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.
Posted by xyyman (Member # 13597) on :
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. ------------------
Posted by Elite Diasporan (Member # 22000) on :
This should be a good discussion. And guys lets keep this civil. And that includes mods.
Posted by sudaniya (Member # 15779) on :
This is really confusing; how can the Dinka be Basal Eurasian?
Posted by xyyman (Member # 13597) on :
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.”
Posted by Swenet (Member # 17303) on :
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.
Posted by xyyman (Member # 13597) on :
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.
Posted by xyyman (Member # 13597) on :
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. Posted by Elmaestro (Member # 22566) on :
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.
Posted by Swenet (Member # 17303) on :
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:
Posted by Elmaestro (Member # 22566) on :
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.
Posted by Elmaestro (Member # 22566) on :
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.
Posted by Swenet (Member # 17303) on :
quote:Originally posted by xyyman: 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.
See the links in my previous post.
Posted by Swenet (Member # 17303) on :
quote:Originally posted by Elmaestro:
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?
Posted by Elmaestro (Member # 22566) on :
You said
"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.
Posted by Swenet (Member # 17303) on :
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.
Posted by Elmaestro (Member # 22566) on :
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.
Posted by Elmaestro (Member # 22566) on :
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
Posted by xyyman (Member # 13597) on :
“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.
Posted by xyyman (Member # 13597) on :
".now we are back to calling autosomal "populations" uniparentals(L1)....
..."
He does that. I don't understand why....
Posted by Swenet (Member # 17303) on :
quote:Originally posted by Elmaestro:
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.
Posted by Tukuler (Member # 19944) on :
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.
Posted by Elmaestro (Member # 22566) on :
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.
Posted by the lioness, (Member # 17353) on :
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
Posted by Swenet (Member # 17303) on :
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.
Posted by Swenet (Member # 17303) on :
@Lioness, I'm not going to stay in this misinformation thread than I have to.
Posted by the lioness, (Member # 17353) on :
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
Posted by Elmaestro (Member # 22566) on :
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
Posted by Swenet (Member # 17303) on :
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.
Posted by the lioness, (Member # 17353) on :
Swenet is scared to answer that basic question, it's disappointing
Posted by Tukuler (Member # 19944) on :
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.
Is this a scientific Haggard?
Posted by Tukuler (Member # 19944) on :
quote:Originally posted by the lioness,: Swenet is scared to answer that basic question, it's disappointing
Baiting and ad hominen by mgmt is disappointing.
Posted by the lioness, (Member # 17353) on :
who asked you? your moderation was royal mess
Posted by xyyman (Member # 13597) on :
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.
Posted by Tukuler (Member # 19944) on :
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 by xyyman (Member # 13597) on :
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?
Posted by Tukuler (Member # 19944) on :
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..
Posted by Elite Diasporan (Member # 22000) on :
quote:Originally posted by Elmaestro: [QB]
EliteDiasporan I'm trying to be non-confrontational... please tell me that you see that I was trying my best here.
All I see no rowdy back and forth flamewars. Just the both of you having a tense disagreement.
@Lioness @Tukuler
Take this somewhere else.
Posted by xyyman (Member # 13597) on :
??
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..
Posted by Elmaestro (Member # 22566) on :
quote:Originally posted by Tukuler: 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.
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.
Posted by xyyman (Member # 13597) on :
This paragraph is hilarious......
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)."
Posted by xyyman (Member # 13597) on :
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."
Posted by xyyman (Member # 13597) on :
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.
Posted by Tukuler (Member # 19944) on :
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.
Posted by Doug M (Member # 7650) on :
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.
Posted by Elmaestro (Member # 22566) on :
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.
Posted by Elmaestro (Member # 22566) on :
@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.
Posted by Doug M (Member # 7650) on :
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.
Posted by Tukuler (Member # 19944) on :
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.
Political objections overruled.
Posted by Elmaestro (Member # 22566) on :
That's completely wrong.
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 try Posted by Tukuler (Member # 19944) on :
quote:Originally posted by Doug M:
the equation that Near Eastern is minus African ancestry is not quite correct.
