posted
This is a continuation of this discussion as well as a few other things I wanted to point out. I'm guessing that I'm not clear when I type certain things so I hope to quickly break down a few things via discussion in here in regards to somethings.
1. South sudanese Nilotes are not quintessential "Nilo-Saharans." I mentioned recently, (I don't remember if it was on here in the Holocene thread or elsewhere) That the south Sudanese might be distinct on the Nilo-Saharan stratigraph. Since Dobon 2015 it seems that everyone has the Idea that Nilo-Saharan ancestry peaks in the Nilotic populations of South Sudan, like the Dinka. This is an incomplete assessment, given the fact that component drops heavily as you move away from south Sudan even in Nilo-Saharan speaking populations elsewhere.
2. SSA Substructure. Something Else that was brought up a few times... most notably seen here. Capras coment in relation to this chart "Baria can't be seen as entirely downstream of Mota" The Baria like other S.Sudanese Nilotes Can't fit down stream of Mota (nor Hadza). They have ancestry related to but probably distinct from Rainforest Foragers. This actually goes for Yoruba as well with out the Archaic admixture. A good portion of Ancestry in these populations are from a group that is downstream from Mota-like (Omotic) populations and a population somewhere upstream... See the following chart for a visual representation. (click to expand)
3. 'OOA drift in Africa'. Another thing that I mentioned before was that certain Nilo-Saharan or Omotic groups seem to only be a "bottleneck away from being Near Eastern/Natufian." One thing that is obvious to me now, is that the homogenization process that gave rise to modern Eurasians did not happen entirely in isolation from other Africans.
so, What does that mean?
This goes back to the Basal Eurasian issue. If this homogenization process happened significantly earlier than the OOA migration, we should expect to see interaction between these African groups. -Meaning, that we can be looking at populations IN Africa with Homogenized Ancestry mistaken for Non-African ancestry.
Up until the Taforalt genome, the closest individuals to whatever/whoever this population was were the Natufians... and that's by default given their age and proximity to Africa. This is THE reason why certain African populations shows very high Natufian components (in ADMIXTURE) as opposed to whatever population they actually have recent Eurasian Admixture from.
4. The HADZA Effect The Hadza are interesting to me because they are a population that cannot be recognized and adequately be accounted for in many mainstream, cookie cutter models. They throw wrenches in many analysis, they're essentially disregarded or explained away with some exotic rationale. The Hadza have the benefit of being old and isolated enough to retain unbothered Ancient East African ancestry. This is upstream of Mota but Downstream from rainforest foragers like Mbuti.
Unlike most other African populations they don't owe a huge portion of their ancestry to a population that diverged before them, However up until 2kya they also lack homogenized(OOA-like) ancestry. So phylogenetically this will put Hadza somewhere above the root separating Basal Eurasian/OOA-ish from other Africans. Hence why the Iranians who show the most "Basal-Eurasian" fit best by default in this run from Lazaridis.
Also Capra previously pointed out To me that Dinka should be looked at as technically Basal Eurasian, judging by this graph... As I stated earlier the dinka have ancestry that is both upstream and downstream from mota, which will result in them being an outlier as the Hadza are. Though the Latter were essentially completely upstream before 500bc or so.
5.The relationship between genetic distance and heterogeneity. This is probably the most important issue as it relates to Ancient genomes. It's something that have been talked about recurrently. but is not fully realized when addressing what it means for the relationship between ancient populations and Africans. Most recently we seen an example in this thread. In that self contained study we see that the genetic distance of Africans and Europeans is greater than that of any other two non African groups, however Europeans and Africans are joined closest in fig 1b. You can see this expressed in many forms of analysis, including pcas and treemix.
there was a time when Fst. was incorrectly used to explain population history. Distance in regards to Fst are inflated when looking at populations that are more heterogeneous. Ironically, this problem also rears itself in formal stats as shared alleles are magnified by homogeneity. Also when dealing with ancient populations we have to consider ancestry that is not present in modern day populations at all. the Ifri m Amr mousa (IAM) specimen from fregel 2017 makes this blatant. which brings me to my final thought.
6. Basal Eurasian, North African or just Africans? I mentioned quite a few times that I believed BE is probably just a statistical population and not a tangible single population who widely contributed to West Eurasian ancestry. which is why I've also said that we can get a population that seems to be completely Eurasian with 100% Basal Eurasian and that different African populations can accompany and or be responsible for Basal Eurasian signals. When it comes to North Africans, I believe that we'll find that some of their ancestry could have diverged prior to that of some SSA ancestry and that they were more than just Eurasian genomes in Africa before OOA. Hence what we see with the Neolithic Moroccans (IAM) and their ridiculous Fst distances. as well as the Taforalt appearing 15-20% Hadza.
