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I'm interested in horizontal gene transfer in bacteria, viruses, and organisms such as Bdelloid Rotifers. I've just read in Carl Zimmer's 'A Planet of Viruses' the following passage:

As a host cell manufactures new viruses, it sometimes accidentally adds some of its own genes to them. The new viruses carry the genes of their hosts as they swim through the ocean, and they insert them, along with their own, into the genomes of their new hosts. By one estimate, viruses transfer a trillion trillion genes between host genomes in the ocean every year.

It's interesting to consider the scale of DNA-swapping that has occurred given the frequency by which it happens and the evolutionary timescale.

Are there any examples of genes in the human genome that we know were deposited by viruses that would have given an evolving human a physical/mental advantage? Where did they come from? What benefit did they provide?

I'm interested in genetic additions from non-human-ancestor species, rather than the transfer of genes that occurred as mutations from other humans.

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The number of candidates that help humans cognitively is hotter in comparing humans to other primates. Though it happens trillions of times a year, its much more common with bacteria and fungi than animals, so the catalog of human vertical transfers is small. –  shigeta May 22 '12 at 14:11
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The processes that control the germline of metazoans (multicellular animals) are highly regulated compared to single cell bacteria and eukaryotes as well as plants.

At this point there are no clear stories of gene transfer into a complex animal, though there are some for plants:

"animals and fungi seem to be largely unaffected, with a few exceptions, while lateral gene transfer frequently occurs in protists with phagotrophic lifestyles, possibly with rates comparable to prokaryotic organisms."

Bacteria fungi and plants are more permissive and more susceptible to gene transfer and it probably is more important to their evolutionary path.

Its been estimated that as much as eight percent of the human genome has been affected by viral integration. But viral genomes are highly selected against carrying non essential material - other genes rarely come along for the ride it seems. What is probably more influential is that viral insertions could participate in rewiring the regulatory network of animal cells, not adding genes, but modifying the conditions under which they are active.

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Human endogenous retroviruses (HERVs) have been an interesting (and expanding) topic of research in evolutionary biology and medicine. A retrovirus has an RNA genome in the virus particle, and integrates with the host cell's DNA upon infection to hijack the transcription/translation machinery and produce copies of itself. For this reason, it is not possible to "cure" a cell of a retroviral infection; instead all of the infected cells must be destroyed or commit suicide through apoptosis, also known as programmed cell death. Common examples of retroviruses include HIV (causative agent of AIDS), HTLV (human T-cell leukemia virus), and the Hepatitis B virus.

Viral infections are most common in somatic cells, where any change in the DNA sequence is not passed along to the next generation. However, any retroviral infection in germ cells (eggs, sperm, and the progenitor cells that make them) could be passed on to the next generation, and over time spread throughout a population. Some HERV fragments are apparently completely inactive (at least as far as we are able to tell currently), and are a possible source for some of the so-called "junk" or non-coding non-regulatory DNA that makes up a significant part of our genome - one estimate claims that 8% of our genetic material is of retroviral origin. Other HERVs have been implicated in various pathological conditions, including multiple sclerosis.

I'm not sure that any human genes have been found that were picked up by a virus, stayed with it for a time (and potentially mutated), then was reinserted back into the human genome, if that's what you're asking. There are certainly many cases of genes and gene fragments (coding regions, promotors, enhancers, etc.) being moved around as a result of viral integration/splicing. http://en.wikipedia.org/wiki/Endogenous_retrovirus#Genome_Evolution is a large, rather well-written section with numerous links to the primary literature showing how our genome has been altered over the years by HERVs.

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