From an article in the NYTimes Magazine about Carl Woese:
What made Woese the foremost challenger and modifier of Darwinian orthodoxy — as Einstein was to Newtonian orthodoxy — is that his work led to recognition that the tree’s cardinal premise is wrong. Branches do sometimes fuse. Limbs do sometimes converge. The scientific term for this phenomenon is horizontal gene transfer (H.G.T.). DNA itself can indeed move sideways, between limbs, across barriers, from one kind of creature into another.Those were just two of three big surprises that flowed from the work and the influence of Woese — the existence of the archaea (that third kingdom of life) and the prevalence of H.G.T. (sideways heredity). The third big surprise is a revelation, or anyway a strong likelihood, about our own deepest ancestry. We ourselves — we humans — probably come from creatures that, as recently as 41 years ago, were not known to exist. How so? Because the latest news on archaea is that all animals, all plants, all fungi and all other complex creatures composed of cells bearing DNA within nuclei — that list includes us — may have descended from these odd, ancient microbes. Our limb, eukarya, seems to branch off the limb labeled archaea. The cells that compose our human bodies are now known to resemble, in telling ways, the cells of one group of archaea known as the Lokiarcheota, recently discovered in marine ooze, almost 11,000-feet deep between Norway and Greenland near an ocean-bottom hydrothermal vent. It’s a little like learning, with a jolt, that your great-great-great-grandfather came not from Lithuania but from Mars.We are not precisely who we thought we were. We are composite creatures, and our ancestry seems to arise from a dark zone of the living world, a group of creatures about which science, until recent decades, was ignorant. Evolution is trickier, far more complicated, than we realized. The tree of life is more tangled. Genes don’t just move vertically. They can also pass laterally across species boundaries, across wider gaps, even between different kingdoms of life, and some have come sideways into our own lineage — the primate lineage — from unsuspected, nonprimate sources. It’s the genetic equivalent of a blood transfusion or (to use a different metaphor preferred by some scientists) an infection that transforms identity. They called it “infective heredity.”
Lateral transfer of useful traits must have been the norm billions of years ago, and still the norm for many unicellular organisms, including eukaryotic ones. It has been demonstrated that viruses which affect archaea don't actually usually explode them in the process, as eubacterial phages normally do. Instead they create communal networks, with the archaea forming tubules which convey genes to each other mediated by the viral capsids in some manner. In this way any new immigrant into a territory occupied by established archaea can be given traits which will help them survive. No known archaeal species causes acute disease so far as is known. Instead they prefer the hard-scrabble life, as opposed to eubacterial which are opportunistic invaders.
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