I think that the reference on the "Tree of Life - Eukaryote" page that states amitochondriate acquired then lost mitochondria is innacurate. I highly doubt that this sequence of evolutionary events (lost their mitochondria - reduction) ever occurred and it appears that this subject is currently hotly debated. The very prestiguous Woods Hole Oceanographic Institution states that:
"It is now widely accepted that the eukaryotes we call protists are far more diverse in cellular organization than the non-protist eukaryote groups—namely animals, plants and fungi. A variety of heterotrophic protists lack classical mitochondria, inhabiting low- oxygen environments such as the guts and tissues of animals, marine or freshwater sediments, and the lower reaches of stratified water bodies. Over the last two decades these 'amitochondriate' organisms have been of great interest to evolutionary biologists, as some may have diverged before the acquisition of the mitochondrion and consequently represent very early stages in the evolution of the eukaryotic cell. Some amitochondriate groups—particularly the largely parasitic trichomonads, diplomonads, and microsporidia— have indeed tended to form the most basal branches in evolutionary trees of eukaryotes, based on molecular sequence comparisons. However the validity of these deep branches has, of late, been vigorously challenged, as has the contention that these organisms lack any trace of having had mitochondria. To date, almost all of the research into amitchondriate protists has focused on those groups with parasitic members. However surveys of sediments and anoxic water bodies reveal a considerable and drastically understudied diversity of free-living, low-oxygen protists, frequently of unclear affinities. In several instances, electron-microscopical studies indicate the absence of classical mitochondria. Detailed morphological data in concert with molecular phylogenies, covering both free-living and parasitic taxa, are leading us towards a more authoritative state regarding the affinities of the amitochondriate protists and whether any groups remain candidates for being primitively amitochondriate relicts of early eukaryotic evolution.”
From: “The evolutionary importance and affinities of 'amitochondriate' protists,”by Virginia Edgcomb, Andrew Roger, and Alastair Simpson. Woods Hole Oceanographic Institution, University of Sydney, Australia, November 4, 1998.
http://www.mbari.org/seminars/1998/nov4_simpson.html
"Phylogenetic evidence is presented that primitively amitochondriate eukaryotes containing the nucleus, cytoskeleton, and endomembrane system may have never existed. Instead, the primary host for the mitochondrial progenitor may have been a chimeric prokaryote, created by fusion between an archaebacterium and a eubacterium, in which eubacterial energy metabolism (glycolysis and fermentation) was retained. A Rickettsia-like intracellular symbiont, suggested to be the last common ancestor of the family Rickettsiaceae and mitochondria, may have penetrated such a host (pro-eukaryote), surrounded by a single membrane, due to tightly membrane-associated phospholipase activity, as do present-day rickettsiae. The relatively rapid evolutionary conversion of the invader into an organelle may have occurred in a safe milieu via numerous, often dramatic, changes involving both partners, which resulted in successful coupling of the host glycolysis and the symbiont respiration. Establishment of a potent energy-generating organelle made it possible, through rapid dramatic changes, to develop genuine eukaryotic elements. Such sequential, or converging, global events could fill the gap between prokaryotes and eukaryotes known as major evolutionary discontinuity."
