Another helpful idea would be for one of these foundations to establish a data bank. Notice what is missing in the NSF policy is any discussion of a data archive. Other areas of NSF and NIH have such archives and maintain policies of mandatory deposition of data. This is most prominent for genetics, with the GenBank archive and journal publication of most results conditional on mandatory submission of data to the archive. Thus, there is no logical impediment to the creation of such a resource by a federal agency. The fact that they chose not to implement such a policy, I find significant.
April 17, 2005
The sharing of anthropological material and datasets
John Hawks has a very informative new post about the new NSF guidelines for the sharing of anthropological data. This paragraph really nails down the problem:
April 16, 2005
Genographic project video presentation
can be found here. Some extra information plus a Q&A session near the end.
It is interesting that all six people (whose results were revealed during the presentation) loved what they heard. The African discovered that he belonged to haplogroup B which was frequent in his hunter-gather people from Tanzania; the Mongolian discovered that he belonged to haplogroup C3 and was a descendant of Genghis Khan to boot; the Native American discovered that he belonged to haplogroup Q, which is the main Native American lineage and he was descended from Siberian mammoth hunters of the Ice Age. The three Europeans got something interesting to think about too: one was a Western European R1b concordant with his English ancestry (the same as Dr. Wells), the second one was descended from the important Inventors of Agriculture, and the third one's ancestor was a Kurgan horse-rider and alleged Proto-Indo-European.
It would be much more realistic to show some unexpected results, e.g., a Native American who was descended from a European, or a European who was descended from an African. What goes through the mind of a black man when he is told that his forefather was white? What happens to a would-be-jihadi when he is told that he is carrying Crusader DNA? What are the consequences when a people who think that they are descended from Alexander the Great are told that they are actually not? (or these people, for that matter) Perhaps, they will console themselves with some educational programs.
Will the Genographic project concentrate only on "success" stories, such as the alleged descent of the modern Lebanese from the Phoenicians, or the Lemba from ancient Israelites? Or, will we learn some more sobering facts too, say the potential discovery of a few erectus sequences hidden in the 100,000 soon-to-be-gathered samples?
It is interesting that all six people (whose results were revealed during the presentation) loved what they heard. The African discovered that he belonged to haplogroup B which was frequent in his hunter-gather people from Tanzania; the Mongolian discovered that he belonged to haplogroup C3 and was a descendant of Genghis Khan to boot; the Native American discovered that he belonged to haplogroup Q, which is the main Native American lineage and he was descended from Siberian mammoth hunters of the Ice Age. The three Europeans got something interesting to think about too: one was a Western European R1b concordant with his English ancestry (the same as Dr. Wells), the second one was descended from the important Inventors of Agriculture, and the third one's ancestor was a Kurgan horse-rider and alleged Proto-Indo-European.
It would be much more realistic to show some unexpected results, e.g., a Native American who was descended from a European, or a European who was descended from an African. What goes through the mind of a black man when he is told that his forefather was white? What happens to a would-be-jihadi when he is told that he is carrying Crusader DNA? What are the consequences when a people who think that they are descended from Alexander the Great are told that they are actually not? (or these people, for that matter) Perhaps, they will console themselves with some educational programs.
Will the Genographic project concentrate only on "success" stories, such as the alleged descent of the modern Lebanese from the Phoenicians, or the Lemba from ancient Israelites? Or, will we learn some more sobering facts too, say the potential discovery of a few erectus sequences hidden in the 100,000 soon-to-be-gathered samples?
Spencer Wells responds
Spencer Wells responds to some questions posed in the GENEALOGY-DNA list:
Here are some answers to a few questions on the listserv:See also the FTDNA Genographic FAQ.
* We will be testing ancient remains. Alan Cooper, one of the pioneers in this field and arguably the best of the best technically speaking, will be heading up this center. As of May, Alan will be based at the University of Adelaide in Australia (he was formerly at Oxford). We will be attempting to obtain ancient genetic material, both mtDNA and nuclear, from human and non-human (esp. domesticated animal) remains.
* The public testing will be for the standard 12 FTDNA STRs (in the case of men) and HVR-1 sequences (in the case of women), with predicted haplogroups based on these results. New algorithms have been developed by the IBM team to allow us to predict haplogroups with great precision, but in those cases where we are uncertain, additional SNP typing will be conducted to confirm.
