EVEs Are Bone of Our Bones and Flesh of Our Flesh

When we think of the human genome, we generally have in mind the collection of genes that make us human. What most people don't realize is that a significant portion of their genome (at least 8%) actually comes from viruses, and these parts are called endogenous viral elements (EVEs). EVEs, and other genetic elements like them [1] (which all together make up around half (!) of the human genome), can help establish genetic relationships because they are like molecular fossils. In fact, the term 'paleovirology' has been coined to describe their study. A paper from 2010, aside from being interesting in its own right, has a great illustration that helps to convey this concept [2].

The left side is not very important for our purposes, but basically it shows various types of viruses and the pathways that can land their genetic material into a host genome. The box in the middle-bottom represents double-stranded DNA where the viral sequence has integrated into a host genome.

The right side of the figure represents what happens after that. When the virus integrates into a host genome, it doesn't instantly become part of the genome of the whole population. At first, only one individual in the population has the virus in its genome in a particular spot. However, when that individual has offspring it can pass on the viral element as if it was just another gene. Simply by chance (or perhaps due to selection) the new genetic variant containing the EVE can become more common in the population. (That exact scenario is currently happening in koalas.) Not every individual has it, just like not every human has color blindness, type A blood, blue eyes, or blond hair. Eventually, though, the variant may go extinct, or it may become fixed, which means that every member of the population has it. From that point on, all descendants will have the viral element in the same spot of the genome (unless it is secondarily deleted, which generally leaves a genetic scar).

So looking again at the right side, we can see a rabbit-like species that eventually gave rise to three daughter species. The population giving rise to species C branched off before the EVE invaded the genome, so it is clean (in that specific genetic location). When the EVE first invaded the host genome, it was passed along to descendants until it became fixed--present in all members of the species. So when species A and B branched off, both were marked by the EVE. If you knew nothing about how species A, B, and C were related to each other beforehand, the presence of the EVE in identical spots in the genome would tip you off. After all, the genome is a large place and the likelihood that two EVEs would independently end up in the exact same location are pretty small. This also works for populations within a species as well.

With improvements in technology over the last 10-15 years, scientists have been sequencing the genomes of all kinds of animals to see what is in them. It turns out that EVEs are all over the place. Scientists looking for the presence of one type of human EVE in other primates got results like what is shown below. In case it isn't obvious, the entry of each virus group is mapped onto the primate family tree, and it communicates much of the same information as the figure above, with humans and chimpanzees most closely related because they share the most EVEs [source].

Probably most of the EVEs are just genomic junk hanging around. Sometimes they can cause problems by disrupting a needed gene or its regulation (see: cancer). However, occasionally they can be helpful. For example, in mammalian evolution retroviruses have repeatedly, and independently, donated a gene that is used in placenta formation.

Their critical role in fetal development, their ability to reveal common ancestry, and the fact that they are an integral part of us--all of this makes EVE a fitting name.


Notes:
1. Things like transposons, LINEs, and SINEs (especially Alu elements).
2. Katzourakis A, Gifford RJ (2010) Endogenous Viral Elements in Animal Genomes. PLoS Genet 6(11): e1001191.

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