This is the kind of quantitative study that I really like. There is so much anecdotal talk and debate about whether people from this region/country/continent/class/religion etc. are more beautiful/attractive/intelligent/etc. but with the exception of IQ and personality traits, I have seen very little quantitative evidence for these assertions.
Like g where an individual's correlated performance in multiple test items allows us to extract a common underlying intelligence factor, correlated measures of attractiveness across many observers could in principle allow us to extract an individuals BQ (beauty quotient) in a controlled social science experiment.
Personality and Individual Differences doi:10.1016/j.paid.2008.05.005
A beauty-map of London: Ratings of the physical attractiveness of women and men in London’s boroughs
Viren Swami and Eliana G. Hernandez
Abstract
In 1908, Francis Galton discussed anecdotal data he had collected for the compilation of a ‘beauty-map of the British Isles’. Based on his discussion, the present study attempted to compile a more empirical beauty-map of London. A community sample of 461 Londoners completed a questionnaire in which they rated the physical attractiveness of women and men in London’s 33 boroughs, as well as their familiarity with those boroughs. Results showed a significant interaction between borough and rated sex, with women being rated as more attractive across boroughs, and three boroughs in particular (the City of London, the City of Westminster, and Kensington and Chelsea) being rated high in physical attractiveness. Overall, ratings of attractiveness were significantly positively correlated with familiarity of boroughs, as well as objective measures of borough affluence (specifically, annual gross pay and average house prices) but not of borough health (life expectancy). These results are discussed in relation to the association between wealth and attractiveness, as well as Galton’s original beauty-map.
Link
July 17, 2008
Y chromosomes of Sudanese
American Journal of Physical Anthropology
Y-chromosome variation among Sudanese: Restricted gene flow, concordance with language, geography, and history
Hisham Y. Hassan et al.
Abstract
We study the major levels of Y-chromosome haplogroup variation in 15 Sudanese populations by typing major Y-haplogroups in 445 unrelated males representing the three linguistic families in Sudan. Our analysis shows Sudanese populations fall into haplogroups A, B, E, F, I, J, K, and R in frequencies of 16.9, 7.9, 34.4, 3.1, 1.3, 22.5, 0.9, and 13% respectively. Haplogroups A, B, and E occur mainly in Nilo-Saharan speaking groups including Nilotics, Fur, Borgu, and Masalit; whereas haplogroups F, I, J, K, and R are more frequent among Afro-Asiatic speaking groups including Arabs, Beja, Copts, and Hausa, and Niger-Congo speakers from the Fulani ethnic group. Mantel tests reveal a strong correlation between genetic and linguistic structures (r = 0.31, P = 0.007), and a similar correlation between genetic and geographic distances (r = 0.29, P = 0.025) that appears after removing nomadic pastoralists of no known geographic locality from the analysis. The bulk of genetic diversity appears to be a consequence of recent migrations and demographic events mainly from Asia and Europe, evident in a higher migration rate for speakers of Afro-Asiatic as compared with the Nilo-Saharan family of languages, and a generally higher effective population size for the former. The data provide insights not only into the history of the Nile Valley, but also in part to the history of Africa and the area of the Sahel.
Link
Y-chromosome variation among Sudanese: Restricted gene flow, concordance with language, geography, and history
Hisham Y. Hassan et al.
Abstract
We study the major levels of Y-chromosome haplogroup variation in 15 Sudanese populations by typing major Y-haplogroups in 445 unrelated males representing the three linguistic families in Sudan. Our analysis shows Sudanese populations fall into haplogroups A, B, E, F, I, J, K, and R in frequencies of 16.9, 7.9, 34.4, 3.1, 1.3, 22.5, 0.9, and 13% respectively. Haplogroups A, B, and E occur mainly in Nilo-Saharan speaking groups including Nilotics, Fur, Borgu, and Masalit; whereas haplogroups F, I, J, K, and R are more frequent among Afro-Asiatic speaking groups including Arabs, Beja, Copts, and Hausa, and Niger-Congo speakers from the Fulani ethnic group. Mantel tests reveal a strong correlation between genetic and linguistic structures (r = 0.31, P = 0.007), and a similar correlation between genetic and geographic distances (r = 0.29, P = 0.025) that appears after removing nomadic pastoralists of no known geographic locality from the analysis. The bulk of genetic diversity appears to be a consequence of recent migrations and demographic events mainly from Asia and Europe, evident in a higher migration rate for speakers of Afro-Asiatic as compared with the Nilo-Saharan family of languages, and a generally higher effective population size for the former. The data provide insights not only into the history of the Nile Valley, but also in part to the history of Africa and the area of the Sahel.
Link
July 16, 2008
Y chromosomes and Athapaskans
From the EurekAlert release:
From the paper:
Wikipedia on Athapaskan languages.
American Journal of Physical Anthropology
Distribution of Y chromosomes among native North Americans: A study of Athapaskan population history
Ripan Singh Malhi et al.
Abstract
In this study, 231 Y chromosomes from 12 populations were typed for four diagnostic single nucleotide polymorphisms (SNPs) to determine haplogroup membership and 43 Y chromosomes from three of these populations were typed for eight short tandem repeats (STRs) to determine haplotypes. These data were combined with previously published data, amounting to 724 Y chromosomes from 26 populations in North America, and analyzed to investigate the geographic distribution of Y chromosomes among native North Americans and to test the Southern Athapaskan migration hypothesis. The results suggest that European admixture has significantly altered the distribution of Y chromosomes in North America and because of this caution should be taken when inferring prehistoric population events in North America using Y chromosome data alone. However, consistent with studies of other genetic systems, we are still able to identify close relationships among Y chromosomes in Athapaskans from the Subarctic and the Southwest, suggesting that a small number of proto-Apachean migrants from the Subarctic founded the Southwest Athapaskan populations.
