Athena of Rites of Passage has a post critiquing the recent Neolithic aDNA paper (via Palanthsci). Her take is a bit different from mine. It makes good points as well -- focusing on the small sample size and the complexity of probable cultural interactions in the Neolithic.
Here's a good quote:
The authors argue that simulations confirm that the first farmers had limited success in leaving a genetic mark on the female lineages of modern Europeans. What are these simulations? What are their parameters? Given that their genetic data is basically flawed, this part of the argument just exacerbates whole, flawed mess. And now comes the punch line: "One possible explanation is that the farming culture itself spread without the people originally carrying these ideas." Huh? Once again... huh? They then go on to suggest "pioneer groups" who really impressed the oh-so-backward Mesolithic populations to the extent that they saw the error of their ways and they took up farming. Whooosh, we turn back the clock to ideas of farmer-missionaries.
We will always have the problem of small samples and complex interactions. All the more reason to be cautious in interpreting results.