An editorial in the NY Times is supposedly meant to show how genetic testing "disproves" the concept of race. A professor gave admixture tests to his students, and some of them were surprised to find out that they had admixture other than what they thought, e.g., blacks with 50% European admixture or a white with 14% African admixture.
Of course, these results actually prove the existence of race. It would be interesting to see how many of the students had anything other than the majority of their ancestry from their self-identified racial group; my guess, based on many autosomal studies to date, is that this percentage would be minimal.
It is of course expected that individuals will have variable proportions of admixture. After all, races are not species, and people from different races have interbed in the past and are continuing to interbreed in the present.
Genetic testing has in fact vindicated the findings of traditional physical anthropology. Physical anthropologists have long believed in continental races, although they may have differed as to the number of these races. Whenever individuals from around the world are clustered based on a large number of loci, invariably the major races emerge as clusters of genetic similarity. Whenever the self-reported race of individuals is compared with their "genotypic" cluster, invariably the two agree.
In regions of the world such as Central Asia, East Africa, or Latin America where traditional physical anthropology has believed that intermixture of races has created mixed-race populations, genetics has invariably shown the hybridity of these populations. Groups such as African Americans who were known to have acquired a large degree of Caucasoid admixture due to the social definition of a "black" in the United States, have been shown to be a group with around 20-25% European admixture.
So, the concept of 'race' has not been debunked by modern genetics. Rather, it has been victoriously confirmed.
Update:
John Hawks has much to say about this "debunking" of race, also addressing some problems of the DNA Print test.
July 31, 2005
July 28, 2005
Pre-Roman Iberian mtDNA
A new study has been published on the ancient DNA of Iberia. Here is a link to several other ancient DNA articles reported previously on this blog:
This appears to be in general agreement with the recent paper on the origin of African mtDNA in Iberia. The absence of mtDNA haplogroup V, common today in Iberia, is confirmed. Interestingly haplogroup H1, which is a subclade of the frequent haplogroup H was also found in the prehistoric sample. H1 is believed to have originated in Iberia.
Annals of Human Genetics (Early View)
The Genetics of the Pre-Roman Iberian Peninsula: A mtDNA Study of Ancient Iberians
M. L. Sampietro et al.
Summary
The Iberians developed a surprisingly sophisticated culture in the Mediterranean coast of the Iberian Peninsula from the 6th century BC until their conquest by the Romans in the 2nd century BC. They spoke and wrote a non-Indo-European language that still cannot be understood; their origins and relationships with other non-Indo-European peoples, like the Etruscans, are unclear, since their funerary practices were based on the cremation of bodies, and therefore anthropology has been unable to approach the study of this people. We have retrieved mitochondrial DNA (mtDNA) from a few of the scarce skeletal remains that have been preserved, some of them belonging to ritualistically executed individuals. The most stringent authentication criteria proposed for ancient DNA, such as independent replication, amino-acid analysis, quantitation of template molecules, multiple extractions and cloning of PCR products, have been followed to obtain reliable sequences from the mtDNA hypervariable region 1 (HVR1), as well as some haplogroup diagnostic SNPs. Phylogeographic analyses show that the haplogroup composition of the ancient Iberians was very similar to that found in modern Iberian Peninsula populations, suggesting a long-term genetic continuity since pre-Roman times. Nonetheless, there is less genetic diversity in the ancient Iberians than is found among modern populations, a fact that could reflect the small population size at the origin of the population sampled, and the heterogenic tribal structure of the Iberian society. Moreover, the Iberians were not especially closely related to the Etruscans, which points to considerable genetic heterogeneity in Pre-Roman Western Europe.
Link
The most frequent haplogroup is H (52.9%), followed by U (17.6%), J (11.8%), and pre-HV, K and T at the same frequency (5.9%). No samples were found to correspond to other haplogroups that are widely present in the Iberian peninsula populations (Table 7), such as V, X, I or W. The North African U6 subhaplogroup and Sub-Saharan African L lineages are also absent from the ancient Iberians analyzed so far; therefore, the possible entry of U6 lineages prior to the Muslim conquest in the 8th century A.D., as suggested by some authors, remains unproven. However, it is recognized that the sample size is at present too small to exclude any competing hypothesis about a possible North African genetic contribution to the genesis of the Iberian peninsula populations.
