Reconstructing Prehistoric African Population Structure

[drobbah]

3100 yr old Tanzanian pastoralist genome has been analyzed.I was hoping to see some sort of E-M35/T-M70 lineage from the Tanzanian nomad but instead the Kenyan genome came out as E1b1b1b2

 

"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%)"

The study also claimed the Somalis have around 13-16% Iran_N ancestry.Doesn't seem realistic in my honest opinion...

"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)."

[Awale]

This is pretty funny for me because I emailed Pontus Skoglund about something a while back and he just recently replied and one of his two emails said:

tomorrow we have a paper on African ancient DNA that is coming out in Cell which might be of interest to you.

Great to see this study, anyway. Will have to properly read it and look at its data before posting again, though.

The study also claimed the Somalis have around 13-16% Iran_N ancestry.Doesn't seem realistic in my honest opinion...

Agreed.

[blackflash16]

Here are the qpAdm results cited in the paper:

 

	Table S5. Details of ancestry proportions inferred using qpAdm.
	Target population	P-value for chosen model	Number of sources	Source 1	Source 1 ancestry	Source 1 SE	Source 2	Source 2 ancestry	Source 2 SE	Source 3	Source 3 ancestry	Source 3 SE	Outgroup population in worst outlier for f4(Target population, fitted Target Population; Base (Mbuti), Outgroup)	Z-score for worst outlier	Number of SNPs (Ancient individuals are enriched for 1.2M SNPs, present-day populations genotyped for ~600k)
	Kenya_400BP	0.263546414	1	Ethiopia_4500BP	100.0%	0.0%									27,532
	Tanzania_Pemba_1400BP	0.070819424	1	Ethiopia_4500BP	100.0%	0.0%									22,680
	Hadza1	0.044373607	1	Ethiopia_4500BP	100.0%	0.0%									74,967
	Tanzania_Pemba_600BP	0.356951982	1	Mende	100.0%	0.0%									102,412
	Malawi_Chewa	0.818452487	1	Mende	100.0%	0.0%									69,106
	Malawi_Ngoni	0.683597822	1	Mende	100.0%	0.0%									77,158
	Malawi_Tumbuka	0.596606063	1	Mende	100.0%	0.0%									70,736
	Malawi_Yao	0.56514891	1	Mende	100.0%	0.0%									69,887
	Yoruba	0.699650257	1	Mende	100.0%	0.0%									65,208
	Esan	0.889835332	1	Mende	100.0%	0.0%									73,045
	Gambian	0.010650124	1	Mende	100.0%	0.0%									74,979
	Luo	0.020767054	1	Mende	100.0%	0.0%									72,548
	BantuKenya	0.062937628	1	Mende	100.0%	0.0%									74,528
	BantuSA_Ovambo	0.459703325	1	Mende	100.0%	0.0%									82,121
	Himba	0.025321143	1	Mende	100.0%	0.0%									77,920
	Wambo	0.311331451	1	Mende	100.0%	0.0%									73,539
	BantuSA_Herero	0.038491594	1	Mende	100.0%	0.0%									83,930
	Tanzania_Luxmanda_3100BP	0.027331465	2	Ethiopia_4500BP	62.2%	1.4%	PPNB	37.8%	1.4%				South_Africa_2000BP	2.5	124,595
	Tanzania_Luxmanda_3100BP_PMD	0.164555237	2	Ethiopia_4500BP	62.8%	1.8%	PPNB	37.2%	1.8%				Anatolia_Neolithic	-57.7	60,127
	South_Africa_1200BP	0.797655643	2	South_Africa_2000BP	59.7%	2.3%	Tanzania_Luxmanda_3100BP	40.3%	2.3%				Ust_Ishim	1.1	87,068
	South_Africa_1200BP_PMD	0.79752436	2	South_Africa_2000BP	46.0%	7.4%	Tanzania_Luxmanda_3100BP	54.0%	7.4%				Punjabi	1.3	14,391
	Tanzania_Zanzibar_1400BP	0.1349785	2	Ethiopia_4500BP	69.2%	3.0%	South_Africa_2000BP	30.8%	3.0%				PPNB	-1.7	108,179