.
Don't buy the Brooklyn Bridge. There ain't no such equation in Lazaridis (2014) Supplementary Info 13.
Non critical acceptance of rampant Sardines through out Inner Africa is the result of too much Lazar-ade and too little multidisciplinary investigations.
Posted by Elmaestro (Member # 22566) on :
I also want to inform you that if your interpretation was right, then it'd literally only solidify my position as introduced in the OP. as I can really just say Basal Eurasian estimates require SSA ancestry... But that's simply not the case here.
just misinterpretation.
Posted by Tukuler (Member # 19944) on :
quote:Originally posted by Elmaestro:
Face saving essay denying what the authors 'plain print w/o a lotta who shot John.
I don't care what you say they said.
Thing is I care what Laz Patterson Reich said. I tried my best to show you by simply color coding the plain print but you know more and refuse to listen or even consider stepping back and taking time out to digest what they write.
Posted by Tukuler (Member # 19944) on :
quote:Originally posted by Elmaestro: facesaving fluff
Unlike you I m not interpreting.
I directly quoted Laz Patterson Reich.
You made shit up in their name.
Not trying to convince you. Setting the record straight simply posting screenshots from the supplement.
You're free to cling to your own fabrications.
Posted by Elmaestro (Member # 22566) on :
you know what, tukuler....
Explain detail by detail how they solved for near eastern.
Also explain what Lazaradis mean by this
". 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)."
Don't comment on what you think I'm trying to do or etc.
Publically show us how would you solve for NE in Stuttgart. And explain what lazaradis is saying in the paragraph before Figure S13.1.
Don't bracket and color code... just show me how the equation will yeild NE estimates IN stuttgart.
Posted by Elmaestro (Member # 22566) on :
why is the African Admixture in Bedouin B according to lazaridis a "complication?
and I quote AGAIN
"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). "
"A complication of using the BedouinB population for this purpose is that it has some African admixture,"
---------------
Matter of fact... Show us in YOUR interpretation how you'd find the ratio of Loschbour in Near Eastern!!? How did lazaridis find the ratio of Loschbour in Near eastern tukuler!??
Posted by Tukuler (Member # 19944) on :
Forget who's the better rhetorician.
How you gonna tell me to ignore the authors? That's a warning sign of personal bias right there.
Let's follow actual author text for the 4th time hoping it will sink in after a while.
Look at the blue box and underscore elMaestro. The authors say the ratio of (S13.1) and (S13.2) is the Near Eastern admixture of Stuttgart.
Look at the red box elMaestro. The authors say (S13.2) is estimated subtracting Yoruba from Bedouin B.
Look at the green boxes elMaestro. That's the math for Loschbour and Near Eastern admixture/shared ancestry.
Don't use logic. Stick to the math.
Loschbour in NE is detected by BedB minus YRI. You believe BedB minus YRI detects NE in Stuttgart. The authors make no such claim and explicitly state and table as YRI increase NE in Stuttgart increases.
Stuttgart isn't even a factor in (S13.3) & (S13.4).
You can believe what you wanna.
Your argument is against the authors.
I suggest you take notes while studying not merely reading the entire SI13 section so as not to mistake what's being laid, Admixture proportions for Stuttgart.
Posted by Elmaestro (Member # 22566) on :
scrap what I beleive for a second... You don't care to know the actual math behind solving this if it's coming from me.. I'll accept that.
But lets look at what YOUR saying.
"Loschbour in NE is detected by BedB minus YRI"
and here
"Look at the blue box elMaestro. The authors say the ratio of (S13.1) and (S13.2) is the Near Eastern admixture of Stuttgart. "
If we're solving for the ratio of (loschbour in NE) and (Luschbour in Stuttgart) to get the amount of NE in Stuttgart, what'll happen to the African/Yoruban in this equation?
just use logic.
Posted by Tukuler (Member # 19944) on :
One more time forget the logic (indirect inference) authors didn't conclude. the math is whats pertinent and the authors give it no logical inference necessary.