Link
The new findings reinforce the hypothesis that the Athapaskan migration involved a relatively small group that nonetheless was very successful at assimilating and intermixing with native groups already living in the southwest. The newcomers were so influential that the Athapaskan language family now dominates many parts of the Southwest. Now called Apacheans, the Navajo and Apache descendants of the early migrants are dispersed throughout the central Southwest and speak languages closely related to the Chipewyan, an Athapaskan language found in the subarctic.
...
Other patterns emerged from the Y chromosome analysis. One genetic signature associated with European males was detected in native males throughout North America, but was found at the highest frequency in groups living nearest to Hudson Bay, where trade between Europeans and the region's indigenous peoples was established in the early 17th century.
From the paper:
Gene map interpolations (Fig. 2A–C) indicate that the frequency of haplogroup Q is highest in Southwestern North America/Mesoamerica. The frequency of haplogroup C is highest in Northwestern North America and the frequency of haplogroup R, the presence of which is attributed to European admixture, reaches its maximum in Northeastern North America. In total, 73% percent of the populations analyzed exhibited haplogroup R, which ranges in frequency from 4 to 88% (Table 1).
...
Y chromosome haplogroup C is observed at a moderate frequency in the Subarctic Athapaskan groups and at a low frequency in the Navajo and Apache, but is otherwise absent from the Southwest. Nearly all Navajo and Apache Y chromosomes within haplogroup C belong to a specific, well-defined subclade (Zegura et al., 2004). Hence, it is likely that ancestral Subarctic Athapaskan speakers provided the source for Y chromosome haplogroup C as well as the mtDNA A2a subclade in Apachean groups.
However, Apachean groups cluster with other Southwest and Mesoamerican groups in the principal coordinates analysis, rather than with Athapaskans from the Subarctic. This suggests that the majority of non-C Y chromosomes in the Navajo and Apache were contributed by non-Athapaskan populations in the Southwest, which mirrors the presence in the Apachean of mtDNA lineages belonging to haplogroups B and C.
Wikipedia on Athapaskan languages.
American Journal of Physical Anthropology
Distribution of Y chromosomes among native North Americans: A study of Athapaskan population history
Ripan Singh Malhi et al.
Abstract
In this study, 231 Y chromosomes from 12 populations were typed for four diagnostic single nucleotide polymorphisms (SNPs) to determine haplogroup membership and 43 Y chromosomes from three of these populations were typed for eight short tandem repeats (STRs) to determine haplotypes. These data were combined with previously published data, amounting to 724 Y chromosomes from 26 populations in North America, and analyzed to investigate the geographic distribution of Y chromosomes among native North Americans and to test the Southern Athapaskan migration hypothesis. The results suggest that European admixture has significantly altered the distribution of Y chromosomes in North America and because of this caution should be taken when inferring prehistoric population events in North America using Y chromosome data alone. However, consistent with studies of other genetic systems, we are still able to identify close relationships among Y chromosomes in Athapaskans from the Subarctic and the Southwest, suggesting that a small number of proto-Apachean migrants from the Subarctic founded the Southwest Athapaskan populations.
Link
Individualists and egalitarians are more optimistic
Personality and Individual Differences doi:10.1016/j.paid.2008.05.008
Is optimism universal? A meta-analytical investigation of optimism levels across 22 nations
Ronald Fischer et al.
Abstract
A meta-analysis of dispositional optimism levels as measured by the life orientation test (LOT, Scheier & Carver, 1985) across 22 countries (k = 213; N = 89,138) is reported. Using mixed effect modeling, overall culture differences were small. Greater individualism (Hofstede, 1980) was associated with greater optimism. Greater egalitarianism (versus hierarchy, Schwartz, 1994) was consistently associated with higher optimism. Claims of fundamental cultural differences were not supported. Implications for cross-cultural research and applications are discussed.
Link
Is optimism universal? A meta-analytical investigation of optimism levels across 22 nations
Ronald Fischer et al.
Abstract
A meta-analysis of dispositional optimism levels as measured by the life orientation test (LOT, Scheier & Carver, 1985) across 22 countries (k = 213; N = 89,138) is reported. Using mixed effect modeling, overall culture differences were small. Greater individualism (Hofstede, 1980) was associated with greater optimism. Greater egalitarianism (versus hierarchy, Schwartz, 1994) was consistently associated with higher optimism. Claims of fundamental cultural differences were not supported. Implications for cross-cultural research and applications are discussed.
Link
28,000 year-old Cro-Magnon mtDNA from Italy
The researchers could verify that the sequence of the Cro-Magnon (which was the Cambridge Reference Sequence, common among modern Caucasoids) was genuine, since it was different from that of all possible contaminating individuals who handled the find since 2003.
This raises an interesting methodological problem. Should researchers with common mtDNA sequences be handling ancient remains? It seems like blind good luck that no one out of individuals had the quite common CRS. In the recent mtDNA paper on the Mycenaeans for example, they were able to identify contaminant sequences by the fact that the author and experimenter had a particular mutation; if she was plain CRS, they wouldn't have been able to disprove possible contamination for the CRS individual from Mycenae.
Ascertaining authenticity is challenging. In an ideal situation the sample is handled by only a single individual, and one who is unlikely to possess the same mtDNA type as the sample. An obvious solution to this would be to recruit a person of remote geographic origin to do the lab work, e.g. a Japanese person to work on European samples and vice versa.
PLoS ONE 3(7): e2700. doi:10.1371/journal.pone.0002700
A 28,000 Years Old Cro-Magnon mtDNA Sequence Differs from All Potentially Contaminating Modern Sequences
David Caramelli et al.
Abstract
Background
DNA sequences from ancient speciments may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal) and early modern (Cro-Magnoid) Europeans.
