posted
Human genetic variation particularly in Africa is still poorly understood. This is despite a consensus on the large African effective population size compared to populations from other continents. Based on sequencing of the mitochondrial Cytochrome C Oxidase subunit II (MT-CO2), and genome wide microsatellite data we observe evidence suggesting the effective size (Ne) of humans to be larger than the current estimates, with a foci of increased genetic diversity in east Africa, and a population size of east Africans being at least 2-6 fold larger than other populations. Both phylogenetic and network analysis indicate that east Africans possess more ancestral lineages in comparison to various continental populations placing them at the root of the human evolutionary tree. Our results also affirm east Africa as the likely spot from which migration towards Asia has taken place. The study reflects the spectacular level of sequence variation within east Africans in comparison to the global sample, and appeals for further studies that may contribute towards filling the existing gaps in the database. The implication of these data to current genomic research, as well as the need to carry out defined studies of human genetic variation that includes more African populations; particularly east Africans is paramount.
--Jibril Hirbo5, Sara Tishkoff et al.
The Episode of Genetic Drift Defining the Migration of Humans out of Africa Is Derived from a Large East African Population Size
PLoS One. 2014; 9(5): e97674. Published online 2014 May 20. doi: 10.1371/journal.pone.0097674
quote:Originally posted by Troll Patrol # Ish Gebor: Human genetic variation particularly in Africa is still poorly understood. This is despite a consensus on the large African effective population size compared to populations from other continents. Based on sequencing of the mitochondrial Cytochrome C Oxidase subunit II (MT-CO2), and genome wide microsatellite data we observe evidence suggesting the effective size (Ne) of humans to be larger than the current estimates, with a foci of increased genetic diversity in east Africa, and a population size of east Africans being at least 2-6 fold larger than other populations. Both phylogenetic and network analysis indicate that east Africans possess more ancestral lineages in comparison to various continental populations placing them at the root of the human evolutionary tree. Our results also affirm east Africa as the likely spot from which migration towards Asia has taken place. The study reflects the spectacular level of sequence variation within east Africans in comparison to the global sample, and appeals for further studies that may contribute towards filling the existing gaps in the database. The implication of these data to current genomic research, as well as the need to carry out defined studies of human genetic variation that includes more African populations; particularly east Africans is paramount.
--Jibril Hirbo5, Sara Tishkoff et al.
The Episode of Genetic Drift Defining the Migration of Humans out of Africa Is Derived from a Large East African Population Size
PLoS One. 2014; 9(5): e97674. Published online 2014 May 20. doi: 10.1371/journal.pone.0097674
Good find. This confirms Tishkoff's earlier studies.
Another interesting thing she says:
"It is not only genetic data that lends support to an east African origin of humans but the unparalleled ethnic and linguistic diversity that remains one of the highest worldwide. Interestingly the two most ancestral sequences in the NJ tree figure refer to Nubian individuals. Nubia is currently identified with one of the most ancient human settlements, the Say culture. Recently, a related compound associated with a lithic middle Stone Age ndustry was discovered in Dhofar Oman and taken as an evidence of human migration out of Africa through an Arabian route [46]. Overall, the various genetic markers used in the current analysis support the observation of human effective population size larger than previously estimated, and emphasize the importance of sampling populations of putative deep ancestry."
^^Anyone have any info on the Say culture?
Posts: 5905 | From: The Hammer | Registered: Aug 2008
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posted
I would not place too much confidence in this paper.This paper is pure conjecture.
The major problem with the paper is that the authors assume the populations they sampled have always lived in East Africa.
This is false . A simple perusal of the archaeological literature would have shown that the present populations entered East Africa from the east and the Sahara in the past 5000 years.
In addition, the earliest sites of human occupation in India are related to South African cultures, not East African cultures so the entire hypothesis lacks support.
A close read of the literature associated with the Green Sahara, would have made this clear since it records the expansion of civilizations from the Saharan highlands down into th nubian region. For example, the linguistic evidence and archaeology indicate that Afro-Asiatic speakers only recently migrated to their present centers of habitation.
Posts: 13012 | From: Chicago | Registered: Jan 2006
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The map on the right includes recent gene flow coming from the Levant and going in to the horn as Tishkoff indicated simple models are less likely.
The intermediate position, between African and non-African populations, Ethiopian Jews and Somalis occupy could be due either to shared common ancestry or to recent gene flow.
So when you say " the 'intermediate' position of Ethiopians and Somalis has nothing to do with race but to their position in the flow Out of Africa, you misrepresent Tishkoff's remarks and suggest a simple model of the opposite extreme
This is evident if we look at the complete quote and the right hand map showing Hg F going into the region from the Levant. You don't have the color key so just showing tha map doesn't explain it, the map however still betrays your point
quote: The intermediate position, between African and non-African populations, that the Ethiopian Jews and Somalis occupy in the PCA plot also has been observed in other genetic studies (Ritte et al. 1993; Passarino et al. 1998) and could be due either to shared common ancestry or to recent gene flow. The fact that the Ethiopians and Somalis have a subset of the sub-Saharan African haplotype diversity—and that the non-African populations have a subset of the diversity present in Ethiopians and Somalis—makes simple-admixture models less likely; rather, these observations support the hypothesis proposed by other nuclear-genetic studies (Tishkoff et al. 1996a, 1998a, 1998b; Kidd et al. 1998)—that populations in northeastern Africa may have diverged from those in the rest of sub-Saharan Africa early in the history of modern African populations and that a subset of this northeastern-African population migrated out of Africa and populated the rest of the globe. These conclusions are supported by recent mtDNA analysis (Quintana-Murci et al. 1999).
-- 2000 Short Tandem-Repeat Polymorphism/Alu Haplotype Variation at the PLAT Locus: Implications for Modern Human Origins
S. A. Tishkoff et al.
Because Tishkoff said simple-admixture models are less likely it doesn't mean there is no recent admixture into the region. That would be a simple model
It means that the reason for the divergance of Ethiopian Jews and Somalis from Sub Saharans is complex, involving divergance early in the history of modern African populations
and from recent gene flow which has been very significant in some populaltions of Ethiopians and Somalis
Posts: 42919 | From: , | Registered: Jan 2010
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Any black and white analysis of the situation will always represent a wrong and gross simplification of the situation.