The actual math explained by the authors overrides your logical inference. Didn't they teach you that in university or technology institute? .
Nothing written by the authors support you.
Loschbour in NE is detected by BedB minus YRI. You believe BedB minus YRI detects NE in Stuttgart. The authors make no such claim and explicitly state and table: as YRI increases in BedB, NE increases in Stuttgart. Posted by Elmaestro (Member # 22566) on :
"A complication of using the BedouinB population for this purpose is that it has some African admixture," -LAZARIDIS
^This was written by the authors.
1.you don't understand the math. 2.you don't care to understand the math 3.you ignore context that goes against your interpretation.
...I don't think there's much more I can say. I explained to you very well why your take on the quote is a misunderstanding
I explained to you how these numbers(γ) indicated by the red arrows were used in the equation. ...You don't care
You (though your interepretation of the equations are wrong) inadvertently explained how these numbers were used in the equation to your own contradiction ...but none of that matters because of your personal interpretation of a quote;
"The amount of Near Eastern admixture estimated for Stuttgart can be seen in Table S13.2 and ranges between 55-100% with estimates increasing as the amount of estimated African admixture in BedouinB increases."
despite me and you both showing that that African Admixture was being subtracted in the equation.
At this point I have nothing more to add. I tried man.
Posted by Elmaestro (Member # 22566) on :
"You(ElMaestro) believe BedB minus YRI detects NE in Stuttgart" -Tukuler
quote: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.
Posted by Tukuler (Member # 19944) on :
I thought you were done. Ego won't let you rest.
Yeah you tried buy I don't buy bridges or used cars.
Better try the rubes.
Posted by Tukuler (Member # 19944) on :
quote: elMaestro projects:
You don't care to know the actual math behind solving this if it's coming from me.. I'll accept that.
1.you don't understand the math. 2.you don't care to understand the math 3.you ignore context that goes against you're interpretation
Yeah, everybody who don't agree w/u is stupid
Take the chip off your shoulders
Please I have a science degree and 17 years experience with a multinational IT corp and I don't understand the math?
You wanna get personal and project how you feel about me as what I think of you? It's not about you and your peregrinations or non-sequitors.
That's why you can produce no quote from the authors without smearing your foot all in it.
Have you gathered requirements? Have you written user guides? Have you written instruction manuals? Have you written installation procedures for worldwide project releases and upgrades?
Thing is I know I'm not infallible and have admitted to error on ES when I fuck up.
You think everybody's stupid but you're the Master.
You tried and miserably failed to make liars of Laz Patterson Reich by introducing non- sequitors and running from their short descript statement: as YRI increases in BedB so NE increases in Stuttgart.
And as I predicted you conclude they was jus playin.
Posted by Tukuler (Member # 19944) on :
Nuff said.
Posted by Elmaestro (Member # 22566) on :
Why can't we keep the topic on Lazaridis 2014 please... you honestly think I'm getting personal with you?
I'm short winded when it comes to explaining things to people I don't care for.
Yet, I'm taking extensive time out of my life to try to explain to you that your interpretation is wrong...
Most other posters don't care or don't understand what we're even talking about here... I have no ego to protect.
I roll back when I'm checked... I admit when I'm wrong... I express the fact that I don't know things. This is not a big deal.
you still haven't come to terms with this quote from the same paper.
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)
[..]
We estimate y=4.2%, or 5.1%, or 7.3%, as mentioned previously; these differ by only a few percent, but because they are used to subtract a portion of African ancestry from the BedouinB that is quite divergent from Eurasians, these small differences have substantial effects.
"A complication of using the BedouinB population for this purpose is that it has some African admixture," -Lazaridis
My goal isn't to make you look stupid. I have no chip.. I've just been trying to explain the saaaame f4 equations over and over.
Dont put all that personal baggage on me... I'll accept failure as a communicator and will suggest you settle this by contacting lazaridis or someone for confirmation... but leave all that personal junk out of this mane... it's exhausting.
Posted by Tukuler (Member # 19944) on :
quote:elMaestro projects:
You don't care to know the actual math behind solving this if it's coming from me.. I'll accept that.
