posted
Remember that north african sample from Kerkouane which you believed was a black numidian and who wasn't modeled like modern north africans ?
I told you that the model was obviously flawed and the fact that he plots with modern NAs was quite telling ...here we do have his results and like I said he's similar to modern north africans :
Closest populations to him :
That's a sample that literally predates the numidian kingdom and yet he's already similar to us.
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
posted
you need some URLs in the OP with article title about Kerkouane so other people reading this thread can easily go to the source article and easily find the place in the article (page #) which mentions a North African sample from Kerkouane
as the supplement shows, they only reported mitochondrial DNA
Posts: 42919 | From: , | Registered: Jan 2010
| IP: Logged |
quote:Originally posted by the lioness,: you need some URLs in the OP with article title about Kerkouane so other people reading this thread can easily go to the source article and easily find the place in the article (page #) which mentions a North African sample from Kerkouane
as the supplement shows, they only reported mitochondrial DNA
It's from this paper :
A Genetic History of Continuity and Mobility in the Iron Age Central Mediterranean M. Moots et al, preprint March 15, 2022
quote:For R11759, who projects near modern Mozabite and Moroccan populations in PCA space, [...] When compared to other ancient individuals using qpWave analysis (Fig. 5), this individual forms a clade with ancient Canary Island inhabitants thought to be representative of the original founding population (25). The Canary Islands were originally settled in the 1st millennium BCE by a population genetically ancestral to today’s Amazigh populations of Saharan Africa (26).
and the study doesn't report mtdna I think you confuse it with another paper
[ 17. June 2022, 04:35 PM: Message edited by: the lioness, ]
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
However, don't speak for me; "black Numidian" is not something I would say ..or type for that matter.
-How do the other "North Africans" in the study perform in whatever program that is (G25??)
-Why don't you see the fact that modern North Africans with additional SSA ancestry being so close to this sample as an incongruity?
-Mozab still can't be modeled as 70% IAM 30% EEF.
-also Lioness please move this thread to Egyptology. I see you've already started editing comments.
Posts: 1781 | From: New York | Registered: Jul 2016
| IP: Logged |
quote:Originally posted by Elmaestro: [QB] Interesting.
However, don't speak for me; "black Numidian" is not something I would say ..or type for that matter.
You literally agreed with the "black" numidian quote of punos rey...
quote:Originally posted by Elmaestro: -How do the other "North Africans" in the study perform in whatever program that is (G25??)
The samples from that paper were as expected mixed with greek settlers from Sicily some being almost fully sicilian while others had important amount of north african ancestry. Here their results :
quote:Originally posted by Elmaestro: -Why don't you see the fact that modern North Africans with additional SSA ancestry being so close to this sample as an incongruity?
Which population exactly are you talking about ?
quote:Originally posted by Elmaestro: -Mozab still can't be modeled as 70% IAM 30% EEF.
The results simply shows that this sample wasn't 70% IAM 30% EFF and this is not surprising since that flawed model lacked basic populations to properly model north africans.
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
Also the model Didn't lack "basic populations" . The core issue is that Mozab cannot be modeled with that level of two way admixture.
The reason why these academic papers use basic two-four way models is to avoid over-fitting and anachronistic modeling. To compound the initial question which you were confused about, what was the ethnogensis of such ancient North Africans (EEF + IBM + Steppe + YRI)? Look at the results you posted above, how are you asking me which modern day North Africans am I talking about? Which ever group that resemble him, keep in mind Your claim was that he's the same as modern North Africans and Guanches.
Posts: 1781 | From: New York | Registered: Jul 2016
| IP: Logged |
Also the model Didn't lack "basic populations" . The core issue is that Mozab cannot be modeled with that level of two way admixture. The reason why these academic papers use basic two-four way models is to avoid over-fitting and anachronistic modeling.
It lacks a natufian component and Morocco_LN is certainly not a good component to model them you certainly won't avoid over-fitting with such component.
quote:Originally posted by Elmaestro: To compound the initial question which you were confused about, what was the ethnogensis of such ancient North Africans (EEF + IBM + Steppe + YRI)? Look at the results you posted above, how are you asking me which modern day North Africans am I talking about? Which ever group that resemble him, keep in mind Your claim was that he's the same as modern North Africans and Guanches.
Again my question is which population do you think has "additional SSA ancestry" ? Did you ask this because the first populations aren't morocco_north or coastal algerians ?
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
posted
This is what separates researchers from enthusiasts
There are only a few North African groups who do not typically show "elevated levels of SSA ancestry due to the trans-Saharan slave trade" - They're in quotes cuz that's not my thought.
You posted results which highlights closeness between the ancient individual, Mozabites and Matmata Berbers. Why are you asking me such a question?
Each column within the modern North African square represents a different NA population. Notice how it doesn't really matter which North African group I'd draw the comparison with? The demographic history is quite obvious yet has been obfuscated over and over again by amateurs who frankly don't understand how the tools they use even work. On one end folks can swear up and down that there was no significant admixture from European/Arab sources in recent times (Arab conquest.) But still on the other end the SSA signals are of recent times (Arab Conquest.) So why do we see a trend in which these ancient North African individuals plot or score significant closeness with Modern North Africans as you brag about?
What's special about the Admixture chart above is that it excludes SSA populations... Notice how we see a story reflective of a demographic difference? The fact that you can fit a Carthagian with groups who honestly have no reason being donors (Yoruba, Natufian) due to geo-temporal and spacial improbability should alert you to the fact that there's something not being told correctly.