This appears to be in general agreement with the recent paper on the origin of African mtDNA in Iberia. The absence of mtDNA haplogroup V, common today in Iberia, is confirmed. Interestingly haplogroup H1, which is a subclade of the frequent haplogroup H was also found in the prehistoric sample. H1 is believed to have originated in Iberia.
Annals of Human Genetics (Early View)
The Genetics of the Pre-Roman Iberian Peninsula: A mtDNA Study of Ancient Iberians
M. L. Sampietro et al.
Summary
The Iberians developed a surprisingly sophisticated culture in the Mediterranean coast of the Iberian Peninsula from the 6th century BC until their conquest by the Romans in the 2nd century BC. They spoke and wrote a non-Indo-European language that still cannot be understood; their origins and relationships with other non-Indo-European peoples, like the Etruscans, are unclear, since their funerary practices were based on the cremation of bodies, and therefore anthropology has been unable to approach the study of this people. We have retrieved mitochondrial DNA (mtDNA) from a few of the scarce skeletal remains that have been preserved, some of them belonging to ritualistically executed individuals. The most stringent authentication criteria proposed for ancient DNA, such as independent replication, amino-acid analysis, quantitation of template molecules, multiple extractions and cloning of PCR products, have been followed to obtain reliable sequences from the mtDNA hypervariable region 1 (HVR1), as well as some haplogroup diagnostic SNPs. Phylogeographic analyses show that the haplogroup composition of the ancient Iberians was very similar to that found in modern Iberian Peninsula populations, suggesting a long-term genetic continuity since pre-Roman times. Nonetheless, there is less genetic diversity in the ancient Iberians than is found among modern populations, a fact that could reflect the small population size at the origin of the population sampled, and the heterogenic tribal structure of the Iberian society. Moreover, the Iberians were not especially closely related to the Etruscans, which points to considerable genetic heterogeneity in Pre-Roman Western Europe.
Link
Diversity of tribal Indians
Annals of Human Genetics (Early view)
Diversity and Divergence Among the Tribal Populations of India
W.S. Watkins et al.
Summary
Tribal populations of the Indian subcontinent have been of longstanding interest to anthropologists and human geneticists. To investigate the relationship of Indian tribes to Indian castes and continental populations, we analyzed 45 unlinked autosomal STR loci in 9 tribal groups, 8 castes, and 18 populations from Africa, Europe and East Asia. South Indian tribal populations demonstrate low within-population heterozygosity (range: 0.54 - 0.69), while tribal populations sampled further north and east have higher heterozygosity (range: 0.69 - 0.74). Genetic distance estimates show that tribal Indians are more closely related to caste Indians than to other major groups. Between-tribe differentiation is high and exceeds that for eight sub-Saharan African populations (4.8% vs. 3.7%). Telugu-speaking populations are less differentiated than non-Telugu speakers (FST: 0.029 vs. 0.079), but geographic distance was not predictive of genetic affinity between tribes. South Indian tribes show significant population structure, and individuals can be clustered statistically into groups that correspond with their tribal affiliation. These results are consistent with high levels of genetic drift and isolation in Indian tribal populations, particularly those of South India, and they imply that these populations may be potential candidates for linkage disequilibrium and association mapping.
Link
Diversity and Divergence Among the Tribal Populations of India
W.S. Watkins et al.
Summary
Tribal populations of the Indian subcontinent have been of longstanding interest to anthropologists and human geneticists. To investigate the relationship of Indian tribes to Indian castes and continental populations, we analyzed 45 unlinked autosomal STR loci in 9 tribal groups, 8 castes, and 18 populations from Africa, Europe and East Asia. South Indian tribal populations demonstrate low within-population heterozygosity (range: 0.54 - 0.69), while tribal populations sampled further north and east have higher heterozygosity (range: 0.69 - 0.74). Genetic distance estimates show that tribal Indians are more closely related to caste Indians than to other major groups. Between-tribe differentiation is high and exceeds that for eight sub-Saharan African populations (4.8% vs. 3.7%). Telugu-speaking populations are less differentiated than non-Telugu speakers (FST: 0.029 vs. 0.079), but geographic distance was not predictive of genetic affinity between tribes. South Indian tribes show significant population structure, and individuals can be clustered statistically into groups that correspond with their tribal affiliation. These results are consistent with high levels of genetic drift and isolation in Indian tribal populations, particularly those of South India, and they imply that these populations may be potential candidates for linkage disequilibrium and association mapping.