Methodology/Principal Findings
We typed the mitochondrial DNA (mtDNA) hypervariable region I in a 28,000 years old Cro-Magnoid individual from the Paglicci cave, in Italy (Paglicci 23) and in all the people who had contact with the sample since its discovery in 2003. The Paglicci 23 sequence, determined through the analysis of 152 clones, is the Cambridge reference sequence, and cannot possibly reflect contamination because it differs from all potentially contaminating modern sequences.
Conclusions/Significance:
The Paglicci 23 individual carried a mtDNA sequence that is still common in Europe, and which radically differs from those of the almost contemporary Neandertals, demonstrating a genealogical continuity across 28,000 years, from Cro-Magnoid to modern Europeans. Because all potential sources of modern DNA contamination are known, the Paglicci 23 sample will offer a unique opportunity to get insight for the first time into the nuclear genes of early modern Europeans.
Link
This raises an interesting methodological problem. Should researchers with common mtDNA sequences be handling ancient remains? It seems like blind good luck that no one out of individuals had the quite common CRS. In the recent mtDNA paper on the Mycenaeans for example, they were able to identify contaminant sequences by the fact that the author and experimenter had a particular mutation; if she was plain CRS, they wouldn't have been able to disprove possible contamination for the CRS individual from Mycenae.
Ascertaining authenticity is challenging. In an ideal situation the sample is handled by only a single individual, and one who is unlikely to possess the same mtDNA type as the sample. An obvious solution to this would be to recruit a person of remote geographic origin to do the lab work, e.g. a Japanese person to work on European samples and vice versa.
PLoS ONE 3(7): e2700. doi:10.1371/journal.pone.0002700
A 28,000 Years Old Cro-Magnon mtDNA Sequence Differs from All Potentially Contaminating Modern Sequences
David Caramelli et al.
Abstract
Background
DNA sequences from ancient speciments may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal) and early modern (Cro-Magnoid) Europeans.
Methodology/Principal Findings
We typed the mitochondrial DNA (mtDNA) hypervariable region I in a 28,000 years old Cro-Magnoid individual from the Paglicci cave, in Italy (Paglicci 23) and in all the people who had contact with the sample since its discovery in 2003. The Paglicci 23 sequence, determined through the analysis of 152 clones, is the Cambridge reference sequence, and cannot possibly reflect contamination because it differs from all potentially contaminating modern sequences.
Conclusions/Significance:
The Paglicci 23 individual carried a mtDNA sequence that is still common in Europe, and which radically differs from those of the almost contemporary Neandertals, demonstrating a genealogical continuity across 28,000 years, from Cro-Magnoid to modern Europeans. Because all potential sources of modern DNA contamination are known, the Paglicci 23 sample will offer a unique opportunity to get insight for the first time into the nuclear genes of early modern Europeans.
Link
July 15, 2008
Narcissistic people aren't really more beautiful
Personality and Individual Differences doi:10.1016/j.paid.2008.05.018
Narcissistic men and women think they are so hot – But they are not
April Bleske-Rechek et al.
Abstract
Narcissists think they are more knowledgeable, better leaders, and more attractive than others are. Higher narcissism scores in celebrities than in non-celebrities (Young & Pinsky, 2006) raise the question of whether narcissistic individuals actually are, to some degree, more knowledgeable or attractive than other individuals are. Because little research has investigated the degree to which narcissists’ ratings of their attractiveness are inflated relative to others’ ratings of their attractiveness, we asked men and women to evaluate their own attractiveness, and then we asked two separate panels of judges to view and rate facial shots of these men and women. More narcissistic men and women rated themselves as more attractive than less narcissistic individuals did, but outside judges did not rate more and less narcissistic individuals as any different in attractiveness.
Link
Narcissistic men and women think they are so hot – But they are not
April Bleske-Rechek et al.
Abstract
Narcissists think they are more knowledgeable, better leaders, and more attractive than others are. Higher narcissism scores in celebrities than in non-celebrities (Young & Pinsky, 2006) raise the question of whether narcissistic individuals actually are, to some degree, more knowledgeable or attractive than other individuals are. Because little research has investigated the degree to which narcissists’ ratings of their attractiveness are inflated relative to others’ ratings of their attractiveness, we asked men and women to evaluate their own attractiveness, and then we asked two separate panels of judges to view and rate facial shots of these men and women. More narcissistic men and women rated themselves as more attractive than less narcissistic individuals did, but outside judges did not rate more and less narcissistic individuals as any different in attractiveness.
Link
Craniometry of the Ainu
American Journal of Physical Anthropology
Craniometric variation of the Ainu: An assessment of differential gene flow from Northeast Asia into Northern Japan, Hokkaido
Tsunehiko Hanihara et al.
Abstract
In and after the latest Neolithic period in Japan (B.P. 2,300 years), there were two distinct waves of migration from eastern Asia. One is well known as successive episodes in which indigenous inhabitants of main-island Japan were intruded on by new arrivals with advanced technology, and of a different genetic stock. Another migration of people and culture, identified as the Okhotsk culture, reached the northeastern part of Hokkaido. As opposed to main-island Japan, the morphological continuity from the Neolithic to recent inhabitants in Hokkaido (Ainu) is notable, so that the evidence of admixture easily could have escaped notice. In this study, the effects of gene flow from an outside source on the pattern of among-group variation of Hokkaido Ainu are examined by means of two models. One is the R-matrix model comparing observed and expected craniometric variation for estimating differential external gene flow into a region. The other is a simple simulation model that estimates admixture in a population with two parental populations. The two approaches give similar results. The results suggest the possibility of admixture between the migrants from Northeast Asia, the Okhotsk culture people, and the indigenous inhabitants in Hokkaido during the 5th to 12th centuries A.D., at least in northeastern Hokkaido. Such gene flow may have a certain degree of effect on the genetic structure of recent Ainu. The findings further suggest morphological heterogeneity in Northeast Asia during the Holocene that has relevance for understanding the morphological heterogeneity seen through time in the New World.
