Biologists suspect that endosymbiosis gave rise to mitochondria before plastids partly because

1. Knoll AH. 2014. Paleobiological perspectives on early eukaryotic evolution. Cold Spring Harb. Perspect. Biol. 6, a016121 ( 10.1101/cshperspect.a016121) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

2. Lane N. 2014. Bioenergetic constraints on the evolution of complex life. Cold Spring Harb. Perspect. Biol. 6, a015982 ( 10.1101/cshperspect.a015982) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

3. Wideman JG, Leung KF, Field MC, Dacks JB. 2014. The cell biology of the endocytic system from an evolutionary perspective. Cold Spring Harb. Perspect. Biol. 6, a016998. ( 10.1101/cshperspect.a016998) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

4. Koonin EV. 2012. The logic of chance: the nature and origin of biological evolution. Upper Saddle River, NJ: FT Press. [Google Scholar]

5. Adl SM, et al. 2005. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J. Eukaryot. Microbiol. 52, 399–451. ( 10.1111/j.1550-7408.2005.00053.x) [PubMed] [CrossRef] [Google Scholar]

6. Archibald JM. 2014. One plus one equals one: symbiosis and the evolution of complex life. Oxford, UK: Oxford University Press. [Google Scholar]

7. Altmann R. 1890. Die Elementarorganismen und ihre Beziehungen zu den Zellen. Leipzig, Germany: Verlag von Veit & Comp. [Google Scholar]

8. Höxtermann E, Mollenhauer D. 2007. Symbiose und Symbiogenese—Entdeckung und Entwicklung eines biologischen Problems. In Evolution durch Kooperation und Integration (eds Geus A, Höxtermann E), p. 258 Marburg an der Lahn: Basilisken-Presse. [Google Scholar]

9. Schwendener S. 1867. Über die wahre Natur der Flechten. Verhandlungen der Schweizerischen Naturforschenden Gesellschaft in Rheinfelden 51, 88–90. [Google Scholar]

10. De Bary A. 1878. Über Symbiose. Tageblatt der 51. Versammlung deutscher Naturforscher und Aerzte in Cassel, pp. 121–126. [Google Scholar]

11. Schimper AFW. 1883. Über die Entwickelung der Chlorophyllkörner und Farbkörper. Bot. Z 41, 105–120, 121–136, 137–152, 153–162. [Google Scholar]

12. Schimper AFW. 1885. Untersuchungen über die Chlorophyllkörner und die ihnen homologen Gebilde. Jahrb. wiss. Bot. 16, 1–247. [Google Scholar]

13. Mereschkowsky C. 1905. Über Natur und Ursprung der Chromatophoren im Pflanzenreiche. Biol. Centralbl. 25, 593–604. [Google Scholar]

14. Martin W, Kowallik K. 1999. Annotated English translation of Meresch­kowsky's 1905 paper ‘Über Natur und Ursprung der Chromatophoren im Pflanzenreiche’. Eur. J. Phycol. 34, 287–295. ( 10.1080/09670269910001736342) [CrossRef] [Google Scholar]

15. Mereschkowsky C. 1910. Theorie der zwei Plasmaarten als Grundlage der Symbiogenesis, einer neuen Lehre von der Entstehung der Organismen. Biol. Centralbl. 30, 353–442. [Google Scholar]

16. Geus A, Höxtermann E. 2007. Evolution durch Kooperation und Integration. Marburg an der Lahn: Basilisken-Presse. [Google Scholar]

17. Schlacht A, Herman EK, Klute MJ, Field MC, Dacks JB. 2014. Missing pieces of an ancient puzzle: Evolution of the eukaryotic membrane-trafficking system. Cold Spring Harb. Perspect. Biol. 6, a016048 ( 10.1101/cshperspect.a016048) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

18. De Duve C. 2007. The origin of eukaryotes: a reappraisal. Nat. Rev. Genet. 8, 395–403. ( 10.1038/nrg2071) [PubMed] [CrossRef] [Google Scholar]

19. Margulis L, Chapman M, Guerrero R, Hall J. 2006. The last eukaryotic common ancestor (LECA): acquisition of cytoskeletal motility from aerotolerant spirochetes in the Proterozoic Eon. Proc. Natl Acad. Sci. USA 103, 13 080–13 085. ( 10.1073/pnas.0604985103) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

20. Lindmark DG, Müller M. 1973. Hydrogenosome, a cytoplasmic organelle of the anaerobic flagellate Tritrichomonas foetus, and its role in pyruvate metabolism. J. Biol. Chem. 248, 7724–7728. [PubMed] [Google Scholar]

21. Müller M, et al. 2012. Biochemistry and evolution of anaerobic energy metabolism in eukaryotes. Microbiol. Mol. Biol. Rev. 76, 444–495. ( 10.1128/MMBR.05024-11) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

22. Martin W, Hoffmeister M, Rotte C, Henze K. 2001. An overview of endosymbiotic models for the origins of eukaryotes, their ATP-producing organelles (mitochondria and hydrogenosomes) and their heterotrophic lifestyle. Biol. Chem. 382, 1521–1539. ( 10.1515/BC.2001.187) [PubMed] [CrossRef] [Google Scholar]

23. Martin W, Rotte C, Hoffmeister M, Theissen U, Gelius-Dietrich G, Ahr S, Henze K. 2003. Early cell evolution, eukaryotes, anoxia, sulfide, oxygen, fungi first (?), and a tree of genomes revisited. IUBMB Life 55, 193–204. ( 10.1080/1521654031000141231) [PubMed] [CrossRef] [Google Scholar]

