the Csango and the Szekely), settled in the historical region of Transylvania in Romania, were generated and analyzed following high quality sequencing standards. Phylogenetic analyses were used for haplogroup determination, quasi-median network analyses were applied for the visualization of character conflicts, and median joining reconstructions were used for depicting haplotype structures. Affiliation of haplotypes to major west Eurasian haplogroups was confirmed using coding region SNPs. Gene flow between the two populations was low and biased towards a higher migration rate from the Csango to the Szekely than vice versa. Phylogeographic analyses revealed effects of genetic isolation within the Csango population, which is, in its genetic structure, clearly different from the Szekely population. The pronounced genetic divergence between the two populations is in sharp contrast to the expectation of high genetic similarity due to the close geographic proximity of their native homelands. The population data will be incorporated in the EMPOP database (http://www.empop.org).
Link
May 21, 2007
Distribution of Genghis Khan's descendants
Genetika. 2007 Mar;43(3):422-6.
[Distribution of the male lineages of Genghis Khan's descendants in northern Eurasian populations]
[Article in Russian]
[No authors listed]
Data on the variation of 12 microsatellite loci of Y-chromosome haplogroup C3 were used to screen lineages included in the cluster of Genghis Khan's descendants in 18 northern Eurasian populations (Altaian Kazakhs, Altaians-Kizhi, Teleuts, Khakassians, Shorians, Tyvans, Todjins, Tofalars, Sojots, Buryats, Khamnigans, Evenks, Mongols, Kalmyks, Tajiks, Kurds, Persians, and Russians; the total sample size was 1437 people). The highest frequency of haplotypes from the cluster of the Genghis Khan's descendants was found in Mongols (34.8%). In Russia, this cluster was found in Altaian Kazakhs (8.3%), Altaians (3.4%), Buryats (2.3%), Tyvans (1.9%), and Kalmyks (1.7%).
Link
[Distribution of the male lineages of Genghis Khan's descendants in northern Eurasian populations]
[Article in Russian]
[No authors listed]
Data on the variation of 12 microsatellite loci of Y-chromosome haplogroup C3 were used to screen lineages included in the cluster of Genghis Khan's descendants in 18 northern Eurasian populations (Altaian Kazakhs, Altaians-Kizhi, Teleuts, Khakassians, Shorians, Tyvans, Todjins, Tofalars, Sojots, Buryats, Khamnigans, Evenks, Mongols, Kalmyks, Tajiks, Kurds, Persians, and Russians; the total sample size was 1437 people). The highest frequency of haplotypes from the cluster of the Genghis Khan's descendants was found in Mongols (34.8%). In Russia, this cluster was found in Altaian Kazakhs (8.3%), Altaians (3.4%), Buryats (2.3%), Tyvans (1.9%), and Kalmyks (1.7%).
Link
Prehistoric settlement of Australia
Proc Natl Acad Sci U S A. 2007 May 11; [Epub ahead of print]
Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis.
Hudjashov G, Kivisild T, Underhill PA, Endicott P, Sanchez JJ, Lin AA, Shen P, Oefner P, Renfrew C, Villems R, Forster P.
Published and new samples of Aboriginal Australians and Melanesians were analyzed for mtDNA (n = 172) and Y variation (n = 522), and the resulting profiles were compared with the branches known so far within the global mtDNA and the Y chromosome tree. (i) All Australian lineages are confirmed to fall within the mitochondrial founder branches M and N and the Y chromosomal founders C and F, which are associated with the exodus of modern humans from Africa approximately 50-70,000 years ago. The analysis reveals no evidence for any archaic maternal or paternal lineages in Australians, despite some suggestively robust features in the Australian fossil record, thus weakening the argument for continuity with any earlier Homo erectus populations in Southeast Asia. (ii) The tree of complete mtDNA sequences shows that Aboriginal Australians are most closely related to the autochthonous populations of New Guinea/Melanesia, indicating that prehistoric Australia and New Guinea were occupied initially by one and the same Palaeolithic colonization event approximately 50,000 years ago, in agreement with current archaeological evidence. (iii) The deep mtDNA and Y chromosomal branching patterns between Australia and most other populations around the Indian Ocean point to a considerable isolation after the initial arrival. (iv) We detect only minor secondary gene flow into Australia, and this could have taken place before the land bridge between Australia and New Guinea was submerged approximately 8,000 years ago, thus calling into question that certain significant developments in later Australian prehistory (the emergence of a backed-blade lithic industry, and the linguistic dichotomy) were externally motivated.
