I think the 2nd wave influenced Vinca, Cucuteni-Tripolye, Hamangia, Boian and Gumelnita cultures.
So, steppe people were also affected by the second wave.
I think this may be the earliest arrival of 2nd wave into the Balkans :
https://en.wikipedia.org/wiki/Dudești_culture
They were herders in Wallachia (lower Danube)
I think they were influenced by a different wave, a later wave, but was that different wave Tepecik or was it Barcin or Kumtepe like? Or were there three slightly different waves? I don't know. Does the archaeology help?
I can't find specific dates for each sample. I wish they'd provided that. So, basically, all we know is:
Boncuklu: 8300-7500 BC. Central Anatolia-Forager-elementary farming and some experimentation with pig domestication.
Tepecik:7500-5800 BC-Central Anatolia- Mixed and complex plant and animal exploitation practices (hunting and gathering, cereal agriculture and domesticated animals...significant interaction with communities further east at the headwaters of the Tigris, perhaps having to do with obsidian.
Barcin: 6400 BC Pottery Neolithic in NW, not Central Anatolia.
Kumtepe: 5700 BC Copper Age NW Anatolia
Did you take a look at the Admixture Chart?
http://www.cell.com/cms/attachment/2062474746/2064493946/gr3_lrg.jpg
I think it's important to note that the Boncuklu and Tepecik analysis is based on both whole genome and shotgun sequencing analysis. Was that always the case in all the papers in the past? Did they use the same set of samples for the modern populations? Could some of the discrepancies be accounted for by that fact?
It looks as if they're saying that over time the "WHG like" percentage of the Boncuklu samples dropped a bit. Given the archaeology that I'll reference below, I think it's pretty clear that with the Pottery Neolithic there was migration from elsewhere, probably from the Tigris Euphrates area but perhaps also from the Levant which changed them slightly. By the time of Tepecik Central Anatolia was definitely less WHG.
The EN samples seem to have quite a bit of variation. North-West Anatolian Pottery Neolithic Barcin is sort of in-between Boncuklu and Tepecik, and Kumtepe and Mentese, also further north, are sort of back up to the Boncuklu levels. What were the people who took off for Europe like? We know that there was a migration, pre-pottery Neolithic, from the coastal northern Levant where Syria meets Anatolia and which went to Cyprus among other places. We don't have samples from there. Does anyone know if there are even any available from that place and time? One might think they would have been more like Boncuklu, but they're also pretty close to where we might find Levant Neolithic. As for the movement of Pottery Neolithic like people out of the Near East, were they more Tepecik like or Barcin like? From what I remember of the archaeology there's very little to show any interactions between Barcin and the Balkans, for example. So, perhaps they were Tepecik like, but I don't know. I used to have the dates for the various early pre-pottery and pottery Neolithic settlements clear in my mind, but now I'd have to look them up. If anyone has a handle on it, please post.
The FST charts are interesting too. Look at where both Boncuklu and Tepecik have the strongest correlation. It's certainly not the Near East. Also, I just noticed that for all the talk about how Levantine the Cypriots are, by this measure they are a lot more European than Levantine. Obviously, of course, this is just part of their genetic variation.
Kumtepe is a whole other issue. The authors don't say, but is this Kumtepe 6? The authors do definitely see a closer correlation between Otzi/Remedello and Kumtepe, but can we tell from the analysis whether there was an actual movement of Kumtepe like people into southeastern Europe, or could it be that Boncuklu, Tepecik and some WHG picked up in Europe "looks like" Copper Age Kumtepe. On the other hand, there we have Otzi and Remedello with copper implements and other "hallmarks" of supposedly "Indo-European" culture, and yet no sign of "steppe" admixture at all, or so minor that it could be noise. So, could all of that have come from Northwestern Anatolia? Certainly, this paper underscores that, as Dienekes showed years ago, and as I've continued to say, Otzi has some CHG, which other MN samples do not.
Anyway, the paper has some nice data on the archaeology, which hints at the source of the minor changes in the genetics.
Farming came late to Anatolia: "The Epipalaeolithic of the plateau and its coastal fringes is poorly documented [S23]. However, one site on the plateau has been excavated at Pınarbaşı in the Konya Plain, where unlike the partially contemporary Levantine Early Natufian, there is no evidence of sedentary practices or intensive plant exploitation [S24]. The earliest sedentarising communities on the plateau appear in the 10th-9th millennia cal BC and are represented also by occupation at Pınarbaşı which lacks evidence of cultivation or herding [S25]."
The "Basal Eurasian" must have arrived before the Pre-Pottery Neolithic: "The Pre-Pottery Neolithic period (PPN) of the plateau is better understood. Among the human groups and cultures of the Konya Plain there are indications of highly diverse but indigenous communities during this phase of uptake of sedentism, of cultivation and of herding."
"There is thus substantial evidence for interactions between central Anatolia, the south coast of Turkey, the Levant and areas south-east of the Taurus from the Epipalaeolithic into the Pottery Neolithic [S32]."
"A diversity of cultures can be described in the Anatolian plateau during the subsequent Pottery Neolithic, considered to span from c.7000 to c.6000 cal BC. In Çatalhöyük in the Konya Plain [S34,35] we find rectilinear closely packed house clusters as at 8th millennium Aşıklı Höyük, and domestic organization that resembles 9th- 8th millennium Boncuklu. In contrast, Tepecik-Çiftlik and Köşk Höyük in Volcanic Cappadocia have independent houses and open areas, pointing to cultural differences with the Konya plain...Recent work has detected many new settlements in the Volcanic Cappadocia region; these are thought to be related to migrating individuals and small groups, possibly moving over quite significant distances, attracted by the local obsidian sources."