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Promenade
21-09-17, 20:59
Reconstructing Prehistoric African Population Structure, Skoglund et al. - http://www.cell.com/cell/fulltext/S0092-8674(17)31008-5

Levantine Ancestry (I'm guessing Natufian) found in an African individual from 1000BC. If the latter hypothesis given here is correct perhaps it is a signal of shared ancestry from the first Afro-Asiatic Speakers?

"Western-Eurasian-related ancestry is pervasive in eastern Africa today (Pagani et al., 2012, Tishkoff et al., 2009), and the timing of this admixture has been estimated to be ∼3,000 BP on average (Pickrell et al., 2014). We found that the ∼3,100 BP individual (Tanzania_Luxmanda_3100BP), associated with a Savanna Pastoral Neolithic archeological tradition, could be modeled as having 38% ± 1% of her ancestry related to the nearly 10,000-year-old pre-pottery farmers of the Levant (Lazaridis et al., 2016), and we can exclude source populations related to early farmer populations in Iran and Anatolia. These results could be explained by migration into Africa from descendants of pre-pottery Levantine farmers or alternatively by a scenario in which both pre-pottery Levantine farmers and Tanzania_Luxmanda_3100BP descend from a common ancestral population that lived thousands of years earlier in Africa or the Near East. We fit the remaining approximately two-thirds of Tanzania_Luxmanda_3100BP as most closely related to the Ethiopia_4500BP (p = 0.029) or, allowing for three-way mixture, also from a source closely related to the Dinka (p = 0.18; the Levantine-related ancestry in this case was 39% ± 1%) (Table S4)."

Also Somalians are best modeled with Iran Neo ancestry, seems CHG like ancestry didnt just creep into Southern Europe and the Steppes... it eventually made it's way south to Africa as well

"While these findings show that a Levant-Neolithic-related population made a critical contribution to the ancestry of present-day eastern Africans (Lazaridis et al., 2016), present-day Cushitic speakers such as the Somali cannot be fit simply as having Tanzania_Luxmanda_3100BP ancestry. The best fitting model for the Somali includes Tanzania_Luxmanda_3100BP ancestry, Dinka-related ancestry, and 16% ± 3% Iranian-Neolithic-related ancestry (p = 0.015). This suggests that ancestry related to the Iranian Neolithic appeared in eastern Africa after earlier gene flow related to Levant Neolithic populations, a scenario that is made more plausible by the genetic evidence of admixture of Iranian-Neolithic-related ancestry throughout the Levant by the time of the Bronze Age (Lazaridis et al., 2016) and in ancient Egypt by the Iron Age (Schuenemann et al., 2017)."

Also some significant discoveries about the ancient genetic make up of Africa. San related ancestry used to be found in much larger percentages all over prehistoric east africa. A South to North East cline of African ancestry used to exist mirroring the modern day South to North West cline of African Ancestry, but Bantu Migrations seems to have mostly replaced these people.

"We find that ancestry closely related to the ancient southern Africans was present much farther north and east in the past than is apparent today. This ancient southern African ancestry comprises up to 91% of the ancestry of Khoe-San groups today (Table S5 (http://www.cell.com/cms/attachment/2108833685/2082649544/mmc5.xlsx)), and also 31% ± 3% of the ancestry of Tanzania_Zanzibar_1400BP, 60% ± 6% of the ancestry of Malawi_Fingira_6100BP, and 65% ± 3% of the ancestry of Malawi_Fingira_2500BP (Figure 2 (http://www.cell.com/cms/attachment/2108833685/2082649521/gr2.jpg)A). Notably, the Khoe-San-related ancestry in ancient individuals from Malawi and Tanzania is symmetrically related to the two previously identified lineages present in the San (Z < 2; Figure S2 (http://www.cell.com/cms/attachment/2108833685/2082649524/figs2.jpg)), estimated to have diverged at least 20,000 years ago (Mallick et al., 2016, Pickrell et al., 2012, Schlebusch et al., 2012), implying that this was an ancient divergent branch of this group that lived in eastern Africa at least until 1,400 BP. However, it was not present in all eastern Africans, as we do not detect it in the ∼400-year-old individual from coastal Kenya nor in the present-day Hadza"

