quote:

---

Originally posted by beyoku:

Here is the study that has the ADMIXTURE data.
https://www.nature.com/articles/ncomms15694

Skip right to the SUPP that has the mass of data and all populations in ADMIXTURE.

---

Thx 4/t link to Schueneman&Krause 2017.

I only see K=16. I like to see several K's when I go over-interpreting STRUCTURE.
At level 16 global there's a lot of continental substructure. Plus without lower K's
I can't track progression of colors in populations as K increases. That's important
as will be seen examining Natufians in other researchers STRUCTURE graphs.
Colors can change frequency, pop in, and drop out of any population.

I invite comments and especially critique.

If anyone contributes please stay directly on
topic at least 4/t first 25 posts, thank you.
 

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Posted by Tukuler (Member # 19944) on :
 
Only peoples with a majority or plurality of the brown in Natufians are shown.
List is in descending order sorted by their common 'Natufian Brown' color K.


 

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Posted by Tukuler (Member # 19944) on :
 
These ancients and moderns have 50% brown at the least. From Beta Israel to
the 'Jews' of Yemen, Saudis, and Somalis. These and Beduin B are the living
reps of the brown dominant in the Natufian and Neolithic Levant samples.

I think the component originated where the Bab el Mandeb strait separates the
Red Sea from the Aden Gulf, formerly the Erythraean Strait. I choose to call the
color Erythrea Brown. I think it started on the African side and spread north with
the West African Monsoon. The continental Africans who settled the Levant
mingling with the locals to birth the Natufians probably introduced it there.

Map 1. Surmised Erythrea West in red arc and surrounding topography.


Map 2. Erythrea West cut out of 1970's political map.


Map 3. East Erythrea in blue arc and surrounding topography.


Natufians are known to be crossbred. If the royal blue Anatoli element reps
Natufian 'Eurasian' parentage then surely the brown reps African heritage.

All the peoples below have only two or three major components.

Natufian: Erythrea Brown + Anatoli Royal Blue
Levant N: Erythrea Brown + Anatoli Royal Blue
AbusirEg: Erythrea Brown + Anatoli Royal Blue + Caucasus Sky Blue

Beduin B: Erythrea Brown + Caucasus Sky Blue + Anatoli Royal Blue
Teimani: Erythrea Brown + Caucasus Sky Blue + Anatoli Royal Blue
Saudi: Erythrea Brown + Caucasus Sky Blue + Anatoli Royal Blue

Beta Israel: Erythrea Brown + Volta-Niger Red + Hadza Steel
Somali: Erythrea Brown + Volta-Niger Red + Hadza Steel



Bronze Age Levant has less than 50% Erythrea and interjects the Maghreb geography
coming next. Other than that it'd be with the Levantine-Abusir brown/royal/sky set.

Though placed here for their majority brown, Beduin B, Yemenite Jew, and Saudi
would otherwise fit in the upcoming Mashreq brown/sky/ set.
 

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Posted by Tukuler (Member # 19944) on :
 
Maghreb group


 

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Posted by Tukuler (Member # 19944) on :
 
Mashreq group


 

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Posted by Tukuler (Member # 19944) on :
 
roundup
 

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Posted by xyyman (Member # 13597) on :
 
"I only see K=16. I like to see several K's when I go over-interpreting STRUCTURE.
At level 16 global there's a lot of continental substructure. Plus without lower K's
I can't track progression of colors in populations as K increases. That's important
as will be seen examining Natufians in other researchers STRUCTURE graphs.
Colors can change freq, pop in and drop out of any population."


-------------
I agree but they(researchers) lately don't show lower K's. I have noticed this trend. They no longer show a clean copy of TreeMix either. Their intention is to sway readers
 

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Posted by Elite Diasporan (Member # 22000) on :
 
Very good thread.
 

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Posted by xyyman (Member # 13597) on :
 
No!! Royal blue and Sky blue is also African. Why? See chart below. It is found in West Africa also but in trace amounts. It is found in Mandingo and Gambians and of course indigenous South Africans. Everything found outside Africa is found IN Africa. Blue is probable part of the Paleolithic African element lost through drift ?






 

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Posted by beyoku (Member # 14524) on :
 
XYYMAN - are you taking into account Statistical Noise and recent known admixture in these tested populations.
 

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Posted by -Just Call Me Jari- (Member # 14451) on :
 

quote:

---

Originally posted by Elite Diasporan:
Very good thread.

---

quote:

---

Originally posted by beyoku:
XYYMAN - are you taking into account Statistical Noise and recent known admixture in these tested populations.

---

quote:

---

Originally posted by Elmaestro:
I like the analysis but I don't like the source... I've posted about this many times.

1.The Natufian brown... isn't distinctly natufian. It's composite.
a. Mota possesses it -Mota is unadmixed according to HOII.
b. Certain beduin groups can outscore Natufians for that component.

2.Until we got aDNA from Neolithic/LSA north Africa. Natufians where the oldest samples with important African (including SSA) admixture. However later populations, the ones that would later recieve NAtufian-like admixture, like Greeks, Arabians, Anatolians, Bedouins recombined with various Africans.

This will make Africans with non African admixture significantly Natufian by default.
Somalians don't have 40-60% NAtufian admixture
Nubians and North cushitic speakers don't have 50-65% NAtufian Admixture
Nor do they even share the non-African admixture that they have received.

Which is why formal stats particular F3 will show that the Beja for example clearly have East Med European Admixture and Horners clearly have Arabian Affinity.

All in all with more African aDNA we'll see as clear as day that there is no such thing as a Natufian component.

@Xyyman any African with skyblue has eurasian Admixture... don't ruin a fine thread with your dishonesty.

In regards to the mandinka, The can be 100% African true... but they definately have somewhat recent North African Admixture. The thing about west Africans in most unsupervised charts is that they're heavily biased against Non-Africans (and non west Af. African genes shared in non Africans). So any relationship between them and Eurasian will be hidden. I can break down why that is in another thread.... but I say that to sy this... If a west African shows signs of mixture in ADMIXTURE... they're ver very very likely to actually be mixed.