...there's more that could be said, but I'll wait for discussion points to see if my rationale is clear at this point.
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posted
Sometimes I am led to believe you and Swenet are the same person. Write so eloquent but when you dig deeper you realize that there is so much contradiction.
This is a contradiction! --------- 1. South sudanese Nilotes are not quintessential "Nilo-Saharans." …..Versus …..this is an incomplete assessment, given the fact that component drops heavily as you move away from south Sudan even in Nilo-Saharan speaking populations elsewhere. -----------------------
You know YRI are not the only SSA and that East African SSA are distinct from West African SSA. East Africans SSA do NOT seem to be admixed with the same archaic Africans as West Africans. Which African SSA?. West or East? ------- 2. SSA Substructure. --------
Agreed!!
--------- 3. 'OOA drift in Africa'. -------------
Agreed! Unsupervised Data Coming out from several years ago has shown the isolated Hadza and Sandwe contain more “European’ ancestry than AFRAMS ---------------------------- 4. The HADZA Effect The Hadza are interesting to me because they are a population that cannot be recognized and adequately be accounted for in many mainstream, cookie cutter models --------------------------
Are making this up?????? --------- However up until 2kya they also lack homogenized(OOA-like) ancestry. ---------
Agreed!!! Sforza data and many STR dataset show the same. Not to mention McEvoy et al. Geography don’t lie…and genes mimic geography -------- however Europeans and Africans are joined closest in fig 1b. You can see this expressed in many forms of analysis, including pcas and treemix. ------
Agreed!!!! -------------------- I believe that we'll find that some of their ancestry could have diverged prior to that of some SSA ancestry and that they were more than just Eurasian genomes in Africa before OOA. Hence what we see with the Neolithic Moroccans (IAM) and their ridiculous Fst distances. as well as the Taforalt appearing 15-20% Hadza. ------------------
-------------------- 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
This should be a good discussion. And guys lets keep this civil. And that includes mods.
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posted
Again to be clear. Tanzanians like Hadza and Sandwe carry more “European” ancestry than AFRAMS. This has been observed several years ago. We also see that Tanzanian-Luxmanda(dated 3100BCE) carry more than 60% “Sardinian”/European ancestry(not East Asian like Japanese) but carry a pure African mtDNA lineage L2a. Can’t get more African than L2a(the supposed Bantu West African migration marker . lol!)
So that statement is BS…eh!....... I disagree with(being civil)
Not to mention 5000years earlier, further south than where the Hadza lived …….in Malawi. These African individuals (8100BP) already carried Sardinian ancestry!!!!!!
Quote ;
“Hadza – However up until 2kya they also lack homogenized(OOA-like) ancestry.”
-------------------- 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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Yet elMaestro is trying to say the net split time of Yoruba is younger than Basal Eurasian and that Dinka are "technically Basal Eurasian". Again, we know that is simply not true. Demonstrably NOT true. SMH.
Of course, elMaestro is going to insist that these bizarre and forced arguments aren't his own politics talking.
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posted
Don’t get caught up in the label given “Basal Eurasian”. Basal Eurasian is found as far south as Malawi 8100 years ago in Africa. That is why Skoglund et al speculated that the genetic material MAY have an African origin(or Near East) because of the genetic chronology(time stamp). If Luxmanda carried L2a that would put Basal Eurasian deeper within Africa.
ElMaesrtro is right Basal Eurasian is African but NOT Dinka(Sudan). It is from further south.
-------------------- 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
I agree ... YRI is YOUNGER than Basal Eurasian.
BTW - What genetic proof do you have that YRI older than Basal Eurasian?
We have seen ancient DNA has shown PN2/E1b1* in Sudan area in the Neolithic. The Natufians(carry related Basal Eurasian) were rich in YAP/PN2.
-------------------- 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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quote:Originally posted by sudaniya: This is really confusing; how can the Dinka be Basal Eurasian?
They aren’t Basal Eurasian. Just to be clear. Their ancestors are composed of populatations that split near the time of Basal Eurasian and before East Africans.
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posted
BTW, for people who don't know how to read this. All this says in regards to Hadza is that Mota forms clade with Hotu to the exclusion of Hadza and Dinka. That's all it says.
It doesn't prove that Hadza have no Eurasian ancestry It doesn't prove that Hadza are "sister to pre-OOA" (whatever that means) The stat goes against many of the things that are said here.
quote:Originally posted by xyyman: [QB] Sometimes I am led to believe you and Swenet are the same person. Write so eloquent but when you dig deeper you realize that there is so much contradiction.