It's clear that ancient East Africa has since about 60kya been the source of both OOA migrants and most Sub-Saharan Africans as well as been recipient of back migrations of Eurasians into East Africa in the last 3000 years (LINK).
In this table we can see the proportion of (recent) Eurasian admixtures in various African populations.
quote:To assess the effect of gene flow on population differentiation in SSA, we masked Eurasian ancestry across the genome (Supplementary Methods and Supplementary Note 6). This markedly reduced population differentiation, as measured by a decline in mean pairwise FST from 0.021 to 0.015 (Supplementary Note 6), suggests that Eurasian ancestry has a substantial impact on differentiation among SSA populations.
An Fst population differentiation of 0.015 and even 0.021 is very low. East and West African populations, and African populations in general, are very close to each others. Especially if you remove the more recent Eurasian component from the migrations by Semitic (ethio-semitic) and Muslim Arabs speakers into the East African region in the last 3000 years.
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quote:Originally posted by Amun-Ra The Ultimate: Any black and white analysis of the situation will always represent a wrong and gross simplification of the situation.
It's clear that ancient East Africa has since about 60kya been the source of both OOA migrants and most Sub-Saharan Africans as well as been recipient of back migrations of Eurasians into East Africa in the last 3000 years (LINK).
In this table we can see the proportion of (recent) Eurasian admixtures in various African populations.
quote:To assess the effect of gene flow on population differentiation in SSA, we masked Eurasian ancestry across the genome (Supplementary Methods and Supplementary Note 6). This markedly reduced population differentiation, as measured by a decline in mean pairwise FST from 0.021 to 0.015 (Supplementary Note 6), suggests that Eurasian ancestry has a substantial impact on differentiation among SSA populations.
An Fst population differentiation of 0.015 and even 0.021 is very low. East and West African populations, and African populations in general, are very close to each others. Especially if you remove the more recent Eurasian component from the migrations by Semitic (ethio-semitic) and Muslim Arabs speakers into the East African region in the last 3000 years.
Are you claiming that the Semitic speaking Africans came from outside Africa?
What is the evidence of this migration?
The archaeological evidence points to migrations into Arabia, not Arabia back into Africa.
What are the dates for these Eurasian back migrations supported by archaeological evidence?
Amun-Ra The Ultimate your claims are based on the idea by these authors that West Africans show admixture with West Africans. These authors claim this may be impossible because their is no archaeological evidence linking these people, or situating the Khoisan in West Africa. They are wrong the Khoisan probably migrated into West Africa before they settled in Iberia and founded Aurignacian civilization and introduced L3(M,N) to Western Eurasia.
In addition to haplogroups M1, M* and N in Sub-Saharan Africa we also find among the Senegambians hapotype AF24 (DQ112852) , which is delineated by a DdeI site at 10394 and AluI site of np 10397. The AF-24 haplotype is a branch of the African subhaplogroup L3 (Chen, 2000). This is the same delineation of haplogroup M*. It is clear from the molecular evidence that the M1, M and N haplogroups are found not only in Northeast Africa, but across Africa from East to West (Winters, 2007). Haplogroup LOd is found at the root of human mtDNA. Gonder et al (2006) maintains that LOd is “the most basal branch of the gene tree”. The TMRCA for LOd is 106kya. This makes haplotype AF-24 much older than L3a and probably explains why this haplotype is found among the Khwe/Khoisan (Chen et al,2000). The TMRCA of LOd dates to 106kya. As a result, anatomically modern humans (amh) had plenty of time to spread this haplogroup to Senegal. In West Africa the presence of amh date to the Upper Palaeolithic (Giresse,2008).
The archaeological evidence makes it clear that amh had ample opportunity to spread LOd and L3(M,N) which has an affinity to AF-24 (Chen,2000), to West Africa during this early period of demic diffusion of amh in Africa. The earliest evidence of human activity in West Africa is typified by the Sangoan industry (Phillipson,2005). The amh associated with the Sangoan culture may have deposited Hg LOd and haplotype AF-24 in Senegal thousands of years before the exit of amh from Africa. This is because it was not until 65kya that the TMRCA of non-African L3(M,N) exited Africa (Kivisild et al, 2006). Anatomically modern humans arrived in Senegal during the Sangoan period. Sangoan artifacts spread from East Africa to West Africa between 100-80kya. In Senegal Sangoan material has been found near Cap Manuel (Giresse, 2008), Gambia River in Senegal (Davies,1967; Wai-Ogussu,1973); and Cap Vert (Phillipson,2005).
quote:Originally posted by Clyde Winters: I would not place too much confidence in this paper.This paper is pure conjecture.
The major problem with the paper is that the authors assume the populations they sampled have always lived in East Africa.
This is false . A simple perusal of the archaeological literature would have shown that the present populations entered East Africa from the east and the Sahara in the past 5000 years.
quote:Originally posted by Clyde Winters:
quote:Originally posted by the lioness,:
quote:Originally posted by Clyde Winters:
present populations entered East Africa from the east
What do you mean? East of East Africa, if you go east of East Africa you're in the sea
Sorry I meant West.
OK let's look at what you really meant
quote: The major problem with the paper is that the authors assume the populations they sampled have always lived in East Africa.
This is false . A simple perusal of the archaeological literature would have shown that the present populations entered East Africa from the Westt and the Sahara in the past 5000 years.
Herto skull, Ethiopia: Dated at between 160,000 and 154,000 years old Lucy, Ethiopia 3.2 million years ago
The oldest fossil remains of anatomically modern humans are the Omo remains, Ethiopia, which date to 195,000 (±5,000) years ago and include two partial skulls as well as arm, leg, foot and pelvis bones.