	Malawi_Fingira_6100BP	0.120308552	2	Ethiopia_4500BP	39.5%	5.5%	South_Africa_2000BP	60.5%	5.5%				Iran_Neolithic	-1.4	25,077
	Malawi_Hora_8100BP	0.048618646	2	Ethiopia_4500BP	46.6%	2.8%	South_Africa_2000BP	53.4%	2.8%				Dinka	2.7	90,781
	Malawi_Fingira_2500BP	0.041801755	2	Dinka	35.0%	2.8%	South_Africa_2000BP	65.0%	2.8%				Mende	2.2	94,371
	Mandenka	0.698583702	2	Mende	97.2%	0.6%	PPNB	2.8%	0.6%				Dinka	-1.9	68,671
	Biaka	0.263704374	2	Mbuti	72.1%	2.4%	Mende	27.9%	2.4%				Iran_Neolithic	-1.9	68,488
	Hadza	0.02738864	2	Dinka	19.3%	8.5%	Ethiopia_4500BP	80.7%	8.5%				Ust_Ishim	2.7	69,413
	Masai	0.014608198	2	Dinka	50.9%	2.1%	Tanzania_Luxmanda_3100BP	49.1%	2.1%				Ami	-2.4	69,646
	Datog	0.128763111	2	Dinka	34.0%	3.0%	Tanzania_Luxmanda_3100BP	66.0%	3.0%				Mixe	-2.0	75,739
	Kikuyu	0.018943915	2	Mende	62.8%	2.0%	Tanzania_Luxmanda_3100BP	37.2%	2.0%				Dinka	-3.0	77,057
	Ju_hoan_North	0.050248981	2	South_Africa_2000BP	90.9%	1.2%	Tanzania_Luxmanda_3100BP	9.1%	1.2%				Denisova	3.3	66,308
	Ju_hoan_South	0.060549412	2	South_Africa_2000BP	89.5%	1.2%	Tanzania_Luxmanda_3100BP	10.5%	1.2%				Denisova	2.9	72,546
	Taa_North	0.048898318	2	South_Africa_2000BP	88.1%	1.2%	Tanzania_Luxmanda_3100BP	11.9%	1.2%				Denisova	2.7	69,475
	Naro	0.092694084	2	South_Africa_2000BP	88.0%	1.2%	Tanzania_Luxmanda_3100BP	12.0%	1.2%				Denisova	2.5	70,640
	Afar_WGA	0.035029029	2	Ganj_Dareh_Iran_Neolithic	21.1%	2.5%	Tanzania_Luxmanda_3100BP	78.9%	2.5%				Dinka	-3.9	72,683
	Luhya	0.588961185	2	Dinka	39.8%	5.9%	Mende	60.2%	5.9%				South_Africa_2000BP	1.6	72,591
	Gana	0.177044532	2	Dinka	38.4%	1.6%	South_Africa_2000BP	61.6%	1.6%				Anatolia_Neolithic	-1.5	71,036
	Khwe	0.08673416	2	Dinka	62.1%	1.5%	South_Africa_2000BP	37.9%	1.5%				Ethiopia_4500BP	2.1	70,886
	Xuun	0.047257056	2	Dinka	29.9%	1.6%	South_Africa_2000BP	70.1%	1.6%				Denisova	1.6	66,801
	Hoan	0.183725467	2	Dinka	27.8%	1.9%	South_Africa_2000BP	72.2%	1.9%				Mixe	1.5	70,984
	Taa_West	0.141966574	2	Dinka	18.5%	1.8%	South_Africa_2000BP	81.5%	1.8%				Denisova	2.0	67,814
	Taa_East	0.023684896	2	Dinka	22.1%	1.9%	South_Africa_2000BP	77.9%	1.9%				Mixe	2.5	70,560
	Mbuti	0.144248841	2	Mende	47.5%	2.7%	South_Africa_2000BP	52.5%	2.7%				Iran_Neolithic	2.4	71,998
	Damara	0.684312915	2	Mende	92.4%	1.8%	South_Africa_2000BP	7.6%	1.8%				Denisova	1.7	70,908
	BantuSA	0.749653639	2	Mende	80.6%	1.7%	South_Africa_2000BP	19.4%	1.7%				Denisova	2.2	72,668
	Tswana	0.643588346	2	Mende	79.0%	1.8%	South_Africa_2000BP	21.0%	1.8%				Denisova	2.5	72,673
	Kgalagadi	0.250834567	2	Mende	65.3%	1.7%	South_Africa_2000BP	34.7%	1.7%				Denisova	3.1	72,699
	Somali	0.015401137	3	Dinka	21.7%	3.5%	Ganj_Dareh_Iran_Neolithic	16.2%	2.6%	Tanzania_Luxmanda_3100BP	62.1%	5.6%	Mende	-2.1	68,793
	Burbur_WGA	0.114531304	3	Anatolia_Neolithic	1.3%	58.1%	Dinka	19.7%	5.0%	PPNB	79.0%	62.8%	Iran_Neolithic	2.0	73,083
	Gui	0.034545878	3	Mbuti	27.1%	9.2%	South_Africa_2000BP	61.4%	8.0%	Tanzania_Luxmanda_3100BP	11.5%	1.8%	Mixe	2.1	70,837
	Shua	0.093270308	3	Mende	49.5%	2.8%	South_Africa_2000BP	35.8%	1.8%	Tanzania_Luxmanda_3100BP	14.8%	1.5%	Denisova	2.2	68,906
	Khomani	0.100823752	3	Dinka	13.9%	3.3%	South_Africa_2000BP	64.5%	1.9%	Tanzania_Luxmanda_3100BP	21.5%	2.0%	Ethiopia_4500BP	1.6	67,477
	Sandawe	0.045962257	3	Dinka	37.2%	3.6%	Mbuti	22.4%	2.3%	Tanzania_Luxmanda_3100BP	40.4%	2.0%	Punjabi	-1.7	66,718

