% Before the discovery of the Lokiarchaeota, symbiogenetic models proposing a direct endosymbiosis of the mitochondrial ancestor within one archaeon had gained popularity [24,26,50] (Figure 2B). They imply a triggering effect of eukaryogenesis for mitochondrial endosymbiosis. However, the fact that the newly discovered archaea possess several homologs to membrane remodeling and cytoskeleton-related eukaryotic proteins has opened the possibility for a proto-eukaryotic lineage endowed with phagocytosis to evolve from within archaea, which seems to be the currently favored hypothesis [9,10]. In this case, mitochondria would incorporate later (Figure 2A). The difference between the two situations is far from irrelevant because the driving forces underlying eukaryogenesis and the predictions of the two models are very different. In the former case, mitochondrial symbiosis would be the cause of eukaryogenesis; in the latter, the consequence. In the former case, amitochondriate eukaryotes would have never existed; in the latter, the possibility that archaea-derived amitochondriate proto-eukaryotes exist is real. In models invoking a bacterial host for the archaeon (Figure 2C), the mitochondrial symbiosis is a second, independent event; mitochondria would therefore come later, but, as in the case of autogenous models, the time between the start of eukaryogenesis and the mitochondrial stabilization is difficult to determine. The strong alphaproteobacterial signal in eukaryotic genomes [33,51] would tend to suggest a relatively late mitochondrial incorporation event.
% The origin of the nucleus remains mysterious. While it was present in LECA, and evolved as part of the endomembrane system involving many protein components of archaeal and bacterial ancestry [52], most models do not provide any (or any convincing) selective force for the evolution of this defining character. Two driving forces have been evoked by autogenous models. Cavalier-Smith proposed that the nucleus evolved to prevent DNA damage caused by cytoskeletal pulling [53], an idea adopted by others [26]. However, eukaryotic chromosomes are able to overcome mechanical stresses during mitosis, when the nuclear envelope disintegrates in many protists, and even in species where the chromosomes are permanently uncondensed. In addition, eukaryotes (as do prokaryotes) have efficient DNA repair systems to cope with single- and double-strand breaks occurring during the mechanically-challenging DNA-dependent processes (replication, transcription, recombination), and many eukaryotes have genomes with several dozens of chromosomes, which reduces the individual size of DNA molecules, diminishing breakage probability. Jékely proposed that the nucleus appeared to safeguard ribosome biogenesis, preventing the formation of chimeric ribosomes during mitochondrial endosymbiosis [54]. However, the formation of chimeric ribosomes could have been more simply achieved by retaining the ribosomal protein genes in the mitochondrial genome, as is the case with the ribosomal RNA and other protein genes for which cytosolic synthesis and transport back to the mitochondrion poses a problem.
% In the framework of the hydrogen hypothesis, the nucleus was proposed to appear de novo through the synthesis of bacterial-like lipids that would form vesicles in the archaeal cytoplasm (Figure 2B). The nuclear compartment would have evolved to decouple transcription and translation, thus preventing the synthesis of aberrant proteins as introns appeared [55]. However, this explanation is at odds with the fact that a single intron in an essential gene is deleterious if transcription and translation are not already uncoupled and a splicing system is not in place. Thus, the decoupling of transcription and translation by the nuclear membrane must precede intron invasion. Such an idea was put forward in the framework of the syntrophy hypothesis, which proposes the endosymbiotic origin of the nucleus [31] (Figure 2C). Endosymbiotic models for the origin of the nucleus easily account for the presence of a different compartment [21,28,31], but the difficulty here lies in how to explain what drives the endosymbiosis and the origin of the endomembrane system
% http://www.sciencedirect.com/science/article/pii/S0169534715002384?via%3Dihub#bib0535
% It possessed all the paradigmatic eukaryotic features, including the nucleus (with nuclear lamina and nuclear pores), a complex endomembrane system, and a sophisticated tubulin/actin-based cytoskeleton. In relation to the endomembrane system, LECA possessed developed endocytic and exocytic pathways as well as concomitant vesicle-trafficking networks (including Golgi apparatus, lysosomes, and autophagosomes) which also involved the cytoskeleton. The cytoskeleton was also essential for phagocytosis, and the presence of this mechanism indicates that LECA was most likely heterotrophic and fed on organic matter, perhaps as a predator of other cells. Its metabolism was most likely aerobic because it possessed oxygen-respiring mitochondria. The cytoskeleton had also a key role in mitosis, cell cytokinesis, and cell motility (probably by several flagella). Meiosis was likely present, opening the possibility for some form of sexual reproduction. The genome contained introns, making necessary a splicing system, likely integrated in a sophisticated gene regulation machinery that also included the activity of small non-coding RNAs and RNA interference. This list is not exhaustive because many other processes, such as ubiquitination and proteasome-mediated degradation, were also present. Coding for all those characters, some of them based on the participation of hundreds of different proteins, requires a very large number of genes. Conservative estimates suggest that the eukaryotic ancestor had a genome with at least 4000–5000 genes [52,79]. This implies that LECA was complex, fully comparable to many modern eukaryotes, and that the toolkit for eukaryotic cell components was established very early.
% Alphaproteobacterial genomes range from ∼1.3 Mb (parasitic Rickettsia and free-living Pelagibacter spp.) to >9 Mb, but the largest mitochondrial genomes have only ∼100 genes (some excavate protists) and the smallest – animal and apicomplexan mitochondrial genomes – have only 13 and 3 protein-coding genes, respectively. Genome extinction was achieved in many hydrogenosomes and other mitochondria-related organelles (MROs) found in some parasitic and/or anaerobic protists [4,77,82]. 