Link
Ancient European DNA mutation causes ataxia
American Journal of Human Genetics (Online Early)
Mitochondrial DNA Polymerase W748S Mutation: A Common Cause of Autosomal Recessive Ataxia with Ancient European Origin
Anna H. Hakonen et al.
Mutations in the catalytic subunit of the mitochondrial DNA polymerase γ (POLG) have been found to be an important cause of neurological disease. Recently, we and collaborators reported a new neurodegenerative disorder with autosomal recessive ataxia in four patients homozygous for two amino acid changes in POLG: W748S in cis with E1143G. Here, we studied the frequency of this allele and found it to be among the most common genetic causes of inherited ataxia in Finland. We identified 27 patients with mitochondrial recessive ataxia syndrome (MIRAS) from 15 Finnish families, with a carrier frequency in the general population of 1 : 125. Since the mutation pair W748S+E1143G has also been described in European patients, we examined the haplotypes of 13 non-Finnish, European patients with the W748S mutation. Haplotype analysis revealed that all the chromosomes carrying these two changes, in patients from Finland, Norway, the United Kingdom, and Belgium, originate from a common ancient founder. In Finland and Norway, long, common, northern haplotypes, outside the core haplotype, could be identified. Despite having identical homozygous mutations, the Finnish patients with this adult- or juvenile-onset disease had surprisingly heterogeneous phenotypes, albeit with a characteristic set of features, including ataxia, peripheral neuropathy, dysarthria, mild cognitive impairment, involuntary movements, psychiatric symptoms, and epileptic seizures. The high carrier frequency in Finland, the high number of patients in Norway, and the ancient European founder chromosome indicate that this newly identified ataxia should be considered in the first-line differential diagnosis of progressive ataxia syndromes.
Link
Mitochondrial DNA Polymerase W748S Mutation: A Common Cause of Autosomal Recessive Ataxia with Ancient European Origin
Anna H. Hakonen et al.
Mutations in the catalytic subunit of the mitochondrial DNA polymerase γ (POLG) have been found to be an important cause of neurological disease. Recently, we and collaborators reported a new neurodegenerative disorder with autosomal recessive ataxia in four patients homozygous for two amino acid changes in POLG: W748S in cis with E1143G. Here, we studied the frequency of this allele and found it to be among the most common genetic causes of inherited ataxia in Finland. We identified 27 patients with mitochondrial recessive ataxia syndrome (MIRAS) from 15 Finnish families, with a carrier frequency in the general population of 1 : 125. Since the mutation pair W748S+E1143G has also been described in European patients, we examined the haplotypes of 13 non-Finnish, European patients with the W748S mutation. Haplotype analysis revealed that all the chromosomes carrying these two changes, in patients from Finland, Norway, the United Kingdom, and Belgium, originate from a common ancient founder. In Finland and Norway, long, common, northern haplotypes, outside the core haplotype, could be identified. Despite having identical homozygous mutations, the Finnish patients with this adult- or juvenile-onset disease had surprisingly heterogeneous phenotypes, albeit with a characteristic set of features, including ataxia, peripheral neuropathy, dysarthria, mild cognitive impairment, involuntary movements, psychiatric symptoms, and epileptic seizures. The high carrier frequency in Finland, the high number of patients in Norway, and the ancient European founder chromosome indicate that this newly identified ataxia should be considered in the first-line differential diagnosis of progressive ataxia syndromes.
Link
July 22, 2005
Reliability of P25 marker
A new study deals with some problems of the P25 marker which defines haplogroup R1b. Normally, a SNP is considered rare enough that its presence unambiguously establishes descent from a common ancestor, and its absence establishes non-descent. However, it is possible for a back-mutation to occur. In this case, there is a relationship of descent, but it appears that there is no such relationship. The authors of the new study discovered at least two cases of this happening, and they recommend that a different marker, M269 be used in the future.
Forensic Sci Int. 2005 Jul 15; [Epub ahead of print]
The case of the unreliable SNP: Recurrent back-mutation of Y-chromosomal marker P25 through gene conversion.
Adams SM et al.