Posts: 42919 | From: , | Registered: Jan 2010
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quote:Originally posted by zarahan- aka Enrique Cardova:
Another interesting thing she says:
"It is not only genetic data that lends support to an east African origin of humans but the unparalleled ethnic and linguistic diversity that remains one of the highest worldwide. Interestingly the two most ancestral sequences in the NJ tree figure refer to Nubian individuals. Nubia is currently identified with one of the most ancient human settlements, the Say culture. Recently, a related compound associated with a lithic middle Stone Age ndustry was discovered in Dhofar Oman and taken as an evidence of human migration out of Africa through an Arabian route [46]. Overall, the various genetic markers used in the current analysis support the observation of human effective population size larger than previously estimated, and emphasize the importance of sampling populations of putative deep ancestry."
^^Anyone have any info on the Say culture?
Table 1 shows the population parameters and selective neutrality test (Tajima’s D) based on MT-CO2 variation of all continental groups, mean values and test of significance for the obtained values. Tajima’s D (Table 1) scored negative values consistent with human expansion within and outside of Africa (or exchange of alleles between neighboring demes, see discussion below) with satisfactory statistical scores. The transition to transversion ratio of 2:1 in our reported Single Nucleotide Polymorphisms (SNPs) is consistent with being at the root of the gene tree and with neutral evolution distance based analysis using FST for mtDNA sequences and RST for microsatellite data were carried out for subsequent MDS plotting and a population by population correlation comparison using Mantel Test. The result showed no correlation with a P value of 0.66 similar to comparison between mitochondria and Y chromosome variations reported earlier [16].
[...]
The third cluster (C), includes members of almost all world populations particularly non-Africans who share a major haplo- type that seems to have originated within an east African gene pool (Table S1 and Figure 3).
[...]
Mutations and Haplotypes Frequencies in the MT-CO2
The sheer number of haplotypes, a basic measurement of genetic diversity, is also taken as an indication of Ne. As mitochondria are non-recombining the number of mutations and haplotypes is quite correlated. In the MT-CO2 sequence 68 haplotypes were estimated using Arlequin ver3.11 and assigned numbers from 1 to 68. Haplotype relative and absolute frequencies in the studied populations were also calculated. Strikingly, of the total 68 haplotypes, 43 occurred solely in east Africa (Table S1) of which 25 were in Sudanese, 9 in Eritreans and 5 in Ugandans and one Kenyan. The rest of the haplotypes were derived from or included east Africans with exception of 13 haplotypes, 4 in Africa 2 in Australia, 3 in Europe 1 in Arabia 1 America/Africa and 1 Europe/Africa. Of the 42 haplotype defining mutations (Table S2) in Sudanese and Eritreans 11 (26.2%) were non-synonymous (replacements) occurring in trans-membrane domain of COII protein while 31 (73.8%) were synonymous with transitions representing the majority of the mutations. Out of the 42 mutations (Table S2), 31 were previously reported in the literature and 11 were novel. All mutations in Ugandan MT-CO2 samples are synonymous and reported at http://dspace.nwu.ac.za/handle/10394/4221). All published haplogroups associated with the mutations are indicated in Table S2.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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You make a number of valid points. But the movement of the Sangoan culture from South Africa into the North and West Africa would support an early migration of Khoisan into these areas. It would also explain why the oldest y-haplogroups are found among Khoisan and Atlas Berbers.
Granted the Swahilli may have interacted with the Khoisan but this can not explain Eurasian admixture. This fails to explain the admixture because there are Khoisan in East Africa I believe that fail to show Eurasian admixture, while South African Khoisan do.
Also , if we accept that the Grimaldi, Cro-Magnon etc were Khoisan the Khoisan may have took these haplogroups into Eurasia. As a result, if there was a back migration it took place prior to 3000 years ago, and it was probably Khoisan migrating back to Africa.
Posts: 13012 | From: Chicago | Registered: Jan 2006
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posted
From The African Genome Variation Project shapes medical genetics in Africa http://www.nature.com/nature/journal/v517/n7534/full/nature13997.html This articles is being used by Amun-Ra to suggest that there is considerable Eurasian admixture among African groups. I believe that this so-called admixture with Eurasians results from Africans taking the so-called Eurasian genes into Africa, they also speculate that the Khoisan probably played a role spreading the Eurasian genes, since they acquired the genes through interactions with Afro-Asiatic speakers. (Correct me if I read this wrong.)
They also mention the possible role of Khoisan in West Africa, but believe that there is no genetic evidence supporting such a relationship.
The authors wrote:
quote:
We found evidence for historically complex and regionally distinct admixture with multiple HG and Eurasian populations across SSA (Fig. 2 and Supplementary Note 5). Specifically, ancient Eurasian admixture was observed in central West African populations (Yoruba; ~7,500–10,500 years ago), old admixture among Ethiopian populations (~2,400–3,200 years ago) consistent with previous reports10, 12, and more recent complex admixture in some East African populations (~150–1,500 years ago) (Fig. 2, Extended Data Fig. 7 and Supplementary Note 5). Our finding of ancient Eurasian admixture corroborates findings of non-zero Neanderthal ancestry in Yoruba, which is likely to have been introduced through Eurasian admixture and back migration, possibly facilitated by greening of the Sahara desert during this period13, 14.
We also find evidence for complex and regionally distinct HG admixture across SSA (Fig. 2, Extended Data Figs 7 and Supplementary Note 5), with ancient gene flow (~9,000 years ago) among Igbo and more recent admixture in East and South Africa (multiple events ranging from 100 years ago to 3,000 years ago), broadly consistent with historical movements reflecting the Bantu expansion. An exploration of the likeliest sources of admixture in our data suggested that HG admixture in Igbo was most closely represented by modern day Khoe-San populations rather than by rainforest HG populations (Supplementary Note 5). Given limited archaeological and linguistic evidence for the presence of Khoe-San populations in West Africa, this extant HG admixture might represent ancient populations, consistent with the presence of mass HG graves from the early Holocene period comprising skeletons with distinct morphological features15, and with evidence of HG rock art dating to this period in the western Sahara16, 17. In East Africa, our analyses suggested that Mbuti rainforest HG populations most closely represented ancient HG mixing populations (Supplementary Note 5), with admixture dating to ~3,000 years ago, suggesting that HG ancestry here is likely to be older than previously reported18. The primary source of HG admixture in Zulu and Sotho populations was from Khoe-San populations (Fig. 2 and Supplementary Note 5), consistent with linguistic assimilation of click consonants among these populations.
quote: Although the history of the Bantu expansion is probably complex, assessments of population admixture can provide new insights. We note historically complex and regionally distinct admixture with multiple HG and Eurasian populations across SSA, including ancient HG and Eurasian ancestry in West and East Africa and more recent complex HG admixture in South Africa. As well as explaining genetic differentiation among modern populations in SSA, these admixture patterns provide genetic evidence for early back-to-Africa migrations, the possible existence of extant HG populations in western Africa—compatible with archaeological evidence15, and patterns of gene flow consistent with the Bantu expansion, including genetic assimilation of populations resident across the region.