The one for Somalis in particular:

Somali

0.015401137

3

Dinka

21.7%

3.5%

Ganj_Dareh_Iran_Neolithic

16.2%

2.6%

Tanzania_Luxmanda_3100BP

62.1%

5.6%

Mende

-2.1

68,793

[Awale]

Yeah, I finally got to that part:

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).

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).

Seems rather implausible. I'd like to see what we'll get with Treemix and nMonte, though. But I'm not surprised that there's something more basal about the South-Erythraeaic speaking pastoralist's West-Eurasian ancestry. Lank and I noticed several years ago with ADMIXTURE alone that there was something minutely different about the admixture in Southeast Africans and Somalis (Somalis sometimes looked a little more "Med", for example) but 16% extra Neolithic-Zagrosian and some extra Dinka-like ancestry makes no sense. For one, our region is mostly, not entirely, a dead-zone for Western-African related ancestry so direct admixture from full-on Dinka-like people after this South-Erythraeic speaker's ancestors left the Horn makes little sense so maybe it's just a sign of this pastoralist being admixed somehow with extra Mota-like ancestry, idk. The 16% extra Neolithic-Zagrosian makes no sense, though. The only things that could probably cause that would the Proto-Ethiopiansemitic speaking community and perhaps also admixture acquired during the Islamic period but neither make sense because:

1) Somalis never language-shifted. How on Earth are we carrying so much ancient Zagrosian ancestry possibly owed to the Proto-Ethiopiansemitic speaking community, especially while other analyses and lines of evidence (like uniparentals) never picked up on it?

2) There's just been no proof in either Uniparentals or auDNA up to this point that our ancestors notably out-mixed during the Islamic Period (~700 CE and beyond).