24. Martin W. 2007. Eukaryote and mitochondrial origins: Two sides of the same coin and too much ado about oxygen. In Primary producers of the sea (eds Falkowski P, Knoll AH), pp. 53–73. New York, NY: Academic Press. [Google Scholar]

25. Martin W, Müller M. 1998. The hydrogen hypothesis for the first eukaryote. Nature 392, 37–41. ( 10.1038/32096) [PubMed] [CrossRef] [Google Scholar]

26. Tovar J, Fischer A, Clark CG. 1999. The mitosome, a novel organelle related to mitochondria in the amitochondrial parasite Entamoeba histolytica. Mol. Microbiol. 32, 1013–1021. ( 10.1046/j.1365-2958.1999.01414.x) [PubMed] [CrossRef] [Google Scholar]

27. Tovar J, León-Avila G, Sánchez LB, Sutak R, Tachezy J, van der Giezen M, Hernández M, Müller M, Lucocq JM. 2003. Mitochondrial remnant organelles of Giardia function in iron–sulphur protein maturation. Nature 426, 172–176. ( 10.1038/nature01945) [PubMed] [CrossRef] [Google Scholar]

28. van der Giezen M. 2009. Hydrogenosomes and mitosomes: conservation and evolution of functions. J. Eukaryot. Microbiol. 56, 221–231. ( 10.1111/j.1550-7408.2009.00407.x) [PubMed] [CrossRef] [Google Scholar]

29. Embley TM, van der Giezen M, Horner DS, Dyal PL, Foster P. 2003. Mitochondria and hydrogenosomes are two forms of the same fundamental organelle. Phil. Trans. R. Soc. Lond. B 358, 191–202. ( 10.1098/rstb.2002.1190) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

30. Williams TA, Foster PG, Cox CJ, Embley TM. 2013. An archaeal origin of eukaryotes supports only two primary domains of life. Nature 504, 231–236. ( 10.1038/nature12779) [PubMed] [CrossRef] [Google Scholar]

31. Guy L, Saw JH, Ettema TJG. 2014. The archaeal legacy of eukaryotes: a phylogenomic perspective. Cold Spring Harb. Perspect. Biol. 6, a016022 ( 10.1101/cshperspect.a016022) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

32. McInerney JO, O'Connell M, Pisani D. 2014. The hybrid nature of the Eukaryota and a consilient view of life on Earth. Nat. Rev. Microbiol. 12, 449–455. ( 10.1038/nrmicro3271) [PubMed] [CrossRef] [Google Scholar]

33. Simpson AGB, Roger AJ. 2004. The real ‘kingdoms’ of eukaryotes. Curr. Biol. 14, R693–R696. ( 10.1016/j.cub.2004.08.038) [PubMed] [CrossRef] [Google Scholar]

34. Lane N, Martin W. 2010. The energetics of genome complexity. Nature 467, 929–934. ( 10.1038/nature09486) [PubMed] [CrossRef] [Google Scholar]

35. Martin W, Koonin EV. 2006. Introns and the origin of nucleus–cytosol compartmentalization. Nature 440, 41–45. ( 10.1038/nature04531) [PubMed] [CrossRef] [Google Scholar]

36. Thiergart T, Landan G, Schenk M, Dagan T, Martin WF. 2012. An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin. Genome Biol. Evol. 4, 466–485. ( 10.1093/gbe/evs018) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

37. Rivera MC, Jain R, Moore JE, Lake JA. 1998. Genomic evidence for two functionally distinct gene classes. Proc. Natl Acad. Sci. USA 95, 6239–6244. ( 10.1073/pnas.95.11.6239) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

38. Maier U-G, Zauner S, Woehle C, Bolte K, Hempel F, Allen JF, Martin WF. 2013. Massively convergent evolution for ribosomal protein gene content in plastid and mitochondrial genomes. Genome Biol. Evol. 5, 2318–2329. ( 10.1093/gbe/evt181) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

39. Gilson PR, Maier UG, McFadden GI. 1997. Size isn't everything: Lessons in genetic miniaturisation from nucleomorphs. Curr. Opin. Genet. Dev. 7, 800–806. ( 10.1016/S0959-437X(97)80043-3) [PubMed] [CrossRef] [Google Scholar]

40. Martin W. 1999. A briefly argued case that mitochondria and plastids are descendants of endosymbionts, but that the nuclear compartment is not. Proc. R. Soc. Lond. B 266, 1387–1395. ( 10.1098/rspb.1999.0792) [CrossRef] [Google Scholar]

41. Ku C, Nelson-Sathi S, Roettger M, Garg S, Hazkani-Covo E, Martin WF. In press. Endosymbiotic gene transfer from prokaryotic pangenomes: inherited chimaerism in eukaryotes. Proc. Natl Acad. Sci. USA. ( 10.1073/pnas.1421385112) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

42. Hansmann S, Martin W. 2000. Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis. Int. J. Syst. Evol. Microbiol. 50, 1655–1663. ( 10.1099/00207713-50-4-1655) [PubMed] [CrossRef] [Google Scholar]

43. Charlebois RL, Doolittle WF. 2004. Computing prokaryotic gene ubiquity: rescuing the core from extinction. Genome Res. 14, 2469–2477. ( 10.1101/gr.3024704) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

44. Cicarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283–1287. ( 10.1126/science.1123061) [PubMed] [CrossRef] [Google Scholar]

45. Esser C, et al. 2004. A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol. Biol. Evol. 21, 1643–1660. ( 10.1093/molbev/msh160) [PubMed] [CrossRef] [Google Scholar]

