Below the fold you will find some excerpts from Eugene Koonin’s article, The origin and early evolution of eukaryotes in the light of phylogenomics.
There is a sharp divide in the organizational complexity of the cell between eukaryotes, which have complex intracellular compartmentalization, and even the most sophisticated prokaryotes (archaea and bacteria), which do not. A typical eukaryotic cell is about 1,000-fold bigger by volume than a typical bacterium or archaeon, and functions under different physical principles: free diffusion has little role in eukaryotic cells, but is crucial in prokaryotes. The compartmentalization of eukaryotic cells is supported by an elaborate endomembrane system and by the actin-tubulin-based cytoskeleton. There are no direct counterparts of these organelles in archaea or bacteria.
Phylogenomic reconstructions show that the characteristic eukaryotic complexity arose almost ‘ready made’, without any intermediate grades seen between the prokaryotic and eukaryotic levels of organization. Explaining this apparent leap in complexity at the origin of eukaryotes is one of the principal challenges of evolutionary biology.
For many years, evolutionary biologists tended to favor the so called crown group phylogeny. The ‘crown’ of this evolutionary tree included animals (Metazoa) and plants (Viridiplantae), fungi and various assortments of protists, depending on the methods used for tree construction. The rest of the protists, such as microsporidia, diplomonads and parabasalia, were considered ‘early branching eukaryotes’; for some of them, this conclusion was reached because they appeared to lack mitochondria and were therefore thought to have evolved before the mitochondrial symbiosis. The scenario resulting from the crown group phylogeny was called the archezoan scenario: the archaezoan was defined as a hypothetical ancestral form that lacked mitochondria but possessed the other signature features of the eukaryotic cell.
There are therefore no grounds to consider any group of eukaryotes primitive, a presymbiotic archezoan. Rather, taking into account the small genomes and high rate of evolution characteristic of most of the protist groups thought to be early branching, and their parasitic lifestyle, it is becoming increasingly clear that most or perhaps all of them evolved from more complex ancestral forms by reductive evolution. Reductive evolution refers to the evolutionary modality typical of parasites: they tend to lose genes, organelles and functions when the respective functionalities are taken over by the host. So the archezoan (crown group) phylogeny seems to have been disproved, and deep phylogeny and the theories of the origin of eukaryotes effectively had to start from scratch.
The results of all these reconstructions consistently point to a complex LECA, in terms of both the sheer number of ancestral genes and, perhaps even more importantly, the ancestral presence of the signature functional systems of the eukaryotic cell (see below).
Given that the current estimate for the gene complement of LECA must be conservative, the genome of LECA is likely to have been as complex as those of typical extant free-living unicellular eukaryotes.
This conclusion is supported by reconstructions from comparative genomics of the ancestral composition of the key functional systems of the LECA, such as the nuclear pore, the spliceosome, the RNA interference machinery, the proteasome and the ubiquitin signaling system, and the endomembrane apparatus. The outcomes of these reconstructions are all straightforward and consistent, even when different topologies of the phylogenetic tree of eukaryotes were used as the scaffold for the reconstruction: LECA already possessed all these structures in its fully functional state, possibly as complex as the counterparts in modern eukaryotes.
So as you can see, I was correct in noting that LECA was about as complex as a modern day unicellular eukaryote. So it’s time to begin considering how this cell was front-loaded to emerge.