Reconstructing early events in eukaryotic evolution

Resolving the order of events that occurred during the transition from prok aryotic to eukaryotic cells remains one of the greatest problems in cell ev olution. One view, the Archezoa hypothesis, proposes that the endosymbiotic origin of mitochondria occurred relatively late in eukaryotic evolution an d that several mitochondrion-lacking protist groups diverged before the est ablishment of the organelle. Phylogenies based on small subunit ribosomal R NA and several protein-coding genes supported this proposal, placing amitoc hondriate protists such as diplomonads, parabasalids, and Microsporidia as the earliest diverging eukaryotic lineages. However, trees of other molecul es, such as tubulins, heat shock protein 70, TATA box-binding protein, and the largest subunit of RNA polymerase II, indicate that Microsporidia are n ot deeply branching eukaryotes but instead are close relatives of the Fungi . Furthermore, recent discoveries of mitochondrion-derived genes in the nuc lear genomes of entamoebae, Microsporidia, parabasalids, and diplomonads su ggest that these organisms likely descend from mitochondrion-bearing ancest ors. Although several protist lineages formally remain as candidates for Ar chezoa, most evidence suggests that the mitochondrial endosymbiosis took pl ace prior to the divergence of all extant eukaryotes. In addition, discover ies of proteobacterial-like nuclear genes coding for cytoplasmic proteins i ndicate that the mitochondrial symbiont may have contributed more to the eu karyotic lineage than previously thought. As genome sequence data from para basalids and diplomonads accumulate, it is becoming clear that the last com mon ancestor of these protist taxa and other extant eukaryotic groups alrea dy possessed many of the complex features found in most eukaryotes but lack ing in prokaryotes. However, our confidence in the deeply branching positio n of diplomonads and parabasalids among eukaryotes is weakened by conflicti ng phylogenies and potential sources of artifact. Our current picture of ea rly eukaryotic evolution is in a state of flux.