Link
Craniometric variation of the Ainu: An assessment of differential gene flow from Northeast Asia into Northern Japan, Hokkaido
Tsunehiko Hanihara et al.
Abstract
In and after the latest Neolithic period in Japan (B.P. 2,300 years), there were two distinct waves of migration from eastern Asia. One is well known as successive episodes in which indigenous inhabitants of main-island Japan were intruded on by new arrivals with advanced technology, and of a different genetic stock. Another migration of people and culture, identified as the Okhotsk culture, reached the northeastern part of Hokkaido. As opposed to main-island Japan, the morphological continuity from the Neolithic to recent inhabitants in Hokkaido (Ainu) is notable, so that the evidence of admixture easily could have escaped notice. In this study, the effects of gene flow from an outside source on the pattern of among-group variation of Hokkaido Ainu are examined by means of two models. One is the R-matrix model comparing observed and expected craniometric variation for estimating differential external gene flow into a region. The other is a simple simulation model that estimates admixture in a population with two parental populations. The two approaches give similar results. The results suggest the possibility of admixture between the migrants from Northeast Asia, the Okhotsk culture people, and the indigenous inhabitants in Hokkaido during the 5th to 12th centuries A.D., at least in northeastern Hokkaido. Such gene flow may have a certain degree of effect on the genetic structure of recent Ainu. The findings further suggest morphological heterogeneity in Northeast Asia during the Holocene that has relevance for understanding the morphological heterogeneity seen through time in the New World.
Link
July 14, 2008
Ancient mtDNA from Southeast Asia
American Journal of Physical Anthropology
Genetic history of Southeast Asian populations as revealed by ancient and modern human mitochondrial DNA analysis
Patcharee Lertrit et al.
Abstract
The 360 base-pair fragment in HVS-1 of the mitochondrial genome were determined from ancient human remains excavated at Noen U-loke and Ban Lum-Khao, two Bronze and Iron Age archaeological sites in Northeastern Thailand, radio-carbon dated to circa 3,500-1,500 years BP and 3,200-2,400 years BP, respectively. These two neighboring populations were parts of early agricultural communities prevailing in northeastern Thailand from the fourth millennium BP onwards. The nucleotide sequences of these ancient samples were compared with the sequences of modern samples from various ethnic populations of East and Southeast Asia, encompassing four major linguistic affiliations (Altaic, Sino-Tibetan, Tai-Kadai, and Austroasiatic), to investigate the genetic relationships and history among them. The two ancient samples were most closely related to each other, and next most closely related to the Chao-Bon, an Austroasiatic-speaking group living near the archaeological sites, suggesting that the genetic continuum may have persisted since prehistoric times in situ among the native, perhaps Austroasiatic-speaking population. Tai-Kadai groups formed close affinities among themselves, with a tendency to be more closely related to other Southeast Asian populations than to populations from further north. The Tai-Kadai groups were relatively distant from all groups that have presumably been in Southeast Asia for longer-that is, the two ancient groups and the Austroasiatic-speaking groups, with the exception of the Khmer group. This finding is compatible with the known history of the Thais: their late arrival in Southeast Asia from southern China after the 10th-11th century AD, followed by a period of subjugation under the Khmers.
Link
Genetic history of Southeast Asian populations as revealed by ancient and modern human mitochondrial DNA analysis
Patcharee Lertrit et al.
Abstract
The 360 base-pair fragment in HVS-1 of the mitochondrial genome were determined from ancient human remains excavated at Noen U-loke and Ban Lum-Khao, two Bronze and Iron Age archaeological sites in Northeastern Thailand, radio-carbon dated to circa 3,500-1,500 years BP and 3,200-2,400 years BP, respectively. These two neighboring populations were parts of early agricultural communities prevailing in northeastern Thailand from the fourth millennium BP onwards. The nucleotide sequences of these ancient samples were compared with the sequences of modern samples from various ethnic populations of East and Southeast Asia, encompassing four major linguistic affiliations (Altaic, Sino-Tibetan, Tai-Kadai, and Austroasiatic), to investigate the genetic relationships and history among them. The two ancient samples were most closely related to each other, and next most closely related to the Chao-Bon, an Austroasiatic-speaking group living near the archaeological sites, suggesting that the genetic continuum may have persisted since prehistoric times in situ among the native, perhaps Austroasiatic-speaking population. Tai-Kadai groups formed close affinities among themselves, with a tendency to be more closely related to other Southeast Asian populations than to populations from further north. The Tai-Kadai groups were relatively distant from all groups that have presumably been in Southeast Asia for longer-that is, the two ancient groups and the Austroasiatic-speaking groups, with the exception of the Khmer group. This finding is compatible with the known history of the Thais: their late arrival in Southeast Asia from southern China after the 10th-11th century AD, followed by a period of subjugation under the Khmers.
Link
July 11, 2008
mtDNA haplogroup H1 and ischemic stroke protection
BMC Med Genet. 2008 Jul 1;9(1):57. [Epub ahead of print]
Mitochondrial haplogroup H1 is protective for ischemic stroke in Portuguese patients.
Rosa A, Fonseca BV, Krug T, Manso H, Gouveia L, Albergaria I, Gaspar G, Correia M, Viana-Baptista M, Moiron Simoes R, Nogueira Pinto A, Taipa R, Ferreira C, Ramalho Fontes J, Rui Silva M, Gabriel JP, Matos I, Lopes G, Ferro JM, Vicente AM, Oliveira SA.