What you failed to understand is that in academia they're aware of the potential inconsistency. They overrated the "Saharaness" of that individual because if he represented a resident North African it'd dampen the currently accepted model of complete neolithic turn-over by populations akin to KEB.
The results shown above is the reason why by academically accepted methods it is impossible to model Modern NA's with such high levels of IAM. even if you look at ANA estimates you'll see Modern NA's score less, though Ancient NA and modern NAs are "the same.."
Posts: 1781 | From: New York | Registered: Jul 2016
| IP: Logged |
Each column within the modern North African square represents a different NA population. Notice how it doesn't really matter which North African group I'd draw the comparison with? The demographic history is quite obvious yet has been obfuscated over and over again by amateurs who frankly don't understand how the tools they use even work. On one end folks can swear up and down that there was no significant admixture from European/Arab sources in recent times (Arab conquest.) But still on the other end the SSA signals are of recent times (Arab Conquest.) So why do we see a trend in which these ancient North African individuals plot or score significant closeness with Modern North Africans as you brag about?
First of all it all depends on the north african populations you included in this square which does not seem exhaustive obviously. Secondly all I said was based on papers which concluded that this slave trade did impact north africans but afaik mozabites or matmata berbers are not concerned by this.
In the pic I posted why do you think "moroccan", "moroccan_south", "tunisian_douz", etc are so far from the sample ? Because for instance "moroccan" in the dataset of davidsky are 9 samples from Casablanca an area known for having excess arab and black ancestry. So you're confused because you do not put this into context, you have to first know each berber group to understand what you're dealing with. The impact of these events isn't as general as you think.
So there is no surprise those samples plot with mozabites or matmata berbers those are perfectly indigenous profile and among the closest samples to me many are mozabite or matmata as you can see :
Also the other samples we got from Numidia and austria show different results when it comes to their closest populations simply reflecting the local variations.
quote:Originally posted by Elmaestro: What's special about the Admixture chart above is that it excludes SSA populations... Notice how we see a story reflective of a demographic difference?
actually your pic isn't really accurate (I suppose whoever made it simply put any north african sample without contextualizing it ) also it lacks the two copper age samples. And who denied demographic difference ?
quote:Originally posted by Elmaestro: The fact that you can fit a Carthagian with groups who honestly have no reason being donors (Yoruba, Natufian) due to geo-temporal and spacial improbability should alert you to the fact that there's something not being told correctly.
I don't understand why you assume such populations couldn't be donor ?? Phoenicians themselves were full of natufian ancestry and what about the profile of those black populations that probably migrated further north after the dessication of the sahara ? You seriously expect them to be dinka-like ? What about capsians ? Moreover I hope you understand by now that carthaginians were more like punicized north africans than something else.
quote:Originally posted by Elmaestro: What you failed to understand is that in academia they're aware of the potential inconsistency. They overrated the "Saharaness" of that individual because if he represented a resident North African it'd dampen the currently accepted model of complete neolithic turn-over by populations akin to KEB.
The results shown above is the reason why by academically accepted methods it is impossible to model Modern NA's with such high levels of IAM. even if you look at ANA estimates you'll see Modern NA's score less, though Ancient NA and modern NAs are "the same.."
That simply means we do a better job than them how many times I've pointed out their inconsistencies and lack of knowledge ? I'm already aware of this I simply keep my critical thinking and cross-check with datas I've gathered from other papers and books.
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
posted
I posed a question & I just realized that I told you what might be going on by accident in my previous response.
real quick the chart is published here and it contains all of the NA populations you'll find in Human origins and the 1240K datasets. TBH, it's the most honest structural side by side analysis of North Africans I've seen.
nonetheless, you're grasping at straws as I knew you would. You won't straight up say that Mozabites don't have additional SSA ancestry from recent times so the argument is now that certain populations with even more SSA related admixture in recent times are farther away from the Kerkouane
I'm not going for that.
My guy if you are attributing the closeness to locality then I'd expect you point out local populations in respects to Kerkouane who show the least evidence of SSA geneflow in recent times.... Like the Chenini Berbers of Douiret. But you're hyped on the public Mozab population who ironically have individuals grouped in that population who show considerable variation (that's why they seem close to everybody in amateur runs.) Not only that but the more local Matmata draws closer to SSA admixed north Africans... in fact we have putative evidence of their SSA ancestry as we do the Mozab.
quote:Admixture estimates suggest that the Arab and sub-Saharan Africa contribution to the genetic structure of Matmata occurred around the mid-eleventh century, which is close to the timing of the Hilalian invasion (1052 CE) (Laroui 1977, Abdel Waheb 2004); the Bedouin tribes were particularly aggressive over the conquered local Berber groups in order to significantly accelerate the Arabization process and thus linguistic assimilation (Abun-Nasr 1971).
Fact of the matter is, though your (G25?) results give the impression that these populations were all the same, that is simply not the case. You're looking at a punic sample and posted results including primarily Mesolithic populations from more local non SSA populations (Natufian, Taforalt), Neolithic European and modern SSA samples. And the European samples aren't even geographically relevant for a punic sample despite the vast availability of Eurasian particularly European samples at our disposal. What's going here is called confirmation bias. I told you already, that natufian and SSA signal is likely reflective of local North African variation. The need to patch up or cover for extraneous variants results in over-fitting.
