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edao
04-08-13, 13:42
http://upload.wikimedia.org/wikipedia/commons/thumb/e/e2/Namibian_Bushmen_Girls.JPG/300px-Namibian_Bushmen_Girls.JPG
Various Y-chromosome studies showed that the San carry some of the most divergent (oldest) Y-chromosome haplogroups. These haplogroups are specific sub-groups of haplogroups A and B, the two earliest branches on the human Y-chromosome tree.

Mitochondrial DNA studies also showed evidence that the San carry high frequencies of the earliest haplogroup branches in the human mitochondrial DNA tree. The most divergent (oldest) mitochondrial haplogroup, L0d, has been identified at its highest frequencies in the southern African San groups.


In a study published in March 2011, Brenna Henn and colleagues found that the ǂKhomani Bushmen, as well as the Sandawe and Hadza peoples of Tanzania, were the most genetically diverse of any living humans studied. This high degree of genetic diversity hints at the origin of anatomically modern humans. source (http://en.wikipedia.org/wiki/South_african_bushmen)



"The Khoi-San peoples of southern Africa are descendants of the earliest diversification event in human history, a new study shows. This event occurred about 100 000 years ago, well before modern humans began migrating out of Africa.

The major divergences among different groups of people in Africa have important implications and consequences in terms of human evolutionary history, said Mattias Jakobsson of Uppsala University in Sweden.

The human population has been structured for a long time and it is possible that modern humans emerged from a non-homogeneous group," Jakobsson said in a University of the Witwatersrand news release." source (http://www.health24.com/Lifestyle/Environmental-health/News/Khoi-San-genetics-shed-light-on-evolution-20130210)

SCIENTISTS have completed the most comprehensive genetic study of the Khoe-San peoples, confirming that they are descendants of one of the earliest known splits among the branches of anatomically modern humans. source (http://www.bdlive.co.za/national/science/2012/09/21/study-sheds-light-on-khoe-san-genetics)

Maciamo
05-02-14, 15:45
A new study (http://www.pnas.org/content/early/2014/01/29/1313787111.full.pdf+html) identified a small percentage (1 to 5% in average) of West Eurasian ancestry in the Khoisans, peaking at 14% in the Nama people (http://en.wikipedia.org/wiki/Nama_people) of southern Africa.

According to the article (http://www.newscientist.com/article/dn24988-humanitys-forgotten-return-to-africa-revealed-in-dna.html) in the New Scientist, this West Eurasian admixture resembles sequences from southern Europeans, including Sardinians, Italians and people from the Basque region. The study mentions that it could be southern European or Levantine in origin. They estimate that the introgression of these Mediterranean genes occurred some time between 900 and 1,800 years ago - a surprisingly recent, yet undocumented event. This would date from the late Roman, Byzantine or Moorish period. There is no mention of admixture from North Africa or the Arabian peninsula though.

I find it odd that an international team of geneticists from such institutions as Harvard Medical School, MIT, Max Planck Institute for Evolutionary Anthropology and CNRS do not have the means to distinguish between Iberian, Basque, Sardinian, North or South Italian, Greco-Anatolian or Levantine admixture. This is usually easily feasible with amateur programmes such as the Dodecad or Eurogenes. How is it possible that geneticists at high-tech institutions like that lag so much behind ?

Angela
05-02-14, 21:49
A new study (http://www.pnas.org/content/early/2014/01/29/1313787111.full.pdf+html) identified a small percentage (1 to 5% in average) of West Eurasian ancestry in the Khoisans, peaking at 14% in the Nama people (http://en.wikipedia.org/wiki/Nama_people) of southern Africa.

According to the article (http://www.newscientist.com/article/dn24988-humanitys-forgotten-return-to-africa-revealed-in-dna.html) in the New Scientist, this West Eurasian admixture resembles sequences from southern Europeans, including Sardinians, Italians and people from the Basque region. The study mentions that it could be southern European or Levantine in origin. They estimate that the introgression of these Mediterranean genes occurred some time between 900 and 1,800 years ago - a surprisingly recent, yet undocumented event. This would date from the late Roman, Byzantine or Moorish period. There is no mention of admixture from North Africa or the Arabian peninsula though.

I find it odd that an international team of geneticists from such institutions as Harvard Medical School, MIT, Max Planck Institute for Evolutionary Anthropology and CNRS do not have the means to distinguish between Iberian, Basque, Sardinian, North or South Italian, Greco-Anatolian or Levantine admixture. This is usually easily feasible with amateur programmes such as the Dodecad or Eurogenes. How is it possible that geneticists at high-tech institutions like that lag so much behind ?

The admixture into the Khoi San which is dated to 900 to 1800 years ago was not a movement directly into them from a Mediterranean like population. Rather, these alleles were transmitted to them indirectly via East Africans.

