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Neanderthal Population Data Raises Doubt about Human-Neanderthal Interbreeding

As a high school student, I was frequently summoned to the principal’s office—usually because he thought I was responsible for carrying out some type of misdeed. And, more often than not, he was right. Guilty as charged!

Invariably, my response was to lie and deny—and I learned quickly that if I was going to talk my way out of trouble, my story had to hang together. It’s impossible to maintain plausible deniability if your facts don’t mesh.

As it turns out, those anthropologists who claim that modern humans and Neanderthals interbred have the same problem as mischievous students who are poor liars—their story doesn’t quite hang together. Molecular anthropologists claim they have detected signatures for interbreeding in the Neanderthal and modern human genomes, but other data challenge this idea. As a case in point, new research into the population size and distribution of Neanderthal groups raises serious doubts about the likelihood that modern humans and Neanderthals would have ever encountered one another, let alone interbred.1

The Case for Human-Neanderthal Interbreeding

The first compelling evidence for interbreeding between human and Neanderthals came in 2010, when researchers completed the draft sequence of the Neanderthal genome.2 This low-quality genome was a composite, constructed from the DNA isolated from three Neanderthal individuals.

A comparison of the composite genome with representative human genomes revealed that Neanderthal DNA has more in common with non-African people groups than those from African populations. One way of accounting for this difference is to assume that limited interbreeding occurred between humans and Neanderthals. Specifically, geneticists posit that these interbreeding events took place in the eastern portion of the Middle East, roughly 45,000 to 80,000 years ago, as humans began migrating around the world. This introgression would explain why non-African populations display what appears to be a 1 to 4 percent genetic contribution from Neanderthals while African people groups display no contribution whatsoever.

At the beginning of 2014, researchers published a high-quality genome sequence for an individual Neanderthal recovered in the Altai Mountains of Siberia. Analysis of this genome confirms the results from the draft genome sequence;3  namely, humans and Neanderthals interbred as humans migrated out of Africa, resulting in a 1 to 2 percent Neanderthal contribution to the human genome.

In addition to the statistical association between the Neanderthal and Eurasian genomes, other researchers claim more direct evidence for interbreeding. These investigators maintain that they have identified distinct genetic regions in the human genome derived from Neanderthal DNA.4

How Well Established Is the Case for Human-Neanderthal Interbreeding?

On the surface, the evidence for interbreeding between humans and Neanderthals seems “air-tight.” In fact, many anthropologists regard human-Neanderthal interbreeding as part of their discipline’s “orthodoxy.” Yet, there may be another way to explain the supposed Neanderthal signature in the human genome. As previously discussed, the statistical association between Neanderthal and Eurasian genomes may be a consequence of the substructure of African population groups, not interbreeding.

Additionally, a number of other studies have yielded results that don’t quite fit the interbreeding scenario. For example, the recent re-dating of two key sets of Neanderthal remains from the northwestern foothills of the Caucasus Mountains and Iberia, respectively, indicates that Neanderthals may have gone extinct much earlier than thought. If an earlier extinction is the case, then humans and Neanderthals couldn’t have co-existed in Europe or Iberia, raising the intriguing possibility that humans and Neanderthals didn’t co-exist in the Middle East either. And, of course, if humans and Neanderthals didn’t co-exist, they couldn’t interbreed. (To get details on these studies go here and here.)

A recent study conducted by a large team of collaborators from Europe and China adds one more complication to the mix.5 The researchers used a method to selectively fish out the protein-coding DNA sequences from Neanderthal remains recovered in Spain and Croatia. They isolated over 17,000 protein-coding genes and analyzed them along with the same genes from the Altai Mountains specimen (which provided the DNA for the high-quality Neanderthal genome sequence). Then, they compared the Neanderthal genetic variability with the corresponding genetic variability of present-day humans. The researchers observed that the genetic variability among Neanderthals was remarkably low, suggesting these hominids lived in small populations, isolated from one another.

In addition to this result, analysis of the Altai Mountain specimen’s high-quality genome indicates that Neanderthals frequently mated with close relatives.6 This scenario comports well with the idea that these creatures lived in small, isolated groups.

In 2009, researchers studied the genetic diversity of Neanderthal mitochondrial DNA sequences.7 This work yielded the same result as studies of Neanderthal nuclear DNA. Based on the variability of Neanderthal mitochondrial DNA, it appears the effective population size of Neanderthals across Europe and Asia may have been as low as 3,500 at any one point in time.

The low population densities of Neanderthals greatly reduces the likelihood that migrating modern humans would have encountered these creatures, making it hard to imagine how interbreeding could have occurred. Keep in mind that the population sizes of migrating humans must have been small as well.

Did humans and Neanderthals interbreed? While many anthropologists think they did, I think it is still premature to draw this conclusion. The latest insight into the size and distribution of Neanderthal groups (along with the timing of Neanderthal extinctions) punches holes in a story widely accepted among many anthropologists and the general public.


What does it matter if humans and Neanderthal interbred? This question has important consequences for both evolutionary and creation models. RTB scholars discussed some of these implications on the May 10, 2010 episode of Science News Flash.


  1. Sergi Castellano et al., “Patterns of Coding Variations in the Complete Exomes of Three Neanderthals,” Proceedings of the National Academy of Sciences, USA 111 (May 6 2014): 6666–71.
  2. Richard E. Green, “A Draft Sequence of the Neandertal Genome,” Science 328 (May 7, 2010): 710–22.
  3. Kay Prüfer et al., “The Complete Genome Sequence of a Neanderthal from the Altai Mountains,” Nature 505 (January 2, 2014): 43–49.
  4. Sriram Sankararamen et al., “The Genomic Landscape of Neanderthal Ancestry in Present-Day Humans,” Nature 507 (March 20, 2014): 354–57.
  5. Castellano et al., “Patterns of Coding Variations.”
  6. Prüfer et al., “The Complete Genome Sequence.”
  7. Adrian W. Briggs et al., “Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes,” Science 325 (July 17, 2009): 318–21.