Balter, Michael. 2013. Farming’s tangled European roots. Science 342. 181-182.
Bollongino, Ruth, Olaf Nehlich, Michael P. Richards, Jörg Orschiedt, Mark G. Thomas, Christian Sell, Zuzana Fajkosová, Adam Powell, Joachim Burger. 2000 years of parallel societies in Stone Age Central Europe Science 10/2013; DOI:10.1126/science.1245049.
Brandt, Guido, Wolfgang Haak, Christina J. Adler, Christina Roth, Anna Szécsényi-Nagy, Sarah Karimnia, Sabine Möller-Rieker, Harald Meller, Robert Ganslmeier, Susanne Friederich, Veit Dresely, Nicole Nicklisch, Joseph K. Pickrell, Frank Sirocko, David Reich, Alan Cooper, Kurt W. Alt. 2013. Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity. Science 342. 257-261.
They don't mention language, but the findings have big implications for the Indo-Europeanization of Europe. The Brandt et al. paper surveys mitochondrial DNA from 364 people found in one region of Germany (southwestern Sachsen-Anhalt) over four millennia, from 5500 to 1500 BCE. Early in that period is when the first farmers, ultimately from the Near East, arrived on the scene. The authors find a drop in the haplogroups associated with the earlier hunter-gatherer population at this time. Surprising is that 2,000 years later, we see a big bounce back of hunter-gatherer mtDNA and decline of farmer mtDNA. By the early Bronze Age, yet other groups come into the picture and eventually become more common than either. They outline four 'genetic shifts' in the area that "highlight the biological cohesiveness of archeological cultures", namely the familiar groups — the Linear Pottery, Funnel Beaker, Corded Ware and Bell-Beaker Cultures (2013:261). If you have access to the electronic version, there's a beautiful graphic of this.
Bollongino et al. examine DNA and other evidence from 29 people found in a single cave in western Germany from the Mesolithic and Neolithic periods. The results show that both earlier hunter-gatherer cultures and farmer cultures coexisted for a couple thousand years. Far more interesting is that they apparently had very distinct diets — domesticated animals for the farmers but lots of fish for the hunter-gatherers.
Taken together, these studies seem to suggest that there may have been a rapid incursion of farmers coming from the southeast, but not rapid displacement of the native populations nor of their cultures. This could well mean that there was sustained contact, probably close contact, for millennia. A lot of work on European linguistic prehistory assumes, one way or another, a relatively fast pattern of language shift. I think this makes that scenario more complicated.
More importantly, and something that gets lost in the discussions too often in discussions on this topic, is it looks like there was a lot of diversity in contacts. Balter quotes Peter Bogucki as arguing that "people may not have moved around in cohesive groups and that small bands of wanderers may have had the cumulative effect of 'smearing' genetic signatures over large areas.
It's so rare to see something that looks like actual progress in understanding these issues in European prehistory and I'm daring to hope for the moment that this is such progress.