I guess one person's "nitpicking" is another person's attempt at clarity and trying to get even the details right. We're all different in how we approach the material.
I came across some posts by RK at eurogenes that might clarify things.
I hope that RK doesn't mind my lifting part of his posts. It's a compliment.
This relates to the "ethnogenesis" of the "Anatolian Neolithic" group.
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There's some complexity with regard to 'circular admixture' between Levant_N, Natufian and Anatolia_Neolithic, and also Iran_N, CHG, and Iran_Chalcolithic, but the qpWave rank indicates that there really isn't much more complexity left once we use Levant_N and Iran_N as the bottom two corners. Anatolia_Neolithic still requires a currently unsampled population slightly further west than WHG on the WHG-EHG cline to get represented accurately, but not much else seems missing."
"Matt" made an interesting response to this:
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Less EHG ancestry than Switzerland_HG, which is modelled as having less than Loschbour. (Or conversely, less close to the WHG who are ancestral to EHG, I guess?). I don't think this will actually prove to be necessary though, and that this will all depend on what they find when they rerun and republish with the dataset from Fu et al."
I think it makes sense if we remember that the population in Anatolia was "WHG like", but not WHG.
Also,
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About Anatolia_Neolithic, I think the proportions are probably incorrect, but the source populations are probably correct. I agree that the proximate population source for EEF is Anatolia_Neolithic, but I expect some extra Iran_N would probably fit in the Danubian Neolithic on top of Anatolia_N if we tried."
He's talking about a mix of Iran Neolithic and Levant Neolithic (plus some "WHG like") admixture.
In my opinion, the specific, proximate source for at least Cardial might not yet have been sampled, i.e. it's in the Aegean or eastern mainland Greek Neolithic, and the Marmara samples are a bit different. Until we get them though I don't think there's any problem with using the ANF's as our best source so far.
As I have pointed out as well, although these early farming people were pretty homogeneous, they weren't identical.
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Previously there was a strange but very consistent tendency for all steppe groups, including yamnaya and Khvalynsk, to favour some EEF groups over others; Iceman was always the EEF pop closest to the steppe. Also some C European EEF groups were more 'Caucasus' than others, where 'Caucasus' is an ADMIXTURE component that is not very ANE-shifted despite centering there. Now that EEF is seen to be a mix of Iran_N and Levant_N, there is probably slight variation in the proportions depending on location, with Cardial farmers more Levantine and Danubian more Iran_N, I would bet."
That could be because the Danubian might derive more of its ancestry from the northwest Anatolia samples, and the Cardial ones from the Aegean group.
As to the comment about the Basal Eurasians, I don't recall mixing up dates or saying that the original Basal Eurasians were always farmers. No group was "always farmers".
All groups were originally hunter gatherers. What I was speculating is that the group or groups which developed agriculture had very high Basal Eurasian percentages.
On a related note, again from RK:
"But they do get consensus figures from matching qpAdm, f4s and ADMIXTUREGRAPH, so I am inclined to trust the higher figures. We would probably need a >>80% Basal Eurasian genome to settle the figures very well, probably from the Persian Gulf or Arabia."
As to the spread of farming:
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My guess is that, as small groups of humans passed through the Neolithic 'cultural bottleneck', the deformation of both genes and memes was so strong, and the resulting society so difficult for H-G societies to replicate, that all instances of highly developed agropastoral lifestyle involved at least some vertical genetic and memetic transmission, and accompanying demographic change in the ancestry stream at some point. "
"I expect that, once the preceding middle Eastern HGs are compared against the neolithic successors, extremely strong signs of recent selection will emerge. There are sharp boundaries in the presence of small %s of Basal ancestry in reindeer herders vs Siberian HGs, which seem to suggest some pre-adaptation is necessary for sustained agropastoralism in closed cultural groups, even today."
So I and LeBrok have been saying for a couple of years.
On the migration to the north into the steppe groups:
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the proximate contributor is probably an agricultural population on the Iran_N Levant_N clinal crescent that diffused into the Caucasus and further northwards, thus tying the Basal ancestry in pre-IEs to agropastoral groups, instead of an older diffusion from Kotias HGs only."
So, it may not be Iran Chalcolithic, but it's not Kotias CHG hunter-gatherer. It's a later farming group, not a very early hunter-gatherer group.
On why Kotias is sometimes a better fit:
"Later populations favouring Kotias over Ganj Dareh in Llorente et al. is probably an artifact caused by Kotias being a mix of Iranian+EHG/WHG+Levantine ancestry, which will have the effect of pulling Kotias away from the Iran_N corner towards the centre of the cloud of populations, where most later groups lie."
This I'm not sure about, but it seems reasonable.
As to why the models don't work with M/L steppe groups like Sintashta, Andronovo, or even Srubnaya related groups he doesn't really opine much that I can find.
One reason might be that we don't yet have the genome of the proximate but related source (related to Andronovo or Sintashta, I mean). Or perhaps they have it but aren't yet ready to release it. The answers might also be clearer once we have a genome from BMAC and IVC.
"The existence of a Basal-EHG admixed population deep into Iran also makes a very old ANE presence in Central Asia somewhat more likely, especially if the Basal ancestry peters out as one moves deeper into the North and East. My guess is that the IVC will be Iran_N+Onge and BMAC will be Iran_N+ANE/EHG, reflecting admixture from the prior HG populations in each location. "
He also dives into the controversy over Proto-Afro-Asiatic. Again, I've always thought it probably moved with Levantine people south rather than the other direction, perhaps from the Sinai with even more Natufian like people.
I do think that the "steppe" proportions in even southern South Asian tribals has to do partly with pre-existing "ANE like" ancestry.