In “Q&A: Who is H. sapiens really, and how do we know?” (BMC Biology 2011, 9:20doi:10.1186/1741-7007-9-20), Mason Liang and Rasmus Neilsen explain reasons for thinking that humans and Neanderthals interbred:
Is it true that modern humans have Neanderthals and other archaic species in their direct ancestry?
According to two recently published papers by Green et al. and Reich et al., the answer to this question is yes. Human genomes are in part composed of DNA from other archaic hominin species that traditionally have not been counted among our ancestors, although the proportion of archaic DNA in the genome depends on your ethnicity. On the basis of analyses of ancient DNA, Green et al. report that, on average, 1 to 5% of the genomes of non-African individuals are descended from a Neanderthal, and Reich et al. report that 4 to 6% of the genomes of Melanesians are derived from a newly discovered archaic hominin population dubbed the Denisovans. Denisovans and Neanderthals are the only archaic species investigated so far, but future investigations may reveal contributions of DNA from other species, perhaps even from species that have never been characterized well morphologically.
Lots of useful information here, clearly written.
Bornagain was wondering about this. If he is here, he might like to comment.