The Y-chromosomal binary marker P25 is a paralogous sequence variant, rather than a SNP: three copies of the P25 sequence lie within the giant palindromic repeats on Yq, and one copy has undergone a C to A transversion to define haplogroup R1b (designated C/C/A). Since gene conversion is known to be active in the palindromic repeats, we reasoned that P25 might be liable to back-mutation by gene conversion, yielding the ancestral state C/C/C. Through analysis of a set of binary markers in Y-chromosomes in two large samples from Great Britain and the Iberian Peninsula we show that such conversion events have occurred at least twice, and provide preliminary evidence that the reverse conversion event (yielding C/A/A) has also occurred. Because of its inherent instability, we suggest that P25 be used with caution in forensic studies, and perhaps replaced with the more reliable binary marker M269.
Link
Forensic Sci Int. 2005 Jul 15; [Epub ahead of print]
The case of the unreliable SNP: Recurrent back-mutation of Y-chromosomal marker P25 through gene conversion.
Adams SM et al.
The Y-chromosomal binary marker P25 is a paralogous sequence variant, rather than a SNP: three copies of the P25 sequence lie within the giant palindromic repeats on Yq, and one copy has undergone a C to A transversion to define haplogroup R1b (designated C/C/A). Since gene conversion is known to be active in the palindromic repeats, we reasoned that P25 might be liable to back-mutation by gene conversion, yielding the ancestral state C/C/C. Through analysis of a set of binary markers in Y-chromosomes in two large samples from Great Britain and the Iberian Peninsula we show that such conversion events have occurred at least twice, and provide preliminary evidence that the reverse conversion event (yielding C/A/A) has also occurred. Because of its inherent instability, we suggest that P25 be used with caution in forensic studies, and perhaps replaced with the more reliable binary marker M269.
Link
July 20, 2005
Structure of Mongoloid populations
A previous study discovered a near-perfect differentiation of Japanese from Chinese based on autosomal loci, indicating a strong substructure within the Mongoloid race. Now, researchers have performed clustering with 43 diallelic loci, confirming this structure, and discovering that Koreans and Japanese are more similar to each other than to the Chinese.
Human Genetics (Online first)
Use of autosomal loci for clustering individuals and populations of East Asian origin
Jong-Jin Kim et al.
Abstract We studied the genetic relationships among East Asian populations based on allele frequency differences to clarify the relative similarities of East Asian populations with a specific focus on the relationships among the Koreans, the Japanese, and the Chinese populations known to be genetically similar. The goal is to find markers appropriate for differentiating among the specific populations. In this study, no prior data existed for Koreans and the markers were selected to differentiate Chinese and Japanese. We typed, using AB TaqMan assays, single-nucleotide polymorphisms (SNPs) at 43 highly selected mostly independent diallelic sites, on 386 individuals from eight East Asian populations (Han Chinese from San Francisco, Han Chinese from Taiwan, Hakka, Koreans, Japanese, Ami, Atayal, and Cambodians) and one Siberian population (Yakut). We inferred group membership of individuals using a model-based clustering method implemented by the STRUCTURE program and population clustering by using computer programs DISTANCE, NEIGHBOR, LSSEARCH, and DRAWTREE, respectively, calculating genetic distances among populations, calculating neighbor-joining and least-squares trees, and drawing the calculated trees. On average 52% of individuals in the three Chinese groups were assigned into one cluster, and, respectively, 78 and 69% of Koreans and Japanese into a different cluster. Koreans differentiated from the Chinese groups and clustered with the Japanese in the principal component analysis (PCA) and in the best least-squares tree. The majority of Koreans were difficult to distinguish from the Japanese. This study shows that a relatively few highly selected markers can, within limits, differentiate between closely related populations.
Link
Human Genetics (Online first)
Use of autosomal loci for clustering individuals and populations of East Asian origin
Jong-Jin Kim et al.
Abstract We studied the genetic relationships among East Asian populations based on allele frequency differences to clarify the relative similarities of East Asian populations with a specific focus on the relationships among the Koreans, the Japanese, and the Chinese populations known to be genetically similar. The goal is to find markers appropriate for differentiating among the specific populations. In this study, no prior data existed for Koreans and the markers were selected to differentiate Chinese and Japanese. We typed, using AB TaqMan assays, single-nucleotide polymorphisms (SNPs) at 43 highly selected mostly independent diallelic sites, on 386 individuals from eight East Asian populations (Han Chinese from San Francisco, Han Chinese from Taiwan, Hakka, Koreans, Japanese, Ami, Atayal, and Cambodians) and one Siberian population (Yakut). We inferred group membership of individuals using a model-based clustering method implemented by the STRUCTURE program and population clustering by using computer programs DISTANCE, NEIGHBOR, LSSEARCH, and DRAWTREE, respectively, calculating genetic distances among populations, calculating neighbor-joining and least-squares trees, and drawing the calculated trees. On average 52% of individuals in the three Chinese groups were assigned into one cluster, and, respectively, 78 and 69% of Koreans and Japanese into a different cluster. Koreans differentiated from the Chinese groups and clustered with the Japanese in the principal component analysis (PCA) and in the best least-squares tree. The majority of Koreans were difficult to distinguish from the Japanese. This study shows that a relatively few highly selected markers can, within limits, differentiate between closely related populations.
