Viruses have a strong role in Evolution

A story making the rounds reports on a study that suggests that viruses may have had a very strong influence on human evolution.  The Economic Times reports the following:

In a new study, researchers apply big-data analysis to reveal the full extent of viruses' impact on the evolution of humans and other mammals.

The findings suggest an astonishing 30 per cent of all protein adaptations since humans' divergence with chimpanzees have been driven by viruses.

"When you have a pandemic or an epidemic at some point in evolution, the population that is targeted by the virus either adapts, or goes extinct," said David Enard, a postdoctoral fellow at Stanford University.

“We knew that, but what really surprised us is the strength and clarity of the pattern we found,” said Enard.

This is not so surprising. We already know that endogenous retroviruses have had a very large role to play in human evolution and that the pattern of their dispersal provides some of the best evidence of common ancestry.

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
http://dx.doi.org/10.1002/cfg.216

Initial Evolution of Life Non-Darwinian??

Spock: "Well, its life, Jim, but not as we know it." New Scientist has an article on the evolution of early life in which it is posited by several researchers that this progressed in strikingly non-Darwinian fashion. Mark Buchanan writes:

JUST suppose that Darwin's ideas were only a part of the story of evolution. Suppose that a process he never wrote about, and never even imagined, has been controlling the evolution of life throughout most of the Earth's history. It may sound preposterous, but this is exactly what microbiologist Carl Woese and physicist Nigel Goldenfeld, both at the University of Illinois at Urbana-Champaign, believe. Darwin's explanation of evolution, they argue, even in its sophisticated modern form, applies only to a recent phase of life on Earth.

What is not so clear from the initial section of the article is that this applies to the microbiological world almost exclusively. The authors argue that, at an early stage of evolution, horizontal gene transfer was largely responsible for the genetic code being spread among all organisms:

"In some sense," says Woese, "the genetic code is a fossil or perhaps an echo of the origin of life, just as the cosmic microwave background is a sort of echo of the big bang. And its form points to a process very different from today's Darwinian evolution." For the researchers the conclusion is inescapable: the genetic code must have arisen in an earlier evolutionary phase dominated by horizontal gene transfer.

Given the behavior of viruses (H1N1 for example) in which genes are swapped between different viral strains and that of ERVs in which viral RNA is written into the DNA of living organisms, perhaps this is not as surprising as it sounds. The authors are quick to note that the vast majority of evolution is now Darwinian in nature but that we see evidence of how things may have started out. Read the whole thing.

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Bornaviruses and Human Evolution

Wired has an article on a startling discovery in virology—that viruses other than retroviruses can attach themselves to their host DNA. Tina Hesman writes:

Bornaviruses, a type of RNA virus that causes disease in horses and sheep, can insert their genetic material into human DNA and first did so at least 40 million years ago, the study shows. The findings, published January 7 in Nature, provide the first evidence that RNA viruses other than retroviruses (such as HIV) can stably integrate genes into host DNA. The new work may help reveal more about the evolution of RNA viruses as well as their mammalian hosts.

“Our whole notion of ourselves as a species is slightly misconceived,” says Robert Gifford, a paleovirologist at the Aaron Diamond AIDS Research Center, affiliated with Rockefeller University in New York City. Human DNA includes genetic contributions from bacteria and other organisms, and humans have even come to rely on some of these genes for basic functions like fighting infections.

Retroviral segmants have been found to be involved in placental development as well and make up a sizable percentage of our DNA. I have posted about ERVs before, here and here. This just shows how "mutt"-like our DNA is and will certainly rattle some cages.

More on the ERV - Human Interaction

The Irish Times has a story on how Endogenous Retroviruses have become part of the human genome. They write:

If you think that viruses have played no part in human evolution think again. Up to 46 per cent of our DNA was actually provided some time in the past by invading viruses, Ryan says. In comparison, just 1.5 per cent of our genomes arise from the genes we inherit from our primate and animal ancestors.

Ryan argues that Human Endogenous Retroviruses, or Hervs, are a viral integration process integral to the genome of all mammals. It came about by an extensive series of retroviral epidemics that infected our ancestors over tens of millions of years. This means that the virus is something more than just a pest.

ERVs have been used extensively as evidence for evolution, since we share a large number of ERVs with the higher primates and the insertion points are always the same. But as evil as they are, they also play continuous roles in our genome:

Ryan suggests that certain viruses play vital roles in human activity. “There are eight full-length viruses in the human placenta playing different roles, such as a human virus that codes for syncytin 1, which fuses cells together to create a protective layer between mother and baby,” says Ryan. “Proof of the symbiotic inclusion of such viruses as part of our DNA is the fact they have been conserved throughout evolution.”

ID has difficulty explaining ERVs because they cause such harm to any given generation and they are clearly detrimental to health in the short term. Here is a reminder of how important ERVs are to evolutionary studies.

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