For a long time, we believed that Neanderthals and Homo Sapiens (modern humans) were two separate species. With the advent of DNA sequencing, however, it was discovered that Sapiens interbred with Neanderthals as they migrated from Africa 60,000 years ago. Another previously unknown hominid species, known as Denisovans, was also discovered at that time, and it interbred with Sapiens and Neanderthals, too.
Gene sequencing shows that non-African genomes today contain about 2% Neanderthal DNA, and people from Papua, New Guinea, and Australia are about 3% Denisovan. Studies on modern African DNA are taking longer because climate, geography and politics make locating skeletons much more difficult.
We are able to look in the other direction as well thanks to new technologies in genetic sequencing and computation. It appears that Sapiens contributed their genes to Neanderthal DNA more than 200,000 years ago. There is also evidence that another unknown hominid species interbred with everyone else, making up 4%–8% of modern human DNA.
Clearly, prehistoric peoples met and mixed a great deal more than we previously thought. In fact, we might not actually be all that separate. As biologist Adam Siepel has said, “It suggests that maybe Neanderthals actually are us. As different as they are, maybe they’re just another version of us.”
Neanderthals appear to have migrated to Eurasia around 100,000–200,000 years ago and Homo Sapiens stayed in Africa until about 60,000 years ago. So, interbreeding didn't happen for tens of thousands of years, during which time they evolved some major differences, leading us to believe they represented completely different strands of hominid development. Not so, apparently! Denisovans were discovered in 2010, adding to the complex picture of human evolution. Genetic archaeologists believe they've also found DNA from a different ancient hominid in our genes. As technology continues to advance, we'll be able to get a clearer picture even further back in time. So who knows what we'll find out about ourselves in the future!