Link
Y-haplogroups of some European population
A new paper in the Forensic Science International gives some interesting results
Forensic Science International (Article in Press, Corrected Proof)
A collaborative study of the EDNAP group regarding Y-chromosome binary polymorphism analysis
María Brion et al.
Abstract
A collaborative study was carried out by the European DNA Profiling Group (EDNAP) in order to evaluate the performance of Y-chromosome binary polymorphism analysis in different European laboratories. Four blood samples were sent to the laboratories, to be analysed for 11 Y-chromosome single nucleotide polymorphisms (SNPs): SRY-1532, M40, M35, M213, M9, 92R7, M17, P25, M18, M153 and M167. All the labs were also asked to submit a population study including these markers.
All participating laboratories reported the same results, indicating the reproducibility and robustness of Y-chromosome SNP typing.
A total of 535 samples from six different European populations were also analysed. In Galicia (NW Spain) and Belgium, the most frequent haplogroup was R1b*(xR1b1,R1b3df). Haplogroup F*(xK) is one of the most frequent in Austria and Denmark, while the lowest frequency appear in Belgium.
Haplogroup frequencies found in this collaborative study were compared with previously published European Y-chromosome haplogroup data.
Link
- Detection of 1 haplogroup A* and 2 BCD chromosomes in Germany (3.2% non-Caucasoid paternal admixture)
- Detection of 1 E*(xE3b) chromosome in Austria (0.8% non-Caucasoid paternal admixture)
- Detection of 1 R1a*(xR1a1) chromosome in Norway; usually R1a chromosomes also harbor the defining mutation for R1a1, but it appears that this is not always the case.
Forensic Science International (Article in Press, Corrected Proof)
A collaborative study of the EDNAP group regarding Y-chromosome binary polymorphism analysis
María Brion et al.
Abstract
A collaborative study was carried out by the European DNA Profiling Group (EDNAP) in order to evaluate the performance of Y-chromosome binary polymorphism analysis in different European laboratories. Four blood samples were sent to the laboratories, to be analysed for 11 Y-chromosome single nucleotide polymorphisms (SNPs): SRY-1532, M40, M35, M213, M9, 92R7, M17, P25, M18, M153 and M167. All the labs were also asked to submit a population study including these markers.
All participating laboratories reported the same results, indicating the reproducibility and robustness of Y-chromosome SNP typing.
A total of 535 samples from six different European populations were also analysed. In Galicia (NW Spain) and Belgium, the most frequent haplogroup was R1b*(xR1b1,R1b3df). Haplogroup F*(xK) is one of the most frequent in Austria and Denmark, while the lowest frequency appear in Belgium.
Haplogroup frequencies found in this collaborative study were compared with previously published European Y-chromosome haplogroup data.
Link
July 19, 2005
Neighborhood segregation in the United States
Blacks are currently the most segregated population in the United States, but they have also experienced the largest decline in segregation, leading to the projection that Latinos will become the most segregated population in the future.
Timberlake and Iceland examined all 323 of the nation's metropolitan areas, using Census data from 1970-2000. They searched for trends by exploring four key measures of residential inequality: dissimilarity, entropy, isolation and net difference. The researchers focused on four racial and ethnic groups: Caucasians, African Americans, Asians and Latinos. "African Americans continue to be the most segregated group from whites, but we also found that on average, African Americans have experienced greater declines in segregation," Timberlake says. "So, if that trend continues, Latinos will become the most segregated population by the middle-to-end of the next decade," he says.
Culture switching
An interesting press release about an experiment in Hong Kong:
In the journal American Psychologist (July 2000), they showed how it might work. Hong Kong students, who are raised in traditional Chinese families but also immersed in Western education and culture, were shown photos of icons that were culturally neutral, American or Chinese before seeking their opinion of what was happening in a photograph of a lone fish swimming ahead of others.