\begin{hangparas}{0.5cm}{1}Abreu F, Martins JL, Silveira TS, Keim CN, de Barros HG, Filho FJ, Lins U. 2007. 'Candidatus \textit{Magnetoglobus multicellularis}', a multicellular, magnetotactic prokaryote from a hypersaline environment. \textit{Int J Syst Evol Microbiol} \textbf{57}(Pt 6):1318--1322.
\end{hangparas}

% Allen JF. 2015. Why chloroplasts and mitochondria retain their own genomes and genetic systems: colocation for redox regulation of gene expression. \textit{Proc Natl Acad Sci U S A} \textbf{112}:10231--10238. 

\begin{hangparas}{0.5cm}{1}Andersson SG, Kurland CG. 1999. Origins of mitochondria and hydrogenosomes. \textit{Curr Opin Microbiol} \textbf{2}(5):535--541.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Angert ER. 2012. DNA replication and genomic architecture of very large bacteria. \textit{Annu Rev Microbiol} \textbf{66}:197--212.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Arias Del Angel JA, Escalante AE, Mart\'inez-Castilla LP, Ben\'itez M. 2017. An Evo-Devo Perspective on Multicellular Development of Myxobacteria. \textit{J Exp Zool B Mol Dev Evol} \textbf{328}(1--2):165--178. % doi: 10.1002/jez.b.22727. 
\end{hangparas}

% Booth A, Doolittle WF. 2015. Eukaryogenesis, how special really? \textit{Proc Natl Acad Sci U S A} \textbf{112}(33):10278--10285. % doi: 10.1073/pnas.1421376112. Epub 2015 Apr 16.

% Booth A, Doolittle WF. 2015. Reply to Lane and Martin: Being and becoming eukaryotes. \textit{Proc Natl Acad Sci U S A} \textbf{112}(35):E4824. % doi: 10.1073/pnas.1513285112.

\begin{hangparas}{0.5cm}{1}Cavalier-Smith T. 1987. Eukaryotes with no mitochondria. \textit{Nature} \textbf{326}(6111):332--333.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Cavalier-Smith T. 1989. Molecular phylogeny. Archaebacteria and Archezoa. \textit{Nature} \textbf{339}(6220):l00--101
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Clements KD, Bullivant S. 1991. An unusual symbiont from the gut of surgeonfishes may be the largest known prokaryote. \textit{J Bacteriol} \textbf{173}(17):5359--5362.
\end{hangparas}