The initial signal of West Eurasian admixture which they are picking up was into East African populations, and is dated from 2700 to 3300 years ago.


From the paper...
We reconstruct the allele frequencies of the putative west Eurasian population in eastern Africa and show that this
population is a good proxy for the west Eurasian ancestry in southern Africa. The most parsimonious explanation for these findings is that west Eurasian ancestry entered southern Africa indirectly through eastern Africa...and that west Eurasian ancestry entered eastern Africa on average 2,700 to 3,300 years ago.

So they are not talking about a back to Africa migration during the Roman era. This is a migration around 1000 B.C. which was large enough that some East African populations are almost 50% West Eurasian. This explains the 23andme results for East Africans that showed essentially the same thing.

As for the source, the extensive modelling can be found in the supplement. Depending on the African population that was being targeted, one or another of the southern European populations provided the best fit, along with the Druze, but the differences were small. From the paper...the f3 statistics in nearly all eastern African populations involve a southern European or Levantine population as one reference.

As I mentioned above, the authors also reconstructed the allele frequencies of the west Eurasian population involved in the admixture in eastern Africa, and discovered that this hypothetical population is a better proxy for the West Eurasian admixture than any modern southern European or Levantine population.

From that, I think we can extrapolate that the population responsible for the west Eurasian admixture in Africa no longer exists. After taking into account, as the authors do, the archaeological evidence for migration from Arabia and the southern Levant into Africa, and the linguistic evidence as well, it would appear, as the authors posit, that the source of the migration was in those areas, but that the population that then existed in those areas is significantly different from the current, modern populations.

The prior work from the Reich lab has already shown that modern Near Eastern populations are not a good proxy for the EEF. Now, we find that they are not a good proxy for the source of the west Eurasian admixture in Africa. That suggests to me that the modern Levant and even Arabia have significantly changed even from 1000 B.C. to the present. Although some input from south Asia and perhaps ANE input as well may be contributing factors, it seems to me that the biggest change may have been the intrusion of SSA lineages in more modern times, although that is speculation at this point.

Maciamo
06-02-14, 10:24
The admixture into the Khoi San which is dated to 900 to 1800 years ago was not a movement directly into them from a Mediterranean like population. Rather, these alleles were transmitted to them indirectly via East Africans.

The initial signal of West Eurasian admixture which they are picking up was into East African populations, and is dated from 2700 to 3300 years ago.


From the paper...
We reconstruct the allele frequencies of the putative west Eurasian population in eastern Africa and show that this
population is a good proxy for the west Eurasian ancestry in southern Africa. The most parsimonious explanation for these findings is that west Eurasian ancestry entered southern Africa indirectly through eastern Africa...and that west Eurasian ancestry entered eastern Africa on average 2,700 to 3,300 years ago.

So they are not talking about a back to Africa migration during the Roman era. This is a migration around 1000 B.C. which was large enough that some East African populations are almost 50% West Eurasian. This explains the 23andme results for East Africans that showed essentially the same thing.

As for the source, the extensive modelling can be found in the supplement. Depending on the African population that was being targeted, one or another of the southern European populations provided the best fit, along with the Druze, but the differences were small. From the paper...the f3 statistics in nearly all eastern African populations involve a southern European or Levantine population as one reference.

As I mentioned above, the authors also reconstructed the allele frequencies of the west Eurasian population involved in the admixture in eastern Africa, and discovered that this hypothetical population is a better proxy for the West Eurasian admixture than any modern southern European or Levantine population.

From that, I think we can extrapolate that the population responsible for the west Eurasian admixture in Africa no longer exists. After taking into account, as the authors do, the archaeological evidence for migration from Arabia and the southern Levant into Africa, and the linguistic evidence as well, it would appear, as the authors posit, that the source of the migration was in those areas, but that the population that then existed in those areas is significantly different from the current, modern populations.

The prior work from the Reich lab has already shown that modern Near Eastern populations are not a good proxy for the EEF. Now, we find that they are not a good proxy for the source of the west Eurasian admixture in Africa. That suggests to me that the modern Levant and even Arabia have significantly changed even from 1000 B.C. to the present. Although some input from south Asia and perhaps ANE input as well may be contributing factors, it seems to me that the biggest change may have been the intrusion of SSA lineages in more modern times, although that is speculation at this point.

I admit that I didn't have time to read the paper. But if the admixture is southern European, it could not have been inherited from East Africans, since the latter lack European admixture. East Africans have essentially Near Eastern and Arabic admixture, represented by Y-DNA haplogroups T and J1. The Dodecad also shows that the Masaai (MKK) have 3.8% of Southwest Asian admixture, 0.4% of South Asian and 0.1% of West Asian, which corresponds to an introgression from the southern Arabian peninsula. The Ethiopians, who are known to possess only J1 and T among non-African male lineages, have 23.5% of Southwest Asian, 2% of Mediterranean and 0.4% of West Asian. Both the Masaai and Ethiopians completely lack West European and East European admixtures.