46. Pisani D, Cotton JA, McInerney JO. 2007. Supertrees disentangle the chime­rical origin of eukaryotic genomes. Mol. Biol. Evol. 24, 1752–1760. ( 10.1093/molbev/msm095) [PubMed] [CrossRef] [Google Scholar]

47. Cotton JA, McInerney JO. 2010. Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. Proc. Natl Acad. Sci. USA 107, 17 252–17 255. ( 10.1073/pnas.1000265107) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

48. Lane CE, Archibald JM. 2008. The eukaryotic tree of life: endosymbiosis takes its TOL. Trends Ecol. Evol. 23, 268–275. ( 10.1016/j.tree.2008.02.004) [PubMed] [CrossRef] [Google Scholar]

49. Embley TM, Hirt RP. 1998. Early branching eukaryotes? Curr. Opin. Genet. Dev. 8, 624–629. ( 10.1016/S0959-437X(98)80029-4) [PubMed] [CrossRef] [Google Scholar]

50. Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM. 2008. The archaebacterial origin of eukaryotes. Proc. Natl Acad. Sci. USA 105, 20 356–20 361. ( 10.1073/pnas.0810647105) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

51. Williams TA, Embley M. 2014. Archaeal ‘dark matter’ and the origin of eukaryotes. Genome Biol. Evol. 6, 474–481. ( 10.1093/gbe/evu031) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

52. Kelly S, Wickstead B, Gull K. 2011. Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes. Proc. R. Soc. B 278, 1009–1018. ( 10.1098/rspb.2010.1427) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

53. Martin W. 2005. Archaebacteria (Archaea) and the origin of the eukaryotic nucleus. Curr. Opin. Microbiol. 8, 630–637. ( 10.1016/j.mib.2005.10.004) [PubMed] [CrossRef] [Google Scholar]

54. Pederson T. 2011. The nucleus introduced. Cold Spring Harb. Perspect. Biol. 5, a000521 ( 10.1101/cshperspect.a000521) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

55. Cavalier-Smith T. 1987. The origin of eukaryote and archaebacterial cells. Ann. NY Acad. Sci. 503, 17–54. ( 10.1111/j.1749-6632.1987.tb40596.x) [PubMed] [CrossRef] [Google Scholar]

56. Cavalier-Smith T. 1988. Origin of the cell-nucleus. Bioessays 9, 72–78. ( 10.1002/bies.950090209) [PubMed] [CrossRef] [Google Scholar]

57. Cavalier-Smith T. 2002. The phagotrophic origin of eukaryotes and phylogenetic classification of protozoa. Int. J. Syst. Evol. Microbiol. 52, 297–354. ( 10.1099/ijs.0.02058-0) [PubMed] [CrossRef] [Google Scholar]

58. Cavalier-Smith T. 2004. Only six kingdoms of life. Proc. R. Soc. B 271, 1251–1262. ( 10.1098/rspb.2004.2705) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

59. Gould GW, Dring GJ. 1979. Possible relationship between bacterial endospore formation and the origin of eukaryotic cells. J. Theor. Biol. 81, 47–53. ( 10.1016/0022-5193(79)90079-1) [PubMed] [CrossRef] [Google Scholar]

60. Zillig W, Klenk H-P, Palm P, Leffers H, Pühler G, Gropp F, Garrett RA. 1989. Did eukaryotes originate by a fusion event? Endocyt. Cell Res. 6, 1–25. [Google Scholar]

61. Gupta RS, Golding GB. 1996. The origin of the eukaryotic cell. Trends Biochem. Sci. 21, 166–171. ( 10.1016/S0968-0004(96)20013-1) [PubMed] [CrossRef] [Google Scholar]

62. Fuerst JA, Webb RI. 1991. Membrane-bounded nucleoid in the eubacterium Gemmata obscuriglobus. Proc. Natl Acad. Sci. USA 88, 8184–8188. ( 10.1073/pnas.88.18.8184) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

63. Santarella-Mellwig R, Pruggnaller S, Roos N, Mattaj IW, Devos DP. 2013. Three-dimensional reconstruction of bacteria with a complex endomembrane system. PLoS Biol. 11, e1001565 ( 10.1371/journal.pbio.1001565) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

64. Devos DP. 2013. PVC bacteria: Variation of, but not exception to, the Gram-negative cell plan. Trends Microbiol. 22, 14–20. ( 10.1016/j.tim.2013.10.008) [PubMed] [CrossRef] [Google Scholar]

65. Searcy DG, Hixon WG. 1991. Cytoskeletal origins in sulfur-metabolizing archaebacteria. Biosystems 25, 1–11. ( 10.1016/0303-2647(91)90008-9) [PubMed] [CrossRef] [Google Scholar]

66. Lake JA, Rivera MC. 1994. Was the nucleus the first endosymbiont? Proc. Natl Acad. Sci. USA 91, 2880–2881. ( 10.1073/pnas.91.8.2880) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

67. Moreira D, López-García P. 1998. Symbiosis between methanogenic archaea and δ-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis. J. Mol. Evol. 47, 517–530. ( 10.1007/PL00006408) [PubMed] [CrossRef] [Google Scholar]

68. López-García P, Moreira D. 2006. Selective forces for the origin of the eukaryotic nucleus. Bioessays 28, 525–533. ( 10.1002/bies.20413) [PubMed] [CrossRef] [Google Scholar]

