In 1883, the first person to suggested the endosymbiotic nature of eukaryotic cells was the German botanist Andreas Schimper, and in 1926 Russian botanist Konstantin Mereschkowsky and American biologist Ivan Wallin, postulated the idea that symbiosis is the main driving force of evolution in their book “Symbiogenesis and the Origin of Species”. In 1981, American Biologist Lynn Margulis published ”Symbiosis in Cell Evolution” and proposed that the complexity of the eukaryotic cell was assembled over a long time period by symbiotic associations between different kinds of prokaryotes and an amitochondriate protozoa host.
The mosaicism of the eukaryotic genome is challenging. Bacteria, Archaea, and Eukarya share common ancestry but they have very distinctive features. Eukarya are similar to Archaea for some systems like the replication, transcription,and translation apparatuses and to Bacteria for others like metabolism and membrane chemistry (Rochette, 2014), so the different hypotheses are associated with different phylogenomic prediction.
All these hypotheses can be classified into three main classes: hypotheses involving endosymbiosis, which argue that components of the eukaryotic cell arose by engulfment of prokaryotic organisms, hypotheses for autogenous (‘self-birth’) pathways for eukaryotic cell components, and a “ternary” hypotheses suggest that the organism that engulfed the ancestor of mitochondria was itself a chimera of two prokaryotes.
The “hydrogen hypothesis” (Martin and Müller 1998) involves endosymbiosis and implies that ancestral eukaryotic genes are derived from the alphaproteobacterial ancestor of mitochondria and from the methanogenic euryarchaeon that hosted it. The Neomura hypothesis (Cavalier-Smith 2010b) is among the autogenous hypotheses and assumes that Eukarya are the sister group of all Archaea. Finally, a popular ternary hypothesis is the “endokaryotic” hypotheses in which the nucleus derives from an archaeon while the cytoplasm derives from a bacterium (Lake and Rivera 1994).
A recent analysis establishes that there is no phylogenomic support in favor of ternary hypotheses and support that Eukarya branch close to Archaea or basally within them and that some early-mitochondria hypotheses are compatible with current genomic data under certain assumptions (Rochette, 2014).
It’s possible that the last eukaryotic common ancestor (LECA) had a modern nucleus (Mans et al. 2004), a cytoskeleton based on microtubules and actin (Yutin et al. 2009; Hammesfahr and Kollmar 2012), a complete vesicle and membrane-trafficking system allowing for endocytosis (Dacks et al. 2009; Yutin et al. 2009; De Craene et al. 2012), mitochondria (which are derived alphaproteobacteria; Embley and Martin 2006; Gabaldón and Huynen 2007), a modern cell cycle (Eme et al. 2011), and a sexual cycle (Ramesh et al. 2005)
Nicolas C. Rochette, Céline Brochier-Armanet, and Manolo Gouy, Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes, Mol. Biol. Evol. 2014 : mst272
Yonas I. Tekle, Laura Wegener Parfrey, Laura A. Katz, Molecular Data Are Transforming Hypotheses on the Origin and Diversification of Eukaryotes, BioScience(2009),59(6):471 http://dx.doi.org/10.1525/bio.2009.59.6.5