Posts: 1781 | From: New York | Registered: Jul 2016
| IP: Logged |
My guy if you are attributing the closeness to locality then I'd expect you point out local populations in respects to Kerkouane who show the least evidence of SSA geneflow in recent times.... Like the Chenini Berbers of Douiret. But you're hyped on the public Mozab population who ironically have individuals grouped in that population who show considerable variation (that's why they seem close to everybody in amateur runs.) Not only that but the more local Matmata draws closer to SSA admixed north Africans... in fact we have putative evidence of their SSA ancestry as we do the Mozab.
I did not attribute it to locality simply telling you that it wasn't a monolithic people so I'm not expecting every ancient sample from NA to be north moroccan like
quote:Originally posted by Elmaestro: Fact of the matter is, though your (G25?) results give the impression that these populations were all the same, that is simply not the case. You're looking at a punic sample and posted results including primarily Mesolithic populations from more local non SSA populations (Natufian, Taforalt), Neolithic European and modern SSA samples. And the European samples aren't even geographically relevant for a punic sample despite the vast availability of Eurasian particularly European samples at our disposal. What's going here is called confirmation bias. I told you already, that natufian and SSA signal is likely reflective of local North African variation. The need to patch up or cover for extraneous variants results in over-fitting.
What do you imply by "punic sample" ? The sample literally has lower middle eastern influence than me and didn't I bring Capsians or those holocene saharan populations ? So I also acknowledge the possibility of natufian/ssa being of local origin. Now it's not a question of "confirmation bias" (or else all these studies have it) we simply used the most realistic approach with the available samples but what would you propose to model that sample with ? I'm seriously open to any new proposition.
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
posted
Even by adding new samples (I added ancient SSA proxies from west/central and east africa) the results don't change much :
I made the "capsian" proxy by merging KEN_pastoral_N With PPNC which is apparently what some are detecting for the copper age samples and their strange natufian component.
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
quote:Originally posted by Antalas: Even by adding new samples (I added ancient SSA proxies from west/central and east africa) the results don't change much :
I made the "capsian" proxy by merging KEN_pastoral_N With PPNC which is apparently what some are detecting for the copper age samples and their strange natufian component.
It seems like you changed your stance a bit since you first started posting on this site let alone since the Biodiversity days but I digress.
I have to look at the sample myself as I don't use G25 so I'm not familiar with what it does to related samples to compare the results to. but though the last run seems to be favored, there's still a lot going on there, it doesn't make sense in a vacuum. And I can't fully imagine 20% of IAM is being absorbed by EEF though Eurasian proxies do absorb ANA-related components. How much IAM does G25 give the NA samples found in calcholithic Iberia and Sardia with these same source populations?
Posts: 1781 | From: New York | Registered: Jul 2016
| IP: Logged |
I have to look at the sample myself as I don't use G25 so I'm not familiar with what it does to related samples to compare the results to. but though the last run seems to be favored, there's still a lot going on there, it doesn't make sense in a vacuum. And I can't fully imagine 20% of IAM is being absorbed by EEF though Eurasian proxies do absorb ANA-related components. How much IAM does G25 give the NA samples found in calcholithic Iberia and Sardia with these same source populations?
Quite surprising that someone like you still hasn't used that tool and I still don't understand why you stick to that flawed model of 70% IAM anyway here are the results for the copper age samples :
The fits aren't that good but still enough to get an idea.
Here a north african from the 3rd century A.D. in comparison :
I can't have access to the numidian sample for the moment but he was roughly similar to north moroccans and kabyles. Also some of these ancient samples surprisingly had high level of natufian ancestry which was initially assumed to be from phoenicians but that proposition actually doesn't make sense since the level of CHG and iran_N were too low therefore that's why I carefully proposed a hypothetical capsian source (which the copper age samples further reinforce).
Seems like there was already a good amount of variation back then like today and we were too quick to attribute natufian ancestry to arabs.
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
posted
I have no reason to use G25... I have just about every other academic tool at my disposal and know how each of them work. Also many people who use G25 come to bullshit conclusions, especially when it involves Africans.
Nonetheless, now you're starting to make more sense when you post. But I'm not gonna let you slide by allowing you to attribute the loose similarities of these ancient populations to that of modern day individuals.
also I see whats going on here. And I will confirm it on my own in the future. The Kerkouane individual had more recent SSA or "Saharan" ancestry.
Posts: 1781 | From: New York | Registered: Jul 2016
| IP: Logged |
quote:Originally posted by Elmaestro: But I'm not gonna let you slide by allowing you to attribute the loose similarities of these ancient populations to that of modern day individuals.
Why ? What makes you think they were different ? Of course I'm not saying there has been absolutely no changes but all these variations are negligible and these people were overall similar to us.
quote:Originally posted by Elmaestro: also I see whats going on here. And I will confirm it on my own in the future. The Kerkouane individual had more recent SSA or "Saharan" ancestry.
Yes it seems an admixture event with a west african-like source occured much earlier than what people usually think and that's why in another thread I showed that we clearly see a shift from a dinka-like type of ancestry in the neolithic and copper age samples to a west african one in the more recent samples (among the latter we also see specific west african MtDNAs).
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
posted
I have no Idea how G25 gave you those results. I got around to looking at the sample myself and can confirm not only does K11759 score more IAM than the others but one of the best models is a two way fit between Nuragic individuals and IAM a can be up to 78%.