This is a contradiction! --------- 1. South sudanese Nilotes are not quintessential "Nilo-Saharans." …..Versus …..this is an incomplete assessment, given the fact that component drops heavily as you move away from south Sudan even in Nilo-Saharan speaking populations elsewhere. -----------------------
You know YRI are not the only SSA and that East African SSA are distinct from West African SSA. East Africans SSA do NOT seem to be admixed with the same archaic Africans as West Africans. Which African SSA?. West or East?
When did I say they were the same? The gpgraphs above clearly shows that unlike East Africans the YRI has archaic ancestry.
Also the south Sudanese component can’t be considered THE nilosharan component because it isn’t as strong in other Nilo Saharan populations. I don’t see how that translates contradictory.
quote: 4. The HADZA Effect
Are making this up?????? Nah you can check this out --------- However up until 2kya they also lack homogenized(OOA-like) ancestry. ---------
Nah pickrell 2015 dates their Eurasian ancestry to around 2-2.5kya.
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quote:Originally posted by Swenet: BTW, for people who don't know how to read this. All this says in regards to Hadza is that Mota forms clade with Hotu to the exclusion of Hadza and Dinka. That's all it says.
It doesn't prove that Hadza have no Eurasian ancestry It doesn't prove that Hadza are "sister to pre-OOA" (whatever that means) The stat goes against many of the things that are said here.
quote:Originally posted by Elmaestro:
Lol what? Mota + Hotu gives the lowest z score out of every other available combination (w/ mota). That translates to hotu sharing more alleles in relation to mota with the hadza and the Dinka. Like c’mon now.
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quote:Originally posted by Swenet: BTW, for people who don't know how to read this. All this says in regards to Hadza is that Mota forms clade with Hotu to the exclusion of Hadza and Dinka. That's all it says.
It doesn't prove that Hadza have no Eurasian ancestry It doesn't prove that Hadza are "sister to pre-OOA" (whatever that means) The stat goes against many of the things that are said here.
quote:Originally posted by Elmaestro:
Lol what? Mota + Hotu gives the lowest z score out of every other available combination (w/ mota). That translates to hotu sharing more alleles in relation to mota with the hadza and the Dinka. Like c’mon now.
How is more negative value with Hotu as population A mutually exclusive with what I just said?
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"BTW, for people who don't know how to read this. All this says in regards to Hadza is that Mota forms clade with Hotu to the exclusion of Hadza and Dinka."
Clearly that's not all this says.
I know you're very over protective of BE... So it's cool if you disagree, but chill out.
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posted
That is all it says. There is no evidence that Hadza are 'actively involved' in the stat being more negative with Hotu as population A. You can get that stat without Hadza being any of the things you say they are. Passively inheriting L4 and other non-Hadza hgs can just as easily explain this (which it most likely does). But even without L4, it makes sense that many Africans (not just Hadza) will have Hotu as their their most negative population A when their Eurasian admixture is removed. This doesn't have to mean anything about those Africans being "pre-OOA" since Hotu is >60% African.
This guy says I'm "overprotective of BE". I'm not even responding to your posts most of the time when you say weird stuff about BE. You're free to think BE is mtDMA L1 and other non sense all you want. Just don't try to challenge what I say with your non sense politics and expect to be taken seriously.
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quote:Originally posted by Swenet: That is all it says. There is no evidence that Hadza are 'actively involved' in the stat being more negative with Hotu as population A. You can get that stat without Hadza being any of the things you say they are.
I'ts not so much about the Hadza and more about What Basal Eurasian is... Hotu being 60% basal Eurasian and creating the best Z-Scores are no accident.
The hadza have been shown to have divergent ancestry over and over and over again. All they way up till skoglund they're said to have retained strong ancestral East African ancestry. Even Shriner in the article you brought them up in explains that though their ancestry is most similar to omotic it's distinct. And every so often their components appear pervasive in populations like the Natufians in ADMIXTURE/STRUCTURE runs.
If the Hadza are not Basal Eurasian or their progenitors... which I don't beleive because they're not homogenized (and they don't fit too well) then we can theorize that this is probably a result of Hadza receiving a considerable amount of non-African ancestry or conversely that the Hadza might have a close relationship phylogenetically with the ancestors of these populations (or both.)
This is why the F3 is important, it shows that their non-African ancestry is insignifiacnt. according to both Shiriner and skoglund Mota should be a very good proxy (the best) for Hadzas African ancestry, yet still the Hadza have a more positive score than the unadmixed Dinka.
And now we have taforalt genomes that appear to be 20% hadza. I don't beleive it's an accident, the hadza are just the best fit for that ancestry due to their phylogenetic position, being right next to "pre-OOA." as you call it.