Students who had viewed Chinese icons were more likely to see the lone fish as being chased, while those exposed first to American icons saw the lone fish as a leader.
...
For the new study, Hong and Wong worked with 171 Hong Kong Chinese college students who were faced with the prisoner's dilemma: to cooperate or defect. In such a scenario, each player gains if each cooperates, but only the defector gains more if another player cooperates.
Students were paired with friends or strangers and shown either Chinese or American icons; control groups viewed neutral geometric drawings.
Friends participating after viewing Chinese primes not only were more likely to cooperate, they were much more confident that their partners also would choose cooperation strategies than those shown American icons before facing the problem.
When partners were strangers, those viewing the Chinese primes were only slightly more likely (63 percent to 59 percent) to cooperate with each other, the researchers found.
July 18, 2005
Decline in performance of medical examinees in the UK
EurekAlert has a press release on the decline of performance of candidates taking an examination for postgraduate medical study in the United Kingdom:
After a steady increase between 1985 and 1997, the overall performance of postgraduate students taking the Part 1 examination of the Membership of the Royal Colleges of Physicians of the United Kingdom, MRCP (UK), which is a part of higher specialist training, showed a decline from 1997 until 2001. Performance on specific exam questions that were repeated across the years was 14.1% lower in 2001 than in 1996.The causes of this decline are not obvious:
"The 'dog-leg' in performance [in] 1997 was not an artefact of changed Examination Regulations, mix of UK and overseas candidates, or time from qualification until taking the Examination", write the authors. "Study 2 confirmed that performance in 2001 was significantly worse than in 1996, that the poorer performance was found in graduates of UK medical schools, and that candidates passing the Examination in 2001 performed less well than those passing in 1996."Here are some data on the ethnic composition of medical doctors in the UK in recent decades.
DNA Heritage SNP testing
DNA Heritage is now offering SNP (haplogroup) testing services. The list of markers tested is quite impressive. This may be quite an attractive offer for people who want to obtain the highest possible phylogenetic resolution on their Y chromosome.
Also, check out this wonderful demonstration of the distribution of Y-haplogroups around the world. Very convenient as a reference.
Also, check out this wonderful demonstration of the distribution of Y-haplogroups around the world. Very convenient as a reference.
July 16, 2005
25,800-year old Australoid from Thailand
Excavations in the Moh Khiew Cave in Thailand have uncovered a 25,800-year old skeleton. An analysis of these remains has shown that it is unlike Mongoloids, but is similar to a Late Pleistocene Australoid sample from Australia. It is widely believed that southeast Asia was once inhabited by people similar to the Australo-Melanesians, but this early population has been overwhelmed by Mongoloids, especially during the Holocene and afterwards:
Homo (Article in Press)
A morphometric analysis of the Late Pleistocene Human Skeleton from the Moh Khiew Cave in Thailand
Hirofumi Matsumura and Surin Pookajorn
Abstract
Few Late Pleistocene human remains have been found in Southeast Asia and the morphological features of the people of that age are still largely unknown due to the virtual lack of human remains in the area. Recent excavations at the Moh Khiew Cave in Thailand resulted in the discovery of a Late Pleistocene human skeleton in a relatively good state of preservation. An AMS radiocarbon date on the charcoal sample gathered from the burial gave a result of 25,800±600 BP, implying that the inhabitants of Moh Khiew Cave resided in a part of Sundaland during the last glacial age. In debates on the population history of Southeast Asia, it has been repeatedly advocated that Southeast Asia was occupied by indigenous people akin to present-day Australo-Melanesians prior to an expansion of migrants from Northeast Asia into this area. Morphometric analyses were undertaken to test the validity of this hypothesis. In the present study, cranial and dental measurements recorded from the Moh Khiew remains are compared with those of early and modern samples from Southeast Asia and Australia. These comparisons demonstrate that the Moh Khiew specimen resembles the Late Pleistocene series from Coobool Creek, Australia in both cranial and dental measurements. These results suggest that the Moh Khiew skeleton, as well as other fossil remains from the Tabon, Niah and Gua Gunung sites, represents a member of the Sundaland population during the Late Pleistocene, who may share common ancestry with the present-day Australian Aborigines and Melanesians.