1.you don't understand the math. 2.you don't care to understand the math
That isn't you getting personal?
And this is exactly what you're doing 3.you ignore context that goes against you're interpretation while I studied, not merely read, SI 13 taking notes and making comparisons to make sure of the presentation.
You're not showing me anything I haven't delved and strung together. It all supports their, not my, clear cut no wiggle room bottomline.
Bottom line (math already photocopied and posted
Nuff said to the deaf
Posted by Elmaestro (Member # 22566) on :
^because you told me you don't care about what I say about the equations an because I (beleive) I know how to work out the equations, cuz I do them on my spare time... I don't consider those personal statements as far as this discussion is concerned.
^(literal interpretation) Near eastern estimates increase the more Yoruba (green numbers "y") is subtracted.
Therefor;
According to this table 13.2 the more Afrcan Admixture subtracted from Bedouin B increases the amount of NE in Stuttgart.
"The amount of Near Eastern admixture estimated for Stuttgart can be seen in Table S13.2 and ranges between 55-100% with estimates increasing as the amount of estimated African admixture in BedouinB increases." -Lazaridis
Not African Admixture in NE but Bedouin B... which was subtracted in the equation.
Posted by Tukuler (Member # 19944) on :
quote:Elmaestro cover up:
^([my] interpretation) [b]Near eastern estimates increase the more Yoruba (green numbers "y") is subtracted.
VS
[quote]Laz Patterson Reich literal publication:
I choose the professional people who designed the SI, came up with the variable and fixed values for the f4s and equations using the f4, did the replacement runs, tabled the results, etc.
There are times amateur layman successfully contradict the livelihood earning professionals. That's woefully far from this here case.
Posted by Elmaestro (Member # 22566) on :
You got it OG.
I wish you didn't have to smear me though... but I throw in the towel.
Just incase I'm actually wrong and is completely tripping I hope you can break down table 13.2 in a way that explains everything... So that I can learn somehow from my mistake.
Posted by Tukuler (Member # 19944) on :
Gotcha YoungBlood.
Get what you give.
You didn't insult and I didn't smear.
Laz Patterson Reich already broke it down. Please make the effort to study, take notes and crosscheck like I did. It took me a few, considering offline life, but it was rewarding.
Trippin'? shit Trip's me middle name Ooh how I hate when the vacation ends.
Peace
Posted by Elmaestro (Member # 22566) on :
...but I worked the equations back and forth in and out.. yet I still cant come around to your conclusion... It'll really help if you personally broke down the chart... Don't leave me hanging.
Posted by Tukuler (Member # 19944) on :
EDITing done
OK I agree.
The more African removed the purer the Beduin are to pure modern NE.
Tbl S13.2 over estimated Stuttgart = 100% NE where Beduin's African component is axed from K=5.
But Loschbour, Stuttgart, and Beduin are all Eurasian.
The text I kept pushing is poorly worded perhaps better put [if (S13.2) is the ratio's denominator]:
ORIGINAL " The amount of near Eastern admixture estimated for Stuttgart can be seen in table s 13.2 and ranges between 55 to 100% with estimates increasing as the amount of estimated African admixture in Bedouin B increases."
REDACTED " The amount of near Eastern admixture estimated for Stuttgart can be seen in table s 13.2 and ranges between 55 to 100% with estimates increasing as the amount of estimated African admixture taken out of Bedouin B increases."
Why did they word it as the former not the latter? The two mean the exact opposite. The redaction describes the math. The original, as a summation, seems to negate the math.
I don't have resources to dwnld databases to plug values into functions. On top of that I can't factor β or x in backward checks.
Got more abstract thinking to do. More sockeye salmon to eat. I still can't see where (S13.2) and iterations are doing anything other than determining how much Loschbour is in NE. Of course the more African you take out the more Eurasian NE becomes ... Then, the less Loschburg the more NE in ... Application is the bitch.
Might email Laz about application because this isn't as straight forward as I'd like as far as implementing the (S13.1) (S13.2) ratio.