The so-called Eurasian admxture in West Central Africa is probably the presence of R1-M173, V88 and M269. This is speculation because while there may be evidence of hunter-gatherer populations in these areas, their is no evidence of archaeological evidence of a Eurasian back migration into West-Central Africa. This indicates that R1-M173 originated in Africa prior to the OoA event 65kya. The presence of Africans in Brazil 100,000 years ago indicate that Africans had already exited Africa, to the Americas probably 35,000 years before they went to Asia.
.
-------------------- C. A. Winters Posts: 13012 | From: Chicago | Registered: Jan 2006
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posted
Great points Dr Winters. I haven’t raad the paper, but I will now.
But I Agree on most of what you said.
It is wrong to assume these populations ALWAYS existed where they are now.
The Sahara was green and emerging eveidence that is where many of these ancient civilzations originated.
I am on-board now. There is a very deep connection across the Indian Ocean and southern Eastern Africans.
quote:Originally posted by Clyde Winters: .
The major problem with the paper is that the authors assume the populations they sampled have always lived in East Africa.
This is false . A simple perusal of the archaeological literature would have shown that the present populations entered East Africa from the east and the Sahara in the past 5000 years.
In addition, the earliest sites of human occupation in India are related to South African cultures, not East African cultures so the entire hypothesis lacks support.
A close read of the literature associated with the Green Sahara, would have made this clear since it records the expansion of civilizations from the Saharan highlands down into th nubian region. For example, the linguistic evidence and archaeology indicate that Afro-Asiatic speakers only recently migrated to their present centers of habitation.
Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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posted
" Recently, a related compound associated with a lithic middle Stone Age industry was discovered in Dhofar Oman and taken as an evidence of human migration out of Africa through an Arabian route [46]. " (above)
Dhofar/Oman mountains ~ Darfur/Sudan mountains Shaharah tribe collect frankincense/anti-insect, their cattle kept in dome huts fumigated (tetse fly in So Afr.?), people indigo-dye similar to Tuareg of No. Afr.
- - -
"The Khoisan probably were some of the first settlers of the Americas. Between 20-10kya ago."
I guess you refer to some Khoi-like features. But to my knowledge, Khoi-San people have left no evidence or tradition of making and using ocean going wooden ships nor dugout canoes. I conjecture that their ancestors split from the rainforest pygmies out to the peripheral woodland-savannas and added antelope skins to their dome huts during rainy season, and some travelled eastwardly to the Nile, Euphrates, Tigris etc. with skinned woven coracles. But I haven't seen a westerly movement of this.
quote:Originally posted by Clyde Winters: From The African Genome Variation Project shapes medical genetics in Africa http://www.nature.com/nature/journal/v517/n7534/full/nature13997.html This articles is being used by Amun-Ra to suggest that there is considerable Eurasian admixture among African groups. I believe that this so-called admixture with Eurasians results from Africans taking the so-called Eurasian genes into Africa, they also speculate that the Khoisan probably played a role spreading the Eurasian genes, since they acquired the genes through interactions with Afro-Asiatic speakers. (Correct me if I read this wrong.)
They also mention the possible role of Khoisan in West Africa, but believe that there is no genetic evidence supporting such a relationship.
The authors wrote:
quote:
We found evidence for historically complex and regionally distinct admixture with multiple HG and Eurasian populations across SSA (Fig. 2 and Supplementary Note 5). Specifically, ancient Eurasian admixture was observed in central West African populations (Yoruba; ~7,500–10,500 years ago), old admixture among Ethiopian populations (~2,400–3,200 years ago) consistent with previous reports10, 12, and more recent complex admixture in some East African populations (~150–1,500 years ago) (Fig. 2, Extended Data Fig. 7 and Supplementary Note 5). Our finding of ancient Eurasian admixture corroborates findings of non-zero Neanderthal ancestry in Yoruba, which is likely to have been introduced through Eurasian admixture and back migration, possibly facilitated by greening of the Sahara desert during this period13, 14.
We also find evidence for complex and regionally distinct HG admixture across SSA (Fig. 2, Extended Data Figs 7 and Supplementary Note 5), with ancient gene flow (~9,000 years ago) among Igbo and more recent admixture in East and South Africa (multiple events ranging from 100 years ago to 3,000 years ago), broadly consistent with historical movements reflecting the Bantu expansion. An exploration of the likeliest sources of admixture in our data suggested that HG admixture in Igbo was most closely represented by modern day Khoe-San populations rather than by rainforest HG populations (Supplementary Note 5). Given limited archaeological and linguistic evidence for the presence of Khoe-San populations in West Africa, this extant HG admixture might represent ancient populations, consistent with the presence of mass HG graves from the early Holocene period comprising skeletons with distinct morphological features15, and with evidence of HG rock art dating to this period in the western Sahara16, 17. In East Africa, our analyses suggested that Mbuti rainforest HG populations most closely represented ancient HG mixing populations (Supplementary Note 5), with admixture dating to ~3,000 years ago, suggesting that HG ancestry here is likely to be older than previously reported18. The primary source of HG admixture in Zulu and Sotho populations was from Khoe-San populations (Fig. 2 and Supplementary Note 5), consistent with linguistic assimilation of click consonants among these populations.
quote: Although the history of the Bantu expansion is probably complex, assessments of population admixture can provide new insights. We note historically complex and regionally distinct admixture with multiple HG and Eurasian populations across SSA, including ancient HG and Eurasian ancestry in West and East Africa and more recent complex HG admixture in South Africa. As well as explaining genetic differentiation among modern populations in SSA, these admixture patterns provide genetic evidence for early back-to-Africa migrations, the possible existence of extant HG populations in western Africa—compatible with archaeological evidence15, and patterns of gene flow consistent with the Bantu expansion, including genetic assimilation of populations resident across the region.