As for the Khoisans, the Dodecad shows 5% of East African, 0.4% of Southwest Asian, 0.2% of Mediterranean and 0.1% of South Asian. We have known for many years (since Wood et al. 2005 (http://www.nature.com/ejhg/journal/v13/n7/full/5201408a.html)) that the Khoisans possess 6.5% of E1b1b1, 1% of J1 and 2% of R1b-M269 lineages. Their West Eurasian admixture is therefore of two distinct origins. One is Arabic (J1) via the East Africans (E1b1b1), but there is also clearly a West European source that is completely unrelated. It's too bad they didn't test for the deep subclade of Khoisan R1b, but the most likely explanation is that it dates from the European colonial period. The HapMap Khoisan samples were apparently not from the same tribes or region as those tested by Wood et al. as they do not show any sign of he European admixture implied by the presence of R1b-M269.

The HapMap samples only include the foraging San tribes, not the pastoralist Khoi. I would expact a higher East African and Arabic admixture among the pastoralist tribes.

I don't see the point of this new paper by Pickrell et al. if they are not going to look at the origin of their very vague "West Eurasian admixture" into detail. That's really sloppy work.

Angela
06-02-14, 22:36
I think we will have to agree to disagree on the merits of the paper.

The authors don't place the origin of the west Eurasian gene flow in Europe. They place it, as you suggest, in the Levant or Arabia, so the people would have indeed carried Near Eastern haplogroups.

What they are saying, it seems to me, is that autosomally, this migrating Levantine or Arabian population was more similar to southern European populations and the Druze than it is to the current populations of the Levant and Arabia...more similar, but not identical, of course.

One of the ways they arrived at this conclusion was through the construction of a 'virtual' population based on the alleles studied...sort of like the zombie individuals created by Dienekes. This 'virtual' population is the best match to the west Eurasian alleles present in Africans. The problem is that this population no longer exists.

From his posts on other blogs, Joe Pickrell is currently investigating whether the Bedouins would be a good fit for this population if their genomes were stripped of genes which flowed into these areas in periods subsequent to 1000 BC.

Greying Wanderer
08-02-14, 01:06
I think the original intrusion came from Yemen/Saba as a kind of colonial/conquistador type event which eventually spawned Axum. The southern intrusion coming from this derived population.

Over time the daughter colony became stronger than Saba and conquered them displacing the original population.

http://en.wikipedia.org/wiki/Sabaeans

http://en.wikipedia.org/wiki/Kingdom_of_Aksum

Greying Wanderer
08-02-14, 01:09
"But if the admixture is southern European"

I think it just says they are the closest fit among existing populations which could simply mean any displaced population from Yemen/Saba (if that's what happened) ended up in the Southern European gene pool.

Maciamo
08-02-14, 12:06
I think we will have to agree to disagree on the merits of the paper.

The authors don't place the origin of the west Eurasian gene flow in Europe. They place it, as you suggest, in the Levant or Arabia, so the people would have indeed carried Near Eastern haplogroups.

I was misled by the New Scientist article which said:


The unexpected snippets of DNA most resembled sequences from southern Europeans, including Sardinians, Italians and people from the Basque region. Dating methods suggested they made their way into the Khoisan DNA sometime between 900 and 1800 years ago – well before known European contact with southern Africa

I remembered the presence of European R1b among the Khoisans, so after reading the mistaken explanation from the New Scientists I thought that this new paper finally managed to determine when these R1b men mixed with the Khoisans.

In any case this paper is not satisfying from my point of view because it doesn't tell us anything that we didn't already know, and it doesn't distinguish between the Middle Eastern (linked to J1 and T) and European (linked to R1b-M269) admixtures found among the Khoisans. As is often the case it is a waste of research time and funds, which would have been better spent in many other ways.

Maciamo
08-02-14, 16:27
"But if the admixture is southern European"

I think it just says they are the closest fit among existing populations which could simply mean any displaced population from Yemen/Saba (if that's what happened) ended up in the Southern European gene pool.

Another possibility is that the authors of this paper didn't use Saudi or Yemeni samples to compare with the West Eurasian admixtures found in the Khoisans. The only Middle Eastern population mentioned in the paper are the Druzes. The only other populations mentioned in the autosomal comparisons are the Italians, Sardinians, Basques, Orcadians, Russian, Yoruba and Mandenka. Such an omission would be unacceptable from "professionals".