69. Kuwabara T, Minaba M, Ogi N, Kamekura M. 2007. Thermococcus celericrescens sp. nov., a fast-growing and cell-fusing hyperthermophilic archaeon from a deep-sea hydrothermal vent. Int. J. Syst. Evol. Microbiol. 57, 437–443. ( 10.1099/ijs.0.64597-0) [PubMed] [CrossRef] [Google Scholar]

70. Margulis L, Dolan MF, Guerro R. 2000. The chimeric eukaryote: Origin of the nucleus from the karyomastigont in amitochondriate protists. Proc. Natl Acad. Sci. USA 97, 6954–6959. ( 10.1073/pnas.97.13.6954) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

71. Bell PJL. 2001. Viral eukaryogenesis: Was the ancestor of the nucleus a complex DNA virus? J. Mol. Evol. 53, 251–256. ( 10.1111/j.1749-6632.2009.04994.x) [PubMed] [CrossRef] [Google Scholar]

72. Horiike T, Hamada K, Miyata D, Shinozawa T. 2004. The origin of eukaryotes is suggested as the symbiosis of Pyrococcus into γ-proteobacteria by phylogenetic tree based on gene content. J. Mol. Evol. 59, 606–619. ( 10.1007/s00239-004-2652-5) [PubMed] [CrossRef] [Google Scholar]

73. Forterre P, Gribaldo S. 2010. Bacteria with a eukaryotic touch: a glimpse of ancient evolution? Proc. Natl Acad. Sci. USA 107, 12 739–12 740. ( 10.1073/pnas.1007720107) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

74. Kurland CG, Collins LJ, Penny D. 2006. Genomics and the irreducible nature of eukaryote cells. Science 312, 1011–1014. ( 10.1126/science.1121674) [PubMed] [CrossRef] [Google Scholar]

75. Penny D, Collins LJ, Daly TK, Cox SJ. 2014. The relative ages of eukaryotes and akaryotes. J. Mol. Evol. 79, 228–239. ( 10.1007/s00239-014-9643-y) [PubMed] [CrossRef] [Google Scholar]

76. Field MC, Sali A, Rout MP. 2011. On a bender—BARs, ECRTs, COPs, and finally getting your coat. J. Cell Biol. 193, 963–972. ( 10.1083/jcb.201102042) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

77. Forterre P. 2011. A new fusion hypothesis for the origin of Eukaryota: better than previous ones, but probably also wrong. Res. Microbiol. 162, 77–91. ( 10.1016/j.resmic.2010.10.005) [PubMed] [CrossRef] [Google Scholar]

78. 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. Bioessays 33, 810–817. ( 10.1002/bies.201100045) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

79. Embley TM, Martin W. 2006. Eukaryotic evolution, changes and challenges. Nature 440, 623–630. ( 10.1038/nature04546) [PubMed] [CrossRef] [Google Scholar]

80. McFadden GI, van Dooren GG. 2004. Evolution: red algal genome affirms a common origin of all plastids. Curr. Biol. 14, R514–R516. ( 10.1016/j.cub.2004.06.041) [PubMed] [CrossRef] [Google Scholar]

81. Keeling PJ. 2013. The number, speed, and impact of plastid endosymbiosis in eukaryotic evolution. Annu. Rev. Plant. Biol. 64, 583–607. ( 10.1146/annurev-arplant-050312-120144) [PubMed] [CrossRef] [Google Scholar]

82. Zimorski V, Ku C, Martin WF, Gould SB. 2014. Endosymbiotic theory for organelle origins. Curr. Opin. Microbiol. 22, 38–48. ( 10.1016/j.mib.2014.09.008) [PubMed] [CrossRef] [Google Scholar]

83. Wallin IE. 1927. Symbionticism and the origin of species, 171 London, UK: Bailliere, Tindall and Cox. [Google Scholar]

84. Wallin IE. 1925. On the nature of mitochondria. IX. Demonstration of the bacterial nature of mitochondria. Am. J. Anat. 36, 131–139. ( 10.1002/aja.1000360106) [CrossRef] [Google Scholar]

85. Wilson EB. 1928. The cell in development and heredity, 3rd revised edtion New York, NY: Macmillan; (Reprinted 1987 by Garland Publishing, New York.) [Google Scholar]

86. Buchner P. 1953. Endosymbiose der Tiere mit pflanzlichen Mikroorganismen. Basel, Switzerland: Birkhäuser, Basel. [Google Scholar]

87. Lederberg J. 1952. Cell genetics and hereditary symbiosis. Physiol. Rev. 32, 403–430. [PubMed] [Google Scholar]

88. Sagan L. 1967. On the origin of mitosing cells. J. Theoret. Biol. 14, 225–274. ( 10.1016/0022-5193(67)90079-3) [CrossRef] [Google Scholar]

89. Goksøyr J. 1967. Evolution of eucaryotic cells. Nature 214, 1161 ( 10.1038/2141161a0) [PubMed] [CrossRef] [Google Scholar]

90. Knoll AH. 2012. Lynn Margulis, 1938–2011. Proc. Natl Acad. Sci. USA 109, 1022 ( 10.1073/pnas.1120472109) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

91. Margulis L. 1970. Origin of eukaryotic cells. New Haven, CT: Yale University Press. [Google Scholar]

92. de Duve C. 1969. Evolution of the peroxisome. Ann. NY Acad. Sci. 168, 369–381. ( 10.1111/j.1749-6632.1969.tb43124.x) [PubMed] [CrossRef] [Google Scholar]

93. Stanier Y. 1970. Some aspects of the biology of cells and their possible evolutionary significance. Symp. Soc. Gen. Microbiol. 20, 1–38. [Google Scholar]