The so-called Eurasian admxture in West Central Africa is probably the presence of R1-M173, V88 and M269. This is speculation because while there may be evidence of hunter-gatherer populations in these areas, their is no evidence of archaeological evidence of a Eurasian back migration into West-Central Africa. This indicates that R1-M173 originated in Africa prior to the OoA event 65kya. The presence of Africans in Brazil 100,000 years ago indicate that Africans had already exited Africa, to the Americas probably 35,000 years before they went to Asia.
.
Iwo Eleru's place among Late Pleistocene and Early Holocene populations of North and East Africa
quote:Originally posted by Troll Patrol # Ish Gebor:
quote:Originally posted by Clyde Winters: From The African Genome Variation Project shapes medical genetics in Africa http://www.nature.com/nature/journal/v517/n7534/full/nature13997.html This articles is being used by Amun-Ra to suggest that there is considerable Eurasian admixture among African groups. I believe that this so-called admixture with Eurasians results from Africans taking the so-called Eurasian genes into Africa, they also speculate that the Khoisan probably played a role spreading the Eurasian genes, since they acquired the genes through interactions with Afro-Asiatic speakers. (Correct me if I read this wrong.)
They also mention the possible role of Khoisan in West Africa, but believe that there is no genetic evidence supporting such a relationship.
The authors wrote:
quote:
We found evidence for historically complex and regionally distinct admixture with multiple HG and Eurasian populations across SSA (Fig. 2 and Supplementary Note 5). Specifically, ancient Eurasian admixture was observed in central West African populations (Yoruba; ~7,500–10,500 years ago), old admixture among Ethiopian populations (~2,400–3,200 years ago) consistent with previous reports10, 12, and more recent complex admixture in some East African populations (~150–1,500 years ago) (Fig. 2, Extended Data Fig. 7 and Supplementary Note 5). Our finding of ancient Eurasian admixture corroborates findings of non-zero Neanderthal ancestry in Yoruba, which is likely to have been introduced through Eurasian admixture and back migration, possibly facilitated by greening of the Sahara desert during this period13, 14.
We also find evidence for complex and regionally distinct HG admixture across SSA (Fig. 2, Extended Data Figs 7 and Supplementary Note 5), with ancient gene flow (~9,000 years ago) among Igbo and more recent admixture in East and South Africa (multiple events ranging from 100 years ago to 3,000 years ago), broadly consistent with historical movements reflecting the Bantu expansion. An exploration of the likeliest sources of admixture in our data suggested that HG admixture in Igbo was most closely represented by modern day Khoe-San populations rather than by rainforest HG populations (Supplementary Note 5). Given limited archaeological and linguistic evidence for the presence of Khoe-San populations in West Africa, this extant HG admixture might represent ancient populations, consistent with the presence of mass HG graves from the early Holocene period comprising skeletons with distinct morphological features15, and with evidence of HG rock art dating to this period in the western Sahara16, 17. In East Africa, our analyses suggested that Mbuti rainforest HG populations most closely represented ancient HG mixing populations (Supplementary Note 5), with admixture dating to ~3,000 years ago, suggesting that HG ancestry here is likely to be older than previously reported18. The primary source of HG admixture in Zulu and Sotho populations was from Khoe-San populations (Fig. 2 and Supplementary Note 5), consistent with linguistic assimilation of click consonants among these populations.
quote: Although the history of the Bantu expansion is probably complex, assessments of population admixture can provide new insights. We note historically complex and regionally distinct admixture with multiple HG and Eurasian populations across SSA, including ancient HG and Eurasian ancestry in West and East Africa and more recent complex HG admixture in South Africa. As well as explaining genetic differentiation among modern populations in SSA, these admixture patterns provide genetic evidence for early back-to-Africa migrations, the possible existence of extant HG populations in western Africa—compatible with archaeological evidence15, and patterns of gene flow consistent with the Bantu expansion, including genetic assimilation of populations resident across the region.
The so-called Eurasian admxture in West Central Africa is probably the presence of R1-M173, V88 and M269. This is speculation because while there may be evidence of hunter-gatherer populations in these areas, their is no evidence of archaeological evidence of a Eurasian back migration into West-Central Africa. This indicates that R1-M173 originated in Africa prior to the OoA event 65kya. The presence of Africans in Brazil 100,000 years ago indicate that Africans had already exited Africa, to the Americas probably 35,000 years before they went to Asia.
.
Iwo Eleru's place among Late Pleistocene and Early Holocene populations of North and East Africa
quote:Originally posted by DD'eDeN: " Recently, a related compound associated with a lithic middle Stone Age industry was discovered in Dhofar Oman and taken as an evidence of human migration out of Africa through an Arabian route [46]. " (above)
Dhofar/Oman mountains ~ Darfur/Sudan mountains Shaharah tribe collect frankincense/anti-insect, their cattle kept in dome huts fumigated (tetse fly in So Afr.?), people indigo-dye similar to Tuareg of No. Afr.
- - -
"The Khoisan probably were some of the first settlers of the Americas. Between 20-10kya ago."
I guess you refer to some Khoi-like features. But to my knowledge, Khoi-San people have left no evidence or tradition of making and using ocean going wooden ships nor dugout canoes. I conjecture that their ancestors split from the rainforest pygmies out to the peripheral woodland-savannas and added antelope skins to their dome huts during rainy season, and some travelled eastwardly to the Nile, Euphrates, Tigris etc. with skinned woven coracles. But I haven't seen a westerly movement of this.
This is because the Khoisan today do not live in an environment where boats are necessary. The Khoisan have their own traditions. I believe its very interesting they have North African caprines, and the names for their cattle are not related to the Bantu cattle terms.