Then there's that BedouinB multiplier|denominator in the (S13.3)|(S14.4) equivalencies of (S13.2).
Beyond what's evident and obvious in the printed text I just may get a flavour enhancer in my Lazar-ade.
Posted by Elmaestro (Member # 22566) on :
Yeah, the wording in that study is terrible tbh.
Posted by xyyman (Member # 13597) on :
..
quote:Originally posted by Tukuler:
Nuff said.
Posted by Tukuler (Member # 19944) on :
quote:Originally posted by Elmaestro: Yeah, the wording in that study is terrible tbh.
As a statistician, presuming Laz wrote SI 13, that's a technical writing breach. Inversion reduces clarity in technical writing.
Convolution is worse. I can understand TS13.2 if it's for colleague consumption. But does an informed layman need any of that? Why all the YRI talk, its significance in the K=2 to 5 ADMIXTURE results when you're gonna chuck it anyway?
For an element slated for removal why bother to explain its ambiguity at K=4? What does it matter when YRI forms its own color clad when you're gonna extract it anyway?
Plenty more questions developed as I heeded your plea to DO the math (even though I only simulated value) rather than to inspect the math's formulation. Thanks to Marley Mellow Mood green tea this negro's head didn't burst. Not gonna email Laz. Afraid I'll get Clintonisms if any reply at all.
f-stats are powerful though new Reich(?) invention summarized by Patterson(?) The relationships of A B C D and which one placeholds the actual outgroup not just the usual outgroup position tells what can hardly be ascertained with other tools.
For values A B C D different conclusions derive from placements f4(1,2;3,4) f4(2,1;3,4) etc.
Reich & Patterson set up the NE in Stuttgart f4 patterns for Laz the nongeneticist fallguy?
Way too much more to post.
I can only hope future members with the tools and resources join us and we can switch from gladiator mode to jointly working on a project by then.
All my niggas who amateur geneticists hobbyist. Where ya asses at? In all the world there's but we few ESers into this? What's up niggas & negroes? I know y'all lurking this.
@ Xyyman Honestly I'm at a loss right now between inversion and convolution and two solid hours of rereading SI13, SI9, SI11,and SI14. Like Swenet, I begin to suspect Laz disjointed overall production and evolution is not totally the referees fault though we see what they made him change by comparing preprint with print versions.
At any rate, no inversion or convolution about the Roman Empire era African 4th source population for present day Europeans. ???
Meanwhile do me a favor and find afr throughout this entire SI pdf. Later.
Posted by xyyman (Member # 13597) on :
This is more a statistically and/or computer science (not genetics)battle…..and common sense.
1. When they refused or purposely remove or do not collect the most relevant geographical samples we have no other choice but conclude it is intentional. The Abusir is a good example. Instead of isolating a few markers of high frequency found in Yorubans a West African group why didn’t they just isolate markers found in Great Lake African for their hypothesis. We never made the claim that AEians are Yorubans. At least I didn’t!! 2. But sometimes when they do include Great Lakes Africans they include Horners and Nubains etc as …..”Near East”. It is undoubtedly a game. 3. Lazaridis is a computer scientist not a geneticist. There are more than enough statistician/computer scientists out there to run these programs and get some meaningfully answers. Many of these “leading” researchers deliberately misleading the public. But it looks like Lazaridis is in a battle of honesty and facts. Many of the papers he co-authored or was lead author he came clean then later he would retract statements. I have seen the same pattern with Eva Gonzales, Kivilsid, Henn. I believe the guys calling the shots are Reichs and Paabo. ie Reichs Lab and Max Planx. But I said many times we do not need them now. We have enough data and freely available tools. Many of these tools are NOT Windows based so I cannot get into it deeply.
---- “All my niggas who amateur geneticists hobbyist”.
