Bhattacharya D, Yoon HS, Hackett JD (2003) Photosynthetic
eukaryotes unite: endosymbiosis connects the dots. Bioessays 25(1):
50–60
Bodyl A (2005) Do plastid-related characters support the
chromalveolate hypothesis? J Phycol 41:712–718
Bodyl A, Stiller JW, Mackiewicz P (2009) Chromalveolate plastids: direct
descent or multiple endosymbioses? Trends Ecol Evol 24(3):119–121
Bonen L, Doolittle W (1975) On the prokaryotic nature of red algal
chloroplasts. Proc Natl Acad Sci U S A 72:2310–2314
Bornens M, Azimzadeh J (2007) Origin and evolution of the centrosome.
In: Je ´keli G (ed) Eukaryotic membranes and cytoskeleton: origin and
evolution. Land Bioscience, Austin (Tx), pp 119–129
Boudouresque CF, Go ´mez A (1995) Une approche moderne du monde
ve ´ge ´tal. Premie `re Partie. GIS Posidonie Publishing, Marseille
Boullard B (1990) Guerre et paix dans le re `gne ve ´ge ´tal. Edition Marketing, Paris, France
Boxma B, De Graaf RM, van der Staay GWM, van Alen TA, Ricard G,
Gabaldon T, van Hoek AHAM, Moon-van der Staay SY, Koopman
WJH, van Hellemond JJ, Tielens AGM, Friedrich T, Veenhuis M,
Huynen MA, Hackstein JHP (2005) An anaerobic mitochondrion
that produces hydrogen. Nature 434:74–79
Boyen C, Oudot MP, Loiseaux-De Goer S (2001) Origin and evolution
of plastids and mitochondria: the phylogenetic diversity of algae.
Cah Biol Mar 42:11–24
Brocks JJ, Logan GA, Buick R, Summons RE (1999) Archean molecular fossils and the early rise of eukaryotes. Science 285:1033–1036
Buick R (2010) Ancient acritarchs. Nature 463:885–886
Burki F, Okamoto N, Pombert JF, Keeling PJ (2012) The evolutionary
history of haptophytes and cryptophytes: phylogenomic evidence
for separate origins. Proc Royal Soc B 279:2246–2254
Butterfield NJ (2000) Bangiomorpha pubescens n.gen., n. sp.:
implications for the evolution of sex, multicellularity, and the
Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology 26(3):386–404
Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman
JR, Bidwell SL (2007) Draft genome sequence of the sexually
transmitted pathogen Trichomonas vaginalis. Science 315:207–212
Carvalho-Santos Z, Azimzadeh J, Pereira-Leal JB, Bettencourt-Dias M
(2011) Tracing the origin of centrioles, cilia and flagella. J Cell Biol
194(2):165–175
Cavalier-Smith T (1981) Eukaryote kingdoms: seven or nine?
BioSystems 14:461–481
Cavalier-Smith T (2002a) The neomurian origin of archaebacteria, the
negibacterial root of the universal tree and the bacterial megaclassification. Int J Syst Evol Microbiol 52:7–76
Cavalier-Smith T (2002b) The phagotrophic origin of eukaryotes and
phylogenetic classification of protozoa. Int J Syst Evol Microbiol
52:295–354
Ce ´re ´monie H, Buret F, Simonet P, Vogel TM (2004) Isolation of
lightning-competent soil bacteria. Appl Environ Microbiol
70:6342–6346
Chadefaud M (1960) Tome I: Les ve ´ge ´taux non vasculaires.
Cryptogamie. In: Chadefaud M. et Emberger L (eds) Traite ´ de
botanique syste ´matique. Masson et Cie Publishing, Paris, pp –ixv + 1–1018
Chen M, Hiller RG, Howe CJ, Larkum AWD (2005) Unique origin and
lateral transfer of prokaryotic chlorophyll-b and chlorophyll-d light
harvesting systems. Mol Biol Evol 22(1):21–28
Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P
(2006) Toward automatic reconstruction of a highly resolved tree of
Life. Science 311:1283–1286
Claverie JM (2006) Viruses take center stage in cellular evolution.
Genome Biol 7:110
Claverie JM, Abergel C (2009) Mimivirus and its virophage. Annu Rev
Gen 43:49–66
Claverie JM, Abergel C (2010) Mimivirus: the emerging paradox of
quasi-autonomous viruses. Trends Genet 26:431–437
Claverie JM, Otaga H, Audic S, Abergel C, Suhre K, Fournier PE
(2006) Mimivirus and the emerging concept of “giant” virus.