There is a lot we don't know about the Khoisan, and their contributions to the raise of civilization.
present populations entered East Africa from the east
What do you mean? East of East Africa, if you go east of East Africa you're in the sea
The East would mean the coast, you dumbass.
Ancient populations usually moved along the coast or rivers.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:Originally posted by Troll Patrol # Ish Gebor:
quote:Originally posted by the lioness,:
quote:Originally posted by Clyde Winters:
present populations entered East Africa from the east
What do you mean? East of East Africa, if you go east of East Africa you're in the sea
The East would mean the coast, you dumbass.
Ancient populations usually moved along the coast or rivers.
.
read this again jackass >>>
quote:Originally posted by Clyde Winters:
quote:Originally posted by the lioness,:
quote:Originally posted by Clyde Winters:
present populations entered East Africa from the east
What do you mean? East of East Africa, if you go east of East Africa you're in the sea
Sorry I meant West.
Clyde said he meant West, idiot
Yes, I know/ understood what he meant. From west to the east coast, then out migrate.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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There is a lot we don't know about the Khoisan, and their contributions to the raise of civilization.
True, had the same ignorance pervaded Asia we would have heard of a race/people called Chijapanese (Lol).
"The San are another very specific group living in the continent of Africa. They are of small stature, with copper-coloured or yellowish skin, and their hair grows in tufts. In anthropological studies, they are still put together with the Khoi-Khoi in a 'Khoisan race'.
This no doubt comes by extrapolation from the linguistic classification which places the languages of the San and the Khoi-Khoi in a single family characterized by the use of phonemic clicks. The term 'Khoisan', suggested by Shapera and now adopted in many works, is a combination of two Khoi-Khoi words: khoi meaning man, and san, the root sa of which means to gather edible plants, pull up roots, collect fruits, and also to capture small animals.
A human group is accordingly styled by its way of life, its mode of production. In point of fact, however, the San and the Khoi-Khoi have very few common characteristics. Account may be taken of the light colour of their skin, and also the presence of click consonants in both their languages. It should be recalled, however, that this is not a specific characteristic
Examination of the anthropological features of these two groups shows, however, that Khoi-Khoi and San differ in many respects, for instance, in stature, the Khoi-Khoi being distinctly taller than the San. They differ also in regard to cranial characteristics, and Steatopygia , which is very common among the women, whereas the presence of Epicanthus is specific to the San.
Furthermore, the Khoi-Khoi and San languages differ as regards both grammatical structure and vocabulary."
"As to the culture of these peoples, they differ in every way. This was, moreover, noted by the first travellers who visited southern Africa in the seventeenth century, such as Peter Kolb. The Khoi-Khoi lived in kraals, worked metals and raised cattle, whereas the San lived by hunting and gathering and had no fixed dwellings. Thus, neither anthropologists nor linguists can provide sufficient grounds for assuming the existence of a Khoisan group consisting of Khoi-Khoi and San"
"These two groups of peoples have completely different histories. The San are certainly the remnants of the original population of the extreme south of the African continent. They are now confined to the inhospitable and waterless regions of Namibia and the Kalahari. Isolated clusters of them are to be found also in Angola. In former times, they inhabited the savannahs of southern and East Africa as far as the borders of Kenya, as the toponymy and hydronymy of these regions bear witness, the local names of rivers and mountains being borrowed from the languages of the San. T h e clicksounding consonants which are characteristic of the San languages have been borrowed by several Bantu languages. Finally, the rock paintings of the high veld of southern Africa show scenes of armed combat between short, light-skinned San and tall, dark-skinned warriors whose ethnic origin can easily be discerned from the shape of the shields they carry. A small ethnic group, the Hadzabe Bushman or Hadza, living in the region of Lake Eyasi in Tanzania, is a further indication of the extent of former San settlement throughout Africa."
..and Africa shall speak for herself
Posts: 45 | From: South Africa | Registered: Jul 2014
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posted
"The Language of the Hadzabe has not yet been studied in sufficient detail, but there are grounds for thinking that it is related to those of the San. Sometimes support for the thesis that the San once occupied a much larger area than they do today is sought in the presence of round stones, pierced in the centre, throughout East Africa. These ring-shape stone called the !kwe by the San, were used for weighting a stick for digging up edible roots. However, it is not proved that this technique was diffused by the San group. Thus, for instance, among the Galla in southern Ethiopia and in the region of Harar men dig the soil with long stakes called Dongora (Paste 'Weighted Digging Sticks in Ethiopia' on Search or Click 'Advanced Search' and paste 'Sidney R. Waldron' on Author) these stakes are almost always fitted with such ring-shaped stones. The same device is used to weight the pestle for crushing tobacco. Thus it is not possible to uphold the view that the San formerly wandered everywhere where ring-shaped stones of the '!kwe' type are found, or were they?
The earliest population of southern Africa should not, however, be considered solely in terms of the Pygmies in the forests and the San in the savannahs. Other peoples may have existed alongside these. There is, for instance, the fairly recent discovery in Angola of the Kwadi group, which closely resembles the San in its style of life and probably also in Language. At the beginning of the twentieth century, Vedder studied the Otavi, who are the remnants of former groups. These people are of small stature and live by hunting and gathering. Unlike the San, they have a very dark skin and thick lips. The name by which they call themselves is Nu-Khoin, which means 'black people', as opposed to the Khoi-Khoi, whom they called 'red people'. An extremely interesting feature of this group is their system of counting. It differs sharply from the system used by the Khoi-Khoi, who count in tens. Groups such as these, which probably exist also in other areas, throw precious light on the very complex problem of the earliest peoples of the forests and savannahs of central and southern Africa."
Posts: 45 | From: South Africa | Registered: Jul 2014
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quote: Genetic stories, both intimate and universal, were the topic of the day at the New-York Historical Society on Thursday at “It’s All Relatives: The Science Of Your Family Tree,” a program of the 2014 World Science Festival.
Broadcast journalist Randall Pinkston led the conversation, opening with Ancestry.com scientist Catherine Ball and genetic genealogist Cece Moore (also a consultant and script writer on the PBS show Finding Your Roots with Henry Louis Gates, Jr.)