ABSTRACT: BACKGROUND: The genetic contribution to stroke is well established but it has proven difficult to identify the genes and the disease-associated alleles mediating this effect, possibly because only nuclear genes have been intensely investigated so far. Mitochondrial DNA (mtDNA) has been implicated in several disorders having stroke as one of its clinical manifestations. The aim of this case-control study was to assess the contribution of mtDNA polymorphisms and haplogroups to ischemic stroke risk. METHODS: We genotyped 19 mtDNA single nucleotide polymorphisms (SNPs) defining the major European haplogroups in 534 ischemic stroke patients and 499 controls collected in Portugal, and tested their allelic and haplogroup association with ischemic stroke risk. RESULTS: Haplogroup H1 was found to be significantly less frequent in stroke patients than in controls (OR=0.61, 95% CI=0.45-0.83, p=0.001), when comparing each clade against all other haplogroups pooled together. Conversely, the pre-HV/HV and U mtDNA lineages emerge as potential genetic factors conferring risk for stroke (OR=3.14, 95% CI=1.41-7.01, p=0.003, and OR=2.87, 95% CI=1.13-7.28, p=0.021, respectively). SNPs m.3010G>A, m.7028C>T and m.11719G>A strongly influence ischemic stroke risk, their allelic state in haplogroup H1 corroborating its protective effect. CONCLUSION: Our data suggests that mitochondrial haplogroup H1 has an impact on ischemic stroke risk in a Portuguese sample.
Link
Mitochondrial haplogroup H1 is protective for ischemic stroke in Portuguese patients.
Rosa A, Fonseca BV, Krug T, Manso H, Gouveia L, Albergaria I, Gaspar G, Correia M, Viana-Baptista M, Moiron Simoes R, Nogueira Pinto A, Taipa R, Ferreira C, Ramalho Fontes J, Rui Silva M, Gabriel JP, Matos I, Lopes G, Ferro JM, Vicente AM, Oliveira SA.
ABSTRACT: BACKGROUND: The genetic contribution to stroke is well established but it has proven difficult to identify the genes and the disease-associated alleles mediating this effect, possibly because only nuclear genes have been intensely investigated so far. Mitochondrial DNA (mtDNA) has been implicated in several disorders having stroke as one of its clinical manifestations. The aim of this case-control study was to assess the contribution of mtDNA polymorphisms and haplogroups to ischemic stroke risk. METHODS: We genotyped 19 mtDNA single nucleotide polymorphisms (SNPs) defining the major European haplogroups in 534 ischemic stroke patients and 499 controls collected in Portugal, and tested their allelic and haplogroup association with ischemic stroke risk. RESULTS: Haplogroup H1 was found to be significantly less frequent in stroke patients than in controls (OR=0.61, 95% CI=0.45-0.83, p=0.001), when comparing each clade against all other haplogroups pooled together. Conversely, the pre-HV/HV and U mtDNA lineages emerge as potential genetic factors conferring risk for stroke (OR=3.14, 95% CI=1.41-7.01, p=0.003, and OR=2.87, 95% CI=1.13-7.28, p=0.021, respectively). SNPs m.3010G>A, m.7028C>T and m.11719G>A strongly influence ischemic stroke risk, their allelic state in haplogroup H1 corroborating its protective effect. CONCLUSION: Our data suggests that mitochondrial haplogroup H1 has an impact on ischemic stroke risk in a Portuguese sample.
Link
July 10, 2008
Campbell & Tishkoff review paper on African genetic diversity
From the paper:
Several studies of nucleotide and haplotype variation have indicated that ancestral African populations were geographically structured prior to the migration of modern humans out of Africa (70, 71, 79, 157, 197, 237). Additionally, a recent study of 800 short tandem repeat polymorphisms (STRPs) and 400 INDELs genotyped in more than 3000 geographically and ethnically diverse Africans indicates the presence of at least 13 genetically distinct ancestral populations in Africa and high levels of population admixture in many regions (F.A. Reed & S.A Tishkoff, unpublished data). Population clusters are correlated with selfdescribed ethnicity and shared cultural and/or linguistic properties (e.g., Pygmies, Khoisanspeaking hunter-gatherers, Bantu speakers, Cushitic speakers). This study reveals extensive admixture between inferred ancestral populations in most African populations. One exception is amongWest African Niger-Kordofanian (i.e., Bantu) speakers who are more genetically homogeneous compared with other African populations, likely reflecting the recent and rapid spread of Bantu speakers from a common origin in Cameroon/Nigeria (although fine-scale genetic structure can be detected amongst these populations). Thus, the pattern of genetic diversity in Africa indicates that African populations have maintained a large and subdivided population structure throughout much of their evolutionary history (Figure 2).As I have argued before, the great genetic diversity of Sub-Saharan Africans is due to the fact that they are composed of several long-differentiated populations admixed with each other. As Figure 2, mentioned above, indicates, NE Africans are related to Eurasians more closely than other Africans, although there has been subsequent gene flow into NE Africans from other Sub-Saharan Africans. Annual Review of Genomics and Human Genetics Vol. 9 (Volume publication date September 2008) (doi:10.1146/annurev.genom.9.081307.164258) African Genetic Diversity: Implications for Human Demographic History, Modern Human Origins, and Complex Disease Mapping Michael C. Campbell, Sarah A. Tishkoff Comparative studies of ethnically diverse human populations, particularly in Africa, are important for reconstructing human evolutionary history and for understanding the genetic basis of phenotypic adaptation and complex disease. African populations are characterized by greater levels of genetic diversity, extensive population substructure, and less linkage disequilibrium (LD) among loci compared to non-African populations. Africans also possess a number of genetic adaptations that have evolved in response to diverse climates and diets, as well as exposure to infectious disease. This review summarizes patterns and the evolutionary origins of genetic diversity present in African populations, as well as their implications for the mapping of complex traits, including disease susceptibility. Link
July 09, 2008
mtDNA macro-haplogroup R0
R0 is ancestral to the very widespread HV, V, and H which are frequent in Europe, as well as R0a which is frequent in the Middle East.