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quote:Originally posted by Swenet: This guy says I'm "overprotective of BE". I'm not even responding to your posts most of the time when you say weird stuff about BE. You're free to think BE is mtDMA L1 and other non sense all you want. Just don't try to challenge what I say with your non sense politics and expect to be taken seriously. [/QB]
What are you talking about... omfg.
You know what... have your shine fam
..now we are back to calling autosomal "populations" uniparentals(L1)....
...I'm done my nigga
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“Nah pickrell 2015 dates their Eurasian ancestry to around 2-2.5kya.”
Huh?! But Skoglund DIRECTLY date the Eurasian ancestry 8100BCE In Malawi. WT…..
To the newbies. Pickrell used statistical modeling not DIRECT sampling like Skoglund. SMH. Swenet! Swenet! Swenet! Eh! sorry! ElMaestro! Elmaestro! ElMaestro! In other words we know for a FACT Eurasian ancestry was in Malawi 81000 years ago. Long before Pickrell suggested. I believe Pickrell was cited by Skoglund also. Meaning Pickrell is dated is …..outdated.
-------------------- 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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".now we are back to calling autosomal "populations" uniparentals(L1)....
..."
He does that. I don't understand why....
-------------------- 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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quote:Originally posted by Swenet: This guy says I'm "overprotective of BE". I'm not even responding to your posts most of the time when you say weird stuff about BE. You're free to think BE is mtDMA L1 and other non sense all you want. Just don't try to challenge what I say with your non sense politics and expect to be taken seriously.
What are you talking about... omfg.
You know what... have your shine fam
..now we are back to calling autosomal "populations" uniparentals(L1)....
...I'm done my nigga [/QB]
You know what you said. These are the type of weird things you say:
Basal Eurasian isn't a haplogroup. Phylogenetically it can encompass anything from L2-L6 and maybe even L1.
"Basal Eurasian isn't a haplogroup, but it could be L1-linked"
But of course, you never said that. Someone is putting words in your mouth. And these kinds of blatant liberties with the data definitely don't show you're driven by politics. It's just a happy coincidence that reputable commentators and researchers have never said that before.
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
quote:Originally posted by sudaniya: This is really confusing; how can the Dinka be Basal Eurasian?
Since Basal Eurasian is an imaginary population it can't be identified as any real population, similar to the number i.
quote:Originally posted by Swenet:You know what you said. These are the type of weird things you say:
Basal Eurasian isn't a haplogroup. Phylogenetically it can encompass anything from L2-L6 and maybe even L1.
"Basal Eurasian isn't a haplogroup, but it could be L1-linked"
But of course, you never said that. Someone is putting words in your mouth. [/QB]
1."Basal Eurasian isn't a haplogroup, but it could be L1-linked" -When did I say this?
2.Post the links, or quote my whole statements and stop pulling my points out of context. This is the shit you keep doing, I'm not fucking around w/ you. You damn well know that I don't even consider Basal Eurasian a tangible population yet your mission is to wholeheartedly convince others that I believe Basal Eurasians are Dinka and Yorubans. Dude, just fuck off now.
EliteDiasporan I'm trying to be non-confrontational... please tell me that you see that I was trying my best here.
@XYYMAN You looking at apples and oranges... the Malawi fingira are not the Hadza... two different populations with different history. Skoglunds Hadza sample didn't even have Eurasian signatures as a matter of fact.
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Swenet looking at this Lazaridis chart we see some locations shown, West Eurasian, Onge (one of the Andamanese), loschbour is in Luxebourg etc, etc
So on what continent would "Non-African" be on ? and if you can get more specific if possible the likely regions where we see the first "Non-African" , thanks, lioness
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quote:Originally posted by Elmaestro: EliteDiasporan I'm trying to be non-confrontational... please tell me that you see that I was trying my best here.
How about not posting misinformation ask how you score on that.
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posted
@Lioness, I'm not going to stay in this misinformation thread than I have to.
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quote:Originally posted by Swenet: @Lioness, I'm not going to stay in this misinformation thread than I have to.
Ok, understood
looking at this Lazaridis chart on what continent would "Non-African" be on ? and if you can get more specific if possible the likely regions where we see the first "Non-African" , thanks, lioness
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posted
Aren't you supposed to be the knight and shinning armor... the hero of correct information. enlighten her...
you're whole essence is an attempt to put others down apparently... you shallow as fuck. lmao
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posted
Good, you know that I'm an asshole. Good for you. So why still talk to me with your politics, trying to tell me that Hadza are sister to pre-OOA and other misinformation? You don't have to talk to me when I'm making a post. I already told you in 2016 when you were posting misinformation on Mota and Hadza/Sandawe.