Link
The closest sample to the Moh Khiew specimen is the Late Pleistocene Coobool Creek from Australia, and the next closest is the modern Australian Aborigines. The Early to Middle Holocene Southeast Asian samples such as Liang Toge from Flores, Mai Da Dieu from Vietnam and Ban Kao from Thailand are distant from the Moh Khiew specimen.Interestingly, the sample's mtDNA is similar to that of the Semang:
Oota et al. (2001) analysed mtDNA recovered from the Moh Khiew specimen and found continuity with the Semang Negrito foragers living in the Malay Peninsula.
Homo (Article in Press)
A morphometric analysis of the Late Pleistocene Human Skeleton from the Moh Khiew Cave in Thailand
Hirofumi Matsumura and Surin Pookajorn
Abstract
Few Late Pleistocene human remains have been found in Southeast Asia and the morphological features of the people of that age are still largely unknown due to the virtual lack of human remains in the area. Recent excavations at the Moh Khiew Cave in Thailand resulted in the discovery of a Late Pleistocene human skeleton in a relatively good state of preservation. An AMS radiocarbon date on the charcoal sample gathered from the burial gave a result of 25,800±600 BP, implying that the inhabitants of Moh Khiew Cave resided in a part of Sundaland during the last glacial age. In debates on the population history of Southeast Asia, it has been repeatedly advocated that Southeast Asia was occupied by indigenous people akin to present-day Australo-Melanesians prior to an expansion of migrants from Northeast Asia into this area. Morphometric analyses were undertaken to test the validity of this hypothesis. In the present study, cranial and dental measurements recorded from the Moh Khiew remains are compared with those of early and modern samples from Southeast Asia and Australia. These comparisons demonstrate that the Moh Khiew specimen resembles the Late Pleistocene series from Coobool Creek, Australia in both cranial and dental measurements. These results suggest that the Moh Khiew skeleton, as well as other fossil remains from the Tabon, Niah and Gua Gunung sites, represents a member of the Sundaland population during the Late Pleistocene, who may share common ancestry with the present-day Australian Aborigines and Melanesians.
Link
10,300-year old Alaskan had mtDNA haplogroup D
A short piece of news from Nature reports on an analysis of mtDNA from a 10,300-year old Alaskan who belonged to mtDNA haplogroup D, a common Amerindian lineage. More importantly, this old Alaskan shares mutations with 47 living Native Americans who are scattered throughout the continent. This is an important find, which establishes clearly the antiquity of the ancestors of native Americans in the New World.
Molecular Clock reset
John Hawks has written about a new study which has found defects in the way that the molecular clock is used. Read his post about an explanation of the phenomenon which has led to the overestimation of divergence times.
What is important is that the new calibration leads to significantly lower estimates of events in human evolutionary history, bringing the mtDNA time depth of humanity much closer to the present, and closer to the time depth of the human Y chromosome. Perhaps though, the divergence times of human Y chromosomes may also turn out to be overestimated.
Molecular Biology and Evolution 2005 22(7):1561-1568
Time Dependency of Molecular Rate Estimates and Systematic Overestimation of Recent Divergence Times
Simon Y. W. Ho et al.
Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (<1–2 style="font-weight: bold;">modern humans and Neandertals (354 ka; 222–705 ka), Neandertals (108 ka; 70–156 ka), and modern humans (76 ka; 47–110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution. Link
What is important is that the new calibration leads to significantly lower estimates of events in human evolutionary history, bringing the mtDNA time depth of humanity much closer to the present, and closer to the time depth of the human Y chromosome. Perhaps though, the divergence times of human Y chromosomes may also turn out to be overestimated.
Molecular Biology and Evolution 2005 22(7):1561-1568
Time Dependency of Molecular Rate Estimates and Systematic Overestimation of Recent Divergence Times
Simon Y. W. Ho et al.
Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (<1–2 style="font-weight: bold;">modern humans and Neandertals (354 ka; 222–705 ka), Neandertals (108 ka; 70–156 ka), and modern humans (76 ka; 47–110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution. Link
July 15, 2005
Population structure in Interleukin-13 (IL13) locus
This study is interesting, because it provides yet more evidence of the closeness between East Africans and Eurasians:
Genes and Immunity (2005) 6, 53−65
Divergent patterns of linkage disequilibrium and haplotype structure across global populations at the interleukin-13 (IL13) locus
E Tarazona-Santos et al.