BMC Evol Biol. 2008 Jul 4;8(1):191. [Epub ahead of print]
Timing and deciphering mitochondrial DNA macro-haplogroup R0 variability in Central Europe and Middle East.
Brandstaetter A, Zimmermann B, Wagner J, Goebel T, Roeck AW, Salas A, Carracedo A, Parson W.
ABSTRACT: BACKGROUND: Nearly half of the West Eurasian assemblage of human mitochondrial DNA (mtDNA) is fractioned into numerous sub-lineages of the predominant haplogroup (hg) R0. Several hypotheses have been proposed on the origin and the expansion times of some R0 sub-lineages, which were partially inconsistent with each other. Here we describe the phylogenetic structure and genetic variety of hg R0 in five European populations and one population from the Middle East. RESULTS: Our analysis of 1,350 mtDNA haplotypes belonging to R0, including entire control region sequences and 45 single nucleotide polymorphisms from the coding region, revealed significant differences in the distribution of different sub-hgs even between geographically closely located regions. Estimates of coalescence times that were derived using diverse algorithmic approaches consistently affirmed that the major expansions of the different R0 hgs occurred in the terminal Pleistocene and early Holocene. CONCLUSIONS: Given an estimated coalescence time of the distinct lineages of 10 - 18 kya, the differences in the distributions could hint to either limited maternal gene flow after the last glacial maximum due to the alpine nature of the regions involved or to a stochastic loss of diversity due to environmental events and/or disease episodes occurred at different times and in distinctive regions. Our comparison of two different ways of obtaining the timing of the most recent common ancestor confirms that the time of a sudden expansion can be adequately recovered from control region data with valid confidence intervals. For reliable estimates, both procedures should be applied in order to cross-check the results for validity and soundness.
Link
BMC Evol Biol. 2008 Jul 4;8(1):191. [Epub ahead of print]
Timing and deciphering mitochondrial DNA macro-haplogroup R0 variability in Central Europe and Middle East.
Brandstaetter A, Zimmermann B, Wagner J, Goebel T, Roeck AW, Salas A, Carracedo A, Parson W.
ABSTRACT: BACKGROUND: Nearly half of the West Eurasian assemblage of human mitochondrial DNA (mtDNA) is fractioned into numerous sub-lineages of the predominant haplogroup (hg) R0. Several hypotheses have been proposed on the origin and the expansion times of some R0 sub-lineages, which were partially inconsistent with each other. Here we describe the phylogenetic structure and genetic variety of hg R0 in five European populations and one population from the Middle East. RESULTS: Our analysis of 1,350 mtDNA haplotypes belonging to R0, including entire control region sequences and 45 single nucleotide polymorphisms from the coding region, revealed significant differences in the distribution of different sub-hgs even between geographically closely located regions. Estimates of coalescence times that were derived using diverse algorithmic approaches consistently affirmed that the major expansions of the different R0 hgs occurred in the terminal Pleistocene and early Holocene. CONCLUSIONS: Given an estimated coalescence time of the distinct lineages of 10 - 18 kya, the differences in the distributions could hint to either limited maternal gene flow after the last glacial maximum due to the alpine nature of the regions involved or to a stochastic loss of diversity due to environmental events and/or disease episodes occurred at different times and in distinctive regions. Our comparison of two different ways of obtaining the timing of the most recent common ancestor confirms that the time of a sudden expansion can be adequately recovered from control region data with valid confidence intervals. For reliable estimates, both procedures should be applied in order to cross-check the results for validity and soundness.
Link
July 08, 2008
PCA-informative markers for European American substructure
The importance of this work is that while it takes many thousands of markers to identify population structure in closely related groups, a much smaller subset of these markers captures almost all the information in the larger marker set.
Thus, from an economic standpoint, discovery of substructure in an "unexamined" group requires a considerable initial investment of genotyping a large representative sample for a large number of markers. But, subsequent ancestry analysis can profit from the identified smaller subset to economically test new individuals.
Once I look at the details of this paper, I will try to update EURO-DNA-CALC to use this new marker panel.
See the earlier paper by this group on PCA-Correlated SNPs for Structure Identification in Worldwide Human Populations.
PLoS Genet 4(7): e1000114. doi:10.1371/journal.pgen.1000114
Tracing Sub-Structure in the European American Population with PCA-Informative Markers
Peristera Paschou et al.
Abstract
Genetic structure in the European American population reflects waves of migration and recent gene flow among different populations. This complex structure can introduce bias in genetic association studies. Using Principal Components Analysis (PCA), we analyze the structure of two independent European American datasets (1,521 individuals–307,315 autosomal SNPs). Individual variation lies across a continuum with some individuals showing high degrees of admixture with non-European populations, as demonstrated through joint analysis with HapMap data. The CEPH Europeans only represent a small fraction of the variation encountered in the larger European American datasets we studied. We interpret the first eigenvector of this data as correlated with ancestry, and we apply an algorithm that we have previously described to select PCA-informative markers (PCAIMs) that can reproduce this structure. Importantly, we develop a novel method that can remove redundancy from the selected SNP panels and show that we can effectively remove correlated markers, thus increasing genotyping savings. Only 150–200 PCAIMs suffice to accurately predict fine structure in European American datasets, as identified by PCA. Simulating association studies, we couple our method with a PCA-based stratification correction tool and demonstrate that a small number of PCAIMs can efficiently remove false correlations with almost no loss in power. The structure informative SNPs that we propose are an important resource for genetic association studies of European Americans. Furthermore, our redundancy removal algorithm can be applied on sets of ancestry informative markers selected with any method in order to select the most uncorrelated SNPs, and significantly decreases genotyping costs.