Virus Res 117:133–144
Combes C (1995) Les interactions durables. Ecologie et e ´volution du
parasitisme. Masson Publishing, Paris
Combes C (2001) Les associations du vivant. L’art d’e ˆtre parasite.
Flammarion Publishing, Paris
Courties C, Vaquer A, Troussellier M, Lautier J, Chre ´tiennot-Dinet MJ,
Neuveux J, Machado C, Claustre H (1994) Smallest eukaryotic
organism. Nature 370:255
Curtis NE, Massey SE, Pierce SK (2006) The symbiotic chloroplasts in
the Sacoglossan Elysia clarki are from several algal species. Invert
Biol 125(4):336–345
Dagan T, Martin W (2009) Seeing green and red in diatom genomes.
Science 324:1651–1652
Darwin C (1859) On the origin of species by means of natural selection,
or the preservation of favoured races in the struggle for life. John
Murray, London
Daubin V, Gouy M, Perriere G (2001) Bacterial molecular phylogeny
using supertree approach. Genome Inform Ser Workshop Genome
Inform 12:155–164
Di Giulio M (2003) The universal ancestor and the ancestor of bacteria
were hyperthermophiles. J Mol Evol 57:721–730
Doolittle WF (1999) Phylogenetic classification and the universal tree.
Science 284:2124–2128
Dyall SD, Brown MT, Johnson PJ (2004) Ancient invasions: from
endosymbionts to organelles. Science 304:253–257
El Albani A, Bengston S, Canfield DE, Bekker A, Macchiarelli R,
Mazurier A, Hammarlund EU, Boulvais P, Dupuy JJ, Fontaine C,
Fu ¨rsich FT, Gauthier-Lafay F, Janvier P, Javaux E, Ossa Ossa F,
Pierson-Wickmann AC, Riboulleau A, Sardini P, Vachard D,
Whitehoute M, Meunier A (2010) Large colonial organisms with
coordinated growth in oxygenated environments 2.1 Gyr ago.
Nature 466:100–104
Embley TM, Martin W (2006) Eukaryotic evolution, changes and
challenges. Nature 440:623–630
Falkowski PG, Katz ME, Knoll AH, Quigg A, Raven JA, Schofield O,
Taylor FJR (2004) The evolution of modern eukaryotic phytoplankton. Science 305:354–360
Feldmann J, Feldmann G (1946) Recherches sur l’appareil conducteur
des Floride ´es. Rev Cytol 8:159–209
Fischer MG et al (2010) Giant virus with a remarkable complement of
genes infects marine zooplankton. Proc Natl Acad Sci U S A
107:19508–19513
Forterre P, Philippe H (1999) The last universal common ancestor
(LUCA): simple or complex? Biol Bull 196:373–375; discussion:
375–377
Fox GE, Stackbrandt E, Hespell RB, Gibson J, Maniloff J, Dyer TA,
Wolfe RS, Balch WE, Tanner RS, Magrum LJ, Zablen B,
Blakemore R, Gupta R, Bonen L, Lewis BJ, Stahl DA, Luehrsen
KR, Chen KN, Woese CR (1980) The phylogeny of prokaryotes.
Science 209:457–463
Galtier N, Tourasse N, Gouy M (1999) A nonhyperthermophilic common ancestor to extant life forms. Science 283:220–221
Germot A, Philippe H, Le Guyader H (1997) Evidence for loss of
mitochondria in Microsporidia from a mitochondrial-type HSP70
in Nosema locustae. Mol Biochem Parasit 87:159–168
Gorenflot R, Guern M (1989) Organisation et biologie des
Thallophytes. Doin Publishing, Paris
Green BR (2005) Lateral gene transfer in the cyanobacteria: chlorophylls,
proteins and scraps of ribosomal RNA. J Phycol 41:449–452
Haeckel E (1894) Systematische Phylogenie. Entwurf eines naturlichen
Systems der Organismen auf Grund ihrer Stammesgeschichte.
142
C.-F. Boudouresque et al.
eukaryotes unite: endosymbiosis connects the dots. Bioessays 25(1):
50–60
Bodyl A (2005) Do plastid-related characters support the
chromalveolate hypothesis? J Phycol 41:712–718
Bodyl A, Stiller JW, Mackiewicz P (2009) Chromalveolate plastids: direct
descent or multiple endosymbioses? Trends Ecol Evol 24(3):119–121
Bonen L, Doolittle W (1975) On the prokaryotic nature of red algal
chloroplasts. Proc Natl Acad Sci U S A 72:2310–2314
Bornens M, Azimzadeh J (2007) Origin and evolution of the centrosome.