Don't mind me. Continue your misinformation thread. I'm sure there is a lot more misinformation where the OP came from.
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posted
Swenet is scared to answer that basic question, it's disappointing
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
quote:Originally posted by xyyman: We also see that Tanzanian-Luxmanda(dated 3100BCE) carry more than 60% “Sardinian”/European ancestry
OBSERVATIONS
Sardines are THE modern EEF.
Supposedly no modern Inner African in Sardines.
Sardine detected in many modern Africans.
Stuttgart is the EEF poster girl.
NEF contributed to EEF.
NEF levels in EEF were detected by YRI in Beduin B
QUESTIONS:
How does this impact the meaning of Sardine in Africans? or What does this mean re Sardine in modern Africans?
How can Sardine not have a modern African component yet be THE modern EEF?
I'm wary of genetic statistical conclusions on extant populations that are out of sync with linguistics, history, ethnography, anthropology, and archaeology. Not one of these five disciplines attest to rampant S Euro forays deep in Africa before Vasco de Gama.
posted
Sardine do have an African component. Matter of fact Sardinians are an outlier in European DNA. Sardinians are politically European but Geographically African(North) same as Sicilians and Malta
when you read Italians and Iberians carry African DNA they are not talking Mian land Italians from the North They are talking Sardinians and Sicilians.
eg R1b-V88 and E1b1b/b and yDNA A and also autosomally. Read the reports.
BTW - I agree with Lioness. You had a chance to clean up this mess.......but more power to you. You stuck around. I voted for your tenure.
I have to admit under new management it seem much better. Except for the occasional banning of yours truly.
-------------------- 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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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
quote:Originally posted by the lioness,: who asked you? your moderation was royal mess
Trying to distract from what you didn't deny doing; unprovoked baiting and ad homina.
I asked me and I had no admin power to enforce anything.
What are you afraid of? I am so passe. Shut up and be happy. Soon enough you will own all ES.
posted
I want to add that the owners seems to be more supportive to the new administration. I like the “no time out” for editing although someone can go back and make edits and the reader would have long past reading that post and miss the new edits. I also like the personal avatar feature. They also have the function to ‘ban” which you did not have. Were you set up for failure?
-------------------- 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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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
Forget me. "it's impossible to go living through the past." I'm rank and file.
Rey successfully contacted Sami. That was the major breakthrough. Rey is admin in chief.
He and crew can and will do whatever the f they want and will not abide criticism.
I would just like to see consistancy. Either dis cussin battle rap mode or mature discussion mode.
But what about the Sardine observations and questions Mensa? Gimme something developed please..
Sardinia sits at a crossroads in the Mediterranean Sea, the second largest island next to Sicily. Surrounded by sparkling turquoise waters, this Mediterranean jewel lies northwest of the toe of the Italian peninsula boot, about 350 kilometers due west of Rome.
For evolutionary biologists, islands are often intriguing, geographically isolated pockets with unique populations that can be ripe for exploration.
Now, in a new study appearing in the advanced online edition of Molecular Biology and Evolution an international team led by geneticist Anna Olivieri from the University of Pavia tackles a highly interesting question: what were the origins of the Sardinian population in the context of European prehistory and ancient human migrations?
The authors analyzed 3,491 modern, whole mitochondrial DNA genomes from Sardinia (which are only passed down maternally). These were compared with 21 samples of ancient mitogenomes from the island, a large panel of non-Sardinian mitogenomes —-and even Ötzi (the nickname of Europe's oldest natural mummy, the 3,300 BCE-year old "Tyrolean Iceman") —-to better understand their origins.
Their findings show Sardinia as an outlier in the general European genetic landscape. Almost 80 percent of modern Sardinian mitogenomes belong to branches that cannot be found anywhere else outside the island. Thus, they were defined as Sardinian-Specific Haplogroups (SSHs) that most likely arose in the island after its initial occupation. Almost all SSHs coalesce in the post-Nuragic, Nuragic and Neolithic-Copper Age periods. However, some rare SSHs display age estimates older than 7,800 years ago, the postulated archeologically-based starting time of the Neolithic in Sardinia.
"Our analyses raise the possibility that several SSHs may have already been present on the island prior to the Neolithic," said prof. Francesco Cucca, from the Institute of Genetic and Biomedical Research (IRGB), at the CNR in Cagliari (Sardinia).
