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.
Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
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.
Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
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.
posted
"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
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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XYYMAN - are you taking into account Statistical Noise and recent known admixture in these tested populations.
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@ AstenB. yes, Noise can be a possibility but definitely not RECENT admixture. Why? And how can you tell? Simple. Understand that the “width” of the populations in the Cluster Chart(X-axis) is dependent on the number of individuals sampled in that specific population. The researchers typically chose the individuals after they fill out the questionnaire(look at Methods section) about their parentage. In other words they want the most indigenous individuals. Aside from that, another clue is “height”(y-Axis) of the color across the individual(s) in that population. So for example Brown in Madingo and Shau are about the same frequency for ALL individuals in that population. This means that the brown is found throughout every Mandingo which means it is indigenous!!!
These charts are very easy to read.
So no! these are NOT admixed Mandingos. The brown will be seen all through-out Africa with varying frequency. Most likely it is an East African component. Rather than a south African component.
An argument can be made for the Royal blue in “some” Mandingo being noise but since brown and blue a frequently seen together. It cannot be noise for the Royal blue.
That is my lesson for today. Hit me up.
BTW – a recently admixed individual will show up as a “spike” in that color compared to their colleagues in that cluster chart.
These are not admixed Africans!!
quote:Originally posted by beyoku: XYYMAN - are you taking into account Statistical Noise and recent known admixture in these tested populations.
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posted
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?
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So a more accurate title to Schueneman et al should be “ Less Yoruban Chromosome 19 SNPs found in Abusir mummies prior to the Roman Period” Keep in mind the English, Basque, Orcadian and Nordic peoples etc have absolutely zero “brown” component . Yes, English and Northern Europeans have absolute zero genetic relatedness to Abusir. While Madingo and some West Africans do. The brown component found on Chromosome #19 is most likely a Neolithic East African component that is why it is found in Makrani, East Africa and North Africa and the Levant, Southern Europe. Again we are looking at only ONE Chromosome (#19)and not the entire human genome for this study.
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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.
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Before I respond to your waffle above like “recombined”, “skyblue has Eurasian admixture” etc Fact check me on the analysis using one chromosome, #19. You know I have you figured out? Don’t you?
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.
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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?
Your red component comment is wrong. Your Chromosome 19 comment is also incorrect. Fact checked from the data itself:
quote: 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
"genome-wide SNPs" Not "Chromosome 19 SNP's"..... GENOME WIDE SNP's. See also:
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: 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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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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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.
Notes......notes? Grandpa this is Autosomal dna 101 and you have failed to understand the basics which has you all over the place chasing ghosts and phantoms that don’t even exist: African Makrani. I have tried to give you the basic rundown multiple times over multiple years but you want to be a know it all......but still don’t understand how Admixrue as a computer program works.....or the difference between supervised and non supervised......or the differences between “Genome Wide” SNP panels vs “Chromosome 19.....or SNP vs STR...SMH.
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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
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
17 reply posts, only 3 of which add any value to my NATUFIAN BROWN topic then my thread is hijacked to Anatoli/Caucasus blues, red herrings, homophobia, and the [mis]education of Xyyman.
@ ED & Jari Thx 4/t kudos.
@ ED Your Beta Israel observation meant dominant component not significant element, right? Planned doing an Erythrea Brown in 'Jews' post, among others, but right now after the quick and easy diversion I don't even feel like finishing my majority/plurality presentation.
@ EM Thx 4/t critique. This thread was in answer to Xyyman schooling me specifically about hi-freq brown K in Somali and Abusir re Schueneman2017 SupFig 4. A lot of pre-pub hype when thought to be Krause, a lot of post-pub gnashing and wringing after known to be Schuenemann. I had planned to compare Schuenamann's ADMIXTURE to Loosdrecht's contrary one, yours, and any others' ADMIXTURE graphs featuring Natufians.