---

quote:

---

Originally posted by xyyman:
But keep in mind this may be all for nothing. Why? The red component is a “red herring” . That is why it is very very very important to read the METHODS section of these research papers. Understand HOW they are collecting their data and techniques used. And how they are processing the data.

Why is the red component a red herring?…pardon the pun. Lol! Because if you run down the Methods section you will see they are NOT pulling SNPs from the ENTIRE human genome. They are pulling samples from ONE Chromosome. Do you understand how significant that is? If SNPs are pulled across the entire human genome the result will be completely different. The visuals will be different. Understand the game! I need someone to FACT CHECK me on Chromosome #19 but no one has up to this point. ElMaestro? Capra? anyone?

---

quote:

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In order to analyse the nuclear DNA we selected 40 samples with high mtDNA coverage and low mtDNA contamination. Using in solution enrichment for 1.2 million genome-wide SNPs, we obtained between 3,632 and 508,360 target SNPs per sample

---

quote:

---

Finally, we analysed several functionally relevant SNPs in sample JK2911, which had low contamination and relatively high coverage. This individual had a derived allele at the SLC24A5 locus,

---

quote:

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We applied strict criteria for further analysis: we considered only male samples with at least 8% average cytosine deamination rates at the ends of the reads from the untreated library, and with at least 150 SNPs on the X chromosome covered at least twice, in order to estimate contamination levels reliably.

---

As you can see in the image below the X Chromosome is not "Chromosome 19" hence the term "Genome Wide"..



I tried to school you on this last time but you are not paying attention. You are still stuck on DNA 101....you are misleading the forum because of it.
 

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Posted by xyyman (Member # 13597) on :
 
You always have this hard on for me...son. Who said anything about SLC24A5???!!! I am not gay I am anti-gay.

WTF man. Chill out! God damn!

Anyways-
The only question here is Chr #19 and the red component I need fact checked. You checked? Good!! Let me double check my notes.

I will get back to you. I need to go through my notes.
 

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Posted by Fourty2Tribes (Member # 21799) on :
 
Arent those sky blue Africans Khoi? The ethnics are kinda cut off.
 

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Posted by beyoku (Member # 14524) on :
 

quote:

---

Originally posted by xyyman:
You always have this hard on for me...son. Who said anything about SLC24A5???!!! I am not gay I am anti-gay.

WTF man. Chill out! God damn!

Anyways-
The only question here is Chr #19 and the red component I need fact checked. You checked? Good!! Let me double check my notes.

I will get back to you. I need to go through my notes.

---

quote:

---

Originally posted by xyyman:
You always have this hard on for me...son. Who said anything about SLC24A5???!!! I am not gay I am anti-gay.

---

Just say you'll double check your notes and lay off the theatrics. No one wants to hear you talk about your supposed sexuality.No one even asked.
 

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Posted by Tukuler (Member # 19944) on :
 
@ DD
It's no good if its beyond your ken.
Please ask whatever I/we can do
to make this more kennable 4 u.

Me? I don't have a popular writing style so
help me to reach you (and I bet others too).
 

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Posted by Oshun (Member # 19740) on :
 
I have a question: Many of the African groups also have the brown component. Would it derail too much to discuss a little about whether or not there's evidence to show that perhaps the brown is of African origin (and perhaps a subset of African diversity)? I notice that many of the East Africans with brown components seem like they may have more genetic diversity than Natufians, which makes me ponder if the brown part was originally from Egypt or Eastern Africa. Is there a way that can be tested? My only question if this is the case at that point, is why don't Africans with the brown part also have the bright blue outside of northern Africa?
 

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Posted by Tukuler (Member # 19944) on :
 
Well, I call the brown Erythrea because I think it originated in the north
parts of the Horn. The Horn? Guess you could call it the northern East
Africa. Check the maps in post #2. Erythrea West is suggested in red
with arrows pointing to Beta Israel and Somaliland with Puntland). East
Erythrea suggested in blue with Jewish Sanaa and Beduin B arrows.

The bright blue reps Caucasus-Iran originating genomes. The dark blue is
Anatolian in origin. Both of them along with Steppe Hunter Gatherer bright
green help mark the Eurasian in North Africans. The brown and the Atlantic
-Niger red mark their African. Note that Ethiopia Jew has bright blue, hinting
additional brown migrated in as the group formed or maybe marriages with
Yemenite Jews?


Here's a redux showing Schuenemann's Africans having
• just a tiny dash of brown in more than half the group sample
• a weak substratum of brown
• 20-30% brown component
• 40% or more preponderance/dominance of brown

Her Ethiopia Jew is the heavy weight brown champion on the continent.





This brown is looking like a something that connects North Africans and Afro-Asians
to Ethiopian Highland roots. Look for Qemant between Lake Tana and Gondar on that
political map. That's the Ethiopian Jew little resting place.

If major elements of brown start there in Erythrea West then it's on downriver to Egypt's
Delta via the Blue or Black Nile (Atbara) from there. Mushabian, or whoever, brown enters
the Levant meet southbound Anatoli royal blue and voila Natufians!
 

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Posted by Oshun (Member # 19740) on :
 
Actually, I may have answered my own question. If the brown component is "Near Eastern" why isn't there any bright or vibrant deep blue of Levant N in the SSA samples? If the brown component was the result of Near Eastern geneflow into Africa, then we would probably see a lot of deep bright blue in groups like the Somali or Mota, but we don't. Even though groups as ancient as the Natufians have this type of mixture seen throughout the Near East, the SSA that also have the brown component lack the components of the Near East. How would it be the result of back migration when those other components in the MENA samples aren't there? This might mean that either there was a very ancient back migration before those blue components made it into the Near East, or the brown component are African. Or maybe I'm reading too much into that lol.
 