The most plausible candidates would include haplogroups K1a2d and U5b1i1, which together comprise almost 3 percent of modern Sardinians, and possibly others. Such a scenario would not only support archaeological evidence of a Mesolithic occupation of Sardinia, but could also suggest a dual ancestral origin of its first inhabitants. K1a2d is of Late Paleolithic Near Eastern ancestry, whereas U5b1i1 harbours deep ancestral roots in Paleolithic Western Europe.
This work provides evidence that contemporary Sardinians harbour a unique genetic heritage, as a result of their distinct history and relative isolation from the demographic upheavals of continental Europe. Anna Olivieri stresses: "It now seems plausible that human mobility, inter-communication and gene flow around the Mediterranean from Late Glacial times onwards may well have left signatures that survive to this day. Some of these signals are still retained in modern Sardinians."
"Although in the past the stress has often been on the spread of the Neolithic, genetic studies too are beginning to emphasize the complexity and mosaic nature of human ancestry in the Mediterranean, and indeed in Europe more widely," concludes prof. Antonio Torroni, from the University of Pavia. "Future work on ancient DNA should be able to test directly to what extent this more complex model is supported by genetic evidence, and whether our predictions of Mesolithic ancestry in contemporary Sardinians can be sustained."
Explore further: Hair from mummy's clothes provides insights into red deer lineage
More information: Anna Olivieri,† et al, Mitogenome Diversity in Sardinians: a Genetic Window onto an Island's Past, Molecular Biology and Evolution (2017). DOI: 10.1093/molbev/msx082 Journal reference: Molecular Biology and Evolution
But what about the Sardine observations and questions Mensa? Gimme something developed please..
-------------------- 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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NEF levels in EEF were detected by YRI in Beduin B
QUESTIONS:
How does this impact the meaning of Sardine in Africans? or What does this mean re Sardine in modern Africans?
How can Sardine not have a modern African component yet be THE modern EEF?
I'm wary of genetic statistical conclusions on extant populations that are out of sync with linguistics, history, ethnography, anthropology, and archaeology. Not one of these five disciplines attest to rampant S Euro forays deep in Africa before Vasco de Gama.
Is this a scientific Haggard?
Nah it's just misinterperetation. Lazaridis actually used the non-African portion of beduin_B to see if there was geneflow from the Near east to Stuttgart.
Solving for the bold has African ancestry represented by the Yoruba subtracted from Beduin B. the γ estimates are what they reffered to with this quote: "Table S13.2 and ranges between 55-100% with estimates increasing as the amount of estimated African admixture in BedouinB increases."
Basically saying that the more African ancestry removed from bedouin B the closer they are to Stuttgart.
Of course this is before they actually used ancient Near eastern genomes to get better estimates, as we know now stuttgart isn't 100% Near eastern.
So unfortunately that study says nothing about Sardinias(EEF) relationship to Africans but it does show that Basal Eurasian (whatever it is) is homogenized.
Posts: 1781 | From: New York | Registered: Jul 2016
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They want to investigate the relationship between Sardinians and populations outside Sardinia but REMOVED "non-Sardinian" mtDNA from the dataset. Good God! What do you think is "non-Sardinian" mtDNA???? In addition they are hiding data..."data not shown" SMH.
Man! Europeans!!! They really think they are smarter than everyone else.
Quote: " Therefore, to learn more about the ancestry of Sardinians and their genetic links with modern and ancient European (and other) Populations, we analyzed a large dataset of 3,491 novel complete mitogenomes from modern islanders as well as 21mitogenomes from ancient specimens. Among the modern samples, we*** REMOVED*** 1,355 maternally related samples on the bases of pedigree data or kinship evaluation of nuclear genomes, and 44 samples with non-Sardinian maternal origins. We then assessed the phylogenetic relationships of the remaining mitogenomes (2,092 out of the initial 3,491), plus 124 previously published Sardinian mitogenomes, with all publicly available worldwide mitogenomes (more than 26,000 data not shown)."
-------------------- 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
Hint! Hint! NOT from the Near east. Are they reading my postings? mtDNA H1/H3 is from Africa and not from Iberia. They know that!! That is why they said "or from elsewhere" Outside of Iberia in the Western Mediterranean what else is there but Africa and we know it did not originate Iberia.
Quote: "Our detection of potential pre-Neolithic signals in the mitogenome pool of contemporary Sardinians remains to be tested with studies of ancient DNA. If confirmed, a pre-Neolithic presence of H3 (and possibly also of H1 and other lineages, for example within JT) on the island alongside K1a2d and U5b1i1 (and most likely other lineages that we have not detected) Would indicate a more substantial genetic legacy of Mesolithic Sardinians to the modern people of Sardinia. However, it is also important to realise that even if H3 (and H1) arrived in Sardinia only with the Neolithic, they most likely came from either Spain or elsewhere in the western Mediterranean, and **not** from the Near East. This would imply that they are likely the result of autochthonous west Mediterranean Mesolithic acculturation, in the wider European context."