% Collins L, Penny D. 2005. Complex spliceosomal organization ancestral to extant eukaryotes. \textit{Mol Biol Evol} \textbf{22}:1053--1066

\begin{hangparas}{0.5cm}{1}Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM 2008. The archaebacterial origin of eukaryotes. \textit{Proc Natl Acad Sci U S A} \textbf{105}(51):20356--20361.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Da Cunha V, Gaia M, Gadelle D, Nasir A, Forterre P. 2017. Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes. \textit{PLoS Genet} \textbf{13}(6):e1006810. % doi: 10.1371/journal.pgen.1006810. 
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Dacks JB, Field MC, Buick R, Eme L, Gribaldo S, Roger AJ, Brochier-Armanet C, Devos DP. 2016. The changing view of eukaryogenesis -- fossils, cells, lineages and how they all come together. \textit{J Cell Sci} \textbf{129}(20):3695--3703. 
\end{hangparas}

\begin{hangparas}{0.5cm}{1}de Duve C. 2007. The origin of eukaryotes: a reappraisal. \textit{Nat Rev Genet} \textbf{8}(5):395--403. % doi: 10.1038/nrg2071. 
\end{hangparas}

\begin{hangparas}{0.5cm}{1}diCenzo GC, Finan TM. 2017. The Divided Bacterial Genome: Structure, Function, and Evolution. \textit{Microbiol Mol Biol Rev} \textbf{81}(3) pii: e00019-17. % doi: 10.1128/MMBR.00019-17.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Eme L, Sharpe SC, Brown MW, Roger AJ. 2014. On the age of eukaryotes: evaluating evidence from fossils and molecular clocks. \textit{Cold Spring Harb Perspect Biol} \textbf{6}(8) pii: a016139. % doi: 10.1101/cshperspect.a016139.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Eme L, Spang A, Lombard J, Stairs CW, Ettema TJG. 2017. Archaea and the origin of eukaryotes. \textit{Nat Rev Microbiol} \textbf{15}(12):711--723. % doi: 10.1038/nrmicro.2017.133. 
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Fuerst JA. 2013. The PVC superphylum: exceptions to the bacterial definition? \textit{Antonie Van Leeuwenhoek} \textbf{104}(4):451--466. % doi: 10.1007/s10482-013-9986-1. 
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Garg SG, Martin WF. 2016. Mitochondria, the Cell Cycle, and the Origin of Sex via a Syncytial Eukaryote Common Ancestor. \textit{Genome Biol Evol} \textbf{8}(6):1950--1970. % doi: 10.1093/gbe/evw136.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Griese M, Lange C, Soppa J. 2011. Ploidy in cyanobacteria. \textit{FEMS Microbiol Lett} \textbf{323}(2):124--131.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Gross J, Bhattacharya D. 2010. Uniting sex and eukaryote origins in an emerging oxygenic world. \textit{Biol Direct} \textbf{5}:53. % doi: 10.1186/1745-6150-5-53.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Grosberg RK, Strathmann RR. 2007. The evolution of multicellularity: A minor major transition?. \textit{Annu Rev Ecol Evol Syst} \textbf{38}:621--654. % doi:10.1146/annurev.ecolsys.36.102403.114735.
\end{hangparas}

% Hazkani-Covo E, Zeller RM, Martin W. 2010. Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. \textit{PLoS Genet} \textbf{6}:e1000834

\begin{hangparas}{0.5cm}{1}Herrero A, Stavans J, Flores E. 2016. The multicellular nature of filamentous heterocyst-forming cyanobacteria. \textit{FEMS Microbiol Rev} \textbf{40}(6):831--854. % doi: 10.1093/femsre/fuw029. 
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Hjort K, Goldberg AV, Tsaousis AD, Hirt RP, Embley TM. 2010. Diversity and reductive evolution of mitochondria among microbial eukaryotes. \textit{Philos Trans R Soc Lond B Biol Sci} \textbf{365}(1541):713--727. % doi: 10.1098/rstb.2009.0224. 
\end{hangparas}

% Huang CY, Ayliffe MA, Timmis JN. 2004. Simple and complex nuclear loci created by newly transferred chloroplast DNA in tobacco. \textit{Proc Natl Acad Sci U S A} \textbf{101}:9710--9715. 

\begin{hangparas}{0.5cm}{1}Karnkowska A, Vacek V, Zub\'a\v{c}ov\'a Z, Treitli SC, Petr\v{z}elkov\'a R, Eme L, Nov\'ak L, \v{Z}\'arsk\'y V, Barlow LD, Herman EK, Soukal P, Hroudov\'a M, Dole\v{z}al P, Stairs CW, Roger AJ, Eli\'a\v{s} M, Dacks JB, Vl\v{c}ek \v{C}, Hampl V. 2016. A Eukaryote without a Mitochondrial Organelle. \textit{Curr Biol} \textbf{26}(10):1274--1284. % Monocercomonoides sp.
\end{hangparas}



\begin{hangparas}{0.5cm}{1}Koonin EV. 2010. The origin and early evolution of eukaryotes in the light of phylogenomics. \textit{Genome Biol} \textbf{11}(5):209. % doi: 10.1186/gb-2010-11-5-209. 
\end{hangparas}

% Lambowitz AM, Zimmerly S. 2011. Group II introns: mobile ribozymes that invade DNA. \textit{Cold Spring Harb Perspect Biol} \textbf{3}(8):a003616. % doi: 10.1101/cshperspect.a003616.