"Both unsupervised clustering (Figure 1 (http://www.cell.com/cms/attachment/2108833685/2082649523/gr1.jpg)B) and formal ancestry estimation (Figure 2 (http://www.cell.com/cms/attachment/2108833685/2082649521/gr2.jpg)B) suggest that individuals from the Hadza group in Tanzania can be modeled as deriving all their ancestry from a lineage related deeply to ancient eastern Africans such as the Ethiopia_4500BP individual (Figure 3 (http://www.cell.com/cms/attachment/2108833685/2082649522/gr3.jpg)A; Table S5 (http://www.cell.com/cms/attachment/2108833685/2082649544/mmc5.xlsx)). However, this lineage appears to have contributed little ancestry to present-day Bantu speakers in eastern Africa, who instead trace their ancestry to a lineage related to present-day western Africans, with additional components related to the Nilotic-speaking Dinka and to the Tanzania_Luxmanda_3100BP pastoralist (see below; Figure 2 (http://www.cell.com/cms/attachment/2108833685/2082649521/gr2.jpg)). The Sandawe, another population that like the Hadza uses click consonants in their spoken language, are modeled as having ancestry similar to the Hadza but also admixture related to that of neighboring populations (Figure 3 (http://www.cell.com/cms/attachment/2108833685/2082649522/gr3.jpg)A; Table S5 (http://www.cell.com/cms/attachment/2108833685/2082649544/mmc5.xlsx)) consistent with previous findings (Henn et al., 2011, Tishkoff et al., 2009). Population replacement by incoming food producers appears to have been nearly complete in Malawi, where we detect little if any ancestry from the ancient individuals who lived ∼8,100–2,500 BP. Instead, present-day Malawian individuals are consistent with deriving all their ancestry from the Bantu expansion of ultimate western African origin (Figure 3 (http://www.cell.com/cms/attachment/2108833685/2082649522/gr3.jpg))."

West Africans might harbor lineage that split from San as early as 300,000 years ago, the earliest known divergence of modern human lineage still present today.

"we find that ancient southern Africans, who have none of the eastern African admixture that is ubiquitous today, share significantly more alleles with present-day and ancient eastern Africans (including Dinka, Hadza, and Ethiopia_4500BP) than they do with present-day western Africans (Figure 3 (http://www.cell.com/cms/attachment/2108833685/2082649522/gr3.jpg)B; Table S6 (http://www.cell.com/cms/attachment/2108833685/2082649541/mmc6.xlsx)). Even within present-day western Africans, the genetic differences between Yoruba from Nigeria and the Mende from Sierra Leone are inconsistent with descent from a homogeneous ancestral population isolated from ancient southern Africans. The asymmetry between Yoruba and Mende is also observed with non-Africans but is no stronger than in eastern Africans (the most closely related Africans to the ancestral out-of-Africa population), and thus these signals are not driven by admixture from outside Africa and instead likely reflect demographic events entirely within Africa (Figure 3 (http://www.cell.com/cms/attachment/2108833685/2082649522/gr3.jpg)C; Table S6 (http://www.cell.com/cms/attachment/2108833685/2082649541/mmc6.xlsx))."

"The possible basal western African population lineage would represent the earliest known divergence of a modern human lineage that contributed a major proportion of ancestry to present-day humans. Such a lineage must have separated before the divergence of San ancestors, which is estimated to have begun on the order of 200–300 thousand years ago (Scally and Durbin, 2012). Such a model of basal western African ancestry might support the hypothesis that there has been ancient structure in the ancestry of present-day Africans, using a line of evidence independent from previous findings based on long haplotypes with deep divergences from other human haplotypes (Hammer et al., 2011, Lachance et al., 2012, Plagnol and Wall, 2006). One scenario consistent with this result could involve ancestry related to eastern Africans (and the out-of-Africa population) expanding into western Africa and mixing there with more basal lineages. Our genetic data do not support the theory that this putative basal lineage diverged prior to the ancestors of Neanderthals, since the African populations we analyze here are approximately symmetrically related to Neanderthals (Mallick et al., 2016, Prüfer et al., 2014)."

mlukas
21-09-17, 21:15
So I can speculate that proto-Khoisan South African population which diverged 300 000 years ago was represented by Florisbad skull

Angela
22-09-17, 20:37
Thanks, Promenade. Very interesting indeed. All the luminaries in on this one. Getting a lot of press.