The only reason I even double backed on this was due to them showing the most Taf/IAM in an ADMIXTURE run I stated.
There's no need for Yoruba or Shum-Laka in this individual... infact, they usually fail, but when they don't they lower the overall quality of the fit.
Lastly, however more speculatively, I noticed they scrubbed and re-uploaded K11759 and another individual to the Nucleotide archive... maybe there was a mistake with the initial upload.
But hell no.. I was mistaken. There's no evidence on my end for recent west African ancestry.
Posts: 1781 | From: New York | Registered: Jul 2016
| IP: Logged |
quote:Originally posted by Elmaestro: I have no Idea how G25 gave you those results. I got around to looking at the sample myself and can confirm not only does K11759 score more IAM than the others but one of the best models is a two way fit between Nuragic individuals and IAM a can be up to 78%.
The only reason I even double backed on this was due to them showing the most Taf/IAM in an ADMIXTURE run I stated.
There's no need for Yoruba or Shum-Laka in this individual... infact, they usually fail, but when they don't they lower the overall quality of the fit.
Lastly, however more speculatively, I noticed they scrubbed and re-uploaded K11759 and another individual to the Nucleotide archive... maybe there was a mistake with the initial upload.
But hell no.. I was mistaken. There's no evidence on my end for recent west African ancestry.
Which program did you use and which models did you try ? I've already seen you using nuragic in an other flawed model can you pls use a proper european-like sample like barcin_N. As for the ssa did you try with dinka ? It would be nice if you can post some screenshots too.
And yes I've read they reuploaded the whole thing after they mislabelled many of the samples but I don't think that would change anything for this sample.
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
quote:Originally posted by Elmaestro: I have no Idea how G25 gave you those results. I got around to looking at the sample myself and can confirm not only does K11759 score more IAM than the others but one of the best models is a two way fit between Nuragic individuals and IAM a can be up to 78%.
The only reason I even double backed on this was due to them showing the most Taf/IAM in an ADMIXTURE run I stated.
There's no need for Yoruba or Shum-Laka in this individual... infact, they usually fail, but when they don't they lower the overall quality of the fit.
Lastly, however more speculatively, I noticed they scrubbed and re-uploaded K11759 and another individual to the Nucleotide archive... maybe there was a mistake with the initial upload.
But hell no.. I was mistaken. There's no evidence on my end for recent west African ancestry.
Which program did you use and which models did you try ? I've already seen you using nuragic in an other flawed model can you pls use a proper european-like sample like barcin_N. As for the ssa did you try with dinka ? It would be nice if you can post some screenshots too.
And yes I've read they reuploaded the whole thing after they mislabelled many of the samples but I don't think that would change anything for this sample.
We're not on the same level. I run permutations, of-course I used the Dinka in one of the 100s of iterations. I use formal stats and ADMIXTURE as I stated above.
It's funny you're asking that I use Neolithic Anatolian sample as opposed to more localized population lmao. Did people teleport and time-travel from Barcin to Tunisia ffs?? And yes they were used in one of the iterations. G25 is cap.
(also note that the Southern European samples are being ran against each-other. meaning, Meaning Nuragic-Sards score better than Copperage or punic and etc.)
Speaking of flawed models... look at your concoction of samples used in G25. That doesn't even qualify as a model. Can you begin to explain that ethnogenesis using those results?
The simplest answer here is what we knew... Mosaic like distribution of an understudied autochtonous component and EEF or post copperage European ancestry in North Africa before the expansion of m183.
Posts: 1781 | From: New York | Registered: Jul 2016
| IP: Logged |
quote:Originally posted by Elmaestro: We're not on the same level. I run permutations, of-course I used the Dinka in one of the 100s of iterations. I use formal stats and ADMIXTURE as I stated above.
It's funny you're asking that I use Neolithic Anatolian sample as opposed to more localized population lmao. Did people teleport and time-travel from Barcin to Tunisia ffs?? And yes they were used in one of the iterations. G25 is cap.
(also note that the Southern European samples are being ran against each-other. meaning, Meaning Nuragic-Sards score better than Copperage or punic and etc.)
Speaking of flawed models... look at your concoction of samples used in G25. That doesn't even qualify as a model. Can you begin to explain that ethnogenesis using those results?
The simplest answer here is what we knew... Mosaic like distribution of an understudied autochtonous component and EEF or post copperage European ancestry in North Africa before the expansion of m183. [/QB]
What kind of answer is that ? The way you react is really suspicious and if a nuragic + "punic" (of course a mixed sample NA/euro from sardinia) + dinka or mota makes more sense to you than a proper model like the one I posted then we don't have much to discuss here you're indeed not at the same level as me. There is absolutely no reason for G25 to give such different results it worked for all the samples so far and the study also stated that it behaved like guanches, moroccans and mozabites and this is what G25 shows us.
who are most likely the closest people to the first european farmer settlers in the maghreb. As for the rest I really don't see what's problematic about it ?? The guy legit tried to model north africans with nuragic and sardinian punics and dare to ask me how does my model make sense XD
Show the results/screenshots instead of being on the defensive.
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
quote:Originally posted by Elmaestro: We're not on the same level. I run permutations, of-course I used the Dinka in one of the 100s of iterations. I use formal stats and ADMIXTURE as I stated above.