Link
Thus, from an economic standpoint, discovery of substructure in an "unexamined" group requires a considerable initial investment of genotyping a large representative sample for a large number of markers. But, subsequent ancestry analysis can profit from the identified smaller subset to economically test new individuals.
Once I look at the details of this paper, I will try to update EURO-DNA-CALC to use this new marker panel.
See the earlier paper by this group on PCA-Correlated SNPs for Structure Identification in Worldwide Human Populations.
PLoS Genet 4(7): e1000114. doi:10.1371/journal.pgen.1000114
Tracing Sub-Structure in the European American Population with PCA-Informative Markers
Peristera Paschou et al.
Abstract
Genetic structure in the European American population reflects waves of migration and recent gene flow among different populations. This complex structure can introduce bias in genetic association studies. Using Principal Components Analysis (PCA), we analyze the structure of two independent European American datasets (1,521 individuals–307,315 autosomal SNPs). Individual variation lies across a continuum with some individuals showing high degrees of admixture with non-European populations, as demonstrated through joint analysis with HapMap data. The CEPH Europeans only represent a small fraction of the variation encountered in the larger European American datasets we studied. We interpret the first eigenvector of this data as correlated with ancestry, and we apply an algorithm that we have previously described to select PCA-informative markers (PCAIMs) that can reproduce this structure. Importantly, we develop a novel method that can remove redundancy from the selected SNP panels and show that we can effectively remove correlated markers, thus increasing genotyping savings. Only 150–200 PCAIMs suffice to accurately predict fine structure in European American datasets, as identified by PCA. Simulating association studies, we couple our method with a PCA-based stratification correction tool and demonstrate that a small number of PCAIMs can efficiently remove false correlations with almost no loss in power. The structure informative SNPs that we propose are an important resource for genetic association studies of European Americans. Furthermore, our redundancy removal algorithm can be applied on sets of ancestry informative markers selected with any method in order to select the most uncorrelated SNPs, and significantly decreases genotyping costs.
Link
July 07, 2008
Diet in Bronze Age Lerna
Journal of Archaeological Science
Article in Press doi:10.1016/j.jas.2008.06.018
Isotopic Dietary Reconstruction of humans from middle Bronze Age lerna, argolid, greece
S. Triantaphyllou, M.P. Richards, C. Zerner and S. Voutsaki
Abstract
This study presents the results of a carbon and nitrogen stable isotope analysis
of thirty-nine human bone and eight animal samples from Middle Bronze Age (or
Middle Helladic, MH, ca. 2100-1700BC) Lerna, Greece. The isotopic data indicate
that the humans had a C3 terrestrial diet while certain individuals appear to have
significant amounts of animal protein in their diet. With regard to weaning age, the
isotopic values and the estimated age of early enamel disruptions suggest that solid
foods were starting to be used as a substitute for breast milk at or before the ages of
2.5 and 3 years old.
Link
Article in Press doi:10.1016/j.jas.2008.06.018
Isotopic Dietary Reconstruction of humans from middle Bronze Age lerna, argolid, greece
S. Triantaphyllou, M.P. Richards, C. Zerner and S. Voutsaki
Abstract
This study presents the results of a carbon and nitrogen stable isotope analysis
of thirty-nine human bone and eight animal samples from Middle Bronze Age (or
Middle Helladic, MH, ca. 2100-1700BC) Lerna, Greece. The isotopic data indicate
that the humans had a C3 terrestrial diet while certain individuals appear to have
significant amounts of animal protein in their diet. With regard to weaning age, the
isotopic values and the estimated age of early enamel disruptions suggest that solid
foods were starting to be used as a substitute for breast milk at or before the ages of
2.5 and 3 years old.
Link
July 04, 2008
Clicks not a feature of early human language
Annual Review of Anthropology
Vol. 37 (Volume publication date October 2008)
(doi:10.1146/annurev.anthro.37.081407.085109)
A Historical Appraisal of Clicks: A Linguistic and Genetic Population Perspective
Tom Güldemann, Mark Stoneking
Clicks are often considered an exotic feature of languages, and the fact that certain African "Khoisan" groups share the use of clicks as consonants and exhibit deep genetic divergences has been argued to indicate that clicks trace back to an early common ancestral language (Knight et al. 2003). Here, we review the linguistic evidence concerning the use of click sounds in languages and the genetic evidence concerning the relationships of African click-speaking groups. The linguistic evidence suggests that genealogical inheritance and contact-induced transmission are equally relevant for the distribution of clicks in African languages. The genetic evidence indicates that there has been substantial genetic drift in some groups, obscuring their genetic relationships. Overall, the presence of clicks in human languages may in fact not trace back to the dawn of human language, but instead reflect a much later episode in the diversification of human speech.
Link
Vol. 37 (Volume publication date October 2008)
(doi:10.1146/annurev.anthro.37.081407.085109)
A Historical Appraisal of Clicks: A Linguistic and Genetic Population Perspective
Tom Güldemann, Mark Stoneking
Clicks are often considered an exotic feature of languages, and the fact that certain African "Khoisan" groups share the use of clicks as consonants and exhibit deep genetic divergences has been argued to indicate that clicks trace back to an early common ancestral language (Knight et al. 2003). Here, we review the linguistic evidence concerning the use of click sounds in languages and the genetic evidence concerning the relationships of African click-speaking groups. The linguistic evidence suggests that genealogical inheritance and contact-induced transmission are equally relevant for the distribution of clicks in African languages. The genetic evidence indicates that there has been substantial genetic drift in some groups, obscuring their genetic relationships. Overall, the presence of clicks in human languages may in fact not trace back to the dawn of human language, but instead reflect a much later episode in the diversification of human speech.