From:
http://content.febsjournal.org/cgi/content/full/270/8/1599
"“We present a testable model for the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. A chimeric cell evolved via symbiogenesis by syntrophic merger between an archaebacterium and a eubacterium. The archaebacterium, a thermoacidophil resembling extant Thermoplasma, generated hydrogen sulfide to protect the eubacterium, a heterotrophic swimmer comparable to Spirochaeta or Hollandina that oxidized sulfide to sulfur. Selection pressure for speed swimming and oxygen avoidance led to an ancient analogue of the extant cosmopolitan bacterial consortium "Thiodendron latens." By eubacterial-archaebacterial genetic integration, the chimera, an amitochondriate heterotroph, evolved. This "earliest branching protist" that formed by permanent DNA recombination generated the nucleus as a component of the karyomastigont, an intracellular complex that assured genetic continuity of the former symbionts. The karyomastigont organellar system, common in extant amitochondriate protists as well as in presumed mitochondriate ancestors, minimally consists of a single nucleus, a single kinetosome and their protein connector. As predecessor of standard mitosis, the karyomastigont preceded free (unattached) nuclei. The nucleus evolved in karyomastigont ancestors by detachment at least five times (archamoebae, calonymphids, chlorophyte green algae, ciliates, foraminifera). This specific model of syntrophic chimeric fusion can be proved by sequence comparison of functional domains of motility proteins isolated from candidate taxa. Here we outline the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. The common ancestor of all eukaryotes by genome fusion of two or more different prokaryotes became "chimeras" via symbiogenesis. Long term physical association between metabolically dependent consortia bacteria led, by genetic fusion, to this chimera. The chimera originated when an archaebacterium (a thermoacidophil) and a motile eubacterium emerged under selective pressure: oxygen threat and scarcity both of carbon compounds and electron acceptors. The nucleus evolved in the chimera. The earliest descendant of this momentous merger, if alive today, would be recognized as an amitochondriate protist.
Study of conserved protein sequences [a far larger data set than that used by Woese et al.] led Gupta to conclude "all eukaryotic cells, including amitochondriate and aplastidic cells received major genetic contributions to the nuclear genome from both an archaebacterium (very probably of the eocyte, i.e., thermoacidophil group and a Gram-negative bacterium - the ancestral eukaryotic cell never directly descended from archaebacteria but instead was a chimera formed by fusion and integration of the genomes of an archaebacerium and a Gram-negative bacterium.” The eubacterium ancestor has yet to be identified. The archaebacterial sequences, we posit, comes from a Thermoplasma acidophilum-like thermoacidophilic (eocyte) prokaryote. This archaebacterial ancestor lived in warm, acidic, and sporadically sulfurous waters, where it used either elemental sulfur (generating H2S) or less than 5% oxygen (generating H2O) as terminal electron acceptor. As does its extant descendant, the ancient archaebacterium survived acid-hydrolysis environmental conditions by nucleosome-style histone-like protein coating of its DNA and actin-like stress-protein synthesis. The wall-less archaebacterium was remarkably pleiomorphic; it tended into tight physical association with globules of elemental sulfur by use of its rudimentary cytoskeletal system. The second member of the consortium, an obligate anaerobe, required for growth the highly reduced conditions provided by sulfur and sulfate reduction to hydrogen sulfide. Degradation of carbohydrate (e.g., starch, sugars such as cellobiose) and oxidation of the sulfide to elemental sulfur by the eubacterium generated carbon-rich fermentation products and electron acceptors for the archaebacterium. When swimming eubacteria attached to the archaebacterium, the likelihood that the consortium efficiently reached its carbon sources was enhanced. This hypothetical consortium, before the integration to form a chimera, differs little from the widespread and geochemically important "Thiodendron.” The "Thiodendron" stage refers to an extant bacterial consortium that models our idea of an archaebacteria-eubacteria sulfur syntrophic motility symbiosis. The partners in our view merged to become the chimeric predecessor to archaeprotists. The membrane-bounded nucleus, by hypothesis, is the morphological manifestation of the chimera genetic system that evolved from a Thiodendron-type consortium. Each phenomenon we suggest, from free-living bacteria to integrated association, enjoys extant natural analogues.”