It's obviously much bigger than Natufian showing up in these people: it's about African prehistoric genetic structure in general.

The Bantu seem to have mostly wiped out the hunter-gatherer peoples. The same thing happened again and again when farmers encountered hunter-gatherers, although much less so in Europe, probably partly because that Neolithic package wasn't as suited to the climate and terrain of far northern and eastern areas of Europe. Amazing the drop in San like ancestry.

"Our documentation of a radically different landscape of human populations before and after the spread of food producers highlights the difficulty of reconstructing the African past based solely on analysis of present-day populations and the importance of using ancient DNA to study deep African population history in an era in which technological improvements have now made this feasible."

I find this very interesting as well:
" The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others."

There seem to have been repeated flows of West Eurasian ancestry into eastern African, which were transmitted southwards:

"Earlier migration(s), which brought ancestry related to the ancient Near East (Lazaridis et al., 2016, Pagani et al., 2012, Pickrell et al., 2014), brought herding to eastern Africa by ∼4,000 BP (Marshall et al., 1984) and to southern Africa by ∼2,000 BP (Sadr, 2015)."

By earlier they mean before the Bantu migrations, I think.

Another interesting take away:
"While these findings show that a Levant-Neolithic-related populationmade a critical contribution to the ancestry of presentdayeastern Africans (Lazaridis et al., 2016), present-day Cushiticspeakers such as the Somali cannot be fit simply as havingTanzania_Luxmanda_3100BP ancestry. The best fitting modelfor the Somali includes Tanzania_Luxmanda_3100BP ancestry,Dinka-related ancestry, and 16% ± 3% Iranian-Neolithic-relatedancestry (p = 0.015). This suggests that ancestry related to theIranian Neolithic appeared in eastern Africa after earlier geneflow related to Levant Neolithic populations, a scenario that ismade more plausible by the genetic evidence of admixture ofIranian-Neolithic-related ancestry throughout the Levant by thetime of the Bronze Age (Lazaridis et al., 2016) and in ancientEgypt by the Iron Age (Schuenemann et al., 2017).

As to selection, they found selection for certain taste receptors in southern Africa. There's also this:

". The functional category that displays themost extreme allele frequency differentiation between presentdaySan and ancient southern Africans is ‘‘response to radiation’’(Z = 3.3 compared to the genome-wide average). To control forthe possibility that genes in this category show an inflated allelefrequency differentiation in general, we computed the same statisticfor the Mbuti central African rainforest hunter-gatherergroup but found no evidence for selection affecting the responseto radiation category (Figure 4C). Instead, the top category forthe Mbuti is ‘‘response to growth,’’ suggesting the possibilitythat the small stature of rainforest hunter-gatherer populationssuch as the Mbuti may be an acquired adaptation (although wehave no ancient central African genome and thus no informationabout the time frame of selection). We speculate that the signalfor selection in the response to radiation category in the Sancould be due to exposure to sunlight associated with the life ofthe zKhomani and Juj’hoan North people in the Kalahari Basin,which has become a refuge for hunter-gatherer populations inthe last millenia due to encroachment by pastoralist and agriculturalistgroups (Morris, 2002)."