Link
July 03, 2008
Linguistic diversity in the Caucasus
Annual Review of Anthropology
Vol. 37 (Volume publication date October 2008)
(doi:10.1146/annurev.anthro.35.081705.123248)
Linguistic Diversity in the Caucasus
Bernard Comrie
The Caucasus is characterized by a relatively high level of linguistic diversity, whether measured in terms of number of languages, number of language families, or structural properties. This is in stark contrast to low levels of linguistic diversity in neighboring areas (Europe, the Middle East), although the Caucasus does not reach such high levels of linguistic diversity as are found in New Guinea. There is even a variation between greater diversity in the North Caucasus and less diversity in the South Caucasus. Illustrative structural properties show not only idiosyncratic properties of individual languages and families but also features that have spread across the boundaries separating languages and families, sometimes with variation across languages with regard to finer points of detail, although few features characterize the Caucasus as a single linguistic area. Social factors have probably played at least as important a role as has geography in the development of linguistic diversity in the Caucasus.
Link
Vol. 37 (Volume publication date October 2008)
(doi:10.1146/annurev.anthro.35.081705.123248)
Linguistic Diversity in the Caucasus
Bernard Comrie
The Caucasus is characterized by a relatively high level of linguistic diversity, whether measured in terms of number of languages, number of language families, or structural properties. This is in stark contrast to low levels of linguistic diversity in neighboring areas (Europe, the Middle East), although the Caucasus does not reach such high levels of linguistic diversity as are found in New Guinea. There is even a variation between greater diversity in the North Caucasus and less diversity in the South Caucasus. Illustrative structural properties show not only idiosyncratic properties of individual languages and families but also features that have spread across the boundaries separating languages and families, sometimes with variation across languages with regard to finer points of detail, although few features characterize the Caucasus as a single linguistic area. Social factors have probably played at least as important a role as has geography in the development of linguistic diversity in the Caucasus.
Link
July 02, 2008
Waist-to-hip ratio of Miss Koreas
Aesthetic Plast Surg. 2008 Jun 28. [Epub ahead of print]
Anthropometric Analysis of Waist-to-Hip Ratio in Asian Women.
Hong YJ, Park HS, Lee ES, Suh YJ.
BACKGROUND: The universally accepted attractive female figure has a waist-to-hip ratio (WHR) of 0.7 or 0.68 (WHR of the Venus de Milo). Using WHR and other parameters, the authors attempted to investigate chronologic changes in perceptions of the attractive female figure in Korean society, differences between Asian and Western societies in this respect, and changes in attractiveness with respect to body mass index (BMI) and age in the general female Korean population. METHODS: The authors analyzed the anthropometric measurements of 227 Miss Korea winners between 1971 and 2007, 60 candidates of the 2007 Miss Korea contest, 36 candidates of the 2007 Miss France contest, and 1785 normal women in the general population. RESULTS: In the Miss Korea winners' group, the WHR tended toward 0.7. The WHR of the 2007 Miss Korea candidates was statistically smaller than the WHR of the 2007 Miss France candidates. The WHR of normal women was statistically larger than WHR of the 2000s Miss Korea winners. In all age groups of normal women, subjects with a low BMI were not significantly different from the 2000s Miss Koreas in terms of waist circumference, but they had a relatively larger hip circumference. Moreover, subjects with a normal BMI had waist circumferences that were similar to those of the 2000s Miss Koreas but relatively larger hip circumferences, and subjects with high BMI had larger waist and hip circumferences than the 2000s Miss Koreas. CONCLUSION: The perceived attractive female figure in Asia has moved toward the universally accepted ideal WHR. However, there were still some differences between Asian and Western societies in the concept of ideal body figure. Also, a significant difference in body contour was observed between normal women and the ideal figure. This is because hip volume decreases and waist volume increases with age, although waist and hip volumes increase with BMI.
Link
Anthropometric Analysis of Waist-to-Hip Ratio in Asian Women.
Hong YJ, Park HS, Lee ES, Suh YJ.
BACKGROUND: The universally accepted attractive female figure has a waist-to-hip ratio (WHR) of 0.7 or 0.68 (WHR of the Venus de Milo). Using WHR and other parameters, the authors attempted to investigate chronologic changes in perceptions of the attractive female figure in Korean society, differences between Asian and Western societies in this respect, and changes in attractiveness with respect to body mass index (BMI) and age in the general female Korean population. METHODS: The authors analyzed the anthropometric measurements of 227 Miss Korea winners between 1971 and 2007, 60 candidates of the 2007 Miss Korea contest, 36 candidates of the 2007 Miss France contest, and 1785 normal women in the general population. RESULTS: In the Miss Korea winners' group, the WHR tended toward 0.7. The WHR of the 2007 Miss Korea candidates was statistically smaller than the WHR of the 2007 Miss France candidates. The WHR of normal women was statistically larger than WHR of the 2000s Miss Korea winners. In all age groups of normal women, subjects with a low BMI were not significantly different from the 2000s Miss Koreas in terms of waist circumference, but they had a relatively larger hip circumference. Moreover, subjects with a normal BMI had waist circumferences that were similar to those of the 2000s Miss Koreas but relatively larger hip circumferences, and subjects with high BMI had larger waist and hip circumferences than the 2000s Miss Koreas. CONCLUSION: The perceived attractive female figure in Asia has moved toward the universally accepted ideal WHR. However, there were still some differences between Asian and Western societies in the concept of ideal body figure. Also, a significant difference in body contour was observed between normal women and the ideal figure. This is because hip volume decreases and waist volume increases with age, although waist and hip volumes increase with BMI.
Link
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