@ Mensa & Beyoku Alright, some backdrop on 'K-volution' and duck ordering methodology brass tacks is warranted, if borderline. It's certainly helpful . Protect the innocents!
posted
Tukuler, respect for your request to stay on topic. Beyond my ken though.
But I'll mention Natufians we're making flat bread 14,400 years ago from barley & sedge tuber starch & other stuff. Officially that's the oldest bread.
OT:
In my opinion, flat bread was first made in Papua, via sago palm pith processing (associated with evolution of spatula, hoe(d)ad.ze, dugout canoe and initiation of rectilinear structures eg. Longhouses.) between 44ka - 24ka, and brought to India coast, eventually to the Levant. There may or may not be any trace of this genetically.
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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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
@ 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).
posted
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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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
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!
posted
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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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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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]
So this is where I got the Chr#19 from. Panel I and 2 Fu et al and Matheisen et al Anyone done it so far? The target SNPs? I wouldn’t expect Beyoku to answer because he is a wannabe. Still has a hang over those leaked haplgroups wink! Wink! Oshun?….ha! hA! hA! Waste of band-width. Let me run it down. I may be wrong but I will be right back………I was going from memory. I thought I posted it on ESR but it is not there….
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.”
R. Khairat et al., First insights into the metagenome of Egyptian mummies using next-generation sequencing. Journal of applied genetics 54, 309-325 (2013).
I. Mathieson et al., Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499-503 (2015).
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One of the few intelligent questions you ever asked. The blue Royal blue IS present in Gambia and Mandingo and some south Africans.
drift?
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
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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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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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
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...
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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posted
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.
Posts: 2508 | From: . | Registered: Nov 2011
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
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.
Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
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.
posted
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.”
Can anyone explain what is FIN?
Posts: 2508 | From: . | Registered: Nov 2011
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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.
This is still my currecnt analysis of the Data:
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)
2 - They are descendants of ANCIENT prehistoric farming Migrants from the Near East And their ancestry is a composite of ancient farmers from the Near East and the Native African ancestry that would have been mostly found in Egypt during earlier times. Their genomes represent more of a native Northern Egyptian substratum based on the immigrant farmers vs the native African herders and hunter gatherers (They have little pre-neolithic African ancestry). One would expect a North-South Cline of the Nautfian/Anatolian/Iranian type ancestry that was mainly found vs the East and West African ancestry that was hardly found in these remains.
3 - They were mostly native Africans with SW Asian admixture and a portion of their ancestry that is seen as "Eurasian" in this study is instead an ancient shared component of North African origin. Similar to what is found in ancient remains in North Africa (TAFORALT and IAM/KEB). Their autosomal ancestry would be the Northern and Saharan substratum while an older sample could have a higher equatorial affinity.
There a plenty of scenarios that could work but we really have to see the Y-Chromosome markers of the 90 mummies. That would give a good feel of how native their males were to the region and what type of continuity they showed on the continent. For instance: if their Y-DNA was as African (A/B/E) as their mtdna (L/M1/U6) which would be quite low then option (1) could be a possibility. if they were mainly African haplogroups A/B/E then option 3 looks like a good explanation.
Posts: 2463 | From: New Jersey USA | Registered: Dec 2007
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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)
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.
Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
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?
posted
@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: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.
@T-Hotep pretty Much. They're way too similar to Bronze age levantines for this possibility to be ignored. Though they might be ever so slightly more "African" the difference is so miniscule That I find it hard to believe that the Abusir three are reps of a recent result of Admixture with Bronze age near easterners as opposed to just settlement from Bronze age newcomers. Another good explanation is that there have been somewhat consistent Bidrectional geneflow from Lower Egypt and the near East Starting from the Iron Age. And the differences we're seeing is just gradation.
(Then there's also the issue of Levant_BA consistently failing to show an Admixture event Via LD... which hints that they are probably the same population.)
@TheExplorer Bruh there are institutions and well funded highschools who can't get access to a decent lab... what kind advice.... Not to mention. Getting access to samples ancient or modern is not easy... NOR CHEAP.
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