It's funny you're asking that I use Neolithic Anatolian sample as opposed to more localized population lmao. Did people teleport and time-travel from Barcin to Tunisia ffs?? And yes they were used in one of the iterations. G25 is cap.
(also note that the Southern European samples are being ran against each-other. meaning, Meaning Nuragic-Sards score better than Copperage or punic and etc.)
Speaking of flawed models... look at your concoction of samples used in G25. That doesn't even qualify as a model. Can you begin to explain that ethnogenesis using those results?
The simplest answer here is what we knew... Mosaic like distribution of an understudied autochtonous component and EEF or post copperage European ancestry in North Africa before the expansion of m183.
What kind of answer is that ? The way you react is really suspicious and if a nuragic + "punic" (of course a mixed sample NA/euro from sardinia) + dinka or mota makes more sense to you than a proper model like the one I posted then we don't have much to discuss here you're indeed not at the same level as me. There is absolutely no reason for G25 to give such different results it worked for all the samples so far and the study also stated that it behaved like guanches, moroccans and mozabites and this is what G25 shows us.
who are most likely the closest people to the first european farmer settlers in the maghreb. As for the rest I really don't see what's problematic about it ?? The guy legit tried to model north africans with nuragic and sardinian punics and dare to ask me how does my model make sense XD
Show the results/screenshots instead of being on the defensive.
You're reading comprehension is an issue. I'm not reluctant to use Barcin. I used them. They don't offer better fits. I expressed that the Dinka was included in one of my iterations... but doesn't converge on one of the better models I never attempted to model the individual as Punic + Nuragic. I explained that among EEF populations the Nuragic_Sards provide the best fit. PS. This isn't even the best fit, Can you guess the SSA individual(s) who'll drive the probability to about 95%? hint: it isn't Dinka, Yoruba or Mota
I figured out how G25 works... It took me all of 10min's earlier today. I know exactly why it's showing the results it shows now. For the sake of time, Make a list of the populations you wanna see as Source populations. Particularly those included in newer studies. I'll put them through QC and put them to the test. (depending on how quickly I can access them.)
I'm also not sure what you mean by use the LBK individual from this study. 1. they didn't provide any Linearbandkeramik samples and 2.The LBK weren't farmers or EEF. Lastly do you really think that people came directly from Turkey Into NA untouched?
Posts: 1781 | From: New York | Registered: Jul 2016
| IP: Logged |
quote:Originally posted by Elmaestro: You're reading comprehension is an issue. I'm not reluctant to use Barcin. I used them. They don't offer better fits. I expressed that the Dinka was included in one of my iterations... but doesn't converge on one of the better models I never attempted to model the individual as Punic + Nuragic. I explained that among EEF populations the Nuragic_Sards provide the best fit. PS. This isn't even the best fit, Can you guess the SSA individual(s) who'll drive the probability to about 95%? hint: it isn't Dinka, Yoruba or Mota
I figured out how G25 works... It took me all of 10min's earlier today. I know exactly why it's showing the results it shows now. For the sake of time, Make a list of the populations you wanna see as Source populations. Particularly those included in newer studies. I'll put them through QC and put them to the test. (depending on how quickly I can access them.)
I'm also not sure what you mean by use the LBK individual from this study. 1. they didn't provide any Linearbandkeramik samples and 2.The LBK weren't farmers or EEF. Lastly do you really think that people came directly from Turkey Into NA untouched? [/QB]
It's not an issue I was talking about a previous model you made in another thread which surprised me. Since you know a bit about those first european farmers in NA how does "nuragic_sards" make sense to you ? Obviously the first farmers probably already included a small WHG component unlike the anatolian ones so it will most likely prefer nuragic over barcin but still historically the area was obviously not settled by nuragics I hope you understand this because it feels like you're trying to say they were pure IAM and then during the bronze age or later mixed with nuragics.
I honestly have no idea for the SSA individual tell me which one. and what are you talking about ? LBK were farmers from central europe and yes we got their coordinates these are my results when using them :
I asked you to use them because they are most likely the closest folk to the first italian farmers and as you can see the system prefer them over western EEF to model me which confirms a theory that the first farmers in North-West Africa came from sicily/italy bringing the cardial ware and reached during the same era andalusia.
I'm not sure if the fit on your softwares works the same way it does on G25 but myself can get better fits with shitty models which make no sense at all so I don't think you should only rely on this anyway if you want perfectly historical source populations it would be this :
IAM, Eastern EEF (LBK), iberian bell beaker, yoruba/dinka, PPNC, iran_N, WHG,etc but you won't avoid overfitting with this that's why the model I used on G25 is the most basic and accurate one.
Tell me what you get with the first one (barcin,taforalt, etc) then tell me what you get with the second one pls.
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
posted
You're right I got LBK and WHG (Locshbour) mixed up. So the LBK sample was Stuttgart. I can test that. Btw. Because Stuttgart was among the first EEF sample examined it was spoken about a lot on this forum previously. Some people believed there's material evidence for NAfrican admixture.
~
The SSA population I alluded to was Elmentietan. I can run the same successful models on G25 and they work on there too. G25 is liable to overfit and distort ancestral contributions due to the methodology. To show you what I'm talking about using a North African population available on both...
for example: ...In My run I had Early_PN but Elmentietan has a better fit. I'm using this sample because I don't have the KErkouane individuals coordinates for G25
lastly. Three way ref substituting the EEF population with Mamara Barcin aka Anatolia_N ...straight up fails.
