Endogenous retroviruses are weird, but how they got into our genomes and what they mean, evolutionarily, isnt too hard to understand (unless youre an IDiot). A retrovirus has to not only accidentally infect a germ-line cell (sperm/egg), that particular egg/sperm has to successfully mediate fertilization, and where the retrovirus randomly inserts has to not cause trouble for the resulting offspring (cell cycle arrest, cancer, etc), for an endogenous retrovirus to form.
But this scenareo, while highly improbable, has happened lots and lots of times (a large portion of your genome is retroviral), and it logically makes sense. The virus integrating into the host genome is part of a retroviruses life-cycle.
What we hadnt really thought was a possibility before, is a non-retrovirus becoming endogenous. Yes, there are some DNA viruses that associate closely with the host cell DNA without actually integrating, and integration can happen. HPV is normally a DNA virus that associates with our DNA in the form of an episome (snuggles up next to your DNA). HPV causes cancer when it snuggles up a bit too close, and is accidentally integrated. But HPV likes epithelial cells. Cant think of a way it would get into germ line cells (not to say it couldnt).
It just doesnt seem all that likely that a non-retrovirus could get integrated into our genomes and passed on vertically.
GUESS WHAT WE JUST FOOOOOOOOUND!!!!
Quick summary: Borna disease virus, an RNA virus that replicates in the host cell nucleus, stole the reverse transcriptase activity of LINE-1 elements to insert into our ancestors genome ~40 million years ago.
HAHAHAHAHA! *giddy clapping*
They found four of these guys in humans. One on Chromosome 10 (EBLN-1), one on Chromosome 3 (EBLN-2), one on Chromosome 9 (EBLN-3), and one on Chromosome 17 (EBLN-4).
Miracle of miracles, they found four BDV insertions in chimpanzees! One on Chromosome 10 (EBLN-1), one on Chromosome 3 (EBLN-2), one on Chromosome 9 (EBLN-3), and one on Chromosome 17 (EBLN-4).
Wonder of wonders, they found four BDV insertions in orangutans! One on Chromosome 10 (EBLN-1), one on Chromosome 3 (EBLN-2), one on Chromosome 9 (EBLN-3), and one on Chromosome 17 (EBLN-4).
Oh, no! Creationists are just going to have an aneurysm over this!!
A negative sense ssRNA virus had to ‘miraculously’ perform this insanely improbable event dozens of independent times, all of which just so happened to perfectly insert themselves in the same location of the genomes of several different species, and the ones that inserted in the same locations just happen to have the exact same sequences, therefore the Garden of Eden and Jesus Christ died on The Cross for Our Sins.
Or, common descent.
For Petes sake, they found these insertions in everything from squirrels to lemurs to elephants. These insertions go back 40 million years.
Phylogenetic analyses demonstrate that the oldest primate EBLN observed must have appeared in an ancestor of primates after the separation between Strepsirrhini and Haplorrhini, implying that bornaviruses have coexisted with primates for an evolutionary history stretching at least 40 million years. Thus, bornaviruses are the first non-retroviral RNA virus whose existence in prehistoric times has been confirmed.
Linkage: YOOOOOOOOOONG!!! Beat me to it again!!