Mega QAPDM Models thread

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Originally Posted by Croatian Legend

Look you are using one word examples to as an escuse to attack me personally. You know that you have crossed the line. I kept it on topic you went for personal stuff which you have no clue of.

Yes you do act as if you know just by judging how you wrote and attacked me. And you should stop imagining things how someone sounds over a text you seem a little emotional. So i will ask you kindly yet again to keep your manners in.

I have provided enough info on the qpadm vs g25 thing and the whole genetics analysis, where you did not. You proved lazy google search answers.
Yes i do read alot about that topic and if you would to and be more critical and less emotional and just go for the facts you will see what i point to.

And if you look close enough i pointed out way early that G25 is only good for general clustering/distances to poluations nothing more nothing less.
So i have a clear view and opinion on that but your emotions and some fanatsys clouded that the whole thing.

Anyway the problem is sovled let's move back to the general topic which is QPADM!

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If you think this was unprovoked look again. This is your post #158:

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"Sorry but you have no idea or rather you don't actually read scientfic papers because you keep repeating the same nonsense as most here.
Satsurblia is definitly used and also swapped in profesional testing. Satsurblia indicates a pure CHG line and it is used to better seperater CHG from EHG. Also same goes with AHG and EEF: AHG hast an eastern shift and lacks the natufian component that EEF has. It is also used in population/individual testing to see which fits better.

And no genetic scientist uses G25 for professinal work , since you mentioned that it is based on PCA. You do realise that they have there own ways or software to do the PCA. Which is different then G25 from Davidski.
Or rather let me be more clear Davdskis coords are a joke for ancestral calculation no serous scientist uses that. Not to even talk about his methods how he creates the coords. But i won't go into that now.
G25 is only good for general clustering but not to break down your ancestral components."

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That sentence was totally unnecessary, and I told you I have 0 tolerance for condescension. If you or anyone else doesn't see a problem with that then you are totally tone deaf. You could have posted that without sounding like an asshole, and it would have been fine. We wouldn't be at this point now. I told you in the previous post I have delt with slights in the past but not anymore! You say you are not asking for a fight. Those are fighting words to me. You have no business making authoritative statements like "nonsense". The only time I use that word is when I'm discussing Afrocentrism or historical revisionism. There's far more wiggle room with DNA tools.

And on your statement with AHG. It does have levantine affintity. This is from Feldman et al. 2019 https://www.nature.com/articles/s41467-019-09209-7


Inspired by our qualitative observations in PCA and ADMIXTURE analyses, we applied formal statistical frameworks to describe the genetic profiles of the three Anatolian populations and to test and model genetic differences between them. We first characterized the ancestry of AHG. As expected from AHG’s intermediate position on PCA between Epipaleolithic/Neolithic Levantines and WHG, Patterson’s D-statistics13 of the form D (AHG, WHG; Natufian/Levant_N, Mbuti) ≥ 4.8 SE (standard error) and D (AHG, Natufian/Levant_N; WHG, Mbuti) ≥ 9.0 SE (Supplementary Table 3) indicate that AHG is distinct from both the WHG and Epipaleolithic/Neolithic Levantine populations and yet shares extra affinity with each when compared to the other. Then, we applied a qpAdm-based admixture modeling to integrate these D- statistics. qpAdm is a generalization of D/f4-statistics that test whether the target population and the admixture model (i.e., a linear combination of reference populations) are symmetrically related to multiple outgroups13. By doing so, it tests whether the proposed admixture model is adequate to explain the target gene pool and provides admixture coefficient estimates. We find an adequate two-way admixture model (χ2p = 0.158), in which AHG derives around half of his ancestry from a Neolithic Levantine-related gene pool (48.0 ± 4.5%; estimate ± 1 SE) and the rest from the WHG-related one (Supplementary Tables 4, 5). While these results do not suggest that the AHG gene pool originated as a mixture of Levant_N and WHG, both of which lived millennia later than AHG, it still robustly supports that AHG is genetically intermediate between WHG and Levant_N. This cannot be explained without gene flow between the ancestral gene pools of those three groups. This supports a late Pleistocene presence of both Near-Eastern and European hunter-gatherer-related ancestries in central Anatolia. Notably, this genetic link with the Levant pre-dates the advent of farming in this region by at least five millennia.

https://i.postimg.cc/X799DSBc/image.png
my best model so far

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Originally Posted by Gannicus

If you think this was unprovoked look again. This is your post #158:



That sentence was totally unnecessary, and I told you I have 0 tolerance for condescension. If you or anyone else doesn't see a problem with that then you are totally tone deaf. You could have posted that without sounding like an asshole, and it would have been fine. We wouldn't be at this point now. I told you in the previous post I have delt with slights in the past but not anymore! You say you are not asking for a fight. Those are fighting words to me. You have no business making authoritative statements like "nonsense". The only time I use that word is when I'm discussing Afrocentrism or historical revisionism. There's far more wiggle room with DNA tools.