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Posted by xyyman (Member # 13597) on :
 
Ignoring Oshun the clown....And Beyoku the wannabe

--

Ok. FACT CHECK. Here is what I have so far. Those Cluster Chart seemed to cover ONLY 3 males. wow! forgot about that ! Two of which has over 5% contamination. In other words 3 out of 151 mummies were analyzed autosomally of which 2 of 3 had contamination over 5%. Hmmm. Nevertheless that is not my point right now. I am tracking down the target SNPs o fthe 3 males they analyzed. More to come. I need a FACT CHECK. Anyone done it so far?


Quotes
-----------------
Processing and sequencing of the samples. We extracted DNA from 151 mummified human remains and prepared doublestranded Illumina libraries with dual barcodes22,23. Then we used DNA capture techniques for human mitochondrial DNA24 and for 1.24 million genomic single nucleotide polymorphisms (SNPs)25 in combination with Illumina sequencing, through which we successfully obtained complete human mitochondrial genomes from 90 samples and genome-wide SNP data from **three**
male individuals passing quality control.

Who are the three? JK2134, JK2888 and JK2911.

In many samples, nuclear DNA damage was relatively low, indicating modern contamination. We sequenced two libraries per sample: one untreated library to
assess DNA damage, and one library treated with enzymatic

we considered only male samples with at least 8% average cytosine deamination rates at the ends of the reads from the untreated library


Three out of 40 samples fulfilling these criteria had acceptable nuclear contamination rates: Two samples from the Pre-Ptolemaic
Periods (New Kingdom to Late Period) had 5.3 and 0.5% nuclear contamination and yielded 132,084 and 508,360 SNPs, respectively, and one sample from the Ptolemaic Period had 7.3%
Contamination and yielded 201,967 SNPs.

As shown below, to rule out any impact of potential contamination on our results, we analysed the three samples separately or replicated results using
only the least contaminated sample.

Population genetic analysis of nuclear DNA. On the nuclear level we merged the SNP data of our three ancient individuals

In both PCA and ADMIXTURE analyses, we did not find significant differences between the three ancient samples, despite two of them having nuclear contamination
estimates over 5%, which indicates no larger impact of modern DNA contamination.


FROM THE SUPPLEMENTAL
For the nuclear capture two additional libraries for selected 40 samples using 20 ml extract were created as described above with the addition of a UDG treatment27 (see Supplementary Note 2 for details).

Three samples were selected for down-stream analysis: JK2134, JK2888 and JK2911. In all three of these samples, contamination estimates were acceptable, and
similar in both UDG and non-UDG libraries as can be seen in Supplementary Data 2. Furthermore, in all three samples the non-UDG library showed DNA damage
over 8% in the first base pair of reads, which is within the expected range of damage for ancient DNA of this age.


Nuclear data analysis: genotyping. We called genotypes from the UDG treated data for the*** three individuals ***by sampling a random read per SNP in the SNP-capture panel, using a custom tool


The non-UDG and UDG treated libraries were enriched by hybridization to probes targeting approximately 1.24 million genomic SNPs. The target SNPs consist of panel 1 and 2 as described in Mathieson et al. (41) and Fu et al. (12), a large proportion of which are also present on the Affymetrix Human Origins, the Illumina 610-Quad and the Affymetrix 50k array. The probes had a length of 52nt covering a region of 105nt flanking the target SNPs in the center. The
enrichment was performed as described in Fu et al. (25). The two UDG treated libraries per sample were pooled for the capture while the non-UDG treated libraries were captured separately. After the last purification all enriched libraries were pooled for sequencing.
 

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Posted by xyyman (Member # 13597) on :
 
strawman....

quote:

---

Originally posted by the lioness,:
[q] xyyman will you humble yourself and do some remedial on the basics please. You've got red component wrong. Chromosome 19 is not x, get it together [/q]

---

quote:

---

Originally posted by Oshun:
[Q] I have a question: Many of the African groups also have the brown component. Would it derail too much to discuss a little about whether or not there's evidence to show that perhaps the brown is of African origin (and perhaps a subset of African diversity)? I notice that many of the East Africans with brown components seem like they may have more genetic diversity than Natufians, which makes me ponder if the brown part was originally from Egypt or Eastern Africa. Is there a way that can be tested? My only question if this is the case at that point, is why don't Africans with the brown part also have the bright blue outside of northern Africa? [/Q]

---

 

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Posted by xyyman (Member # 13597) on :
 
In running down what the ‘red’ component is in the Abusir , I came across this bombshell. I never knew they REMOVED YRI Components when Mathieson analyzed the 230 ancient European. And here I thought Mathieson was an honest dude. He had me fooled. Just can’t trust ANY European!!!

To those who don’t know, some Scandinavians like Finns carry SSA DNA. Eg ancestral SLC45A2 are found in higher frequency than Germans and English. Yes, the whitest people on the planet carry about 5% ANCESTRAL SLC45A2 IIRC. Nature is a bitch! Lol! Anyways back to Chr#19. Still working on it.

-----
I. Mathieson et al., Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499-503 (2015).

“We defined the ancient source populations by the ‘Selection group 1’ label in
Extended Data Table 1 and Supplementary Table 1 and used the 1000 Genomes
CEU, GBR, IBS and TSI as the present-day populations.We removed SNPs that
were monomorphic in all four of these modern populations as well as in 1000
Genomes Yoruba (YRI). We do not use FIN as one of the modern populations,
because they do not fit this three-population model well.”

----------
 

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Posted by xyyman (Member # 13597) on :
 
So Beyoku you owe me an apology…AGAIN! You know that is why I keep busting your chops. You are such a diezt! Such an ingrate you don’t even know. It wasn’t Chr#19 it was #21. I did the analysis long ago and thought it was posted on ESR. I had to redo it again. I was quoting #19 from memory.
They used Fu et al Method. That is why it is important to read the Methods section if you can understand it….You owe me one!


------------------
Quote:
“The non-UDG and UDG treated libraries were enriched by hybridization to probes targeting approximately 1.24 million genomic SNPs. The target SNPs consist of panel 1 and 2 as described in Mathieson et al. (41) and Fu et al. (12), a large proportion of which are also present on the Affymetrix Human Origins, the Illumina 610-Quad and the Affymetrix 50k array. The probes had a length of 52nt covering a region of 105nt flanking the target SNPs in the center. The
enrichment was performed as described in Fu et al. (25). The two UDG treated libraries per sample were pooled for the capture while the non-UDG treated libraries were captured separately. After the last purification all enriched libraries were pooled for sequencing.”


