A new paper in Science (Brandt et al) talks about genetic changes in European prehistory, mainly by looking at mitochondrial DNA. They do this because mtDNA is easier to recover and sequence than Y-chromosome or autosomal DNA. The most complete story must, however, lie in the autosomal data.
Generally speaking, conquerors seem more likely to incorporate women into their society than men, so the story you get from looking at mtDNA is not going to be the same as that deduced from Y-chromosomes. If it looks as if early farmers from the Impressed Ware and Cardial cultures account for ~30% of European DNA today – judging from mtDNA – the autosomal fraction is likely to be significantly lower than that. The same is probably true for Mesolithic DNA in Europeans – ancestry estimates based on mtDNA are likely to be on the high side.