And on your statement with AHG. It does have levantine affintity. This is from Feldman et al. 2019 https://www.nature.com/articles/s41467-019-09209-7


Inspired by our qualitative observations in PCA and ADMIXTURE analyses, we applied formal statistical frameworks to describe the genetic profiles of the three Anatolian populations and to test and model genetic differences between them. We first characterized the ancestry of AHG. As expected from AHG’s intermediate position on PCA between Epipaleolithic/Neolithic Levantines and WHG, Patterson’s D-statistics13 of the form D (AHG, WHG; Natufian/Levant_N, Mbuti) ≥ 4.8 SE (standard error) and D (AHG, Natufian/Levant_N; WHG, Mbuti) ≥ 9.0 SE (Supplementary Table 3) indicate that AHG is distinct from both the WHG and Epipaleolithic/Neolithic Levantine populations and yet shares extra affinity with each when compared to the other. Then, we applied a qpAdm-based admixture modeling to integrate these D- statistics. qpAdm is a generalization of D/f4-statistics that test whether the target population and the admixture model (i.e., a linear combination of reference populations) are symmetrically related to multiple outgroups13. By doing so, it tests whether the proposed admixture model is adequate to explain the target gene pool and provides admixture coefficient estimates. We find an adequate two-way admixture model (χ2p = 0.158), in which AHG derives around half of his ancestry from a Neolithic Levantine-related gene pool (48.0 ± 4.5%; estimate ± 1 SE) and the rest from the WHG-related one (Supplementary Tables 4, 5). While these results do not suggest that the AHG gene pool originated as a mixture of Levant_N and WHG, both of which lived millennia later than AHG, it still robustly supports that AHG is genetically intermediate between WHG and Levant_N. This cannot be explained without gene flow between the ancestral gene pools of those three groups. This supports a late Pleistocene presence of both Near-Eastern and European hunter-gatherer-related ancestries in central Anatolia. Notably, this genetic link with the Levant pre-dates the advent of farming in this region by at least five millennia.

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Well i will also not tolerate someone attacking me personally and assuming stuff up, period. So point the fingers first at yourself and move on!

Now to the AHG topic you have send.

Yes i am well aware that some science papers point towards natufian others point towards iranian shift. Really depends but i consider it also plausible!
Either way AHG has definitely a stong eastern shift which also shows in my genome. Since i am completely cuf of from the western hemisphere of Europe on my profesional dna result.
I assume it is that and the combination of elevated CHG from CHG heavy steppe source that shows in my genome .

My two contries that show on my Dna result is:

Hungary/Budapest around 31%
Croatia/Dalmatia around 22%
Slovnia/Slovenia at 11%
Bosnia/Mostar at 4%

There are more but i might post later more but those are the ones to name a few. The really interesting part is the deep analysis from the company and this is where it gets interesting.

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Originally Posted by Fistora

https://i.postimg.cc/X799DSBc/image.png
my best model so far

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P- value wise it seems excellent but ry to work on your right to lower your standard error! maybe remove or add some but your definetly on track!

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Originally Posted by Fistora

https://i.postimg.cc/X799DSBc/image.png
my best model so far

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If you get closer to a standard error of 5 or below with keeping your p-value a that level that you are dead on!