So I wonder what caused this if it's legitimate admixture. Weird stuff, I gotta say. But really interesting. On another note, it's great to finally see what archaeology, linguistics, even craniometrics and modern DNA have surmised for a while now backed up by aDNA:

We used our modeling framework to show that the South_Africa_1200BP pastoralist individual from the western Cape is consistent with being a mixture of just two streams of ancestry relative to non-southern African populations, with 40.3% ± 2.3% ancestry related to the Tanzania_Luxmanda_3100BP individual (54% ± 7% when restricting analysis to sequences with postmortem damage) and the remainder being related to the South_Africa_2000BP hunter-gatherers (Table S5). This supports the hypothesis that the Savanna Pastoral Neolithic archaeological tradition in eastern Africa is a plausible source for the spread of herding to southern Africa. Even the Ju|'hoan San group with the least genetic affinity to eastern Africans (Ju_hoan_North), have 9% ± 1% of their ancestry most closely related to Tanzania_Luxmanda_3100BP, consistent with previous findings that the ancestries of all present-day San and Khoe were affected by agro-pastoralist migrations in the last two millennia (Pickrell et al., 2014).

[Lank]

Let's see how well Pagani's 3000 YBP admixture date (repeated ad nauseum by academia) holds up when someone looks at this genome?

This study is a great first step, nice to see an early Cushite exploring Tanzania. Regarding the Somali admixture model, wildly speculating here, but perhaps the model is the problem? The Tanzanian may not be representative of the Cushitic ancestry in Somalis, forcing the addition of implausible, Nilotic and prehistoric Iran-related ancestry. Modern day South Cushites, who still retain a very high level of ancestry similar to this Tanzanian, show admixture with local hunter-gatherers, and vice versa. If the Tanzanian from 3100 ya already had this admixture, he could be a poor fit for the Cushitic ancestry of Somalis.

It would have been a nice start to have an ADMIXTURE analysis with more than just Sardinians as a proxy for Eurasian ancestry... Makes it a bit difficult to differentiate between ancient Levant and Iran/CHG-related ancestries.

[Awale]

Let's see how well Pagani's 3000 YBP admixture date (repeated ad nauseum by academia) holds up when someone looks at this genome?

Inshallah. I was actually surprised they didn't immediately go "Pagani-boi was wrong, baby." in this new paper but I think what held them up is that Somalis look to have a later layer of admixture based on their models. If Somalis and this Tanzanian were identical; they might've claimed Pagani et al.'s findings are implausible since we have a 3,100ybp sample from Tanzania with all the same admixture as modern Erythraeic speaking Horn-Africans like Somalis. But, by their findings, this is still roughly the case as the belief Pagani et al. spread was that all the West-Eurasian admixture hit around 3,000ybp but now, even by their models, it's clear the majority of it is shared with this Tanzanian sample and is most likely much older than the likely ES-speaking-community related signal Pagani et al. noticed all those years ago.

This study is a great first step, nice to see an early Cushite exploring Tanzania. Regarding the Somali admixture model, wildly speculating here, but perhaps the model is the problem? The Tanzanian may not be representative of the Cushitic ancestry in Somalis, forcing the addition of implausible, Nilotic and prehistoric Iran-related ancestry. Modern day South Cushites, who still retain a very high level of ancestry similar to this Tanzanian, show admixture with local hunter-gatherers, and vice versa. If the Tanzanian from 3100 ya already had this admixture, he could be a poor fit for the Cushitic ancestry of Somalis.

It would have been a nice start to have an ADMIXTURE analysis with more than just Sardinians as a proxy for Eurasian ancestry... Makes it a bit difficult to differentiate between ancient Levant and Iran/CHG-related ancestries.

Agreed with everything written above.

