Gene Flow Between Humans and Neandertals?

Remember what FoxP2 is? I wrote a bit about it here. Well, a recent paper shows that the same two amino-acid substitutions occurred in the neandertal FoxP2 homologue that occurred in humans. The commonly accepted hypothesis is that there was no gene flow between humans and neandertals. The paper suggests two hypotheses for why we share the same two amino-acid substitutions with neandertals -- one is based off of the accepted model, which would imply that the amino-acid substitution occurred over 300 thousand years ago. The other is based off of the idea that small amounts of gene flow occurred between the human and neandertal populations. The paper then describes why the second hypothesis is better supported by the data.