Two quotes from "Why Evolution Is True" by Jerry Coyne about ERVs and Natural Selection. Everyone should own this book.

"We also harbor dead genes that came from other species, namely viruses. Some, called 'endogenous retroviruses' (ERVs), can make copies of their genome and insert them into the DNA of species they infect. (HIV is a retrovirus.) If the viruses infect the cells that make sperm and eggs, they can be passed on to future generations. The human genome contains thousands of such viruses, nearly all of them rendered harmless by mutations. They are the remnants of ancient infections. But some of these remnants sit in exactly the same location on the chromosomes of humans and chimpanzees. These were surely viruses that infected our common ancestor and were passed on to both descendants. Since there is almost no chance of viruses inserting themselves independently at exactly the same spot in two species, this points strongly to common ancestry." 
-- Jerry Coyne, University of Chicago biologist

"Chance alone cannot explain the marvelous fit between individuals and their environment. And it doesn't. True, the raw materials for evolution--the variations between individuals--are indeed produced by chance mutations. These mutations occur willy-nilly, regardless of whether they are good or bad for the individual. But it is the filtering of that variation by natural selection that produces adaptations, and natural selection is manifestly not random. It is a powerful molding force, accumulating genes that have a greater chance of being passed on to others, and in so doing making individuals even better able to cope with their environment. It is, then, the unique combination of mutation and selection--chance and lawfulness--that tells us how organisms become adapted."
-- Jerry Coyne