Genetic genealogy is more within reach of the average person than ever, thanks to advances in sequencing technology that have helped the cost of genome sequencing dramatically plummet from nearly $3 billion in 2000 to near $1,000 nowadays. That sort of price reduction is mind-boggling, Ball said. “It’s as if, 15 years from now, I could get my own Mars rover.”
The stories that DNA tells can be surprising. Moore, who was a professional singer before she became a geneticgenealogist, was able to trace a version of the ASAP1 gene, linked to perfect pitch, back through her mother’s side of the family. And her brother-in-law, surprised by a genetic test showing traces of African ancestry, was able to trace his family all the way back to Madison Hemings, the son of U.S. President Thomas Jefferson and his slave Sally Hemings.
Another panelist, Stony Brook University SUNY evolutionary geneticist Brenna Henn, spoke to a broader vision of the family tree—the genetic roots all of mankind. When you start looking at the flow and variation of genes throughout the world, even more interesting stories arise.
“African populations have the most genetic diversity in the world,” Henn said. “If you compared people from the Kalahari Desert to people from Mali, they’d be as different from each other [genetically] as Italians and Chinese people.”
Why are other populations of humans so much less genetically varied than Africans? The answer, Henn explains, lies in our ancestors’ history; the groups of people that migrated out of Africa and spread throughout other continents were smaller subsets of that original, genetically diverse population. Some scientists even estimate that all Native Americans can trace their ancestry back to an effective population of a mere 100 people that crossed over the Bering Strait land bridge from Asia.
…[the drop in cost for genome sequencing] is mind-boggling, Ball said. “It’s as if, 15 years from now, I could get my own Mars rover.”
Such a small sample from a larger population won’t reflect the full spread of gene variation from the larger group. Henn compares it to picking up a small handful of jellybeans out of a big bowl; chances are you probably won’t grab every single color.
Mark Shriver, a Pennsylvania State University geneticist, researches genetic markers for disease. But lately, he’s focusing on certain physical traits: face shape in particular. Shriver’s working on a big project called ADAPT2 that’s aimed at understanding genetic influences behind a person’s physical features. As genetic analyses like Shriver’s become better and better, there are all sorts of possible applications: The Department of Justice, which supports Shriver’s work, is interested in creating better forensic tests that can paint a better portrait of criminal suspects.
But Shriver’s work with the DOJ gave Pinkston pause, “as a guy who has to worry about WWB—walking while black.”
While genetics could, unfortunately, become another tool used to profile black people, Shriver pointed out that it could also be used to steer cops away from harassing innocent African-Americans; genetic evidence has already been used to steer police investigations away from black suspects toward white ones.
Balancing concerns for genetic privacy with ongoing research will continue to weigh heavily in the future. Though federal law (the Genetic Information Non-Discrimination Act) prohibits employers from using genetic information to make hiring, firing, placement and promotion decisions, and also bars insurance companies from charging higher premiums or denying coverage to people on the basis of genetic information, other sticky issues may arise.
It’s difficult, too, to determine just how much our genetic information can really be considered totally our own property.
“If I participate in your study,” Ball said to Shriver, “you’re not only getting my information, but a lot of information from family members that have not consented.”
There is a lot we don't know about the Khoisan, and their contributions to the raise of civilization.
True, had the same ignorance pervaded Asia we would have heard of a race/people called Chijapanese (Lol).
"The San are another very specific group living in the continent of Africa. They are of small stature, with copper-coloured or yellowish skin, and their hair grows in tufts. In anthropological studies, they are still put together with the Khoi-Khoi in a 'Khoisan race'.
This no doubt comes by extrapolation from the linguistic classification which places the languages of the San and the Khoi-Khoi in a single family characterized by the use of phonemic clicks. The term 'Khoisan', suggested by Shapera and now adopted in many works, is a combination of two Khoi-Khoi words: khoi meaning man, and san, the root sa of which means to gather edible plants, pull up roots, collect fruits, and also to capture small animals.
A human group is accordingly styled by its way of life, its mode of production. In point of fact, however, the San and the Khoi-Khoi have very few common characteristics. Account may be taken of the light colour of their skin, and also the presence of click consonants in both their languages. It should be recalled, however, that this is not a specific characteristic
Examination of the anthropological features of these two groups shows, however, that Khoi-Khoi and San differ in many respects, for instance, in stature, the Khoi-Khoi being distinctly taller than the San. They differ also in regard to cranial characteristics, and Steatopygia , which is very common among the women, whereas the presence of Epicanthus is specific to the San.
Furthermore, the Khoi-Khoi and San languages differ as regards both grammatical structure and vocabulary."
"As to the culture of these peoples, they differ in every way. This was, moreover, noted by the first travellers who visited southern Africa in the seventeenth century, such as Peter Kolb. The Khoi-Khoi lived in kraals, worked metals and raised cattle, whereas the San lived by hunting and gathering and had no fixed dwellings. Thus, neither anthropologists nor linguists can provide sufficient grounds for assuming the existence of a Khoisan group consisting of Khoi-Khoi and San"
"These two groups of peoples have completely different histories. The San are certainly the remnants of the original population of the extreme south of the African continent. They are now confined to the inhospitable and waterless regions of Namibia and the Kalahari. Isolated clusters of them are to be found also in Angola. In former times, they inhabited the savannahs of southern and East Africa as far as the borders of Kenya, as the toponymy and hydronymy of these regions bear witness, the local names of rivers and mountains being borrowed from the languages of the San. T h e clicksounding consonants which are characteristic of the San languages have been borrowed by several Bantu languages. Finally, the rock paintings of the high veld of southern Africa show scenes of armed combat between short, light-skinned San and tall, dark-skinned warriors whose ethnic origin can easily be discerned from the shape of the shields they carry. A small ethnic group, the Hadzabe Bushman or Hadza, living in the region of Lake Eyasi in Tanzania, is a further indication of the extent of former San settlement throughout Africa."
quote:Originally posted by Troll Patrol # Ish Gebor: Human genetic variation particularly in Africa is still poorly understood. This is despite a consensus on the large African effective population size compared to populations from other continents. Based on sequencing of the mitochondrial Cytochrome C Oxidase subunit II (MT-CO2), and genome wide microsatellite data we observe evidence suggesting the effective size (Ne) of humans to be larger than the current estimates, with a foci of increased genetic diversity in east Africa, and a population size of east Africans being at least 2-6 fold larger than other populations. Both phylogenetic and network analysis indicate that east Africans possess more ancestral lineages in comparison to various continental populations placing them at the root of the human evolutionary tree. Our results also affirm east Africa as the likely spot from which migration towards Asia has taken place. The study reflects the spectacular level of sequence variation within east Africans in comparison to the global sample, and appeals for further studies that may contribute towards filling the existing gaps in the database. The implication of these data to current genomic research, as well as the need to carry out defined studies of human genetic variation that includes more African populations; particularly east Africans is paramount.