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Originally Posted by Gannicus

And on your statement with AHG. It does have levantine affintity. This is from Feldman et al. 2019 https://www.nature.com/articles/s41467-019-09209-7


Inspired by our qualitative observations in PCA and ADMIXTURE analyses, we applied formal statistical frameworks to describe the genetic profiles of the three Anatolian populations and to test and model genetic differences between them. We first characterized the ancestry of AHG. As expected from AHG’s intermediate position on PCA between Epipaleolithic/Neolithic Levantines and WHG, Patterson’s D-statistics13 of the form D (AHG, WHG; Natufian/Levant_N, Mbuti) ≥ 4.8 SE (standard error) and D (AHG, Natufian/Levant_N; WHG, Mbuti) ≥ 9.0 SE (Supplementary Table 3) indicate that AHG is distinct from both the WHG and Epipaleolithic/Neolithic Levantine populations and yet shares extra affinity with each when compared to the other. Then, we applied a qpAdm-based admixture modeling to integrate these D- statistics. qpAdm is a generalization of D/f4-statistics that test whether the target population and the admixture model (i.e., a linear combination of reference populations) are symmetrically related to multiple outgroups13. By doing so, it tests whether the proposed admixture model is adequate to explain the target gene pool and provides admixture coefficient estimates. We find an adequate two-way admixture model (χ2p = 0.158), in which AHG derives around half of his ancestry from a Neolithic Levantine-related gene pool (48.0 ± 4.5%; estimate ± 1 SE) and the rest from the WHG-related one (Supplementary Tables 4, 5). While these results do not suggest that the AHG gene pool originated as a mixture of Levant_N and WHG, both of which lived millennia later than AHG, it still robustly supports that AHG is genetically intermediate between WHG and Levant_N. This cannot be explained without gene flow between the ancestral gene pools of those three groups. This supports a late Pleistocene presence of both Near-Eastern and European hunter-gatherer-related ancestries in central Anatolia. Notably, this genetic link with the Levant pre-dates the advent of farming in this region by at least five millennia.

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Maybe it would be interesting to model AHG in qpadm an see what seems feasable. Would be interesting what the breakdown is.

Gnereally what is comon that AHG can be modelet as 50 -60% WHG like component and 40 - 50 % Natufian "related".

Gotta correct myself AHG has more Natufian/WHG related and EEF has more of extra Basal Euraisan/Fertile Crescent and less WHG

https://i.postimg.cc/DZwWQJ5Y/image.png

Slight improvement

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Originally Posted by Croatian Legend

Well i will also not tolerate someone attacking me personally and assuming stuff up, period. So point the fingers first at yourself and move on!

Now to the AHG topic you have send.

Yes i am well aware that some science papers point towards natufian others point towards iranian shift. Really depends but i consider it also plausible!
Either way AHG has definitely a stong eastern shift which also shows in my genome. Since i am completely cuf of from the western hemisphere of Europe on my profesional dna result.
I assume it is that and the combination of elevated CHG from CHG heavy steppe source that shows in my genome .

My two contries that show on my Dna result is:

Hungary/Budapest around 31%
Croatia/Dalmatia around 22%
Slovnia/Slovenia at 11%
Bosnia/Mostar at 4%

There are more but i might post later more but those are the ones to name a few. The really interesting part is the deep analysis from the company and this is where it gets interesting.

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To be fair the only time I got nasty with you was from that post I linked. I quoted your first line and we generally had a neutral dialogue up to that point. You insulted me first and I reciprocated.

Go back and look. I was neutral and polite to you up until you said: "Sorry but you have no idea or rather you don't actually read scientfic papers because you keep repeating the same nonsense as most here." That was an insult and rude.
So, my insult to you was after you responded to me in that post.

I'll repeat your insulting and rude comment was post #158 on page 16 and I responded in kind in post #161 on page 17. I was not the first. You crossed a line.

If you go back and re read the thread, the record is plain.

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Originally Posted by Gannicus

To be fair the only time I got nasty with you was from that post I linked. I quoted your first line and we generally had a neutral dialogue up to that point. You insulted me first and I reciprocated.

Go back and look. I was neutral and polite to you up until you said: "Sorry but you have no idea or rather you don't actually read scientfic papers because you keep repeating the same nonsense as most here." That was an insult and rude.
So, my insult to you was after you responded to me in that post.

I'll repeat your insulting and rude comment was post #158 on page 16 and I responded in kind in post #161 on page 17. I was not the first. You crossed a line.

If you go back and re read the thread, the record is plain.

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Look back how and why i said that. You kept repeating your Kotias think. I told you many times before i tried it looked like you ingoned things. Again my comment was not personal like yours becuase you did sound like you don't read that much and just because you overreact and become emotional doesn'tgive you the right assuming things about me. Another indicator was that you went on that using Satsublia is wrong which if you would have read about the scientist that do actually use the sample than you would understand what i meant. As i said that snps don't have a date or age.

Let's just see it as a misunderstanding and move on and continue the topic.

*Handshake emoji*