94. Raff RA, Mahler HR. 1972. The non symbiotic origin of mitochondria. Science 177, 575–582. ( 10.1126/science.177.4049.575) [PubMed] [CrossRef] [Google Scholar]

95. Bogorad L. 1975. Evolution of organelles and eukaryotic genomes. Science 188, 891–898. ( 10.1126/science.1138359) [PubMed] [CrossRef] [Google Scholar]

96. Cavalier-Smith T. 1975. The origin of nuclei and of eukaryotic cells. Nature 256, 463–468. ( 10.1038/256463a0) [PubMed] [CrossRef] [Google Scholar]

97. Bonen L, Doolittle WF. 1975. On the prokaryotic nature of red algal chloroplasts. Proc. Natl Acad. Sci. USA 72, 2310–2314. ( 10.1073/pnas.72.6.2310) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

98. Anderson S, et al. 1981. Sequence and organization of the human mitochondrial genome. Nature 290, 457–465. ( 10.1038/290457a0) [PubMed] [CrossRef] [Google Scholar]

99. John P, Whatley FR. 1975. Paracoccus denitrificans and the evolutionary origin of the mitochondrion. Nature 254, 495–498. ( 10.1038/254495a0) [PubMed] [CrossRef] [Google Scholar]

100. Woese CR. 1977. Endosymbionts and mitochondrial origins. J. Mol. Evol. 10, 93–96. ( 10.1007/BF01751802) [PubMed] [CrossRef] [Google Scholar]

101. Van Valen LM, Maiorana VC. 1980. The Archaebacteria and eukaryotic origins. Nature 287, 248–250. ( 10.1038/287248a0) [PubMed] [CrossRef] [Google Scholar]

102. Doolittle WF. 1980. Revolutionary concepts in evolutionary biology. Trends Biochem. Sci. 5, 146–149. ( 10.1016/0968-0004(80)90010-9) [CrossRef] [Google Scholar]

103. Margulis L. 1981. Symbiosis in cell evolution. San Francisco, CA: Freeman. [Google Scholar]

104. Vellai T, Vida G. 1998. The origin of the eukaryotes: the difference between prokaryotic and eukaryotic cells. Proc. R. Soc. Lond. B 266, 1571–1577. ( 10.1098/rspb.1999.0817) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

105. Searcy DG. 1992. Origins of mitochondria and chloroplasts from sulphurbased symbioses. In The origin and evolution of the cell (eds Hartman H, Matsuno K), pp. 47–78. Singapore: World Scientific. [Google Scholar]

106. Martijn J, Ettema TJG. 2013. From archaeon to eukaryote: The evolutionary dark ages of the eukaryotic cell. Biochem. Soc. Trans. 41, 451–457. ( 10.1042/BST20120292) [PubMed] [CrossRef] [Google Scholar]

107. Gray MW. 2014. The pre-endosymbiont hypothesis: a new perspective on the origin and evolution of mitochondria. Cold Spring Harb. Perspect. Biol. 6, a016097 ( 10.1101/cshperspect.a016097) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

108. Baum DA, Baum B. 2014. An inside-out origin for the eukaryotic cell. BMC Biol. 12, 76 ( 10.1186/s12915-014-0076-2) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

109. Davidov Y, Jurkevitch E. 2009. Predation between prokaryotes and the origin of eukaryotes. Bioessays 31, 748–757. ( 10.1002/bies.200900018) [PubMed] [CrossRef] [Google Scholar]

110. Davidov Y, Huchon D, Koval SF, Jurkevitch E. 2006. A new alpha-proteobacterial clade of Bdellovibrio-like predators: implications for the mitochondrial endosymbiotic theory. Environ. Microbiol. 8, 2179–2188. ( 10.1111/j.1462-2920.2006.01101.x) [PubMed] [CrossRef] [Google Scholar]

111. Pasternak Z, et al. 2014. In and out: An analysis of epibiotic vs periplasmic bacterial predators. ISME J. 8, 625–635. ( 10.1038/ismej.2013.164) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

112. Goldberg AV, et al. 2008. Localization and functionality of microsporidian iron-sulphur cluster assembly proteins. Nature 452, 624–628. ( 10.1038/nature06606) [PubMed] [CrossRef] [Google Scholar]

113. Tsaousis AD, Kunji ERS, Goldberg AV, Lucocq JM, Hirt RP, Embley TM. 2008. A novel route for ATP acquisition by the remnant mitochondria of Encephalitozoon cuniculi. Nature 453, 553–556. ( 10.1038/nature06903) [PubMed] [CrossRef] [Google Scholar]

114. Williams BAP, Hirt RP, Lucocq JM, Embley TM. 2002. A mitochondrial remnant in the microsporidian Trachipleistophora hominis. Nature 418, 865–869. ( 10.1038/nature00949) [PubMed] [CrossRef] [Google Scholar]

115. Brown JR, Doolittle WF. 1997. Archaea and the prokaryote-to-eukaryote transition. Microbiol. Mol. Biol. Rev. 61, 456–502. [PMC free article] [PubMed] [Google Scholar]

116. Martin W, Brinkmann H, Savona C, Cerff R. 1993. Evidence for a chimeric nature of nuclear genomes: Eubacterial origin of eukaryotic glyceraldehyde-3-phosphate dehydrogenase genes. Proc. Natl Acad. Sci. USA 90, 8692–8696. ( 10.1073/pnas.90.18.8692) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

117. Timmis JN, Ayliffe MA, Huang CY, Martin W. 2004. Endosymbiotic gene transfer: Organelle genomes forge eukaryotic chromosomes. Nat. Rev. Genet. 5, 123–135. ( 10.1038/nrg1271) [PubMed] [CrossRef] [Google Scholar]