[blackflash16]

From a cave near the Indian Ocean, north of Mombasa:

I0595, Kenya_400BP

qpAdm: 100% Mota

The individual was a tall, robust young adult male. He was buried in a shallow grave in a crouched position with two hands and one foot in the small of the back and the skull disarticulated and placed by the knees. The individual was buried by sediment containing marine shell beads, small knapped stone tools, and Tana Tradition potsherds. The associated faunal remains are exclusively wild, with the exception of a single possible caprine bone. Large numbers of remains of birds, rodents, and other microfauna suggest that the cave may have only been sporadically occupied when the human remains were deposited. We infer from the material culture and fauna that the cave was occupied by foragers during the time the individual was buried, although food producers were present at nearby settlements such as Mtsengo and Mbuyuni (Helm, 2000). Crop remains of African sorghum, pearl millet and finger millet found at the site suggest these foragers had access to agricultural resources.

Two Individuals from the same cave on Pemba Island:

I0589, Tanzania_Pemba_1400BP.

qpAdm: 100% Mota

This limestone cave at the northern end of Pemba Island in the Zanzibar archipelago has been excavated in multiple campaigns, the most recent two seasons conducted by the ERC-funded Sealinks Project at Oxford University in 2012 and then the Max Planck Institute for the Science of Human History in 2016 (unpublished; see also (Chami et al., 2009)). The sequence shows clear evidence of
human occupation beginning around 1400 BP with an escargotie`re layer of giant African land snail shells, pottery, and disarticulated human remains. Above this layer, the sequence shows regular human use of the cave into the last thousand years.


I2298, Tanzania_Pemba_600BP

qpAdm: 100% Mande

A lower molar from context 301 (Sealinks Project faunal catalog no. 15624), which lies just below the surface and was dated to 639-544 BP (623 ± 20 uncalibrated BP, Wk-43308). Both specimens are associated with a highly unusual faunal assemblage, dominated by fragmented crocodile (Crocodylus cf. niloticus) remains and diverse microfauna, including Rattus rattus (Asian black rat), a
nonnative rodent that must have arrived to the area via maritime exchange routes. There are no taphonomic indicators in the faunal assemblage of hunting by humans, nor of crocodile predation on humans. During both of the occupational phases targeted in this study, there were nearby settlements occupied by farmers whose ancestors likely came from the mainland, for example at the sites of Tumbe (c. 1400-1000 BP) and Chwaka (1000-400 BP) (Fleisher and LaViolette, 2013).

From a cave on Zanzibar Island:

I0589, Tanzania_Zanzibar_1400BP

qpAdm: 69% Mota + 31% South_Africa_2000BP

A complete second phalanx of an adult (Sealinks Project faunal catalog no. 4353). It was recovered from context 1011, in association with local Tana Tradition ceramics typical of the MIA, moderately-sized limestone lithic artifacts, and diverse wild game animals, but no additional human remains (Prendergast et al., 2016). The specimen is directly dated to 1370-1303 BP (1479 ± 23 uncalibrated BP, OxA-31427), thus placing it at the beginning of the MIA phase. While Kuumbi Cave is interpreted as a forager site,
elsewhere on the island at this time, large settlements such as Unguja Ukuu emerge, occupied by farmers whose origins are likely on the mainland (Crowther et al., 2015; Juma, 2004).

East, "West" and "South" African ancestry in the Zanzibar Archipelago within the last 1500 years, along with The Hadza and Cushitic pastoralists on the Tanzanian mainland. SSA party

Shouldn't this thread be in the aDNA sub-forum?

[blackflash16]

The Kenya_500BP individual has |Z|>3 indication of Levant_N admixture (relative to Mota), his assigned Y-DNA is E1b1b:

Kenya_500BP Mota Levant_N Chimp 0.0401 3.643 4219 3894 74432

[blackflash16]

Here are some more d-stats for the Kenyan:

Kenya_500BP Mota Tanzania_Luxmanda_3000BP Chimp 0.0251 2.038 4060 3861 74507
Kenya_500BP Mota Somali Chimp 0.0175 2.040 4834 4668 89810
Kenya_500BP Mota Tanzania_Pemba_700BP Chimp 0.0018 0.139 3277 3265 65242
Kenya_500BP Mota Masai Chimp 0.0062 0.733 4707 4649 89810