The reason why, (put in really simple terms) There's constraints on overfitting, due to snp overlap within the Source and with reference populations (what we used to call outgroups). G25/Vahaduo doesn't account for SNP's at all. It's essentially averages across 24 principle components. I can play around with Modern populations to try to get Barcin_N to fit but that'll defeat the purpose and the fit would probably still be trash anyways.
Posts: 1781 | From: New York | Registered: Jul 2016
| IP: Logged |
quote:Originally posted by Elmaestro: You're right I got LBK and WHG (Locshbour) mixed up. So the LBK sample was Stuttgart. I can test that. Btw. Because Stuttgart was among the first EEF sample examined it was spoken about a lot on this forum previously. Some people believed there's material evidence for NAfrican admixture.
~
The SSA population I alluded to was Elmentietan. I can run the same successful models on G25 and they work on there too. G25 is liable to overfit and distort ancestral contributions due to the methodology. To show you what I'm talking about using a North African population available on both...
for example: ...In My run I had Early_PN but Elmentietan has a better fit. I'm using this sample because I don't have the KErkouane individuals coordinates for G25
lastly. Three way ref substituting the EEF population with Mamara Barcin aka Anatolia_N ...straight up fails.
The reason why, (put in really simple terms) There's constraints on overfitting, due to snp overlap within the Source and with reference populations (what we used to call outgroups). G25/Vahaduo doesn't account for SNP's at all. It's essentially averages across 24 principle components. I can play around with Modern populations to try to get Barcin_N to fit but that'll defeat the purpose and the fit would probably still be trash anyways.
Interesting for the ssa group needed what does this imply ? Do you think there is a link with capsians ? I remember one member on anthrogenica also finding some affinity with KEN_N for these copper age samples. Seems you're right for the model and I tried with my coordinates and got a much worse fit.
Here the coordinate for the kerkouane sample (simulated) : Kerkouane11759_PUNIC-K13-sim_scaled,-0.0664,0.1365,-0.0042,-0.0725,0.0235,-0.0366,-0.0247,0.0072,0.0685,0.0361,0.0079,-0.0041,0.0187,-0.0204,0.0162,-0.0156,0.0053,-0.0222,-0.0508,0 .011,-0.0157,-0.0401,0.0284,-0.008,0.0038
I tried it with your model but the fit is bad too. As for the rest I see but did you try modelling modern samples or even guanches with the model I posted do they also fail. I want to see how the results of this kerkouane sample differ compared to modern or even guanche samples. Also can you try to model me on this ? If you're too lazy to do it no problem.
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
posted
@Elmaestro seems like you need to update your tools lol here the official non simulated results of the kerkouane samples :
As you can see R11759 is similar to modern north africans and guanches and that's a sample from the VIIIth century BC
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
quote:Originally posted by Antalas: @Elmaestro seems like you need to update your tools lol here the official non simulated results of the kerkouane samples :
As you can see R11759 is similar to modern north africans and guanches and that's a sample from the VIIIth century BC
I don't understand what you're getting at. I have to update my tools all the time. What do you mean official non simulated? Also. Any model I create can be replicated with G25... We've already seen this. Also. You shouldn't use models that are *only* feasible with G25, confluence is the key. Also. The study which debut the individuals genome and my findings were independently reputable and similar (see confluence) Also. Why on earth are you still trying to push the idea of 2000+ years of continuity spanning 100s of Kilometers? Also. Why are you still likened to the narrative that Anatolian farmers and Natufians are the direct ancestors of post Bronze age North Africans? Also. relating to what I stated before about continuity... Why can't you see that modern North Africans having similar scores using these sources is problematic?
Posts: 1781 | From: New York | Registered: Jul 2016
| IP: Logged |
posted
You're too emotional calm yourself. It's clear that such continuity and results bothers you because they completely undermine your whole narrative about north africans' genome being shaped by more recent events.
And who said anatolians and natufians were the direct ancestors of post BA north africans ? Such type of ancestry got there through known intermediaries we already talked about this. The thing here is to avoid overfitting and the fits are pretty good.
It's over drop the case.
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
posted
... How can you determine Emotions by reading text. lol Every sentence I typed in the previous post were things I already said and had been saying over and over again. Continuity doesn't bother me but North Africans genomes were shaped by recent events. Stating otherwise is legit counter intelligence. I only want to know why you neglect this in favor of G25 results modeling Iron age samples as Pleistocene and Neolithic samples 4-5K kilometers away?
btw...Who were the known intermediates who contributed to the North African Genepool?
Posts: 1781 | From: New York | Registered: Jul 2016
| IP: Logged |
posted
Continuity is obvious when you take the population as a whole but I'm not denying that some communities/individuals' genomes were shaped by more recent events like the trans-saharan slave trade or the hilalian invasion. I can easily show you some G25 results of algerians or tunisians with an obvious arab or SSA input but most do not show such influence and it seems the current profile was already set during the bronze age; at this point, there is clearly no place for a black north africa as you hope.
Anyway it seems like you're still not familiar with G25 looking at the questions you ask me and check our interactions above I already mentionned the intermediaries. You talked about not getting good fits with the samples I proposed, I then asked you to see if it also fails when you try to model modern north africans and you didn't answer. Really you act suspiciously and appears to be in denial.