* The raw data (STR repeat numbers, differences from CRS, SNPs) will be reported.
* There will be an option to enter ethnographic data when you choose to upload your results to the database. No names (we need to keep it anonymous), but parents'/grandparents' place of birth, ultimate country of origin, specific region/village of origin, language(s) spoken, etc.
* All genealogical work will be conducted through FTDNA's existing procedures, and will require Genographic participants to opt into this aspect. If/when you opt in, you will be shifted over to FTDNA while still maintaining your Genographic record
Hope this helps,
Spencer Wells
April 15, 2005
Ethiopian related posts
Some of my older posts on Ethiopians:
Ethiopian and Yemeni mtDNA
Origin of Ethiopian genetic heterogeneity
COL1A2 Study on Amhara and Oromo Ethiopians
Apolipoprotein Study of Ethiopians
Geography predicts neutral genetic diversity
Oromo and Amhara of Ethiopia
Pleistocene Homo Sapiens from Ethiopia
K2 represents another migration into Africa
Ethiopian and Yemeni mtDNA
Origin of Ethiopian genetic heterogeneity
COL1A2 Study on Amhara and Oromo Ethiopians
Apolipoprotein Study of Ethiopians
Geography predicts neutral genetic diversity
Oromo and Amhara of Ethiopia
Pleistocene Homo Sapiens from Ethiopia
K2 represents another migration into Africa
Uralic related posts
Some of my posts related to Uralic speakers:
The Uralic suicide phenomenon
Uralic haplotypes in Europe
mtDNA subhaplogroup U4 and Uralic origins
Dissection of Y-chromosome haplogroups N and Q
The Finno-Ugrian Suicide Hypothesis
The Proto-Uralic racial type
Craniometric Analysis of Uralic populations
Y Chromosomes in Altai-Sayan
Presence of Tat-C in Ancient Mongolia
New Information on haplogroup N
Y chromosomes in Volga-Ural region
The Uralic suicide phenomenon
Uralic haplotypes in Europe
mtDNA subhaplogroup U4 and Uralic origins
Dissection of Y-chromosome haplogroups N and Q
The Finno-Ugrian Suicide Hypothesis
The Proto-Uralic racial type
Craniometric Analysis of Uralic populations
Y Chromosomes in Altai-Sayan
Presence of Tat-C in Ancient Mongolia
New Information on haplogroup N
Y chromosomes in Volga-Ural region
Jewish related posts
Some of my posts on Jewish genetics:
Haplogroup E3b and Ancient Jews
Jews and Khazars
Samaritan mtDNA and Y chromosomes
mtDNA in Balearic archipelago
Y Chromosomes in Jews/Palestinians/Lebanese
Non-Caucasoid mtDNA admixture in Ashkenazi Jews
Non-Caucasoid Y chromosomes in Ashkenazi Jews
Non-Caucasoid Y chromosomes in Ashkenazi Levites
Haplogroup E3b and Ancient Jews
Jews and Khazars
Samaritan mtDNA and Y chromosomes
mtDNA in Balearic archipelago
Y Chromosomes in Jews/Palestinians/Lebanese
Non-Caucasoid mtDNA admixture in Ashkenazi Jews
Non-Caucasoid Y chromosomes in Ashkenazi Jews
Non-Caucasoid Y chromosomes in Ashkenazi Levites
Howells related posts
Some of my older posts with various analyses on Howells' craniometric data.
Racial Classification: How Easy?
"Discordant" Clines
Who is the most diverse of them all?
Move + New Article
Caucasoid vs. Negroid phenotypic variation
Racial Classification: How Easy?
"Discordant" Clines
Who is the most diverse of them all?
Move + New Article
Caucasoid vs. Negroid phenotypic variation
Update on the Geographic Project public participation kit
According to FTDNA which will be performing the actual testing, males can expect a standard 12 Y-STR test, and females a standard HVR1 test, which are essentially the same tests currently performed by FTDNA for almost the exact same price. I would therefore not encourage people to take this test, unless they were planning to take such a test anyway. In any case, the Genographic Project page suggests that it will inform users about their "deep ancestry", something which cannot be done on the basis of 12 Y-STRs, as the haplotype distributions of many haplogroups overlap.
mtDNA haplogroup K and lower risk of Parkinson's in Italians
See also this other recent study on the same topic.
