Thursday, November 21, 2013

Science Daily: Neanderthal Viruses Found in Modern Humans

A year a half ago, I was sitting in a discussion group in the anthropology department at the University of Tennessee discussing the importance of the Denisova fossil and DNA that was extracted from it.  At that point, it had already been established that Neandertal DNA had been found in modern humans to the tune of between 3 and 9 % depending on the population.  I then publicly wondered when a study of endogenous retroviruses in the Neandertal genome would be forthcoming and whether that would also link them to modern humans.

It has.  Science Daily is reporting on genetic studies that have discovered Neandertal retroviral DNA in modern humans.  From the story:
The researchers compared genetic data from fossils of Neanderthals and another group of ancient human ancestors called Denisovans to data from modern-day cancer patients. They found evidence of Neanderthal and Denisovan viruses in the modern human DNA, suggesting that the viruses originated in our common ancestors more than half a million years ago.
Lets back up.  What are endogenous retroviruses, or ERVs? These are RNA-based viruses that write themselves into the DNA of an individual.  They are thought by some to be directly involved in causing things such as MS and a host of different cancers.  It is not quite clear what kind of role they play in this, however.  It has also been found that some ERV DNA has been co-opted by the reproductive system, and are involved in the creation and stability of the placenta.  They are highly conspicuous and easily recognizable.  ERVs also makes up around eight percent of modern human DNA.

If they get written into the sex chromosome, since they are part of the DNA, they get passed on and, usually over time, lose their virus-causing capabilities, ending up as non-coding parts of the genome.  Sometimes, they don't insert correctly and end up not causing trouble at all.   One of the most interesting things, though is that they insert themselves into the genome in random places.  Therefore, if they show up across related species, it is a marker of evolutionary similarity.  They have, understandably, figured into human evolutionary studies.  ERVs have been found in all of the higher apes that are also found in humans and, broadly, provide evidence of common ancestry with the higher apes.  Here is a paper in Comparative Functional Genomics by Khudosovich et al., explaining the role in detail1.

Now it seems that ERVs that are specific to Neandertals have been found in modern humans.   As with the results of the Neandertal genome, this can only mean one thing: Neandertals directly contributed, in some way, to the ancestry of modern humans.  This has broad implications not just for human evolutionary response but also for theological models involving Adam and Eve.  Conventional science posits that Neandertals appeared around 130 000 years ago in Europe and that, as modern humans moved out of Africa, they met and mated with the resident Neandertals.  The evidence further suggests that, over time, the modern human genome swamped the Neandertal genome and that, in combination with changing climatic conditions and the selective advantage of the modern human genome, Neandertals died out. 

But we know that the last Neandertal died out around 32 000 years ago.  If modern humans carry Neandertal genes (and by extension ERVs), then there must have been modern humans around at least that long.  Further, given that most of these DNA elements are non-coding and insert themselves randomly in the genome, in order to postulate a separate, non-evolutionary, special recent ancestry for modern humans, one must argue that these ERVs were separately inserted into the DNA of Neandertals and modern humans (unintelligent design).

I'm going out into left field now.

Further, if one is to argue that there were only two humans at the beginning of human history, one has to account for how the Neandertal genes got into their descendants.  One could, I suppose, argue that, in the time period between Adam and Eve to Noah, one of Adam's descendants mixed it up with the Neandertals (although one has to account for why they aren't mentioned) and that is how the Neandertal ERVs got there.  There were Neandertals in the Levant, so that is, at least within that framework, possible (Neandertals as Nephilim?).  I will be curious to see if that explanation appears in creationist' writings.

The most parsimonious explanation is that modern humans carry some Neandertal ancestry in them and that this process occurred through evolutionary means. 

1Khodosevich, Konstantin, Lebedev, Yuri and Sverdlov, Eugene (2002) Endogenous Retroviruses and Human Evolution Comparative and Functional Genomics 3(6),494-498


  1. Jim, you slipped up a little saying they get into sex chromosomes - of course they can insert into any chromosome. If it happens in a germline cell, then it can be inherited and possibly later fixed in the population. There are 443,000 fixed sites of insertion (according to a recent review) of ERVs or solo-LTRs in the human genome. Solo LTRs are what remains when the two long terminal repeats of a provirus recombine and delete the rest of the ERV. There are only about 120 fixed human-specific ERV/solo-LTR inserts in humans (,) one of which was just shown to provide an enhancer for a gene that is important in the brain ( There are also some inserts that are polymorphic (not fixed in the population.) The youngest polymorphic insertions are several hundred thousand years old, in the same age range as the initial separation of the Neanderthals. Insertions that are present in modern humans and Neanderthals but not chimps could have occurred during hominin evolution before the divergence between us and Neanderthals, but they could also have been transferred in either direction during the later limited mixing of the two. We need some australopithecine DNA. :)

    It isn't known for sure if there are any ERV copies that can still form functional virus particles or copy to new sites - there are no known cases of a new ERV insertion causing disease (in contrast to Alus, L1s and SVAs.) Of course, our common ancestry with Neanderthals, as with chimps, is shown by several million transposable element insertion sites that we share with them.

  2. Come to think of it, maybe the "sons of god" in Genesis 6 were Neanderthals, and Nephilim means "son of a Neanderthal." I think Dave Barry would say that Sons of the Neanderthals would be a great name for a band.

  3. PNG, I stand corrected.

  4. I meant to convey that, while they can insert into any part of the genome, if they are inserted into a sex chromosome, they get passed on. At least that is my (somewhat sketchy) understanding.

  5. "Sex chromosomes" would normally mean X or Y chromosome. While they can of course insert in those, what matters for inheritance is that the infection and insertion gets into a cell that will give rise to a sperm or an egg (that's what the germline is). Any old chromosome will do so long as it's in a germline cell.

  6. This guy knows where DNA comes from!