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Post by Tukuler on Sept 22, 2017 15:43:04 GMT
Pontus Skoglund et al (2017)
Reconstructing Prehistoric African Population StructureCell Volume 171, Issue 1, p59–71.e21, 21 September 2017 DOI: dx.doi.org/10.1016/j.cell.2017.08.049 | I see only two Africans listed among the team. Chrissy Chiumia and Elizabeth Gomani-Chindebvu are associated with the Malawi Dept of Museums and Monuments in Lilongwe. They aren't 'equally contributing authors but neither are the usual aDNA report suspects Mallick Hellenthal Pääbo Patterson though Pinhasi Krause Reich are noted as Sr authors. After a glance • basal West African (something I guessed from the age of nrY A00 plus the fact of Pleistocene W Afrs becoming Holocene Green Saharans then returning to W Afr) • so-called Eurasian genomes in Africans possibly are pre-OoA African genomes (are they finally peeping said reality - not all OoA genomes left the continent and studies will have to consider which set they're working with) these are the grab bag items for me. That's not to say the 16 Software and Algorithms tools links are throwaways. New to me are the 5 prehistoric Malawi samples that're older than Mota. The three males are all BT. Two had L0d1 mothers, the other's mum was L0k2. One female, an older contemporary of Mota, was L0k1. A female, and oldest of the 8 ancient Malawi samples was mtDNA L0a2. The only sample younger than Mota is an L0f female.
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Post by Tukuler on Sept 22, 2017 21:28:25 GMT
qpAdm
We successfully obtained mixture models for 55 Target populations, comprising
both ancient populations (we excluded Malawi_Chencherere_5200BP due to low
SNP coverage) and populations genotyped on the Affymetrix Human Origins array,
all shown in Table S5. In one analysis, Tanzania_Luxmanda_3100BP was also used
as a target population, and in these analyses it was dropped from the outgroup set.
We highlight some notable mixture models inferred here:
• Kenya_400BP,
Tanzania_Pemba_1400BP and
Hadza1
are all fitted as having ∼100% Ethiopia_4500BP-related ancestry.
The other group of Hadza samples are fitted as having
19% ± 8% Dinka-related ancestry
(the remainder being Ethiopia_4500BP-related).
• Tanzania_Pemba_600BP,
Malawi_Chewa, _Ngoni, _Tumbuka, _Yao,
Yoruba, Esan, Gambian,
Luo, BantuKenya,
BantuSA_Ovambo, Himba, Wambo, BantuSA_Herero
are all fitted as consistent with having ∼100% Mende-related western African-related ancestry.
The Mandenka, from the western African coast,
are fitted as having 2.8% ± 0.6% Levant Neolithic-related ancestry (PPNB).
• The Luhya, an eastern Bantu-speaking group,
are fitted as having 40% ± 6% Dinka-related ancestry,
with the remainder being western African Mende-related ancestry.
• The Biaka, a western rainforest hunter-gatherer group in Cameroon,
is fitted as having 72% ± 2% Mbuti-related ancestry
(the Mbuti are an eastern rainforest hunter-gatherer group),
with the remainder being western African Mende-related ancestry.
• The minimum indigenous southern African ancestry observed
in Khoe-groups and Bantu-speakers in southern Africa
is∼8% ± 2% in the Damara,
and the remainder is western African-related.
• The maximum indigenous southern African ancestry
observed in the present-day populations is the
91% ± 1% inferred for the Ju_hoan_North,
with the remainder being related to Tanzania_Luxmanda_3100BP.
• Some populations in northern and eastern Africa
are fitted as having large proportions of
Tanzania_Luxmanda_3100BP-related ancestry.
This includes the Maasai (49% ± 2%) and Datog (66% ± 3%)
who have ancestry also related to the Dinka;
the Kikuyu (63% ± 2%) who also have ancestry related to the Mende;
and finally, the Afar (79% ± 3%) and Somali (62% ± 6%)
who have large amounts of inferred Tanzania_Luxmanda_3100BP-related ancestry
in addition to ancestry related to the Iran Neolithic.
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Post by Tukuler on Sept 23, 2017 6:19:24 GMT
Early Levantine Farmer-Related Admixture in an ∼3,100-Year-Old Pastoralist from TanzaniaWestern-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). 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). • so-called Eurasian genomes in Africans possibly are pre-OoA African genomes (are they finally peeping said reality - not all OoA genomes left the continent and studies will have to consider which set they're working with)
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Post by Tukuler on Sept 28, 2017 20:56:19 GMT
These are the recovered real nrY haplogroup mutations for the aDNA samples  |
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Post by Tukuler on Sept 28, 2017 21:49:26 GMT
ADMIXTURE graph at K=7 as originally presented and with bars rearranged to group predominant K percentages  Note the very slight East Asian K in • Nama • Maasai • Oromo • Somali The E Asian K bearing individuals of those ethnies also have Sardinian and Luxmanda Ks. No Sardinian K samples are without Luxmanda K. I have to wonder what the E Asian and Sardinia Ks are in some of the samples. Are they really all non-African in origin? |
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Post by Tukuler on Sept 28, 2017 22:59:16 GMT
These f4 statistics suggestions ons were concluded from the
four highest Z scores.
• shared history between MSL and Archaics
• shared history between YRI and Mota/S Afr_2kbp
• BASAL HUMAN flow into MSL more than YRI
• YRI-related flow into Mota and S Afr_2kbp ancestors
• Mota-related flow into YRI more than MSL ancestors
• Mota and MSL are no clade exclusive of S Afr_2kbp
because of excess basal ancestry in Mende
or back and forth flow between Mota-like and S Afr_2kbp
Since other f4 stats rule out Neanderthal or Denisovan flow,
the Archaic sharing history with Mende and Yoruba to a
lesser extent is an African Archaic,
Basal West African, Basal
Human waiting archeoanthropology discovery.
For West Africa population structure this report revealed
• a Basal West African ghost population
• Bight of Benin-like flow into an African ancestral to East and South Africans
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