Around 60,000 years ago, modern humans left Africa, the cradle of our species. As we spread across the face of the Earth, we discovered that we weren’t the first or the only humans to make that sojourn.  From Central Asia to Europe, we met our distant cousins the Neanderthals, descendants of a 500,000 year old migration; further east were the Denisovans, ranging from Sibera to Southeast Asia.  Although these other humans died out around 30,000 years ago, some comfort can be found in the knowledge that a part of them lives on in us.  Genetic evidence uncovered in the past few years suggests that our migrating ancestors may have mated with these other humans during their encounters.  Not everyone was convinced, though, launching an ongoing debate about whether the genetic similarity might be due to common ancestry rather than inbreeding.

Scientist disagree about whether Neanderthals should be considered another species (Homo neanderthalensis) or subspecies of Homo sapiens, but our evolutionary paths are thought to have diverged about 800,000 600,000 years ago.  The name comes from the Neander valley in Germany, where the defining specimen was found in the 1850s.  Thanks to their greater physical strength, popular depictions of Neanderthals have often shown them as brutish, ignoring the fact that they also had larger brains than modern humans. Neanderthals were as intelligent as the modern humans living around them; there is strong evidence that they were artistic, made advanced stone tools and may even have used language the same way we do.  In 2010, a team of researchers led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig announced that our ancestors had interbred with Neanderthals; by sequencing the Neanderthal genome, the team had found that 4% of Neanderthal DNA was shared by living non-African populations.

We know far less about the Denisovans.  They are known from a few fossils (a tooth and fragments of a finger and toe) recently unearthed in the Denisova cave in the Altai mountains of Siberia.  Scientist have been able to tease an amazing amount of information from this paucity of remains; by studying the DNA from these bones, researchers (again led by Svante Pääbo) were able to discover that Denisovans were probably the cousins of Neanderthals, splitting off from them around 640,000 400,000 years ago and heading east after the migration from Africa.  Dr. Pääbo’s team also estimated that genomes of people from New Guinea shared about 5% of their DNA with Denisovans.  This figure was recently revised when the team managed to recover extremely high quality sequence data from the finger bone in a landmark study that has (deservedly) received a great deal of attention.  (Interbreeding wasn’t the only thing they found out about; they also looked at what differences distinguish us from the Denisovans. If you haven’t already read about their work, you really should.)

In a paper recently published in the Proceedings of the National Academy of Sciences, Anders Eriksson and Andrea Manica of the University of Cambridge argue that the DNA we share with Neanderthals and Denivsovans might not be due to interbreeding.  Instead, they suggest that it might come from incomplete genetic mixing in structured populations; using a demographic model, they are able to predict the correct amount of genetic overlap with Neanderthals even without interbreeding.  One way to understand this is by analogy with a deck of playing cards.  A structured population is like a new, unshuffled deck in which the cards are organized by suit.  Two hands of five cards dealt from this deck will have the same suit but only because they came from the same place.  Likewise, Neanderthals and non-African modern humans might share some DNA simply because they happen to have come from the same African subpopulation.  It might help to imagine the migrations in a modern context; two groups descended from migrations out of Mediterranean populations would have more in common with each other than either would with Scandinavians.  “Based on common ancestry and geographic differences among populations within each continent,” said Dr. Manica,  “we would predict out of Africa populations to be more similar to Neanderthals than their African counterparts – exactly the patterns that were observed when the Neanderthal genome was sequenced.”

Of course, these results aren’t conclusive proof that our ancestors didn’t interbreed with other kinds of humans.  This study just demonstrates that the genetic overlap alone isn’t enough evidence for interbreeding, since it could also be due to demographic factors.  Not everyone agrees with the conclusions of this study; Ewen Callway has written eloquently about the ongoing debate, highlighting the important and unfortunate role of publication delays.  In a study available as a preprint, a team led by Dr. Pääbo and David Reich at Harvard estimated the most recent date of gene flow between present-day Europeans and Neanderthals.  Using a statistical analysis of the genomic regions shared with Neanderthals, they conclude that the most recent gene flow happened 47,000-65,000 years ago.  Modern humans and Neanderthals had both moved into Europe by this point.  This means that at least some of the genetic similarity is because of interbreeding, though it doesn’t rule out possibility that population structures in ancient Africa also had an effect.

Though the balance of evidence supports the idea that our ancestors interbred with other kinds of humans, debate may continue about the relative contribution of interbreeding and population structure.  Such dialogue is both healthy and necessary, since it’s what helps us refine our ideas and make scientific progress.  As we continue to learn more about our ancestors and their contemporaries, continuing skepticism and debate will no doubt be invaluable in teasing apart the story of where we came from and what happened to our closest relatives.

[Sorry for the mistaken dates in the original post.]

Refs
Eriksson A, & Manica A (2012). Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Proceedings of the National Academy of Sciences of the United States of America, 109 (35), 13956-60 PMID: 22893688
(and the press release from Cambridge)

Sriram Sankararaman, Nick Patterson, Heng Li, Svante Pääbo, & David Reich (2012). The date of interbreeding between Neandertals and modern humans arXiv arXiv: 1208.2238v1