Link
Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis.
Hudjashov G, Kivisild T, Underhill PA, Endicott P, Sanchez JJ, Lin AA, Shen P, Oefner P, Renfrew C, Villems R, Forster P.
Published and new samples of Aboriginal Australians and Melanesians were analyzed for mtDNA (n = 172) and Y variation (n = 522), and the resulting profiles were compared with the branches known so far within the global mtDNA and the Y chromosome tree. (i) All Australian lineages are confirmed to fall within the mitochondrial founder branches M and N and the Y chromosomal founders C and F, which are associated with the exodus of modern humans from Africa approximately 50-70,000 years ago. The analysis reveals no evidence for any archaic maternal or paternal lineages in Australians, despite some suggestively robust features in the Australian fossil record, thus weakening the argument for continuity with any earlier Homo erectus populations in Southeast Asia. (ii) The tree of complete mtDNA sequences shows that Aboriginal Australians are most closely related to the autochthonous populations of New Guinea/Melanesia, indicating that prehistoric Australia and New Guinea were occupied initially by one and the same Palaeolithic colonization event approximately 50,000 years ago, in agreement with current archaeological evidence. (iii) The deep mtDNA and Y chromosomal branching patterns between Australia and most other populations around the Indian Ocean point to a considerable isolation after the initial arrival. (iv) We detect only minor secondary gene flow into Australia, and this could have taken place before the land bridge between Australia and New Guinea was submerged approximately 8,000 years ago, thus calling into question that certain significant developments in later Australian prehistory (the emergence of a backed-blade lithic industry, and the linguistic dichotomy) were externally motivated.
Link
May 05, 2007
Walking speed in different cities
The New Scientist reports on a study regarding the average walking speed over a distance of 18 meters in different cities. The times to walk 18m are listed below
The website of the study has more info.
1) Singapore (Singapore); 10.55The Arabs' leisurly pace is rather obvious from this list. Also, predictably "tall" nations tend to be on the top of the list, but so is Singapore; perhaps in a crowded city-state fast walking may be a culturally acquired trait.
2) Copenhagen (Denmark); 10.82
3) Madrid (Spain); 10.89
4) Guangzhou (China): 10.94
5) Dublin (Ireland); 11.03
6) Curitiba (Brazil); 11.13
7) Berlin (Germany); 11.16
8) New York (United States of America); 12.00
9) Utrecht (Netherlands); 12.04
10) Vienna (Austria); 12.06
11) Warsaw (Poland); 12.07
12) London (United Kingdom); 12.17
13) Zagreb (Croatia); 12.20
14) Prague (Czech Republic); 12.35
15) Wellington (New Zealand); 12.62
16) Paris (France); 12.65
17) Stockholm (Sweden); 12.75
18) Ljubljana (Slovenia); 12.76
19) Tokyo (Japan); 12.83
20) Ottawa (Canada); 13.72
21) Harare (Zimbabwe); 13.92
22) Sofia (Bulgaria); 13.96
23) Taipei (Taiwan): 14.00
24) Cairo (Egypt); 14.18
25) Sana'a (Yemen); 14.29
26) Bucharest (Romania); 14.36
27) Dubai (United Arab Emirates); 14.64
28) Damascus (Syria); 14.94
29) Amman (Jordan); 15.95
30) Bern (Switzerland); 17.37
31) Manama (Bahrain); 17.69
32) Blantyre (Malawi); 31.60
The website of the study has more info.
Native American DNA in the UK
The BBC has a story on native Britons with Native American mtDNA.
DNA testing has uncovered British descendents of Native Americans brought to the UK centuries ago as slaves, translators or tribal representatives.Also of interest the previous post on Sub-Saharan African Y chromosome haplogroup A in white British surname. Such unusual results are likely to turn up in any population, no matter how homogeneous, provided that a large enough number of individuals are sampled.
Genetic analysis turned up two white British women with a DNA signature characteristic of American Indians.
An Oxford scientist said it was extremely unusual to find these DNA lineages in Britons with no previous knowledge of Native American ancestry.
Indigenous Americans were brought over to the UK as early as the 1500s.
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:
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.
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.
Abstract
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)
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.
Abstract
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:
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.
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.
Link
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.
Link
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.
Link
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).
Link
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).
Link
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.
Link
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.
Link
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.
Link
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.
Link
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.
Link
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.
Link
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.
Link
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.
Link
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