Eur J Hum Genet. 2005 Apr 13; [Epub ahead of print]
Mitochondrial DNA haplogroup K is associated with a lower risk of Parkinson's disease in Italians.
Ghezzi D et al.
It has been proposed that European mitochondrial DNA (mtDNA) haplogroups J and K, and their shared 10398G single-nucleotide polymorphism (SNP) in the ND3 gene, are protective from Parkinson's disease (PD). We evaluated the distribution of the different mtDNA haplogroups in a large cohort of 620 Italian patients with adult-onset (>50, <65>50year old males. In spite of the common 10398G SNP, haplogroups J and K belong to widely diverging mitochondrial clades, a consideration that may explain the different results obtained for the two haplogroups in our cohorts. Our study suggests that haplogroup K might confer a lower risk for PD in Italians, corroborating the idea that the mitochondrial oxidative phosphorylation pathway is involved in the susceptibility to idiopathic PD.
Link
Eur J Hum Genet. 2005 Apr 13; [Epub ahead of print]
Mitochondrial DNA haplogroup K is associated with a lower risk of Parkinson's disease in Italians.
Ghezzi D et al.
It has been proposed that European mitochondrial DNA (mtDNA) haplogroups J and K, and their shared 10398G single-nucleotide polymorphism (SNP) in the ND3 gene, are protective from Parkinson's disease (PD). We evaluated the distribution of the different mtDNA haplogroups in a large cohort of 620 Italian patients with adult-onset (>50, <65>50year old males. In spite of the common 10398G SNP, haplogroups J and K belong to widely diverging mitochondrial clades, a consideration that may explain the different results obtained for the two haplogroups in our cohorts. Our study suggests that haplogroup K might confer a lower risk for PD in Italians, corroborating the idea that the mitochondrial oxidative phosphorylation pathway is involved in the susceptibility to idiopathic PD.
Link
April 13, 2005
The Genographic Project
The Genographic Project is a new initiative by National Geographic and IBM, headed by Dr. Spencer Wells, in which ordinary people can participate, for about $100. For this price you will learn your mtDNA and Y-chromosomal "deep ancestry", and it seems like a really good bargain for anyone interested on the subject, in addition to being part of a real research project!
Until now, the only way to obtain this information was through one of several DNA companies, and at a much higher price. It is not yet clear what information you will get from your sample, so anyone who has already learned their place in the mtDNA and Y-chromosomal phylogeny (::weep:: me) should probably wait before they join in.
Also, of interest in the Genographic Project site, the interactive Atlas of the Human Journey.
UPDATE
Actually, it appears that males only get the Y-chromosomal test and females get the mtDNA test.
Until now, the only way to obtain this information was through one of several DNA companies, and at a much higher price. It is not yet clear what information you will get from your sample, so anyone who has already learned their place in the mtDNA and Y-chromosomal phylogeny (::weep:: me) should probably wait before they join in.
Also, of interest in the Genographic Project site, the interactive Atlas of the Human Journey.
UPDATE
Actually, it appears that males only get the Y-chromosomal test and females get the mtDNA test.
How to participate
Samples will be analyzed for genetic "markers" found in mitochondrial DNA and on the Y chromosome. We will be performing two tests for the public participants:
Males: Y-DNA test. This test allows you to identify your deep ancestral geographic origins on your direct paternal line.
Females: Mitochondrial DNA (mtDNA). This tests the mtDNA of females to identify the ancestral migratory origins of your direct maternal line.
Genes to help tell 'story of everybody'
Indigenous people around the world will be asked to supply a cheek swab to help geneticists answer the question of how humanity spread from Africa.
The National Geographic Society and IBM hope to sample 100,000 people or more and look for ancient clues buried in living DNA to calculate who came from where and when.
For $US100, anyone who wants to can supply his or her own cheek swab for a personalised analysis and perhaps to contribute to the research.
Geneticist and anthropologist Spencer Wells said: "We all came out of Africa but how did we get to where we are today? What we are aiming for is the story of everybody."
Experts in related fields such as population genetics, archaeology, evolution science, linguistics and palaeontology will help in the five-year project.
Fossils provide some clues about where people settled as they evolved and moved from Africa to colonise every continent except Antarctica.