"Like Swenet, I begin to suspect Laz disjointed overall production and evolution is not totally the referees fault though we see what they made him change by comparing preprint with print versions. “
Posted by xyyman (Member # 13597) on :
The CLOSEST living population to the Abusir are "Near East" ...Bedouins. NOT Syrians, Iraqi etc and Turks etc . ..the Africanized Bedouins!!! This is the population they a have labelled "Eurasian" and are talking about the Abusir are has no sub-saharan. Lol! It is impossible. The genetic makeup of the Bedouins indicate they are remnants of North Africans/Africans in the Levant and Arabia.
Quote from Lazaridis 2014. "A complication is that BedouinB is a mixture of NE and African ancestry. We therefore subtracted the effects of African ancestry using estimates of the BedouinB African admixture proportion from ADMIXTURE (SI9) or ALDER68."
Posted by One Third African (Member # 3735) on :
Bumping this thread...
Posted by Yatunde Lisa Bey (Member # 22253) on :
quote:Originally posted by xyyman: The CLOSEST living population to the Abusir are "Near East" ...Bedouins. NOT Syrians, Iraqi etc and Turks etc . ..the Africanized Bedouins!!! This is the population they a have labelled "Eurasian" and are talking about the Abusir are has no sub-saharan. Lol! It is impossible. The genetic makeup of the Bedouins indicate they are remnants of North Africans/Africans in the Levant and Arabia.
Quote from Lazaridis 2014. "A complication is that BedouinB is a mixture of NE and African ancestry. We therefore subtracted the effects of African ancestry using estimates of the BedouinB African admixture proportion from ADMIXTURE (SI9) or ALDER68."
Another interesting read
Posted by Djehuti (Member # 6698) on :
^ Indeed.
Note that while Bedouin A shows Yoruba IDB admixture labeled as "Sub-Saharan", Bedouin B does not but was found to have admixture from other African ancestries including Sub-Saharan East Africans not found in West Africa but only the West African ancestry is labeled "Sub-Saharan".
Posted by Geometer (Member # 23746) on :
^ NIGERIA. We appreciate you (Gauss). 😇
Posted by Djehuti (Member # 6698) on :
Here are a couple of sources dating back to before or at the same time as the Mota study.
There is a new paper dealing with Sudanese genetics, which is of some interest, in my opinion: Hima M.A. Babiker et al., Genetic variation and population structure among Sudanese populations as indicated by the 15 Identifiler STR loci. BMC Investigative Genetics 2011. Open access. Most interestingly they spot a cline and divide (both) between Egypt and Tropical Africa and differential genetics for Somalis, one of three outgroups (the other two being Egyptians and Ugandans from Karamoja region (Nilotic ethnicities).
The structure shows (as much as a mere three components allow) a duality of some clinal value (i.e. not absolute but relative) with a divide cutting across Sudan: not just between North and South according to the latest political split but also placing Darfur, Kordofan and the Nuba along with Tropical Africa as well. Instead Central, North and Eastern Sudanese look much like Egyptians. Somalis are clearly different however but you’d never know based only on K=2. That’s why it is important to explore these analysis to some depth, greater than K=3 in any case, a very shallow depth for such a diverse region.
PC Analysis:
Notice that PC2 and PC3 are of similar values. PC1 however is more than double in importance and marks a cline between Egypt (and the Sudanese Copts) and the Nuba. PC2 and PC3 only show distinctions between Copts and Egyptians and Copts and Somalis respectively. I wonder if this last is caused because of random peculiarities of the 15 ancestry informative markers used in this study, which seem a bit too few not to cause random distortions, specially in such a poorly understood region as is East Africa.
(You can read the rest on Sub-Saharan admixture in the Arab world but I must want to post the following).
Basically, various Muslim West Asian "Arab" populations, as opposed to some of their non-Muslim counterparts (Lebanese Christians, most so far tested Egyptian Copts, Yemenite Jews etc.), show signs of West-Central African-esque admixture probably acquired via the Arab Slave Trade. [note]
The more "ancient" looking East African cluster-related "African" ancestry (pink cluster that forms much of Dinkas' ancestry above) seems markedly older and is present in their non-Muslim minorities at notable levels (~5-15% in Yemenite Jews) who in the eyes of some academics seem like a bit of a throwback to some of these regions' pre-Islamic genetic profiles [3].