From Fu et al
Chromosome 21 Analyses.
To investigate the relationship of the Tianyuan individual to present-day populations, we compared it to chromosome 21 sequences from 11 present-day humans from different parts of the world (a San, a Mbuti, a Yoruba, aMandenka,
and a Dinka from Africa, a French and a Sardinian from Europe, a Papuan, a Dai, and a Han from Asia, and a Karitiana from South America) and a Denisovan individual, each sequenced to 24- to 33-fold genomic coverage (27).


Chromosome 21 Capture and Sequencing.
The ability to sequence nuclear DNA sequences from the Tianyuan individual is limited
by the fact that no more than 0.03% of the DNA extracted is endogenous to the bone. Previous studies (22–24) have shown
that hybridization enrichment can be used to obtain nuclear DNA fragments from ancient samples. However, the commercially
available hybridization systems used in these studies provide only a limited number of capture probes in each hybridization reaction.
Because the enrichment of highly fragmented DNA requires large overlaps between probes, this limits the total size
of genomic regions that can be targeted to a few megabases at best. T

From these libraries as well as the two initial libraries from the femur, we performed two successive enrichments for chromosome
21 fragments (Fig. S5).
 

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Posted by xyyman (Member # 13597) on :
 
So Beyoku….my point is they used specific SNPs to do their analysis on the Abusirs. It was from Chromosome# 21(not #19) . Panel 1 and Panel 2. Now would you shut the Fugk up when I post and take notes. How many times do I have to repeat it. SMH. You are so fugked up in your head you don’t even know it…SMH. Anyways back to the brown component.
 

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Posted by xyyman (Member # 13597) on :
 
I know in your mind you think you got it but you have no clue....and don't know it....SMH

You remind me of those ...non-diasporans. Everyone thinks he is a prophet. I just don't get it...
 

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Posted by Elmaestro (Member # 22566) on :
 
Tukuler just give me the word and I'll clean this thread for you.
 

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Posted by Tukuler (Member # 19944) on :
 
Thx 4 offering.

The fuck with it. Let 'em keep shitting.

The bar is too low to limbo.

I'm satisfied that at least one member had an honest on-topic brainstorm amid the saboteur quagmire.
 

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Posted by Oshun (Member # 19740) on :
 
While I can't speak with certainty for all SSA with traces of vivid blue, if anyone remembers the Mauritania sites, the Soninke originally migrated from more northern areas of Africa. Which means it's likely that at least some of the Mande would've had at least a little contact with northern Africans. It's believable that they would have traces of Near Eastern ancestry. One question I have which was interesting for the Mandinka is, why don't they have more of these colors as well? You would think, that having lived originally in the northern parts of the Sahara, they would look like modern MENA, but they do not. Instead it looks like they were leaving for SSA and lacked enough time to make much contact. That, or mixing with local SSA has dramatically changed them at a genetic level from their ancestors. I forget what the Taforalt looked like, but I don't think they resembled modern MENA very well. So I'm not sure if I could say that this was just a matter of genetic discontinuity among the Mandingo.
 

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Posted by Tukuler (Member # 19944) on :
 
This post is inspired by and sponges off Oshun's observations.
It launches from there but not really in direct reply, an equal if counter current.
I respect everyone's supportable informed views.


My perspective is one of African active agency. Africa as African.
Africa not as a passive receptor object for 'West Eurasians'.
The way I look at it?
There was no such thing as an ancient MENA.
At best, MENA begins well after Islam.

The Sahara was never exclusively Amazigh.
The Sahara, south and central, was mostly 'Sudanese'.
The north Sahara and on to the Libyan coast was mostly 'Gafsian'.
Atlas to coastal Morocco & Algeria, and most of Tunisia had a Neolithic of its own.



Schuenemann's ADMIXTURE @ K=16 differentiates Tamazgha from Afroasia.

Tamazgha is majority Erythrea Brown. See 1stPost graph middle section.
Afroasia is plurality Erythrea Brown. See 1stPost graph bottom section.
nrY E-M35(?) and Afroasian language originate in Northeast Africa.
They spread north from there toward Maghreb and Mashreq.

Tamazgha has much less Caucasus-Iran sky blue than Egypt and Afroasia.
It has slightly more Anatoli royal blue.
Higher frequency of Atlantic-Niger red also distinguishes Tamazgha from Afroasia.
Steppe Hunter Gatherer bright green also strongly differentiates Tamazgha from Afroasia.
It's propably old as the coastal Neolithic.

Atlantic-Niger red stems from further south than Erythrea Brown.
But not very far, Kenya to Tazania.
It's the 'Sudanese' who followed grasslands northward into a Sahara which the West African Monsoon made fertile.
mtDNA L2(?) is pre-Ice Age in near coastal North Africa.
They're as Saharan as anything else and without a need to look Levantine-Iraq-Arabian.

In my day to day experience Moroccans don't look like Saudis.

No reason any Atlantic-Nigers should look like Arab or Araboberber.
In fact just the opposite.
With 16% Niger-Atlantic red Tamazgha should look more Gnawa than the other way around.


Saharan and coastal Classical Era North Africans. Above is a forgotten North African phenotype.


Classical Era coastal Algerians repping The 4 Seasons, a forgotten North African phenotype.



Here are all Schuenemann's south of the Sahara Africans.

Ethiopian Jew is the only pop with a blue substratum. 'MidEast' influx @
6% Caucasus-Iran sky blue. Yet they don't look MENA. Why would they?
They're 92% Erythrea Brown, Atlantic-Niger Red, and Hadza Steel.

Nama and Khomani have sporadic Eurasian genomes, bright green and both the blues, from very recent colonial rapes.