-------------------- 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
Notice also in Fig 3. They did not plot mtDNA H1. Why? The obvious. In certain regions in Africa H1 has higher frequency. Showing that chart will screw with their hypothesis. Lol! They all know I am correct. Europeans are depigmented Africans. Theya re not related to Near Easterners and Basal Eurasian is North African with a origin in the Great Lakes.
-------------------- 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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Tukuler
multidisciplinary Black Scholar
Member # 19944
I'm wary of genetic statistical conclusions on extant populations that are out of sync with • linguistics, • history, • ethnography, • anthropology, and • archaeology. Not one of these five disciplines attest to rampant S Euro forays deep in Africa before Vasco da Gama.
Is this a scientific Haggard?
Nah it's just misinterperetation. Lazaridis actually used the non-African portion of beduin_B to see if there was geneflow from the Near east to Stuttgart.
Solving for the bold has African ancestry represented by the Yoruba subtracted from Beduin B. the γ estimates are what they reffered to with this quote: "Table S13.2 and ranges between 55-100% with estimates increasing as the amount of estimated African admixture in BedouinB increases."
Basically saying that the more African ancestry removed from bedouin B the closer they are to Stuttgart.
What you bolded is for the Loschbour WHG, the Euro component of EEF. Carefully read the text that goes along with the math on p92 where they have (S13.1) and (S13.2)
Forgive me repeating myself but the facs I posted earlier was a tad illegible. So now let's reread the authors misinterpret themselves again.
OIC, that's what they said but they was jus playin.
I'm wary of genetic statistical conclusions on extant populations that are out of sync with • linguistics, • history, • ethnography, • anthropology, and • archaeology. Not one of these five disciplines attest to rampant S Euro forays deep in Africa before Vasco da Gama.
Is this a scientific Haggard?
Nah it's just misinterperetation. Lazaridis actually used the non-African portion of beduin_B to see if there was geneflow from the Near east to Stuttgart.
Solving for the bold has African ancestry represented by the Yoruba subtracted from Beduin B. the γ estimates are what they reffered to with this quote: "Table S13.2 and ranges between 55-100% with estimates increasing as the amount of estimated African admixture in BedouinB increases."
Basically saying that the more African ancestry removed from bedouin B the closer they are to Stuttgart.
What you bolded is for the Loschbour WHG, the Euro component of EEF. Carefully read the text that goes along with the math on p92 where they have (S13.1) and (S13.2)
Forgive me repeating myself but the facs I posted earlier was a tad illegible. So now let's reread the authors misinterpret themselves again.
OIC, that's what they said but they was jus playin.
Which makes sense if there was an ancient African component in the Near East. Modern Yorubas and other "recent" African mixture does not tell you the ancient African mixture unless those ancient Africans were also somehow ancestral to the Yoruba. Hence the latest Iberomaurisan DNA paper.
But by filtering out that African mixture they throw out all African mixture ancient and modern, thus throwing out the baby with the bath water.
Posts: 8889 | Registered: May 2005
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quote:Originally posted by Tukuler:What you bolded is for the Loschbour WHG, the Euro component of EEF. Carefully read the text that goes along with the math on p92 where they have (S13.1) and (S13.2)
Forgive me repeating myself but the facs I posted earlier was a tad illegible. So now let's reread the authors misinterpret themselves again.
OIC, that's what they said but they was jus playin. [/QB]
^^ This is one big equation where x are the surrogate Eurasian populations you'll see in table 13.2 and gamma is one of the three estimates of SSA ancestry in Bedouin B. read below
quote:Recognizing the challenge posed by the lack of accurate surrogates for the ancestral populations, we hypothesized that Stuttgart is a mixture of an unknown hunter-gatherer population that forms a clade with Loschbour in proportion 1-? and an unknown Near Eastern population (NE) in proportion ?. While we do not know the exact NE population contributing ancestry to Stuttgart, we explored using BedouinB as a surrogate, as this is the population that appears at the southern end of the Near Eastern cline in Fig. 1B and has no evidence of eastern non-African ancestry by ADMIXTURE analysis (SI 9). A complication of using the BedouinB population for this purpose is that it has some African admixture, as indicated by the ADMIXTURE analysis (SI 9). We estimated a lower bound (4.2 ± 0.3%) on this admixture proportion using ALDER1, using the Yoruba as a reference population. The advantage of this linkage-disequilibrium based method is that, unlike f4-ratio estimation2, no explicit model of population relationships is needed. We can also use the 5.1% estimate from ADMIXTURE K=3, or 7.3% from ADMIXTURE K=5 (SI 9). The two estimates differ because the Yoruba are inferred to have low levels of West Eurasian admixture at K=3, but to belong 100% to their own ancestral component at K=5. We did not use the K=4 value as in some ADMIXTURE replicates Yoruba formed their own component while in others they did not, whereas they formed their own component in all 100 replicates at K=5. Figure
As you can see here they're trying to use Bedouin B minus any SSA ancestry. The more African that gets subtracted (gamma "γ") the more outstanding the Near eastern estimates are for Stuttgart. What you highlighted literally means the opposite of what you believe it does.