Tanzania_Pemba_1400BP Mota Levant_N Chimp -0.0184 -1.398 2744 2846 52742
Tanzania_Luxmanda_3000BP Somali Mota Chimp -0.0090 -1.970 22038 22437 457675
Tanzania_Luxmanda_3000BP Somali Tanzania_Pemba_1400BP Chimp 0.0169 1.555 2532 2448 51969
Tanzania_Luxmanda_3000BP Somali Kenya_500BP Chimp 0.0093 1.044 3728 3659 74519
Tanzania_Luxmanda_3000BP Somali Hadza Chimp -0.0123 -3.509 22149 22700 457767

[blackflash16]

I uploaded the Luxmanda sample to gedmatch (Kit #: Z626350 ) but I'm not sure I did it right. The calculator results seem to be okay:

Near East Neolithic K13:

Admix Results (sorted):

# Population Percent
1 SUB_SAHARAN 50.15
2 NATUFIAN 30.41
3 ANATOLIA_NEOLITHIC 11.04
4 IRAN_NEOLITHIC 1.51
5 EHG 1.43
6 SHG_WHG 1.41
7 SIBERIAN 1.36
8 PAPUAN 1.33
9 SE_ASIAN 1.23

Least-squares method.

Using 1 population approximation:
1 Somali @ 19.217751
2 Masai @ 22.123108
3 Moroccan @ 32.525169
4 Hadza @ 33.111984
5 Saharawi @ 33.831158
6 Algerian @ 36.990288
7 Mota @ 37.305138
8 Libyan @ 41.139465
9 Yemeni @ 42.639397
10 Egyptian @ 44.120411
11 BedouinA @ 49.894337
12 Jordanian @ 53.766560
13 Palestinian @ 53.870270
14 Jew_Libyan @ 55.550819
15 Gambian @ 55.836201
16 Syrian @ 55.932667
17 Saudi @ 55.962032
18 Jew_Yemenite @ 56.303688
19 Jew_Tunisian @ 56.830215
20 Lebanese @ 57.033176

Using 2 populations approximation:
1 50% Gambian +50% Levant_BA @ 8.558372


Using 3 populations approximation:
1 50% Hadza +25% Levant_N +25% Somali @ 5.534059


Using 4 populations approximation:
++++++++++++++++++++++
1 Hadza + Levant_N + Mota + Somali @ 5.357584
2 Hadza + Hadza + Levant_N + Somali @ 5.534059
3 Levant_N + Mota + Mota + Somali @ 5.573419
4 Gambian + Levant_N + Masai + Somali @ 5.648787
5 Hadza + Levant_N + Masai + Masai @ 5.673450
6 Esan + Levant_BA + Masai + Saharawi @ 5.909684
7 Levant_BA + Masai + Saharawi + Yoruba @ 5.909684
8 Esan + Hadza + Levant_BA + Saharawi @ 5.969609
9 Hadza + Levant_BA + Saharawi + Yoruba @ 5.969609
10 Gambian + Hadza + Levant_BA + Saharawi @ 5.981442
11 Levant_N + Masai + Masai + Mota @ 6.030968
12 Levant_N + Masai + Masai + Masai @ 6.082205
13 Esan + Levant_N + Masai + Somali @ 6.100034
14 Levant_N + Masai + Somali + Yoruba @ 6.100034
15 Esan + Hadza + Levant_N + Saharawi @ 6.359837
16 Hadza + Levant_N + Saharawi + Yoruba @ 6.359837
17 Gambian + Levant_BA + Masai + Saharawi @ 6.407068
18 Esan + Hadza + Levant_N + Libyan @ 6.505563
19 Hadza + Levant_N + Libyan + Yoruba @ 6.505563
20 Gambian + Hadza + Levant_N + Saharawi @ 6.516825

Done.

Elapsed time 0.2023 seconds.

But the one-to-one comparison doesn't at 50/1:

Largest segment = 2.3 cM
Total of segments > 1 cM = 35.2 cM
27 matching segments

I'm guessing there's more that has to be done to the files before uploading for one-to-one comparisons (rather than simply converting to 23andMe format).