Some great graphics. The paper really deserves a read.

https://postimg.org/image/y8tn7wxv9/https://postimg.org/image/y8tn7wxv9/

http://tinypic.com/r/1incw9/9
http://tinypic.com/r/1incw9/9
https://postimg.org/image/y8tn7wxv9/

Angela
22-09-17, 21:51
Some tweets:
Pontus Skoglund‏ @pontus_skoglund (https://twitter.com/pontus_skoglund) Sep 21 (https://twitter.com/pontus_skoglund/status/910926568704188418)More



In our study today we model that earliest diverging modern human lineages are found in western-not southern-Africa


"Iosif Lazaridis‏ @iosif_lazaridis (https://twitter.com/iosif_lazaridis) Sep 21 (https://twitter.com/iosif_lazaridis/status/910924094413180929)More



New by @pontus_skoglund (https://twitter.com/pontus_skoglund) et al. http://www.cell.com/cell/fulltext/S0092-8674(17)31008-5 … (https://t.co/gC70BPiVF8)Ancient E-S African cline has very little overlap with present-day Africans.


So great to see that the Levantine-related ancestry that we detected in 2016 in East Africa also went west ~4,000km, all the way to Morocco

Megalophias
22-09-17, 22:08
The Eurasian admix they found was not Natufian but PPNB, which is more Anatolian-shifted.

The Bantu (in East and Southern Africa) were not just farmers, they were also iron metallurgists, so they had more of an advantage than Neolithic farmers would. Going far south in Africa the climate changes from tropical summer rainfall, good for growing sorghum and millet, to a temperate winter rainfall regime, or to desert. So that's where the juggernaut had to pause. There were San groups in eastern South Africa which only died out/were finally assimilated in the 20th century, and of course in the Kalahari Desert region they are still around. The Khoe pastoralists were on much more even terms with the Bantu and were doing pretty well for themselves prior to European colonization.

Promenade
22-09-17, 23:09
@Angela
Yes a lot of important names, in between this and the paper on North Africa it's a good week for anyone interested in ancient african genetics, although I assume most people already figured that west african migrants largely replaced the ancient people of east africa. The biggest surprise for me is that west africans could have ancestry that diverged from the San as early as 300,00 years ago.


The Eurasian admix they found was not Natufian but PPNB, which is more Anatolian-shifted.

Thank you for clarifying on the exact origins, odd that the papers labels it just "Levantine" and at the same time mentions that it excludes Anatolian ancestry. I think this "Levantine" ancestry and it's association with Semitic/Afro-asiatic languages is strengthened here now that we know it was present in ancient North Africans as well. Perhaps they were also responsible for bringing pastorilism to east Africa as Angela noted.

Now I'm wondering just who brought Iran Neo ancestry to east africa.

LeBrok
23-09-17, 06:47
@Angela

Now I'm wondering just who brought Iran Neo ancestry to east africa.IIRC, Levant Bronze Age had some Iran N.

IronSide
23-09-17, 08:15
Now I'm wondering just who brought Iran Neo ancestry to east africa.

As LeBrok suggested, Levant BA did have some Iran-Neo, Levant BA probably spoke Semitic? Ethiopians (https://en.wikipedia.org/wiki/Ethiopian_Semitic_languages) are Semitic speakers.


While focused on Semitic languages as the only branch of the broader Afroasiatic languages that is also today distributed outside Africa, a recent study by Kitchen et al. proposed through the use of Bayesian computational phylogenetic techniques that "contemporary Ethiosemitic languages of Africa reflect a single introduction of early Ethiosemitic from southern Arabia approximately 2800 years ago", and that this single introduction of Ethiosemitic underwent "rapid diversification" within Eritrea and Ethiopia.

Which means that these early Ethiosemitic speakers themselves migrated to south Arabia from the Levant, and then to East Africa, probably pushed by Old South Arabian (https://en.wikipedia.org/wiki/Old_South_Arabian) speakers, who unlike Ethiopian (South Semitic language) belong to the Central Semitic branch alongside northwest Semitic (Hebrew, Aramaic, Phoenician) and Arabic.

Promenade
23-09-17, 10:34
Okay, but the Iran Neo ancestry seems to have reached the area sometime after the end of the Levant Bronze Age. It had to enter sometime during the Iron Age, Luxmanda is from around the Bronze Age collapse and she has no Iran Neo.

Also if it did come from the Levant we'd also expect an increase in N.W Anatolian farmer ancestry and more Natufian like ancestry, but at the same time I highly doubt it entered unadmixed.