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
quote:Originally posted by Antalas: Continuity is obvious when you take the population as a whole but I'm not denying that some communities/individuals' genomes were shaped by more recent events like the trans-saharan slave trade or the hilalian invasion. I can easily show you some G25 results of algerians or tunisians with an obvious arab or SSA input but most do not show such influence and it seems the current profile was already set during the bronze age; at this point, there is clearly no place for a black north africa as you hope.
Anyway it seems like you're still not familiar with G25 looking at the questions you ask me and check our interactions above I already mentionned the intermediaries. You talked about not getting good fits with the samples I proposed, I then asked you to see if it also fails when you try to model modern north africans and you didn't answer. Really you act suspiciously and appears to be in denial.
Your intermediaries are Stuttgart? or other Neolithics from Czechia? Are you serious?
no, I'm not familiar with G25's arbitrary labels. I don't care to do much more research on it out side of asking "what they mean by non simulated". I can only guess that "non-simulated" means that the populations were included among samples used to calculate eigenvectors. But I could be wrong.
And when I refer to modern samples to infer continuity... I'm clearly referring to populations who would be closest to the Ancient individuals we're talking about... in this case R11759... which population(Individual) is closest to R11759, Antalas?
Posts: 1781 | From: New York | Registered: Jul 2016
| IP: Logged |
quote:Originally posted by Elmaestro: Your intermediaries are Stuttgart? or other Neolithics from Czechia? Are you serious?
no, I'm not familiar with G25's arbitrary labels. I don't care to do much more research on it out side of asking "what they mean by non simulated". I can only guess that "non-simulated" means that the populations were included among samples used to calculate eigenvectors. But I could be wrong.
And when I refer to modern samples to infer continuity... I'm clearly referring to populations who would be closest to the Ancient individuals we're talking about... in this case R11759... which population(Individual) is closest to R11759, Antalas? [/QB]
Pay attention to what the paper says :
quote:This supports a model of agricultural expansion into Central Europe from the Balkans that involved substantial numbers of migrants and strong backward communication during the dissemination of the Linearbandkeramik (LBK) complex, with populations remaining relatively well connected throughout the Neolithic period.
Basically three clusters and combined with archaeological datas it seems the LBK is for the moment the best candidate for the spread of farming in NA during the VII/VIth milleniums BC
Those same farmers who settled in Italy also went further south and ultimately settled in North Africa and Andalusia :
quote:The rapid dispersal of innovations suggests that they were circulated through already existing networks [50]. The earliest presence of Neolithic industries in southern Iberia were dated at least 7500 calibrated ya [51]. All major elements of the Neolithic package arrived in southeastern Spain from the central Mediterranean and reached North Africa through west Mediterranean networks. However, some elements, such as pointed-based vessels, Almagra decoration, and lentils, were subsequently modified in North Africa before being dispersed to Iberia [52].
non-simulated is simply Davidsky converting them directly from the available BAM files and I already posted a distance chart showing the closest population to this sample. Here what the paper says too :
quote:For R11759, who projects near modern Mozabite and Moroccan populations in PCA space, [...] When compared to other ancient individuals using qpWave analysis (Fig. 5), this individual forms a clade with ancient Canary Island inhabitants thought to be representative of the original founding population (25). The Canary Islands were originally settled in the 1st millennium BCE by a population genetically ancestral to today’s Amazigh populations of Saharan Africa (26).
and here a new chart with exclusive samples a friend gathered :
So very close to modern moroccans.
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
posted
It's amazing how you can turn simple questions into a whole objective.
Point is we have 1000's of European samples available. There's no need to mystify the EEF component in NA. You said yourself it is likely that the earliest wave of Neolithization involving cardial ware assemblages were likely those to contribute to Moroccan Neolithic. But somehow you're using LBK (a latter expansion from the balkans) to explain it. And you're doing so because of G25 results. It makes no sense.
For over a decade modern Sardians were used as a proxy for the first EEF settlers in the Mediterranean. Some of the earliest Cardial-impressed ware sites were found there. They also carry Lineages that most recently coalesce with African populations. They (MN_SArd) as well as actual Neolithic Samples from Sicily are decent representatives of early neolithic settlers in Italy... because they are actual Neolithic settlers in Italy, Antalas.
Lastly, if you want you look deeply in to the somewhat simultaneous Neolithization of Northern Morocco and Spain 7.5Kya, I once again have to ask why do you look towards LBK. And why do you think those people aren't represented by actual genetic evidence we have available from those very localities dating to around that same time?!? It's double speak.
Speaking of G25 Does this make sense to you?
Simple question two; I asked about the populations this individual is closest to and you post custom samples lol. The reason why I asked though is clear. Cause I'm speaking about demographic history between the time of x and Modern samples. So if they're closest to southern Moroccans (and some Saharawi), which they are. And we can provide evidence of admxiture between antiquity and the medieval then the point earlier stands.
About simulated and non-simulated: Your explanation doesn't make sense. Downstream analysis of this kind cannot be done without Variant calling (BAM aren't "converted" btw). I'd expect that the variants were called regardless if simuated or not, if not... how did they get the simulated coordinates? Did they guess?
Posts: 1781 | From: New York | Registered: Jul 2016
| IP: Logged |
quote:Originally posted by Elmaestro: It's amazing how you can turn simple questions into a whole objective.
Point is we have 1000's of European samples available. There's no need to mystify the EEF component in NA. You said yourself it is likely that the earliest wave of Neolithization involving cardial ware assemblages were likely those to contribute to Moroccan Neolithic. But somehow you're using LBK (a latter expansion from the balkans) to explain it. And you're doing so because of G25 results. It makes no sense.