118. López-García P, Moreira D. 1999. Metabolic symbiosis at the origin of eukaryotes. Trends Biochem. Sci. 24, 88–93. ( 10.1016/S0968-0004(98)01342-5) [PubMed] [CrossRef] [Google Scholar]

119. Finlay BJ, Embley TM, Fenchel T. 1993. A new polymorphic methanogen, closely related to Methanocorpusculum parvum, living in stable symbiosis within the anaerobic ciliate Trimyema sp. J. Gen. Microbiol. 139, 371–378. ( 10.1099/00221287-139-2-371) [PubMed] [CrossRef] [Google Scholar]

120. von Dohlen CD, Kohler S, Alsop ST, McManus WR. 2001. Mealybug β-proteobacterial endosymbionts contain γ-proteobacterial symbionts. Nature 412, 433–436. ( 10.1038/35086563) [PubMed] [CrossRef] [Google Scholar]

121. Husnik F, et al. 2013. Horizontal gene transfer from diverse bacteria to an insect genome enables a tripartite nested mealybug symbiosis. Cell 153, 1567–1578. ( 10.1016/j.cell.2013.05.040) [PubMed] [CrossRef] [Google Scholar]

122. Yutin N, Wolf MY, Wolf YI, Koonin EV. 2009. The origins of phagocytosis and eukaryogenesis. Biol. Direct 4, 9 ( 10.1186/1745-6150-4-9) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

123. Nelson-Sathi S, Dagan T, Landan G, Janssen A, Steel M, McInerney JO, Deppenmeier U, Martin WF. 2012. Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proc. Natl Acad. Sci. USA 109, 20 537–20 542. ( 10.1073/pnas.1209119109) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

124. Nelson-Sathi S, et al. 2015. Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517, 77–80. ( 10.1038/nature13805) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

125. Say RF, Fuchs G. 2010. Fructose 1,6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme. Nature 464, 1077–1081. ( 10.1038/nature08884) [PubMed] [CrossRef] [Google Scholar]

126. Reher M, Fuhrer T, Bott M, Schönheit P. 2010. The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate-specific aldolase. J. Bacteriol. 192, 964–974. ( 10.1128/JB.01281-09) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

127. Bräsen C, Esser D, Rauch B, Siebers B. 2014. Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation. Microbiol. Mol. Biol. Rev. 78, 89–175. ( 10.1128/MMBR.00041-13) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

128. Hannaert V. 2000. Enolase from Trypanosoma brucei, from the amitochondriate protist Mastigamoeba balamuthi, and from the chloroplast and cytosol of Euglena gracilis: pieces in the evolutionary puzzle of the eukaryotic glycolytic pathway. Mol. Biol. Evol. 17, 989–1000. ( 10.1093/oxfordjournals.molbev.a026395) [PubMed] [CrossRef] [Google Scholar]

129. Lange BM, Rujan T, Martin W, Croteau R. 2000. Isoprenoid biosynthesis: The evolution of two ancient and distinct pathways across genomes. Proc. Natl Acad. Sci. USA 97, 13 172–13 177. ( 10.1073/pnas.240454797) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

130. Waldbauer JR, Newman DK, Summons RE. 2011. Microaerobic steroid biosynthesis and the molecular fossil record of Archean life. Proc. Natl Acad. Sci. USA 108, 13 409–13 414. ( 10.1073/pnas.1104160108) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

131. Poole A, Jeffares D, Penny D. 1999. Early evolution: prokaryotes, the new kids on the block. Bioessays 21, 880–889. ( 10.1002/(SICI)1521-1878(199910)21:10<880::AID-BIES11>3.0.CO;2-P) [PubMed] [CrossRef] [Google Scholar]

132. Lambowitz AM, Zimmerly S. 2011. Group II introns: Mobile ribozymes that invade DNA. Cold Spring Harb. Perspect. Biol. 3, a003616 ( 10.1101/cshperspect.a003616) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

133. Lambowitz AM, Zimmerly S. 2004. Mobile group II introns. Annu. Rev. Genet. 38, 1–35. ( 10.1146/annurev.genet.38.072902.091600) [PubMed] [CrossRef] [Google Scholar]

134. Matsuura M, et al. 1997. A bacterial group II intron encoding reverse transcriptase, maturase, and DNA endonuclease activities: biochemical demonstration of maturase activity and insertion of new genetic information within the intron. Genes Dev. 11, 2910–2924. ( 10.1101/gad.11.21.2910) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

135. Lynch M, Richardson AO. 2002. The evolution of spliceosomal introns. Curr. Opin. Genet. Dev. 12, 701–710. ( 10.1016/S0959-437X(02)00360-X) [PubMed] [CrossRef] [Google Scholar]

136. Audibert A, Weil D, Dautry F. 2002. In vivo kinetics of mRNA splicing and transport in mammalian cells. Mol. Cell. Biol. 22, 6706–6718. ( 10.1128/MCB.22.19.6706-6718.2002) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

137. Collins L, Penny D. 2005. Complex spliceosomal organization ancestral to extant eukaryotes. Mol. Biol. Evol. 22, 1053–1066. ( 10.1093/molbev/msi091) [PubMed] [CrossRef] [Google Scholar]

138. Rogozin IB, Wolf YI, Sorokin AV, Mirkin BG, Koonin EV. 2003. Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr. Biol. 13, 1512–1517. ( 10.1016/S0960-9822(03)00558-X) [PubMed] [CrossRef] [Google Scholar]