Blues are not even a substratum in Mandenka nor Gambian.
6 of 17 Mandenka have Anatoli Royal Blue @ an insignificant 0.6%.
2 of 6 Gambian have royal blue @ 1.2% with another 1 @ 0.3
2 other Gambian have Caucasus-Iran sky blue @ 0.6%
Interaction along the Atlantic from Cape Rhir to Cape Verde (mainland) show a retreat as climate affected economy.



Talk of blues throughout south of Saharan Africans is imaginitive. Any significance of such is imaginary.




Critique invited.
Precision is most welcome.
Ask for clarity or expansion to make sure y'all understand what I'm saying.
Please, don't put words in my mouth.
I just ate, and besides, straw don't taste good. I'd rather stomach crow.
 

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Posted by the questioner (Member # 22195) on :
 
so many people on this website are interested in genetics, yet none have a laboratory.

who here has a laboratory and studies genetics?

until you all have the above, you will never know for certain where these studies's conclusions are coming from.
 

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Posted by Tukuler (Member # 19944) on :
 
I draw my own conclusions.

One of which is Erythrea West housed
south of Sahara African substructure that would become
the northern Click speakers,
central and southern Nilo-Saharans,
and all Afroasian speakers except most Semitic.

The report authors ain't said nothing like that.

I'm a Old Crow trying to learn to fly on hand me down broken wings
Please lend me a helping hand.
What conclusions do you draw from Schuenemann's ADMIXTURE graph?
 

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Posted by Oshun (Member # 19740) on :
 
Unless the Egyptians were ancestral to both Anatolia and the Natufian component, I see this as a reflection of the samples having a lot of mixture with the Near East. While its true the brown could be a reflection of Near Easterners descending from Africa (or that it's from Africa directly), I doubt it's entirely the result of Africans that never left. Just as brown in the absence of bright blues indicate it may've been African an origin, The heavy presence of it in the AE samples suggests some back migration. This sample is mostly Near Eastern and Egyptian. Specifically this sample is from lower Egypt which had more influences from the Near East since the predynastic. The samples being from Lower Egypt isn't an unsupported brainstorm to explain the data, there is plenty of information out there that makes it clear the samples were Lower Egyptians. There are pretty much no other colors in these samples, which to me would point to immigration into an already heavily "Arabized" or mixed group of northern Egyptians. It'd be one thing if they had relatively less of the other colors and were more brown, but there's nearly none of the same diversity and a lot of vibrant blue. Heavy immigration before the New Kingdom is documented in reports by the Egyptians and Egyptological biological data that has remarked on the presence of demographic change that spread into Upper Egypt. So much so that the original southern phenotype existing in the OK was nearly wiped out in most of NK Egypt.

That brown component is probably a mixture of a component indigenous to the Nile Valley (and Africa in general) that is also shared with foreigners that brought vibrant blue shades. Both probably had those blue shades to a certain degree. However, I expect there to be more genetic diversity the closer older samples would have been to Elephantine/Aswan.

quote:

---

We do not use FIN as one of the modern populations,
because they do not fit this three-population model well.”

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quote:

---

Originally posted by beyoku:

1 - They are mainly RECENT migrants from the Near East containing ancestry that is much different from the African Natives. Different from what would be found in the Earlier or southern dynasties. (they have mostly bronze age levantine ancestry)

---

quote:

---

Originally posted by beyoku:
The Brown Component is a statistical anomaly.

The Red Component is not anything special......its just a generic African component centered on Homogeneous West African samples.

---

quote:

---

Like you said, obtaining more Y-DNA haplogroups from this sample would shed more light on these mummies' ancestry. But looking at the ADMIXTURE charts, the three Abusir-el-Meleq mummies' ancestry seems to resemble Levantine people from the Bronze Age than the Neolithic (the latter almost all lack the cyan Iranian-like component). So while I'm not ready yet to write off the entire sample as all recent foreign migrants, I do believe a significant chunk of their unambiguously Levantine-like ancestry can be traced to Bronze Age rather than Neolithic movements.

---

quote:

---

Originally posted by Tukuler:

quote:

---

Originally posted by beyoku:
The Brown Component is a statistical anomaly.

The Red Component is not anything special......its just a generic African component centered on Homogeneous West African samples.

---

.

.


TOPIC REFERENCE: Schuenemann2017 Supplemental Figure 4 ADMIXTURE program graph K=16

Each color is an ancestral population by definition.

What is a statistical anomaly
How is it qualified and quantified?
What makes Erythrea anomalous?
What other topic K's are anomalies and why?


What is special?
How is it qualified and quantified?
What makes Atlantic-Niger not special?
What other topic K's are not special and why not?
Which topic K's are special, by what measurements?

---

quote:

---

Originally posted by Elmaestro:
@Tukuler Consider the temporal aspects of these charts... This is all statistics so we're dealing with "probablies" and not "absolutelies" BUT a huge sign that a STRUCTURAL component is an anomaly is if descendants or later groups can better represent source populations... For exmple Negev Beduoins Tend to score more of the natufian component than Natufians ....clearly they can't be the source or best represent the source of Natufian ancestry... and they clearly show signs of relatively recent admixture from other middle eastern and African groups.

---

quote:

---

Originally posted by xyyman:
Thank you Sage. This is why I keep busting his chops. One stupid unsubstantiated remark after another.

quote:

---

Originally posted by Tukuler:

quote:

---

Originally posted by beyoku:
The Brown Component is a statistical anomaly.

The Red Component is not anything special......its just a generic African component centered on Homogeneous West African samples.

---

.

.


TOPIC REFERENCE: Schuenemann2017 Supplemental Figure 4 ADMIXTURE program graph K=16

Each color is an ancestral population by definition.

What is a statistical anomaly
How is it qualified and quantified?
What makes Erythrea anomalous?
What other topic K's are anomalies and why?


What is special?
How is it qualified and quantified?
What makes Atlantic-Niger not special?
What other topic K's are not special and why not?
Which topic K's are special, by what measurements?

---

---

 

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Posted by Tukuler (Member # 19944) on :
 
Man I sure can't pay you but gratefully appreciate your profession view to name Ms Schue's K colors to adopt and use in this thread?