IronSide
23-09-17, 10:57
Okay, but the Iran Neo ancestry seems to have reached the area sometime after the end of the Levant Bronze Age. It had to enter sometime during the Iron Age, Luxmanda is from around the Bronze Age collapse and she has no Iran Neo.

Also if it did come from the Levant we'd also expect an increase in N.W Anatolian farmer ancestry and more Natufian like ancestry, but at the same time I highly doubt it entered unadmixed.
It came from Yemen during the Iron Age? and it was probably admixed by whatever population was in Yemen at the time, that population may have had Iran-N independently from Semitic migrants from the Levant? I don't know.

The first migrants who didn't have the Iran-N were probably Cushitic speakers, they separated from other Afro-Asiatic groups in PPN Levant before admixture from Iran/Caucasus, the second group were Semitic Ethiopian tribes, who arrived in the Iron Age, bringing with them that admixture.

I guess ...

bicicleur
23-09-17, 12:29
As LeBrok suggested, Levant BA did have some Iran-Neo, Levant BA probably spoke Semitic? Ethiopians (https://en.wikipedia.org/wiki/Ethiopian_Semitic_languages) are Semitic speakers.



Which means that these early Ethiosemitic speakers themselves migrated to south Arabia from the Levant, and then to East Africa, probably pushed by Old South Arabian (https://en.wikipedia.org/wiki/Old_South_Arabian) speakers, who unlike Ethiopian (South Semitic language) belong to the Central Semitic branch alongside northwest Semitic (Hebrew, Aramaic, Phoenician) and Arabic.

it is the time of the Queen of Sheba, and Sheba would have been woutwestern Yemen

bicicleur
23-09-17, 13:49
I wonder if hte basal Africans in west Africa could be related to the people found at Irhoud, who were the forfathers of the Aterian, which lasted in northern Africa till 30 ka.

http://www.nature.com/nature/journal/v546/n7657/full/nature22336.html?foxtrotcallback=true
http://www.nature.com/news/oldest-homo-sapiens-fossil-claim-rewrites-our-species-history-1.22114

Genetiker
23-09-17, 18:45
I'm posting Y-SNP calls here:

Y-SNP calls from prehistoric sub-Saharan Africa (https://genetiker.wordpress.com/2017/09/23/y-snp-calls-from-prehistoric-sub-saharan-africa/)

Ygorbr
24-09-17, 07:09
Now I'm wondering just who brought Iran Neo ancestry to east africa.

I'd bet on Semites for that. In my opinion, dialects of Proto-Afro-Asiatic, a much older language (some estimate it to have been spoken as far as 15,000 years ago), were spread by this ancient expansion formed by mainly Levantine farmer and perhaps later a bit of Anatolian-shifted ancestry. Proto-Semitic, which is a Late Chalcolithic/Early Bronze Age language, was probably the northernmost branch of Afro-Asiatic, in the northern Levant/northern Mesopotamia, and was since its beginning carried on by the expanding Iranian-related ancestry that descended the Anatolian and Iranian plateaus down to the Mesopotamian and Levantine lowlands, adopting (and perhaps in this process also changing) the local Afro-Asiatic languages.

The Semitic expansion to East Africa is thousands of years younger than that of early farmers and pastoralists from the Levant. They were certainly another people also genetically. The ancient PPNB ancestry must've been the one who brought very divergent Afro-Asiatic branches like Cushitic and Omotic, and perhaps only (much) later the slightly more "Semitic-like" Egyptian and Berber branches. The Semitic expansion would've been the last big wave.

Ygorbr
24-09-17, 07:24
It came from Yemen during the Iron Age? and it was probably admixed by whatever population was in Yemen at the time, that population may have had Iran-N independently from Semitic migrants from the Levant? I don't know.

The first migrants who didn't have the Iran-N were probably Cushitic speakers, they separated from other Afro-Asiatic groups in PPN Levant before admixture from Iran/Caucasus, the second group were Semitic Ethiopian tribes, who arrived in the Iron Age, bringing with them that admixture.

I guess ...
I agree. That's also how I "picture" the historical sequence of events indicated by evidences of genetics and linguistics.