139. Roy SW, Gilbert W. 2005. Rates of intron loss and gain: implications for early eukaryotic evolution. Proc. Natl Acad. Sci. USA 102, 5773–5778. ( 10.1073/pnas.0500383102) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

140. Mans BJ, Anantharaman V, Aravind L, Koonin EV. 2004. Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. Cell Cycle 3, 1612–1637. ( 10.4161/cc.3.12.1345) [PubMed] [CrossRef] [Google Scholar]

141. Staub E, Fiziev P, Rosenthal A, Hinzmann B. 2004. Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire. Bioessays 26, 567–581. ( 10.1002/bies.20032) [PubMed] [CrossRef] [Google Scholar]

142. Ptashne M. 2013. Epigenetics: core misconcept. Proc. Natl Acad. Sci. USA 110, 7101–7103. ( 10.1073/pnas.1305399110) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

143. Tielens AGM, Rotte C, van Hellemond JJ, Martin W. 2002. Mitochondria as we don't know them. Trends Biochem. Sci. 27, 564–572. ( 10.1016/S0968-0004(02)02193-X) [PubMed] [CrossRef] [Google Scholar]

144. Martin W, et al. 2002. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc. Natl Acad. Sci. USA 99, 12 246–12 251. ( 10.1073/pnas.182432999) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

145. Rotte C, Stejskal F, Zhu G, Keithly JS, Martin W. 2001. Pyruvate:NADP+ oxidoreductase from the mitochondrion of Euglena gracilis and from the apicomplexan Cryptosporidium parvum: a fusion of pyruvate:ferredoxin oxidoreductase and NADPH-cytochrome P450 reductase. Mol. Biol. Evol. 18, 710–720. ( 10.1093/oxfordjournals.molbev.a003853) [PubMed] [CrossRef] [Google Scholar]

146. Hoffmeister M, van der Klei A, Rotte C, van Grinsven KWA, van Hellemond JJ, Henze K, Tielens AGM, Martin W. 2004. Euglena gracilis rhodoquinone:ubiquinone ratio and mitochondrial proteome differ under aerobic and anaerobic conditions. J. Biol. Chem. 279, 22 422–22 429. ( 10.1074/jbc.M400913200) [PubMed] [CrossRef] [Google Scholar]

147. Atteia A, van Lis R, Gelius-Dietrich G, Adrait A, Garin J, Joyard J, Rolland N, Martin W. 2006. Pyruvate:formate lyase and a novel route of eukaryotic ATP-synthesis in anaerobic Chlamydomonas mitochondria. J. Biol. Chem. 281, 9909–9918. ( 10.1074/jbc.M507862200) [PubMed] [CrossRef] [Google Scholar]

148. Atteia A, et al. 2009. A proteomic survey of Chlamydomonas reinhardtii mitochondria sheds new light on the metabolic plasticity of the organelle and on the nature of the α-proteobacterial mitochondrial ancestor. Mol. Biol. Evol. 29, 1533–1548. ( 10.1093/molbev/msp068) [PubMed] [CrossRef] [Google Scholar]

149. Atteia A, van Lis R, Tielens AGM, Martin WF. 2013. Anaerobic energy metabolism in unicellular photosynthetic eukaryotes. Biochim. Biophys. Acta 1827, 210–223. ( 10.1016/j.bbabio.2012.08.002) [PubMed] [CrossRef] [Google Scholar]

150. Price DC, et al. 2012. Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science 335, 843–847. ( 10.1126/science.1213561) [PubMed] [CrossRef] [Google Scholar]

151. Ku C, Roettger M, Zimorski V, Nelson-Sathi S, Sousa FL, Martin WF. 2014. Plastid origin: who, when and why? Acta Soc. Bot. Pol. 83, 281–289. ( 10.5586/asbp.2014.045) [CrossRef] [Google Scholar]

152. Domman D, Horn M, Embley TM, Williams TA. 2015. Plastid establishment did not require a chlamydial partner. Nat. Comm. 6, 6421 ( 10.1038/ncomms7421) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

153. Deusch O, Landan G, Roettger M, Gruenheit N, Kowallik KV, Allen JF, Martin W, Dagan T. 2008. Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor. Mol. Biol. Evol. 25, 748–761. ( 10.1093/molbev/msn022) [PubMed] [CrossRef] [Google Scholar]

154. Dagan T, et al. 2013. Genomes of stigonematalean cyanobacteria (Subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome Biol. Evol. 5, 31–44. ( 10.1093/gbe/evs117) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

155. Dolezal P, Likic V, Tachezy J, Lithgow T. 2006. Evolution of the molecular machines for protein import into mitochondria. Science 313, 314–318. ( 10.1126/science.1127895) [PubMed] [CrossRef] [Google Scholar]

156. Schleiff EE, Becker TT. 2011. Common ground for protein translocation: Access control for mitochondria and chloroplasts. Nat. Rev. Mol. Cell Biol. 12, 48–59. ( 10.1038/nrm3027) [PubMed] [CrossRef] [Google Scholar]

157. Gould SB, Waller RF, McFadden GI. 2008. Plastid evolution. Annu. Rev. Plant Biol. 59, 491–517. ( 10.1146/annurev.arplant.59.032607.092915) [PubMed] [CrossRef] [Google Scholar]

158. Curtis BA, et al. 2012. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature 492, 59–65. ( 10.1038/nature11681) [PubMed] [CrossRef] [Google Scholar]