% Lane N. 2005. \textit{Power, Sex, Suicide: Mitochondria and the Meaning of Life}. Oxford Univ Press; Oxford.

\begin{hangparas}{0.5cm}{1}Lane N. 2011. Energetics and genetics across the prokaryote-eukaryote divide. \textit{Biol Direct} \textbf{6}:35.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Lane N. 2014. Bioenergetic constraints on the evolution of complex life. \textit{Cold Spring Harb Perspect Biol} \textbf{6}(5):a015982. % doi: 10.1101/cshperspect.a015982.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Lane N, Martin W. 2010. The energetics of genome complexity. \textit{Nature} \textbf{467}(7318):929--934. % doi: 10.1038/nature09486.
\end{hangparas}

% Lane N, Martin WF. 2016. Mitochondria, complexity, and evolutionary deficit spending. \textit{Proc Natl Acad Sci U S A} \textbf{113}(6):E666. % doi: 10.1073/pnas.1522213113. 

\begin{hangparas}{0.5cm}{1}Lane N, Martin WF. 2015. Eukaryotes really are special, and mitochondria are why. \textit{Proc Natl Acad Sci U S A} \textbf{112}(35):E4823. % doi: 10.1073/pnas.1509237112. 
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Lindsay MR, Webb RI, Strous M, Jetten MS, Butler MK, Forde RJ, Fuerst JA. 2001. Cell compartmentalisation in planctomycetes: novel types of structural organisation for the bacterial cell. \textit{Arch Microbiol} \textbf{175}(6):413--429.
\end{hangparas}

% Lynch M. 2007. \textit{The Origins of Genome Architecture}. Sinauer; Sunderland, MA.

% Lynch M. 2007. The frailty of adaptive hypotheses for the origins of organismal complexity. \textit{Proc Natl Acad Sci U S A} \textbf{104}(Suppl 1):8597--8604

% Lynch M, Conery JS 2003. The origins of genome complexity. \textit{Science} \textbf{302}(5649):1401--1404.

% Martin WF. 2017. Symbiogenesis, gradualism, and mitochondrial energy in eukaryote evolution. \textit{Periodicum Biologorum} \textbf{119}(\textbf{3}):141--158 % DOI: 10.18054/pb.v119i3.5694

\begin{hangparas}{0.5cm}{1}Martijn J, Ettema TJ. 2013. From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell. \textit{Biochem Soc Trans} \textbf{41}(1):451--457.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Martin W, Koonin EV. 2006. Introns and the origin of nucleus–cytosol compartmentalization. \textit{Nature} \textbf{440}:41--45
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Martin W, M\"uller M. 1998. The hydrogen hypothesis for the first eukaryote. \textit{Nature} \textbf{392}(6671):37--41.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Martin WF, Tielens AGM, Mentel M, Garg SG, Gould SB. 2017. The Physiology of Phagocytosis in the Context of Mitochondrial Origin. \textit{Microbiol Mol Biol Rev} \textbf{81}(3). pii: e00008--17. % doi: 10.1128/MMBR.00008-17. 
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Mayerhofer LE, Macario AJ, Conway de Macario E. 1992. Lamina, a novel multicellular form of \textit{Methanosarcina mazei} S-6. \textit{J Bacteriol} \textbf{174}(1):309--314.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}McInerney JO, O'Connell MJ, Pisani D. 2014. The hybrid nature of the Eukaryota and a consilient view of life on Earth. \textit{Nat Rev Microbiol} \textbf{12}(6):449--455. % doi: 10.1038/nrmicro3271. 
\end{hangparas}