[f4(African outgroup, X; Loschbour, NE)](1-γ)---> gives you outstanding Near Eastern multiplied by 1-γ to give the non African ratio of Bedouin B [γf4(African outgroup, X; Loschbour, Yoruba)] ---> gives outstanding YRI multiplied by gamma to represent the ratio of ssA in Beduoin B [f4(African outgroup, X; Loschbour, BedouinB) ---> gives outstanding Beduoin B
Bedouin B = Ancient near eastern(NE) + Subsahran African f4(African outgroup, X; Loschbour, BedouinB) = (S13.3) =γf4(African outgroup, X; Loschbour, Yoruba) + (1-γ)f4(African outgroup, X; Loschbour, NE)
Like I said before they are solving for NE So the equation is rewritten as...
Because stuttgart is assumed to be a mixture of Ancient Near eastern and a Eurasian hunter gatherer. Eurasian hunter gathers can be accounted for with Loshbour + Surrogate Eurasians (X). So essentially they're only trying to find what'll remain minus SSA ancestry. and the ratio of that(above equation) compared to f4(African outgroup, X; Loschbour, Stuttgart) that will let you know how much NE ancestry Stuttgart has.
Posts: 1781 | From: New York | Registered: Jul 2016
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posted
@DougM none of this is a big deal now as it's somewhat resolved with the presence of aDNA from the Near east in regards to EEF.
Posts: 1781 | From: New York | Registered: Jul 2016
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posted
Right but the point still stands that there was an ancient African component in that Near Eastern population. So the equation that Near Eastern is minus African ancestry is not quite correct.
Of course as it relates to ancient African genetics in and around North Africa that would be significant. There should be a clinal relationship between ancient North Africa, the Levant and Europe.
Posts: 8889 | Registered: May 2005
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
Like I said. The authors are very plain. NEF in EEF is a ratio of (S13.1) and (S13.2)
Like I told you. The math you keep referring to is just a way to estimate unknown (S13.2) the Loschsbour in Near Eastern.
Of course the less Inner African the more Loschbour and to quote the authors again
quote: The amount of Near Eastern admixture estimated for Stuttgart ... increasing as the amount of estimated African admixture in Bedouin B increases.
No peregrinations necessary. Just believe the authors do mean what they say and all else is but a persons misinterpretation.
This was and remains important because it is valid and it shows Inner African relationship to EEF and thus Sardines allowing questioning of what Sardine in African populations really means.
I tried to break down the problem peice by peice. but you deny my explaination.
Loschbour admixture in NE is not what's being solved.
They are trying to solve for a
the only population that isn't available is Acient Near eatsern(NE).
How would you solve for a using f4 if.
f4(African outgroup, X; Loschbour, Stuttgart) = -aβx
and
f4(African outgroup, X; Loschbour, NE) = -βx
Keep in mind NE doesn't exist in this study... so Bedouin B was used... the reasoning behind the whole equation was explained.
Did you read the quote I posted, particularly the bolded part?
quote:While we do not know the exact NE population contributing ancestry to Stuttgart, we explored using BedouinB as a surrogate, as this is the population that appears at the southern end of the Near Eastern cline in Fig. 1B and has no evidence of eastern non-African ancestry by ADMIXTURE analysis (SI 9). A complication of using the BedouinB population for this purpose is that it has some African admixture, as indicated by the ADMIXTURE analysis (SI 9). We estimated a lower bound (4.2 ± 0.3%) on this admixture proportion using ALDER1, using the Yoruba as a reference population. The advantage of this linkage-disequilibrium based method is that, unlike f4-ratio estimation2, no explicit model of population relationships is needed. We can also use the 5.1% estimate from ADMIXTURE K=3, or 7.3% from ADMIXTURE K=5 (SI 9)
They were never solving for Loshbour Admixture in NE.
They're trying to remove African from Bedouin B to find NE
please actually try to understand what I'm saying. please tryPosts: 1781 | From: New York | Registered: Jul 2016
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