But mysteries remain, for example, about how people first got to Australia 50,000 to 60,000 years ago, or when and from where the first humans arrived in the Americas.
All continents
Linguistics and DNA provide many clues but the so-called Genographic Project will aim to systematically look at all peoples on all continents.
Teams in China, Russia, India, Lebanon, Brazil, South Africa, Paris, Britain and Australia have signed on to help.
Mr Wells says some groups may be hostile to the effort. "There has been a history of exploitation of indigenous groups around the world," he said.
But, he added, experts on dealing with various groups will help sell the idea. "It's a question of explaining the science," he said.
Geneticists will look at little changes in DNA code that have been used by experts to trace human history.
Mitochondrial DNA, handed down virtually unchanged from mothers to their children, is one source that was used to calculate the so-called ancestral Eve, who would have lived in Africa about 180,000 years ago.
Men have their own version, found in the Y chromosome, which is inherited with very little change from father to son.
Tiny mistakes in the code that occur with each generation can be used as a kind of genetic clock to track backward.
People who buy the mail-in swab kit are unlikely to add to the indigenous people's database but can find out something about their own ancient ancestry and perhaps add to the effort, Mr Wells said.
Reuters
The National Geographic Society and IBM hope to sample 100,000 people or more and look for ancient clues buried in living DNA to calculate who came from where and when.
For $US100, anyone who wants to can supply his or her own cheek swab for a personalised analysis and perhaps to contribute to the research.
Geneticist and anthropologist Spencer Wells said: "We all came out of Africa but how did we get to where we are today? What we are aiming for is the story of everybody."
Experts in related fields such as population genetics, archaeology, evolution science, linguistics and palaeontology will help in the five-year project.
Fossils provide some clues about where people settled as they evolved and moved from Africa to colonise every continent except Antarctica.
But mysteries remain, for example, about how people first got to Australia 50,000 to 60,000 years ago, or when and from where the first humans arrived in the Americas.
All continents
Linguistics and DNA provide many clues but the so-called Genographic Project will aim to systematically look at all peoples on all continents.
Teams in China, Russia, India, Lebanon, Brazil, South Africa, Paris, Britain and Australia have signed on to help.
Mr Wells says some groups may be hostile to the effort. "There has been a history of exploitation of indigenous groups around the world," he said.
But, he added, experts on dealing with various groups will help sell the idea. "It's a question of explaining the science," he said.
Geneticists will look at little changes in DNA code that have been used by experts to trace human history.
Mitochondrial DNA, handed down virtually unchanged from mothers to their children, is one source that was used to calculate the so-called ancestral Eve, who would have lived in Africa about 180,000 years ago.
Men have their own version, found in the Y chromosome, which is inherited with very little change from father to son.
Tiny mistakes in the code that occur with each generation can be used as a kind of genetic clock to track backward.
People who buy the mail-in swab kit are unlikely to add to the indigenous people's database but can find out something about their own ancient ancestry and perhaps add to the effort, Mr Wells said.
Reuters
Pathological Flores
John Hawks posts about the pathological nature of the Flores specimens which made the news recently as a new species, Homo floresiensis.
SNP associated with craniofacial form
Genomics. 2005 May;85(5):563-73.
Linkage disequilibrium analysis identifies an FGFR1 haplotype-tag SNP associated with normal variation in craniofacial shape.
Coussens AK et al.
Mutations in FGFR1 and TWIST1 have been reported to affect the timing of calvarial suture fusion resulting in craniosynostosis and facial abnormalities. We screened nonpathologic populations for genetic polymorphisms that may associate with normal craniofacial variation. We identified 17 single-nucleotide polymorphisms (SNPs) in FGFR1, 6 of which were novel (g.8591855G-->A, g.8593685G-->A, g.8602303C-->T, g.8602475A-->G (p.Ile293Val), g.8605849C-->T, g.8607868G-->A). No SNPs were found in TWIST1. FGFR1 SNP haplotypes were reconstructed for Caucasian, Asian, Australian Aboriginal, and African American populations. All populations shared two linkage disequilibrium blocks, with one haplotype-tag SNP (htSNP) tagging each block. The htSNP g.8592931G-->C was found to have a significant negative correlation with the cephalic index for all populations (R = -0.187, p = 0.036), with larger correlations in Asians and females. This finding is a starting point in the identification of a set of SNPs that can be genotyped to determine both normal and disease craniofacial phenotypes.