Also any reason cyan is Iranian over Caucasus?
I don't remember, and too lazy to look up, if proto-Iranians migrated across the Caucasus or only the Zagros.

quote:

---

Originally posted by Tyrannohotep:

quote:

---

Originally posted by beyoku:

1 - They are mainly RECENT migrants from the Near East containing ancestry that is much different from the African Natives. Different from what would be found in the Earlier or southern dynasties. (they have mostly bronze age levantine ancestry)

---

Like you said, obtaining more Y-DNA haplogroups from this sample would shed more light on these mummies' ancestry. But looking at the ADMIXTURE charts, the three Abusir-el-Meleq mummies' ancestry seems to resemble Levantine people from the Bronze Age than the Neolithic

(the latter almost all lack the cyan Iranian-like component).

So while I'm not ready yet to write off the entire sample as all recent foreign migrants, I do believe a significant chunk of their unambiguously Levantine-like ancestry can be traced to Bronze Age rather than Neolithic movements.

---

quote:

---

Originally posted by Elmaestro:
Two offtopic and/or homophobic posts removed

@Tukuler
Anomalous =/= Insignificant
The problem is that the argument can be made that that brown component is misleading as an indicator of source Admixture or even close relatedness.

A coherent conclusion of how that brown component came to be can't be made. So when you say...

"Genetics isn't a vacuum filler. Archeoanthropology, linguistics, and history are proofs of who entered and left the Levant and when they did.
"
-Tukuler

I Agree, Which I why I credit your breakdown however caution literal interpretation of that Brown component. It didn't originate anywhere. It's a computational anomaly, ...a model of incomplete data. We see this with newer studies. AT BEST you can say that the brown component "originates" at the Natufian sites not Erytrea... given the fact that one of the Natufians are 100%, the next highest group are Isreali (correct me if I'm wrong.)

I can pretty much say with confidence that no African population will outscore Near easterners for that same component, not an ancient Erytrean, nor a modern one.

---

quote:

---

Originally posted by Tukuler:

quote:

---

Originally posted by beyoku:
The Brown Component is a statistical anomaly.

The Red Component is not anything special......its just a generic African component centered on Homogeneous West African samples.

---

.

.


TOPIC REFERENCE: Schuenemann2017 Supplemental Figure 4 ADMIXTURE program graph K=16

Each color is an ancestral population by definition.

What is a statistical anomaly
How is it qualified and quantified?
What makes Erythrea anomalous?
What other topic K's are anomalies and why?


What is special?
How is it qualified and quantified?
What makes Atlantic-Niger not special?
What other topic K's are not special and why not?
Which topic K's are special, by what measurements?

---

quote:

---

Originally posted by Tukuler:
OK the weekend's over now.
Beyoku?

quote:

---

Originally posted by Tukuler:

quote:

---

Originally posted by beyoku:
The Brown Component is a statistical anomaly.

The Red Component is not anything special......its just a generic African component centered on Homogeneous West African samples.

---

.

.


TOPIC REFERENCE: Schuenemann2017 Supplemental Figure 4 ADMIXTURE program graph K=16

Each color is an ancestral population by definition.

---

---

quote:

---

What is a statistical anomaly?
How is it qualified and quantified?
What makes Erythrea anomalous?
What other topic K's are anomalies and why?


What is special?
How is it qualified and quantified?
What makes Atlantic-Niger not special?
What other topic K's are not special and why not?
Which topic K's are special, by what measurements?

---

quote:

---

Originally posted by Tukuler:
I just need clarity and expansion on the particulars, which you deleted. thank you.

In regards to the topic graph:

quote:

---

What is a statistical anomaly?
How is it qualified and quantified?
What makes Erythrea anomalous?
What other topic K's are anomalies and why?


What is special?
How is it qualified and quantified?
What makes Atlantic-Niger not special?
What other topic K's are not special and why not?
Which topic K's are special, by what measurements?

---

.
.

Please quote me saying what you question?
It's not me.
It's Schuenemann2017 ADMIXTURE @ K=16 saying Somalis have Erythrea, Atlantic-GreatLakes, and East African Hunter Gatherer ancestral population components.
Her Dinka ancestral population components are Atlantic GreatLakes, East African Hunter Gatherer, Erythrea, and Rainforest Hunter Gatherer.
The ultimate origin of the red as red is East Africa.
That's elementary.
Please supply a collected spit or cheek swabbed Basal Eurasian sample's ADMIXTURE data.
No, but seriously, force fitting BE into the Late Pleistocene and the Holocene?

---

quote:

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Originally posted by xyyman:
Can we spot the double standard and spin?
------------
Quote
@Tukuler
Anomalous =/= Insignificant
The problem is that the argument can be made that that brown component is misleading as an indicator of source Admixture or even close relatedness.

----------------

@xyyman
Anomalous =/= Insignificant
The problem is that the argument can be made that that red component is misleading as an indicator of source Admixture or even close relatedness.

-------

Originally posted by beyoku:
The Brown Component is a statistical anomaly.

The Red Component is not anything special......its just a generic African component centered on Homogeneous West African samples.


" targeted brown component be an anomaly when it makes up about 80% of Bedouins, 95% of Natufians, 60% of Somalis found right across North Africa(50%) including native Canary Islanders and lower frequency in otherSub-Saharan Africans. "

---

quote:

---

Originally posted by Elmaestro:
[Q] [QUOTE]Originally posted by xyyman:
[q] Can we spot the double standard and spin?
------------
Q
As much as all those African populations are the same the spread of that brown component represents the same source population.

[/Q]

---

quote:

---

Originally posted by beyoku:
The Brown Component is a statistical anomaly.

The Red Component is not anything special......its just a generic African component centered on Homogeneous West African samples.

---

quote:

---

Originally posted by Tukuler:
I answered questions from you once though you couldn't bother to answer any questions I asked you and your latest is already covered in the thread.

Keep believing Northeast Africans didn't enter the Levant and engender the Natufians.