Karyomastigonts Preceded Nuclei: The term "karyomastigont" refer to a organellar system observed in certain protists: the mastigont ("cell whip," eukaryotic flagellum, or undulipodium, the [9 (2) + (2)] microtubular axoneme underlain by its [9 (3) + 0)] kinetosome) attached by a "nuclear connector" or "rhizoplast" to a nucleus….The karyomastigont, an ancestral feature of eukaryotes, is present in "early branching protists.” Archaeprotists, are heterotrophic unicells that inhabit anoxic environments. All lack mitochondria. At least 28 families are placed in the phylum Archaeprotista, including archaemoebae (Pelomyxa and Mastigamoeba), metamonads (Retortamonas), diplomonads (Giardia), oxymonads (Pyrsonympha), and the two orders of Parabasalia: Trichomonadida [Devescovina, Mixotricha, Monocercomonas, Trichomonas, and calonymphids (Coronympha, Snyderella)] and Hypermastigida (Lophomonas, Staurojoenina, and Trichonympha). These cells either bear karyomastigonts or derive by differential organelle reproduction (simple morphological steps) from those that do. When, during evolution of these protists, nuclei were severed from their karyomastigonts, akaryomastigonts were generated. Nuclei, unattached, at least temporarily, to undulipodia were freed to proliferate and occupy central positions in cells. Undulipodia, also freed to proliferate, generated larger, faster-swimming cells in the same evolutionary step.
The karyomastigont is the conspicuous central cytoskeleton in basal members of virtually all archaeprotist lineages [three classes: Archamoeba, Metamonads, and Parabasalia. In trichomonads, the karyomastigont, which includes a parabasal body (Golgi complex), coordinates the placement of hydrogenosomes (membrane-bounded bacterial-sized cell inclusions that generate hydrogen). The karyomastigont reproduces as a unit structure. Typically, four attached kinetosomes with rolled sheets of microtubules (the axostyle and its extension the pelta) reproduce as their morphological relationships are retained. Kinetosomes reproduce first, the nucleus divides, and the two groups of kinetosomes separate at the poles of a thin microtubule spindle called the paradesmose. Kinetosomes and associated structures are partitioned to one of the two new karyomastigonts. The other produces components it lacks such as the Golgi complex and axostyle. Nuclear proteobacterial genes were interpreted to have originated from lost or degenerate mitochondria in at least two archaeprotist species Giardia lamblia; Trichomonas vaginalis and in a microsporidian. Hydrogenosomes, at least some types, share common origin with mitochondria. In the hydrogen hypothesis, hydrogenosomes are claimed to be the source of eubacterial genes in amitochondriates. That mitochondria were never acquired in the ancestors we consider more likely than that they were lost in every species of these anaerobic protists. Eubacterial genes in the nucleus that are not from the original spirochete probably were acquired in amitochondriate protists from proteobacterial symbionts other than those of the mitochondrial lineage. Gram-negative bacteria, some of which may be related to ancestors of hydrogenosomes, are rampant as epibionts, endobionts, and even endonuclear symbionts, for example, in Caduceia versatilis.
Karyomastigonts freed (detached from) nuclei independently in many lineages both before and after the acquisition of mitochondria. Calonymphid ancestors of Snyderella released free nuclei before the mitochondrial symbiosis, and Chlamydomonas-like ancestors of other chlorophytes such as Acetabularia released the nuclei after the lineage was fully aerobic. In trophic forms of protists that lack mastigote stages, the karyomastigont is generally absent. An exception is Histomonas, an amoeboid trichomonad cell that lacks an axoneme but bears enough of the remnant karyomastigont structure to permit its classification with parabasalids rather than with rhizopod amoebae. This organellar system appears in the zoospores, motile trophic forms, or sperm of many organisms, suggesting the relative ease of karyomastigont development. The karyomastigont, apparently in some cells, is easily lost, suppressed, and regained. In many taxa of multinucleate or multicellular protists (foraminifera, green algae) and even in plants, the karyomastigont persists only in the zoospores or gametes.
From: “The chimeric eukaryote: Origin of the nucleus from the karyomastigont in amitochondriate protists,” by Lynn Margulis, Michael F. Dolan , and Ricardo Guerrero. Department of Geosciences, Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA 01003; and Department of Microbiology, and Special Research Center Complex Systems (Microbiology Group), University of Barcelona, 08028 Barcelona, Spain. Proceedings of the National Academy of Science, June 20, 2000, vol. 97, no. 13, 6954-6959.
http://www.pnas.org/cgi/content/full/97/13/6954