For over a decade modern Sardians were used as a proxy for the first EEF settlers in the Mediterranean. Some of the earliest Cardial-impressed ware sites were found there. They also carry Lineages that most recently coalesce with African populations. They (MN_SArd) as well as actual Neolithic Samples from Sicily are decent representatives of early neolithic settlers in Italy... because they are actual Neolithic settlers in Italy, Antalas.
Lastly, if you want you look deeply in to the somewhat simultaneous Neolithization of Northern Morocco and Spain 7.5Kya, I once again have to ask why do you look towards LBK. And why do you think those people aren't represented by actual genetic evidence we have available from those very localities dating to around that same time?!? It's double speak.
How can modern sardinians be a good proxy for the first EEF settlers if they absorbed steppe, east med and north african ancestry ? Also was WHG ancestry already part of these EEF settlers' genome ? Anyway yes you can also use the neolithic sardinian/sicilian samples I'm just telling you that among their three clusters the iberian one doesn't seem to be the one we should use.
quote:Originally posted by Elmaestro: Speaking of G25 Does this make sense to you?
your point ? That's not how you should model samples on G25.
quote:Originally posted by Elmaestro Simple question two; I asked about the populations this individual is closest to and you post custom samples lol. The reason why I asked though is clear. Cause I'm speaking about demographic history between the time of x and Modern samples. So if they're closest to southern Moroccans (and some Saharawi), which they are. And we can provide evidence of admxiture between antiquity and the medieval then the point earlier stands.
About simulated and non-simulated: Your explanation doesn't make sense. Downstream analysis of this kind cannot be done without Variant calling (BAM aren't "converted" btw). I'd expect that the variants were called regardless if simuated or not, if not... how did they get the simulated coordinates? Did they guess?
I already posted the closest populations from the paper and G25 then I added these custom samples to further show you to which exact communities this sample clusters with. How would one sample "provide evidence of admixture between antiquity and the medieval" if it's part of the modern north african cluster ? You think from morocco to tunisia and from it to the sahara they all had a chleuh-like profile ? They get the simulated samples through tools available like this one (I suppose) : https://www.exploreyourdna.com/simulated-g25.aspxPosts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
posted
It was thought that their(sard) relative isolation kept them away from certain admixture such as steppe ancestry.
quote:Within this broad framework, the island of Sardinia is thought to have received a high level of EEF ancestry early on and then remained mostly isolated from the subsequent admixture occur- ring on mainland Europe1,2. However, this specific model for Sardinian population history has not been tested with genome-wide wide aDNA data from the island.
10.1038/s41467-020-14523-6 This of-course was due to them displaying statistical straits for being representative of EEF before major revelations by aDNA. What I would admit after some more testing is that Starcevo_Serb + Iraq(Nemrik)_PPN + Kenya PN is the best 3way admixture and preferred by qpADM. While I don't like models which uses purely upstream populations (and those with distant geographical placement), The results were too good to omit.
Your question about WHG being a part of EEF original is actually surprisingly a good question. There might be substructure among WHG in which those who resided a bit further east would contribute to the EEF profile. Like Dzudzuana, best proxy for Pinarbasi was "Basal Eurasian" + Villabruna. Epipaleolithic HG's form Turkey and the surrounding areas were of-course direct ancestors of EEF.
About my G25 post... My point is that the model while fitted well, doesn't make sense. And that is liable to happen due to G25's proclivity to overfitting. I tried to simply explain how Vahaduo works. It seeks average coordinates across each principal component. basically multiply coordinates of source poulations so that the median in the ball park of the test population.
Now that we have "Non-simulated" coordinates the population distances should be different. So your previous post is not significant. Also, you're going in circles. Look, I'm going to try to keep it real simple. These north Africans weren't expected (Academically) to be so close to NA's more shifted to other Africans. Because it had been shown that certain groups were susceptible to SSA and other Admixture in recent times the consensus was that a KEB-like profile would be dominant in NA prior to More recent Halian/SSA/Arab influence. The Guanches were a surprise but was acceptable, but the Calcholithic and later this individual push further into Saharan affinity.
I also further challenge the mainstream understanding by proposing that there was even more European Influence after the Neolithic but prior to the Modern era. See my comments on m183 for example. Lastly there was nothing wrong with "my tools" 😂 as this "Non-Simulated" g25 stuff only gave more validity to my runs.
Posts: 1781 | From: New York | Registered: Jul 2016
| IP: Logged |
posted
Indeed we're going in circles since that was exactly my point since the beginning and I've seen many who tried to push the idea of a KEB-like profile being widespread based on the other Kerkouane samples. Also I don't see why you're talking about "saharan affinity" is it because of the nature of their SSA especially for the two copper age samples ? This kerkouane sample simply has slightly more IBM ancestry than coastal berbers but has similar values to chleuh/saharawis/mozabites and its SSA is in the norm of what we see for modern NAs so I don't see any particular saharan affinity.
If you add this to the other recent samples we got, I still don't understand why you deny any continuity ?? It seems like you're looking for the smallest detail or variation to claim there isn't any.
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
UBBFriend: Email this page to someone!
![[Roll Eyes]](rolleyes.gif)
![[Wink]](wink.gif)
Can you guess the SSA individual(s) who'll drive the probability to about 95%?
Printer-friendly view of this topic