159. Gould SB. 2012. Evolutionary genomics: algae's complex origins. Nature 492, 46–48. ( 10.1038/nature11759) [PubMed] [CrossRef] [Google Scholar]

160. Ball SG, et al. 2013. Metabolic effectors secreted by bacterial pathogens: essential facilitators of plastid endosymbiosis. Plant Cell 25, 7–21. ( 10.1105/tpc.112.101329) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

161. Moreira D, Deschamps P. 2014. What was the real contribution of endosymbionts to the eukaryotic nucleus? Insights from photosynthetic eukaryotes. Cold Spring Harb. Perspect. Biol. 6, a016014 ( 10.1101/cshperspect.a016014) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

162. Deschamps P. 2014. Primary endosymbiosis: have cyanobacteria and chlamydiae ever been roommates? Acta Soc. Bot. Pol. 83, 291–302. ( 10.5586/asbp.2014.048) [CrossRef] [Google Scholar]

163. Degli-Esposti M. 2014. Bioenergetic evolution in proteobacteria and mitochondria. Genome Biol. Evol. 6, 3238–3251. ( 10.1093/gbe/evu257) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

164. Allen JF. 1993. Control of gene-expression by redox potential and the requirement for chloroplast and mitochondrial genomes. J. Theor. Biol. 165, 609–631. ( 10.1006/jtbi.1993.1210) [PubMed] [CrossRef] [Google Scholar]

165. Allen JF. 2003. The function of genomes in bioenergetic organelles. Phil. Trans. R. Soc. Lond. B 358, 19–37. ( 10.1098/rstb.2002.1191) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

166. Lane N. 2015. The vital question: why is life the way it is? London, UK: Profile Books. [Google Scholar]

167. Von Heijne G. 1986. Why mitochondria need a genome. FEBS Lett. 198, 1–4. ( 10.1016/0014-5793(86)81172-3) [PubMed] [CrossRef] [Google Scholar]

168. Koonin EV, Yutin N. 2014. The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes. Cold Spring Harb. Perspect. Biol. 6, a016188 ( 10.1101/cshperspect.a016188) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

169. Williams TA, Foster PG, Nye TMW, Cox CJ, Embley TM. 2012. A congruent phylogenomic signal places eukaryotes within the Archaea. Proc. R. Soc. B 279, 4870–4879. ( 10.1098/rspb.2012.1795) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

170. Petitjean C, Deschamps P, López-García P, Moreira D. 2014. Rooting the domain archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota. Genome Biol. Evol. 7, 191–204. ( 10.1093/gbe/evu274) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

171. Liu YC, Beer LL, Whitman WB. 2012. Methanogens: a window into ancient sulphur metabolism. Trends Micobiol. 20, 251–258. ( 10.1016/j.tim.2012.02.002) [PubMed] [CrossRef] [Google Scholar]

172. Ueno Y, Yamada K, Yoshida N, Maruyama S, Isozaki Y. 2006. Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era. Nature 440, 516–519. ( 10.1038/nature04584) [PubMed] [CrossRef] [Google Scholar]

173. Decker K, Jungermann K, Thauer RK. 1970. Energy production in anaerobic organisms. Angew. Chem. Int. Ed. Engl 9, 138–158. ( 10.1002/anie.197001381) [PubMed] [CrossRef] [Google Scholar]

174. Proskurowski G, Lilley MD, Seewald JS, Fruh-Green GL, Olson EJ, Lupton JE, Sylva SP, Kelley DS. 2008. Abiogenic hydrocarbon production at Lost City hydrothermal field. Science 319, 604–607. ( 10.1126/science.1151194) [PubMed] [CrossRef] [Google Scholar]

175. McCollom TM, Seewald JS. 2013. Serpentinites, hydrogen, and life. Elements 9, 129–134. ( 10.2113/gselements.9.2.129) [CrossRef] [Google Scholar]

176. Schrenk MO, Brazelton WJ, Lang SQ. 2013. Serpentinization, carbon, and deep life. Rev. Mineral. Geochem. 75, 575–606. ( 10.2138/rmg.2013.75.18) [CrossRef] [Google Scholar]

177. Russell MJ, Hall AJ, Martin W. 2010. Serpentinization as a source of energy at the origin of life. Geobiology 8, 355–371. ( 10.1111/j.1472-4669.2010.00249.x) [PubMed] [CrossRef] [Google Scholar]

178. Martin W, Russell MJ. 2007. On the origin of biochemistry at an alkaline hydrothermal vent. Phil. Trans. R. Soc. B 362, 1887–1925. ( 10.1098/rstb.2006.1881) [PMC free article] [PubMed] [CrossRef] [Google Scholar]

179. Lane N, Martin WF. 2012. The origin of membrane bioenergetics. Cell 151, 1406–1416. ( 10.1016/j.cell.2012.11.050) [PubMed] [CrossRef] [Google Scholar]

180. Martin WF, Sousa FL, Lane N. 2014. Energy at life's origin. Science 344, 1092–1093. ( 10.1126/science.1251653) [PubMed] [CrossRef] [Google Scholar]

181. Sousa FL, Martin WF. 2014. Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism. Biochim. Biophys. Acta 1837, 964–981. ( 10.1016/j.bbabio.2014.02.001) [PubMed] [CrossRef] [Google Scholar]

Page 2

Models describing the origin of the nucleus in eukaryotes. (a–o) Schematic of various models accounting for the origin of the nucleus. Archaeal cells/membranes are represented with red, while blue indicates eubacterial cells/membranes. Black membranes are used when the phylogenetic identity of the cell is not clear or not specified. See also [22,53].

Click on the image to see a larger version.