Link
Linkage disequilibrium analysis identifies an FGFR1 haplotype-tag SNP associated with normal variation in craniofacial shape.
Coussens AK et al.
Mutations in FGFR1 and TWIST1 have been reported to affect the timing of calvarial suture fusion resulting in craniosynostosis and facial abnormalities. We screened nonpathologic populations for genetic polymorphisms that may associate with normal craniofacial variation. We identified 17 single-nucleotide polymorphisms (SNPs) in FGFR1, 6 of which were novel (g.8591855G-->A, g.8593685G-->A, g.8602303C-->T, g.8602475A-->G (p.Ile293Val), g.8605849C-->T, g.8607868G-->A). No SNPs were found in TWIST1. FGFR1 SNP haplotypes were reconstructed for Caucasian, Asian, Australian Aboriginal, and African American populations. All populations shared two linkage disequilibrium blocks, with one haplotype-tag SNP (htSNP) tagging each block. The htSNP g.8592931G-->C was found to have a significant negative correlation with the cephalic index for all populations (R = -0.187, p = 0.036), with larger correlations in Asians and females. This finding is a starting point in the identification of a set of SNPs that can be genotyped to determine both normal and disease craniofacial phenotypes.
Link
April 11, 2005
mtDNA haplogroups P and Q in the Southwest Pacific
Mol Biol Evol. 2005 Apr 6; [Epub ahead of print]
Expanding Southwest Pacific mitochondrial haplogroups P and Q.
Friedlaender J et al.
Modern humans have occupied New Guinea and the nearby Bismarck and Solomon archipelagos of Island Melanesia for at least 40,000 years. Previous mitochondrial DNA (mtDNA) studies indicated that two common lineages in this region, haplogroups P and Q, were particularly diverse, with the coalescence for P considered significantly older than that for Q. In this study, we expand the definition of haplogroup Q so that it includes three major branches, each separated by multiple mutational distinctions (Q1, equivalent to the earlier definition of Q, plus Q2 and Q3). We report three whole mtDNA genomes that establish Q2 as a major Q branch. In addition, we describe 314 control region sequences that belong to the expanded haplogroups P and Q from our Southwest Pacific collection. The coalescence dates for the largest P and Q branches (P1 and Q1) are similar to each other ( approximately 50,000 years old), and considerably older than prior estimates. Newly identified Q2, which was found in Island Melanesian samples just to the east, is somewhat younger, by more than 10,000 years. Our coalescence estimates should be more reliable than prior ones because they were based on significantly larger samples, as well as complete mtDNA coding region sequencing. Our estimates are roughly in accord with current suggested dates for the first settlement of New Guinea/Sahul. The phylogeography of P and Q indicates almost total (female) isolation of ancient New Guinea/Island Melanesia from Australia that may have existed from the time of first settlement. While Q subsequently diversified extensively in New Guinea/Island Melanesia, it has not been found in Australia. The only shared mtDNA haplogroup between Australia and New Guinea identified to date remains one minor branch of P.
Link (pdf)
Expanding Southwest Pacific mitochondrial haplogroups P and Q.
Friedlaender J et al.
Modern humans have occupied New Guinea and the nearby Bismarck and Solomon archipelagos of Island Melanesia for at least 40,000 years. Previous mitochondrial DNA (mtDNA) studies indicated that two common lineages in this region, haplogroups P and Q, were particularly diverse, with the coalescence for P considered significantly older than that for Q. In this study, we expand the definition of haplogroup Q so that it includes three major branches, each separated by multiple mutational distinctions (Q1, equivalent to the earlier definition of Q, plus Q2 and Q3). We report three whole mtDNA genomes that establish Q2 as a major Q branch. In addition, we describe 314 control region sequences that belong to the expanded haplogroups P and Q from our Southwest Pacific collection. The coalescence dates for the largest P and Q branches (P1 and Q1) are similar to each other ( approximately 50,000 years old), and considerably older than prior estimates. Newly identified Q2, which was found in Island Melanesian samples just to the east, is somewhat younger, by more than 10,000 years. Our coalescence estimates should be more reliable than prior ones because they were based on significantly larger samples, as well as complete mtDNA coding region sequencing. Our estimates are roughly in accord with current suggested dates for the first settlement of New Guinea/Sahul. The phylogeography of P and Q indicates almost total (female) isolation of ancient New Guinea/Island Melanesia from Australia that may have existed from the time of first settlement. While Q subsequently diversified extensively in New Guinea/Island Melanesia, it has not been found in Australia. The only shared mtDNA haplogroup between Australia and New Guinea identified to date remains one minor branch of P.