Nothing more from me to you until you stop sidestepping and explain your rather emotional response.

=-=

quote:

---

Originally posted by beyoku:
The Brown Component is a statistical anomaly.

The Red Component is not anything special......its just a generic African component centered on Homogeneous West African samples.

---

.

.


TOPIC REFERENCE: Schuenemann2017 Supplemental Figure 4 ADMIXTURE program graph K=16

Each color is an ancestral population by definition.

What is a statistical anomaly
How is it qualified and quantified?
What makes Erythrea anomalous?
What other topic K's are anomalies and why?


What is special?
How is it qualified and quantified?
What makes Atlantic-Niger not special?
What other topic K's are not special and why not?
Which topic K's are special, by what measurements?

---

quote:

---

Originally posted by xyyman:
[Q] "Anomalous =/= Insignificant".

Definition of anomalous
1 : inconsistent with or deviating from what is usual, normal, or expected : irregular, unusual Researchers could not explain the anomalous test results.
2 a : of uncertain nature or classification an anomalous figure in the world of politics
b : marked by incongruity or contradiction : paradoxical

This is what you guys came up with...."anomalous!!!"

You people are obtuse...YOU deeply believe we all fall for your bs

ob·tuse
əbˈt(y)o͞os,äbˈt(y)o͞os/Submit
adjective
1.
annoyingly insensitive or slow to understand.


But

How can the brown component be an anomaly when it makes up about 80% of Bedouins, 95% of Natufians, 60% of Somalis found right across North Africa(50%) including native Canary Islanders and lower frequency in Sub-Saharan Africa. What are you smoking ElMaestro? That is some good stuff.


The problem with some of you white people and Negros is you are really convinced all black people are stupid. We will believe any BS that comes out your mouth.

Anomaly! Ha! HA! HA! HA! …at K16?! SMH []

---

quote:

---

Originally posted by Tukuler:
At the least you must present right here your own independent analysis of Schue's ADMIXTURE graph, sticking to her given sample set, from a multidisciplinary approach if you're able to.

You think my analysis stinks. Fine. Thank you for your critique.

Please also contribute to the Taforalt Brown thread.
No Erythrea K there, you'll like that.
Though in the end you'll probably conclude it stinks too.

---

I think you are kind of talking in riddles.
I will tell you where we agree and where we disagree.

I agree Natufian have African ancestry, Africans migrated through the Sinai into Levant.

Mushabians, likely related to Iberomaurusians, probably the precursors of populations that contributed to the ancestors of Natufian were NOT East African. IMO they may have East African ancestry but primarily be composed of Ancestry native to the North of the Continent, long differentiated from their neighbors to the south. Not Mota, or Dinka, Or Hadza type ancestry that is native to SSA - See Taforlat for what to expect.

The old argument has Cushitic type people in the Horn (think Erythrea) carrying a recent Afroasiatic linguistic package and E-M35 lineages into the Nile Valley, Maghreb and Levant. I think this is where you get your Northern Horn origin for the Brown component regardless of its peak hypothesis : 'Horners being North East Africans.'

The NEW data shows E-M35 having a LONG separation though time and space in the North with MUCH of the E-M35 derived lineages in the horn being much later North African and Saharan derivatives. Therefore adding evidence that Horn Africans are East Africans (Mota/Dinka/Hadza) with North African ancestry. This combination of ancestry CREATES the composite component we identify as Cushitic. This "Cushitic" type ancestry or Erythrea type ancestry, created by the combining of the two regions IMO is not old enough to be in the Horn at the age of Natufian because that admixture event that far south had yet to occur.

SO my guess is Ancient Ethiopians, the age of Natufian.....going back 14 thousand years are going to be (Mota/Dinka/Hadza).....the type of ancestry they could contribute to the North is ONLY going to be (Mota/Dinka/Hadza) because Erythrea is only to be found further North.....so it cant have an origin in the Northern Horn.....if its a later intruder to the Northern Horn. M78 is a late intruder to the Northern Horn. IMO arguing the brown component comes from the Northern Horn is akin to saying Egyptians received M78 from the Somali.

Ancient DNA from North Africa showed Natufian to be admixed with North Africans....a North African component centered on the Maghreb. The latest publication shows Natufian having North African AND MOTA ancestry to the tune of 25-35%

Later Ancient DNA.......I can almost guarantee will bifurcate North African ancestry into that of the Maghreb and that of the lower Nile Valley...Probably increasing the African ancestry in Natufian, absorbing most of the Natufian type ancestry in Horners.

Summed up: Levantines, including Natufian have Egyptian ancestry. Horners have Egyptian ancestry. The Brown component in its African context is Egyptian and not Northern Horn....and Horners have it only because they absorbed Egyptians. The date in which Horn Africans absorbed Egyptians post dates the remains of both Taforalt and Natufian by 1000's of years, with an upper bound of 10,000 years. In the article where they say that Natufian and Taforalt could have a common ancestor perhaps of North African origin........that is your source for much of the ancestry contained within that brown component.

The brown component comes from a Computer algorithm...when you change the K and or introduce additional samples these components will move around like musical chairs. Computer output that has Somali as 40% Yoruba are nearly useless for trying to retrace African migration.
 

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Posted by Tukuler (Member # 19944) on :
 
Upper Egypt Northern Sudan may be as plausible, --with movement SE as well as N onto W and E --, as Erythrea as the 09 brown geographic origin.
Call it Nubia Brown, same difference, same significance.

Schue's Somali bear no 'MidEast' cyan nor Anatoli navy but heavy Atlantic-GreatLakes red, noticeable EAfr HG steel with a Rainforest HG olive substratum.
They have more 09 brown than any NAfrs and all but 3 MidEast populations.
But none of the NAfr ME cyan navy or mint.

Loosdrecht's Natufian composition is here in the Taforalt Brown thread (link).
Schuenemann's ADMIXTURE is the focus of analysis here.
It doesn't support a ~30% African composition.
You're choosing which is right or wrong.
I accept both, "every prophet in her/his house" so to speak.

