Carl Zimmer has an article in Science with a provocative title: On the Origin of Eukaryotes. This is well-timed since it appears just when I've returned from a meeting on this very topic. [Go here if you can't see the article on the Science website.]
One of the things we learned at the meeting is that the Woose tree of life is almost certainly an over-simplification at best and wrong at worst. It is no longer possible to claim that eukaryotes have a simple vertical descent relationship with any archaebacterium (or any bacterium, for that matter).
Instead, the early history of life is characterized by a web or a net involving multiple gene exchanges between all primitive species. After some time, the major divisions of life emerged from this "soup" and became separate lineages with an semi-independent history. This view dates back ten years or so and it's illustrated by a figure that Ford Doolittle published in the February 2000 issue of Scientific American. I've used this figure several times. Here it is again so you can see how it relates to Carl's article.
In the case of eukaryotes, the history is complicated by an endosymbiotic event where a proteobacterium was engulfed and evolved into mitochondria. That explains many of the eukaryotic genes with a clear bacterial origin. Those genes, can be reliably traced to a particular lineage of proteobacteria. What this shows is that by the time of the endosymbiosis most of the main lineages of prokaryotes had emerged from the soup and become fairly well-defined.
This doesn't explain the origins of the host cell. That cell presumably had some of the features of modern eukaryotes. Where did it come from? Was it part of an ancient lineage that formed during the gene exchange period of evolution suggesting that some eukaryotic features are ancient? Was it formed by a fusion between a primitive bacterial cell and a primitive archaebacterium? (Or, did archaebacterial arise from a fusion of a primitive eukaryotic cell and a primitive bacterium?)
Some people even believe that the ancient host progenitor of eukaryotes arose fairly late in the game and was only related to archaebacteria, either through a recent common ancestor or from an archaebaterial species within the archaebacterial clade. This is not consistent with the tree shown above but that's OK.
These two hypotheses on the archaebacterial origin of the host cell are the ones that Carl Zimmer highlights in his article: the Three Domain Tree and the Eocyte Tree.
I don't think either of these trees comes close to representing the true history of eukaryotic cells. I don't think it's even possible to represent that history by a tree. Zimmer mentions this possibility in passing but I don't think he does justice to the controversy over the tree of life.
The controversy is not just about which branch of the archaebacterial tree the eukaryotes came from. It's about whether they came from the archaebacerial lineage at all or whether it's even appropiate to be talking about lineages and trees at this stage of the history of life.
Shifting gears slightly, I'd like to bring up another subject. Here's what Carl writes near the end of his article.
Whatever the exact series of events turns out to be, eukaryotes triggered a biological revolution. Prokaryotes can generate energy only by pumping charged atoms across their membranes. That constraint helps limit their size. As prokaryotes grow in size, their volume increases much faster than their surface area. They end up with too little energy to power their cells. Eukaryotes, on the other hand, can pack hundreds of energy-generating mitochondria into a single cell. And so they could get big, evolving into an entirely new ecological niche.This is a widely believed explanation for the adaptive value of mitochondria and internal membranes. But many species of bacteria have internal membranes and, in the case of photosynthetic species, those internal membranes are packed full of energy-producing proteins.
Why couldn't bacteria have evolved internal membranes in order to get around the size limitation if it was that big of a deal? I don't see anything special about mitochondrial that couldn't have just as easily been handled by infolding of the inner membrane.