Many recent articles maintain that a small percentages of Neanderthal genes (up to 2%) are found in modern non-African people. (I believe that currently there is insufficient genetic material from older hominids, such as H. erectus, to decode a genome).

My question is: how is it known the “Neanderthal genes” found in modern humans got there by way of interbreeding? What distinguishes those genes from genes that both species inherited from a common ancestor? After all, Neanderthals and H. Sapiens are over 99% genetically identical. How is it determined that gene A is found in both because it was from H. erectus, from which both evolved; but gene B was not already present in H. sapiens, so it must have arisen through interbreeding?

  • $\begingroup$ Good question +1. About the claim Neanderthals and H. Sapiens are over 99% genetically identical (and the similar claim about the chimpanzee and human comparison), you should read the post “Same” DNA vs genes $\endgroup$
    – Remi.b
    Apr 20, 2018 at 21:49
  • $\begingroup$ @Remi.b Read that question. It left me very confused. I kind of understand it, but not fully $\endgroup$
    – Tom
    Apr 20, 2018 at 21:51
  • $\begingroup$ You will not have found a value of 40% in any reputable source, and it implies that you have not properly researched your question to mention it without citation. I have edited your question using 2% as the upper limit, consistent with reputable studies, such as the one I cite in my answer. $\endgroup$
    – David
    Apr 22, 2018 at 12:44
  • 1
    $\begingroup$ @David As far as the 40% goes, I'm mostly reading layperson articles because either I don't have access to the scientific ones, or they're just way above my pay scale. I'll look for the one that had that number later, but I think it was not saying that 40% of our genome is Neanderthal, but that 40% of the Neanderthal genome can be found in various modern humans. So I mis-stated that. I'll leave your edit. I just wanted to indicate that I spent days worth of reading online trying to figure this out. $\endgroup$
    – Tom
    Apr 22, 2018 at 16:24
  • $\begingroup$ OK. The three papers I cite are all available in free-to-view format, although in some cases it is as manuscript versions. $\endgroup$
    – David
    Apr 22, 2018 at 16:55

1 Answer 1


Although this question makes some false assumptions, it is fundamentally interesting as the methodology used is neither simple or easy to understand. It is not my area, but I have found it especially interesting to read the long 2010 Science paper by Green et al.. One really needs to read it for oneself (it is free view), but it is not a trivial undertaking.

False assumptions / misconceptions in the question

The main misconception in the question are:

  1. That it is necessary to know anything about the genome of H. erectus to make these conclusions. The methods used do not require this. (Although comparison with chimpanzee is sometimes used to give an indication of whether a genetic change occured in humans or Neanderthals.)
  2. That the similarities and differences under discussion relate to differences in complete genes — “but gene B was not already present in H. sapiens…”. They do not, which makes the analysis more complex to follow.

Towards an explanation

Let me start by addressing the question “What distinguishes those genes (purported to have been acquired by H. sapiens from Neanderthals) from genes that both species inherited from a common ancestor?”. The answer relates to the absence of such genes from modern humans of African origin, and the fact that we know the general evolutionary relationship between neanderthals and modern humans (African and non-African) from a wealth of non-sequence paleontological evidence. This is shown in the diagram below, modified from a recent and recommended review by Nielsen et al. in Nature (2017).

Relationship of humans and neanderthals

Clearly any gene present in the common ancestor to humans and Neanderthals should be present in both African and European populations, unless it had been lost from the African population.

So if the analysis is not done by detecting gain/loss of individual genes, how is it done? Certainly not by overall percentage sequence similarity, because of the high overall similarity and the population variation. It is done by studying SNPs — single nucleotide polymorphisms — in particular genes.

For example, consider a gene that has only a single haplotype in Neanderthals, and originally had a single but different haplotype in humans. (This might determine something like eye colour, although this is not an actual example.) If the other haplotype were acquired by humans as a result of interbreeding, then the modern human population would contain both alleles. When you compared the relationship of the SNPs for this gene between different humans and between humans and Neanderthals you would find different results from those for a gene the variant of which had not been acquired by interbreeding. The acquired gene in humans would be more related to that in Neanderthals than non-acquired genes, but less related to that in other humans (because of its more recent appearance in the population and time for homogenization, I believe).

The African/non-African aspect is explained in the Science paper cited in my introduction, but there is a good visual diagram in a 2014 Nature paper by Sankararaman et al., the manuscript of which can be viewed freely in PMC through the US HHS.

Analysis of Gene Divergence

(1) Sites where a panel of sub-Saharan Africans carries the ancestral allele and where the sequenced Neanderthal and the test haplotype (marked non-African) carry the derived allele are likely to be derived from Neanderthal gene flow; (2) Haplotype divergence patterns. Genomic segments where the divergence of the test haplotype to the sequenced Neanderthal is low while the divergence to a panel of sub-Saharan Africans is high are likely to be introgressed.

These papers contain a wide range of controls, including comparisons of different non-African population groups, and detailed discussion of alternative possibilities.

A final point of interest is that Sankararaman et al. examined some of the genes in which these SNPS suggest Neanderthal origin. They write:

“…genes involved in keratin filament formation and some other biological pathways are significantly enriched in Neanderthal ancestry in European populations, east-Asian populations, or both …. Thus, Neanderthal alleles that affect skin and hair may have helped modern humans to adapt to non-African environments.”


It would be scientifically dishonest not to mention some oddities. One is that the Green et al. paper suggested that gene flow had been uni-directional: from Neanderthals to humans, which is apparently unusual in interbreeding. However a more recent study (Kuhlwilm et al., 2016) shows some human gene flow into Eastern Neanderthals, although not into European Neanderthals. (Thanks to @iayork for pointing this out.). The other is that modern Asians appear to have more Neanderthal DNA than modern Europeans. (This is discussed in the paper already mentioned by Green et al.)

  • $\begingroup$ +1 This makes much sense now. I'm confused about relate to differences in complete genes. Are you talking about the fact that the genes are there, but different alleles of those genes? Because that I understand. I maybe should have said "alleles" in my question. Or are you referring to something different? $\endgroup$
    – Tom
    Apr 22, 2018 at 16:16
  • $\begingroup$ I mean the same genes are there, but there are alleles in Neanderthals that are were not present in the human population before mixing. I had been thinking I could clarify my answer and will do so now. $\endgroup$
    – David
    Apr 22, 2018 at 16:26
  • $\begingroup$ One is that gene flow appears to have been uni-directional: from Neanderthals to humans. Ancient gene flow from early modern humans into Eastern Neanderthals $\endgroup$
    – iayork
    Apr 23, 2018 at 17:53
  • $\begingroup$ @iayork — Thanks for pointing that out. I have ammended my answer accordingly. Do raise any other points you feel I have not addressed correctly or clearly enough. I find the question interesting, but it is not my area of expertise. $\endgroup$
    – David
    Apr 23, 2018 at 20:05

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