--Jibril Hirbo5, Sara Tishkoff et al.
The Episode of Genetic Drift Defining the Migration of Humans out of Africa Is Derived from a Large East African Population Size
PLoS One. 2014; 9(5): e97674. Published online 2014 May 20. doi: 10.1371/journal.pone.0097674
Though I don't doubt this to be the case, I do sometimes find the focus on East Africa to be 'Eurasiocentric' simply because East Africa was the exit point of OOA. I don't know if any of you have seen the (several years old) findings from NatGeo that the alleged cradle of humanity is somewhere in Tanzania.
quote: According to the current data East Africa is home to nearly 2/3 of the world genetic diversity independent of sampling effect. Similar figure have been suggested for sub-Saharan Africa populations [1]. The antiquity of the east African gene pool could be viewed not only from the perspective of the amount of genetic diversity endowed within it but also by signals of uni-modal distribution in their mitochondrial DNA (Hassan et al., unpublished) usually taken as an indication of populations that have passed through ‘‘recent’’ demographic expansion [33], although in this case, may in fact be considered a sign of extended shared history of in situ evolution where alleles are exchanged between neighboring demes [34].
Figure S1 Neighbor joining (NJ). NJ tree of the world populations based on MT-CO2 sequences. The evolutionary relationship of 171 sequences and evolutionary history was inferred using the Neighbor-Joining method. The optimal tree with the sum of branch length = 0.20401570 is shown. The evolutionary distances were computed using the Maximum Composite Likelihood method and are in the units of the number of base substitutions per site. Codon positions included were 1st+2nd+3rd+Noncoding. All positions containing gaps and missing data were eliminated from the dataset. There were a total of 543 positions in the final dataset. Phylogenetic analyses were conducted in MEGA4. Red dots: east Africa, Blue: Africa, Green: Asia, Yellow: Australia, Pink: Europe and gray: America. (TIF)
Figure S2 Multidimensional Scaling Plot (MDS). The 2nd and 3rd coordinates of an MDS plot of 848 nuclear microsatellite loci from 469 individuals of 24 world populations. MDS uses pairwise IBS data based on the 848 loci generated by PLINK software and plotted using R version 2.15.0. The figure, besides a separate clustering of east Africans, indicates the substantial contribution of Africans and east Africans to the founding of populations of Europe and Asia. (TIF)
Figure S3 Multidimensional Scaling Plot (MDS). The 3rd and 4th coordinates of an MDS plot of 848 Microsatellite loci, across the human genome in 469 individuals from 24 populations from Africa, Asia and Europe. MDS uses pairwise IBS data based on the 848 loci generated by PLINK software and plotted using R version 2.15.0. The central position of east Africans and some other Africans emphasizes the founding role of east African gene pool and the disparate alignment on coordinates along which the world populations were founded including populations of Aftica aligning along the 4th dimension. (TIF)
Figure 4. Multidimensional Scaling Plot (MDS). A. First and second coordinates of an MDS plot of 848 Microsatellite Marshfield data set across the human genome for 24 populations from Africa, Asia and Europe. MDS plot was constructed from pairwise differences FST generated by Arlequin program (Table S3). B. First and second coordinates of an MDS plot of 848 Microsatellite loci, across the human genome in 469 individuals from 24 populations from Africa, Asia and Europe. MDS uses pairwise IBS data based on the 848 loci generated by PLINK software and plotted using R version 2.15.0. East Africans cluster to the left of the plot, while Beja (red cluster in the middle), assumes intermediate position. doi:10.1371/journal.pone.0097674.g004
Figure S4 Multidimensional Scaling Plot (MDS). First and second coordinates of an MDS plot based on MT-CO2 data set constructed from pairwise differences FST generated by Arlequin v3.11. Population code as follows: Nara: Nar, Kunama (Kun), Hidarb (Hid), Afar (Afa), Saho (Sah), Bilen (Bil), Tigre (Tgr), Tigrigna (Tig), Rashaida (Rsh), Nilotics (Nil), Beja (Bej), Ethiopians(Eth), Egyptians (Egy), Moroccans (Mor), Southern Africans (Sth), Pygmy (Pyg), Saudi Arabia (Sdi), Asia (Asi), Europe (Eur), Native Americans (NA), Australians (Ast), Nubians (Nub), Nuba (Nba) (TIF)
--Jibril Hirbo, Sara Tishkoff et al.
The Episode of Genetic Drift Defining the Migration of Humans out of Africa Is Derived from a Large East African Population Size
PLoS One. 2014; 9(5): e97674. Published online 2014 May 20. doi: 10.1371/journal.pone.0097674
And surprisingly the following was stated by Brenna Henn, in this interview on population genetics and population structure, considering African populations.
“African populations have the most genetic diversity in the world,” Henn said. “If you compared people from the Kalahari Desert to people from Mali, they’d be as different from each other [genetically] as Italians and Chinese people.”
Why are other populations of humans so much less genetically varied than Africans? The answer, Henn explains, lies in our ancestors’ history; the groups of people that migrated out of Africa and spread throughout other continents were smaller subsets of that original, genetically diverse population.
"AND WITHIN EACH OF THESE GROUPS THERE IS AN AMAZING AMOUNT OF DIVERSITY, [...] THE DIVERSITY IS INDIGNIOUS TO AFRICAN POPULATIONS":
Tracing Family Trees, And Human History, With Genetics
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