This is the paper to which you're referring, right?
"
"Strontium isotopes document greater human mobility at the start of the Balkan Neolithic by Dusan Boric and Douglas Price."
http://www.pnas.org/content/110/9/3298.long
Here is a paragraph describing migration of first Neolithic farmers who came to Hungary, Danubian Gorge area:
"The ensuing period has been referred to as the Final Mesolithic (
16) or Mesolithic–Neolithic transformation phase (
17,
30) and is currently dated to
∼6200–6000/5950 cal B.C., making this phase in the Danube Gorges entirely contemporary with early Neolithic sites in the Morava, middle Danube, and Tisza valleys (
14). Remarkable art in the form of sculpted boulders and innovative architectural features such as red limestone trapezoidal-shaped building floors found at the key site of Lepenski Vir (
SI Appendix, section I and Fig. S2) are attributed to this phase (ref.
31 and
SI Appendix). This is the phase of cultural hybridity in the Danube Gorges. Early Neolithic pottery (
32,
33), polished stone axes (
34), nonlocal good quality yellow white-spotted “Balkan” flint from areas 200 km away from the Danube Gorges in northern Bulgaria (
35) as well as novel, typical Neolithic morphologies in osseous tools were found associated with trapezoidal buildings at the sites of Lepenski Vir and Padina. At the same time, these buildings harnessed many indigenous architectural and material culture elements, whereas
the lack of domesticates (except for dogs) during this phase suggests an unaltered subsistence pattern (
30). Mortuary practices were still characterized by extended supine burials during this period (
SI Appendix, Fig"
I've just re-read the paper, which I should have done before I responded to you, so my apologies. Nowhere in the paper can I see that the authors address the issue of the presence of domesticated animals in the early Neolithic in Greece or generally in the Balkans. They are addressing only one specific area, that around the Danube Gorges, where there was a relatively large group of sedentary fisher gatherers. The authors, through strontium isotope analysis, show that starting from around 6200 BC there were several waves of newcomers. Some new settlements were started on land more amenable to the agricultural package, and these vastly increased over time. However, a few of the prior fisher-gatherer settlements continued to be occupied for some time. It is those settlements whose subsistence strategies they discuss. Even those settlements show some genetic admixture based on the variety of skeleton types, and this increased over time. Eventually, the fisher/hunters, if they did not flee, were totally absorbed by the farmers. This may be the place where the Anatolian farmers picked up their 10% KO1 like European Mesolithic WHG like ancestry.
The paragraph which you cited is referring to the very earliest time of contact, when these people had apparently started to trade for new kinds of goods, and perhaps some wives, but as they were in a phase of "cultural hybridity", according to the authors, they had not yet adopted domesticated animals. They hadn't even adopted farming yet, as the authors make a point of saying that their subsistence strategies hadn't changed.
"
"The ensuing period has been referred to as the Final Mesolithic (16) or Mesolithic–Neolithic transformation phase (17,30) and is currently dated to ∼6200–6000/5950 cal B.C., making this phase in the Danube Gorges entirely contemporary with early Neolithic sites in the Morava, middle Danube, and Tisza valleys (14). Remarkable art in the form of sculpted boulders and innovative architectural features such as red limestone trapezoidal-shaped building floors found at the key site of Lepenski Vir (SI Appendix, section I and Fig. S2) are attributed to this phase (ref. 31 and SI Appendix). This is the phase of cultural hybridity in the Danube Gorges. Early Neolithic pottery (32, 33), polished stone axes (34), nonlocal good quality yellow white-spotted “Balkan” flint from areas 200 km away from the Danube Gorges in northern Bulgaria (35) as well as novel, typical Neolithic morphologies in osseous tools were found associated with trapezoidal buildings at the sites of Lepenski Vir and Padina. At the same time, these buildings harnessed many indigenous architectural and material culture elements, whereas the lack of domesticates (except for dogs) during this phase suggests an unaltered subsistence pattern (30). Mortuary practices were still characterized by extended supine burials during this period (SI Appendix, Fig""
The paper is very confusingly written, but I think if you read it again you'll see what I mean. These people held onto to their prior subsistence patterns for quite a while, before eventually, within a few hundred years, becoming overwhelmed by the sheer numbers around them.
So, I guess my point is that there is no contradiction between this paper and all of the other archaeological work that has been done in the Balkans on this topic.
Ed. Sorry, this was prepared last night and I forgot to post it.