Link (pdf)
Family-based Viking settlement of Shetland and Orkney
Heredity. 2005 Apr 6; [Epub ahead of print]
Genetic evidence for a family-based Scandinavian settlement of Shetland and Orkney during the Viking periods.
Goodacre S et al.
The Viking age witnessed the expansion of Scandinavian invaders across much of northwestern Europe. While Scandinavian settlements had an enduring cultural impact on North Atlantic populations, the nature and extent of their genetic legacy in places such as Shetland and Orkney is not clear. In order to explore this question further, we have made an extensive survey of both Y-chromosomal and mitochondrial DNA (mtDNA) variation in the North Atlantic region. Our findings indicate an overall Scandinavian ancestry of approximately 44% for Shetland and approximately 30% for Orkney, with approximately equal contributions from Scandinavian male and female subjects in both cases. This contrasts with the situation for the Western Isles, where the overall Scandinavian ancestry is less ( approximately 15%) and where there is a disproportionately high contribution from Scandinavian males. In line with previous studies, we find that Iceland exhibits both the greatest overall amount of Scandinavian ancestry (55%) and the greatest discrepancy between Scandinavian male and female components. Our results suggest that while areas close to Scandinavia, such as Orkney and Shetland, may have been settled primarily by Scandinavian family groups, lone Scandinavian males, who later established families with female subjects from the British Isles, may have been prominent in areas more distant from their homeland.
Link
Genetic evidence for a family-based Scandinavian settlement of Shetland and Orkney during the Viking periods.
Goodacre S et al.
The Viking age witnessed the expansion of Scandinavian invaders across much of northwestern Europe. While Scandinavian settlements had an enduring cultural impact on North Atlantic populations, the nature and extent of their genetic legacy in places such as Shetland and Orkney is not clear. In order to explore this question further, we have made an extensive survey of both Y-chromosomal and mitochondrial DNA (mtDNA) variation in the North Atlantic region. Our findings indicate an overall Scandinavian ancestry of approximately 44% for Shetland and approximately 30% for Orkney, with approximately equal contributions from Scandinavian male and female subjects in both cases. This contrasts with the situation for the Western Isles, where the overall Scandinavian ancestry is less ( approximately 15%) and where there is a disproportionately high contribution from Scandinavian males. In line with previous studies, we find that Iceland exhibits both the greatest overall amount of Scandinavian ancestry (55%) and the greatest discrepancy between Scandinavian male and female components. Our results suggest that while areas close to Scandinavia, such as Orkney and Shetland, may have been settled primarily by Scandinavian family groups, lone Scandinavian males, who later established families with female subjects from the British Isles, may have been prominent in areas more distant from their homeland.
Link
Uralic haplotypes in Europe
According to a recent study, two European haplotypes, defined over (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS393) are associated in all but one cases with the Uralic haplogroup N3. These two haplotypes are: 14-14-16-23-11-14-14 and 14-14-16-24-11-14-14.
Searching yhrd, we can obtain the distribution of these haplotypes in Europe. The first haplotype is confined to Scandinavian, Baltic and some Slavic populations, but it is also present in two German samples, Hungary, Turks from Bulgaria, and Szekely (Hungarian origin) from Romania.
The second haplotype has a similar distribution in Scandinavian, Baltic and some Slavic populations, and occurs also in the Pyrenees and in a German sample.
Searching yhrd, we can obtain the distribution of these haplotypes in Europe. The first haplotype is confined to Scandinavian, Baltic and some Slavic populations, but it is also present in two German samples, Hungary, Turks from Bulgaria, and Szekely (Hungarian origin) from Romania.
The second haplotype has a similar distribution in Scandinavian, Baltic and some Slavic populations, and occurs also in the Pyrenees and in a German sample.
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