\begin{hangparas}{0.5cm}{1}McInerney JO, Martin WF, Koonin EV, Allen JF, Galperin MY, Lane N, Archibald JM, Embley TM. 2011. Planctomycetes and eukaryotes: a case of analogy not homology. \textit{Bioessays} \textbf{33}(11):810--817. % doi: 10.1002/bies.201100045.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Mendell JE, Clements KD, Choat JH, Angert ER. 2008. Extreme polyploidy in a large bacterium. \textit{Proc Natl Acad Sci U S A} \textbf{105}(18):6730--6734. % doi: 10.1073/pnas.0707522105. 
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Mereschkowski C. 1905. \"Uber Natur und Ursprung der Chromatophoren im Pflanzenreiche. \textit{Biol Centralbl} \textbf{25}:593--604.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Mereschkowsky K. 1910. Theorie der zwei Plasmaarten als Grundlage der Symbiogenesis, einer neuen Lehre von der Ent‐stehung der Organismen. \textit{Biol Centralbl} \textbf{30}:353--367.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Rast A, Heinz S, Nickelsen J. 2015. Biogenesis of thylakoid membranes. \textit{Biochim Biophys Acta} \textbf{1847}(9):821--830. % doi: 10.1016/j.bbabio.2015.01.007. 
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Rivera MC, Lake JA. 2004. The ring of life provides evidence for a genome fusion origin of eukaryotes. \textit{Nature} \textbf{431}(7005):152--155.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Sagan L. 1967. On the origin of mitosing cells. \textit{J Theor Biol} \textbf{14}(3):255--274.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Schulz HN, Brinkhoff T, Ferdelman TG, Marin\'e MH, Teske A, Jorgensen BB. 1999. Dense populations of a giant sulfur bacterium in Namibian shelf sediments. \textit{Science} \textbf{284}(5413):493--495.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Soppa J. 2014. Polyploidy in archaea and bacteria: about desiccation resistance, giant cell size, long-term survival, enforcement by a eukaryotic host and additional aspects. \textit{J Mol Microbiol Biotechnol} \textbf{24}(5--6):409--419. % doi: 10.1159/000368855. Epub 2015 Feb 17. Review
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Spang A, Saw JH, J\o{}rgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJG. 2015. Complex archaea that bridge the gap between prokaryotes and eukaryotes. \textit{Nature} \textbf{521}(7551):173--179. % doi: 10.1038/nature14447. 
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Van Der Giezen M, Lenton TM. 2012. The rise of oxygen and complex life. \textit{J Eukaryot Microbiol} \textbf{59}(2):111--113. % doi: 10.1111/j.1550-7408.2011.00605.x. 
\end{hangparas}

\begin{hangparas}{0.5cm}{1}von Dohlen CD, Kohler S, Alsop ST, McManus WR. 2001. Mealybug $\beta$-proteobacterial endosymbionts contain $\gamma$-proteobacterial symbionts. \textit{Nature} \textbf{412}:433--436
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Williams TA, Foster PG, Cox CJ, Embley TM. 2013. An archaeal origin of eukaryotes supports only two primary domains of life. \textit{Nature} \textbf{504}(7479):231--236. % doi: 10.1038/nature12779.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Volff JN, Altenbuchner J. 2000. A new beginning with new ends: linearisation of circular chromosomes during bacterial evolution. \textit{FEMS Microbiol Lett} \textbf{186}(2):143--150.
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Woronowicz K, Harrold JW, Kay JM, Niederman RA. 2013. Structural and functional proteomics of intracytoplasmic membrane assembly in \textit{Rhodobacter sphaeroides}. \textit{J Mol Microbiol Biotechnol} \textbf{23}(1--2):48--62. % doi: 10.1159/000346520. 
\end{hangparas}

% Wujek DE. 1979. Intracellular bacteria in the blue-green-alga \textit{Pleurocapsa minor}. \textit{Trans Am Microsc Soc} \textbf{98}:143--145.

\begin{hangparas}{0.5cm}{1}Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV. 2008. The deep archaeal roots of eukaryotes. \textit{Mol Biol Evol} \textbf{25}(8):1619--1630. % doi: 10.1093/molbev/msn108. 
\end{hangparas}

\begin{hangparas}{0.5cm}{1}Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, B\"ackstr\"om D, Juzokaite L, Vancaester E, Seitz KW, Anantharaman K, Starnawski P, Kjeldsen KU, Stott MB, Nunoura T, Banfield JF, Schramm A, Baker BJ, Spang A, Ettema TJ. 2017. Asgard archaea illuminate the origin of eukaryotic cellular complexity. \textit{Nature} \textbf{541}(7637):353--358. % doi: 10.1038/nature21031. 
\end{hangparas}