All the components are from a computer algorithm, so what?
and I wrote about changing K's in the OP, big deal.

All the K9 Erythrea heavy hitters are at either end of the Red Sea.
4 of 5 of these majority brown carriers are at the south end of the Red Sea.
K9 Erythrea Brown.


BTW you really underestimate Hadza.
Rank the 02 Hadza steel carriers and check the pattern.

Can you recommend <5yr old E-M215 reports to bring me up to speed.
 

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Posted by beyoku (Member # 14524) on :
 
Nubia Brown vs Horn Brown are two totally different things. Nubia is at the forefront and source of agriculture/pastoralism/pottery/statehood etc. The Horn is a a very late recipient.

In any case focusing on Natufian Brown and its implications in Africa is as similar as focusing on French Blue (Pagani) and France’s genetic impact on all these Shb Saharan Areas:

http://4.bp.blogspot.com/-VUU1abta_g0/T-NncxwM2lI/AAAAAAAAE5Q/21ZXr6gTDYY/s1600/ethiopians.jpg
 

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Posted by Tyrannohotep (Member # 3735) on :
 
Anyone remember how Ehret placed the origin of Afrasan languages along the Red Sea coast of Sudan to Somalia?

I agree with Beyoku that modern Horners are probably mixed between southward-moving Saharans and whoever was living in the Horn beforehand. But I can see why Tukuler is identifying the "brown component" as Erythrean. Unless Ehret has somehow misplaced the original homeland of Afrasan, it seems reasonable to assume that these proto-Afrasans along the Red Sea coast (along with other Saharans) would have been related to whatever ancestry the brown component represents. Or is this no longer the case?
 

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Posted by beyoku (Member # 14524) on :
 
@Brandon. You could argue it but still you are focusing too much on contemporary Horn Africans. Trombetta and Cruciani (V68/V1515) and Pagani and Taforalt and even the latest Y-DNA on the green Sahara supports data of this type of ancestry entering the Red Sea Coast and Horn somewhat late from the Eastern Sahara and Norh Africa. Why base the name and hypothesize the origin on something they received? it’s like calling Cushitic languages “Horn African” when it clearly looks like they spread south from the Eastern Sahara or Southern Egypt where their earliest forerunners can be found today :Beja. AA looks more to be North African with Levantine and Southern Ethiopian outliers.

FYI V1515 southern migration from the North post dates the age of Natfuian and Taforalt. Horn Africans are some the interesting NOW but as you go back in time their composite type ancestry will dissolve in favor of MOTA/Hadza/Dinka type ancesrty. I think we have seen enough ADMIXTURE Runs and are familiar with Horn African uni-parental profile to know their ancestry having large chunks of West African is not optimal or an accurate indication of where their ancestors come from......it’s a non starter......like the French ancestry in Pagani.
 

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Posted by Tukuler (Member # 19944) on :
 
Upper Egypt Northern Sudan may be as plausible, --with movement SE as well as N onto W and E --, as Erythrea as the 09 brown geographic origin.
Call it Nubia Brown, same difference, same significance.

Non-Schuenemann ADMIXTURE based Eurocentric French diversion absurdity aside, whether choosing Jebel Sahaba or Erythrea West as points of origin, 09 brown reps a major ancestral foundation from NEAfr sources for most the Africans north of the rough Nouakchott to Merca line as well as many Arabian plate peoples.
 

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Posted by beyoku (Member # 14524) on :
 

quote:

---

Originally posted by Tukuler:
Upper Egypt Northern Sudan may be as plausible, --with movement SE as well as N onto W and E --, as Erythrea as the 09 brown geographic origin.
Call it Nubia Brown, same difference, same significance.

Non-Schuenemann ADMIXTURE based Eurocentric French diversion absurdity aside, whether choosing Jebel Sahaba or Erythrea West as points of origin, 09 brown reps a major ancestral foundation from NEAfr sources for most the Africans north of the rough Nouakchott to Merca line.

---

quote:

---

Originally posted by Tukuler:
There is no Maghreb component in Schuenemann's ADMIXTURE.

I'm beginning to think you ignore her graph.

The 08 mint distinguishing northern Africans west of Egypt seems ultimately Steppe derived.
100% or maximum frequency in Steppe & Western Hunter Gatherers.
By appearances, introduced via north Mediterranean contacts.

---

quote:

---

Originally posted by beyoku:

quote:

---

Originally posted by Tukuler:
There is no Maghreb component in Schuenemann's ADMIXTURE.

I'm beginning to think you ignore her graph.

The 08 mint distinguishing northern Africans west of Egypt seems ultimately Steppe derived.
100% or maximum frequency in Steppe & Western Hunter Gatherers.
By appearances, introduced via north Mediterranean contacts.

---

That's is my point .......There is no Maghreb component! That is why this ADMIXTURE run is inadequate in assessing African substructure in Natufian and Africans. I have SEEN the full K=2-XX, at no point did a North African component centered on the Maghreb materialize. I dont even think a Horn African component materialized......Everything was pretty much uninformative due to a lot of the K being sucked up in needless international diversity. I wrote about these details in a thread that seems to be gone as I went through every post in the main thread and didnt find it.

Furthermore, how does the steppe derived argument work in the face of Taforalt/IAM/KEB/Contemporary Maghreb native continuity? It doesn't really. The whole 12kya Eurasian back migration al Henn et al is dead in the water too. The "all SSA comes from Slavery" is also dead in the water. The composite SSA/North African profile found in Taforlat is due to a very old admixture event.

Ultimately any ADMIXTURE results showing North Africans carrying a major component peaking in Natufian has been superseded by the older Taforlat Specimens showing a lot of continuity and the presence of North African ancestry in Natufian. I fail to see why we are discussing Natufian brown (old news) in a bubble outside of the context of Taforalt.

---

quote:

---

Originally posted by xyyman:
huh!?

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quote:

---

Originally posted by beyoku:
This study is ****.

I retract all good I had to say about the authors and how "Smart" they were not to use Yoruba as the lone African SSA reference.

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