Abstract
Interleukin-13 (IL-13) is a cytokine involved in Th2 immune response, which plays a role in susceptibility to infection by extracellular parasites as well as complex diseases of the immune system such as asthma and allergies. To determine the pattern of genetic diversity at the IL13 gene, we sequenced 3950 bp encompassing the IL13 gene and its promoter in 264 chromosomes from individuals originating from East and West Africa, Europe, China and South America. Thirty-one single-nucleotide polymorphisms (SNPs) arranged in 88 haplotypes were indentified, including the nonsynonymous substitution Arg130Gln in exon 4, which differs in frequency across ethnic groups. We show that genetic diversity and linkage disequilibrium (LD) are not evenly distributed across the gene and that sites in the 5' and 3' regions of the gene show strong differentiation among continental groups. We observe a divergent pattern of haplotype variation and LD across geographic regions and we identify a set of htSNPs that will be useful for functional genetic association studies of complex disease. We use several statistical tests to distinguish the effects of natural selection and demographic history on patterns of genetic diversity at the IL13 locus.
Link
As observed in other studies,19 the East African populations are situated closer to the Eurasian populations in the MDS plot compared to West African populations, and the Chinese population has an intermediate position between Amerindian and European populations (Figure 3).
Genes and Immunity (2005) 6, 53−65
Divergent patterns of linkage disequilibrium and haplotype structure across global populations at the interleukin-13 (IL13) locus
E Tarazona-Santos et al.
Abstract
Interleukin-13 (IL-13) is a cytokine involved in Th2 immune response, which plays a role in susceptibility to infection by extracellular parasites as well as complex diseases of the immune system such as asthma and allergies. To determine the pattern of genetic diversity at the IL13 gene, we sequenced 3950 bp encompassing the IL13 gene and its promoter in 264 chromosomes from individuals originating from East and West Africa, Europe, China and South America. Thirty-one single-nucleotide polymorphisms (SNPs) arranged in 88 haplotypes were indentified, including the nonsynonymous substitution Arg130Gln in exon 4, which differs in frequency across ethnic groups. We show that genetic diversity and linkage disequilibrium (LD) are not evenly distributed across the gene and that sites in the 5' and 3' regions of the gene show strong differentiation among continental groups. We observe a divergent pattern of haplotype variation and LD across geographic regions and we identify a set of htSNPs that will be useful for functional genetic association studies of complex disease. We use several statistical tests to distinguish the effects of natural selection and demographic history on patterns of genetic diversity at the IL13 locus.
Link
The southern origin of O3
Haplogroup O3 is the main Y-chromosome lineage present in modern East Asian Mongoloids. A new study sampled extensively East Asian populations to determine the time depth and geographical origin of this ancient and widespread marker.
American Journal of Human Genetics (Onlin early)
Y-Chromosome Evidence of Southern Origin of the East Asian–Specific Haplogroup O3-M122
Hong Shi et al.
The prehistoric peopling of East Asia by modern humans remains controversial with respect to early population migrations. Here, we present a systematic sampling and genetic screening of an East Asian–specific Y-chromosome haplogroup (O3-M122) in 2,332 individuals from diverse East Asian populations. Our results indicate that the O3-M122 lineage is dominant in East Asian populations, with an average frequency of 44.3%. The microsatellite data show that the O3-M122 haplotypes in southern East Asia are more diverse than those in northern East Asia, suggesting a southern origin of the O3-M122 mutation. It was estimated that the early northward migration of the O3-M122 lineages in East Asia occurred ∼25,000–30,000 years ago, consistent with the fossil records of modern humans in East Asia.
Link
American Journal of Human Genetics (Onlin early)
Y-Chromosome Evidence of Southern Origin of the East Asian–Specific Haplogroup O3-M122
Hong Shi et al.
The prehistoric peopling of East Asia by modern humans remains controversial with respect to early population migrations. Here, we present a systematic sampling and genetic screening of an East Asian–specific Y-chromosome haplogroup (O3-M122) in 2,332 individuals from diverse East Asian populations. Our results indicate that the O3-M122 lineage is dominant in East Asian populations, with an average frequency of 44.3%. The microsatellite data show that the O3-M122 haplotypes in southern East Asia are more diverse than those in northern East Asia, suggesting a southern origin of the O3-M122 mutation. It was estimated that the early northward migration of the O3-M122 lineages in East Asia occurred ∼25,000–30,000 years ago, consistent with the fossil records of modern humans in East Asia.
Link
Subscribe to:
Posts (Atom)