In: Je ´keli G (ed) Eukaryotic membranes and cytoskeleton: origin and
evolution. Land Bioscience, Austin (Tx), pp 119–129
Boudouresque CF, Go ´mez A (1995) Une approche moderne du monde
ve ´ge ´tal. Premie `re Partie. GIS Posidonie Publishing, Marseille
Boullard B (1990) Guerre et paix dans le re `gne ve ´ge ´tal. Edition Marketing, Paris, France
Boxma B, De Graaf RM, van der Staay GWM, van Alen TA, Ricard G,
Gabaldon T, van Hoek AHAM, Moon-van der Staay SY, Koopman
WJH, van Hellemond JJ, Tielens AGM, Friedrich T, Veenhuis M,
Huynen MA, Hackstein JHP (2005) An anaerobic mitochondrion
that produces hydrogen. Nature 434:74–79
Boyen C, Oudot MP, Loiseaux-De Goer S (2001) Origin and evolution
of plastids and mitochondria: the phylogenetic diversity of algae.
Cah Biol Mar 42:11–24
Brocks JJ, Logan GA, Buick R, Summons RE (1999) Archean molecular fossils and the early rise of eukaryotes. Science 285:1033–1036
Buick R (2010) Ancient acritarchs. Nature 463:885–886
Burki F, Okamoto N, Pombert JF, Keeling PJ (2012) The evolutionary
history of haptophytes and cryptophytes: phylogenomic evidence
for separate origins. Proc Royal Soc B 279:2246–2254
Butterfield NJ (2000) Bangiomorpha pubescens n.gen., n. sp.:
implications for the evolution of sex, multicellularity, and the
Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology 26(3):386–404
Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman
JR, Bidwell SL (2007) Draft genome sequence of the sexually
transmitted pathogen Trichomonas vaginalis. Science 315:207–212
Carvalho-Santos Z, Azimzadeh J, Pereira-Leal JB, Bettencourt-Dias M
(2011) Tracing the origin of centrioles, cilia and flagella. J Cell Biol
194(2):165–175
Cavalier-Smith T (1981) Eukaryote kingdoms: seven or nine?
BioSystems 14:461–481
Cavalier-Smith T (2002a) The neomurian origin of archaebacteria, the
negibacterial root of the universal tree and the bacterial megaclassification. Int J Syst Evol Microbiol 52:7–76
Cavalier-Smith T (2002b) The phagotrophic origin of eukaryotes and
phylogenetic classification of protozoa. Int J Syst Evol Microbiol
52:295–354
Ce ´re ´monie H, Buret F, Simonet P, Vogel TM (2004) Isolation of
lightning-competent soil bacteria. Appl Environ Microbiol
70:6342–6346
Chadefaud M (1960) Tome I: Les ve ´ge ´taux non vasculaires.
Cryptogamie. In: Chadefaud M. et Emberger L (eds) Traite ´ de
botanique syste ´matique. Masson et Cie Publishing, Paris, pp –ixv + 1–1018
Chen M, Hiller RG, Howe CJ, Larkum AWD (2005) Unique origin and
lateral transfer of prokaryotic chlorophyll-b and chlorophyll-d light
harvesting systems. Mol Biol Evol 22(1):21–28
Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P
(2006) Toward automatic reconstruction of a highly resolved tree of
Life. Science 311:1283–1286
Claverie JM (2006) Viruses take center stage in cellular evolution.
Genome Biol 7:110
Claverie JM, Abergel C (2009) Mimivirus and its virophage. Annu Rev
Gen 43:49–66
Claverie JM, Abergel C (2010) Mimivirus: the emerging paradox of
quasi-autonomous viruses. Trends Genet 26:431–437
Claverie JM, Otaga H, Audic S, Abergel C, Suhre K, Fournier PE
(2006) Mimivirus and the emerging concept of “giant” virus.
Virus Res 117:133–144
Combes C (1995) Les interactions durables. Ecologie et e ´volution du
parasitisme. Masson Publishing, Paris
Combes C (2001) Les associations du vivant. L’art d’e ˆtre parasite.
Flammarion Publishing, Paris
Courties C, Vaquer A, Troussellier M, Lautier J, Chre ´tiennot-Dinet MJ,
Neuveux J, Machado C, Claustre H (1994) Smallest eukaryotic
organism. Nature 370:255
Curtis NE, Massey SE, Pierce SK (2006) The symbiotic chloroplasts in
the Sacoglossan Elysia clarki are from several algal species. Invert
Biol 125(4):336–345
Dagan T, Martin W (2009) Seeing green and red in diatom genomes.
Science 324:1651–1652
Darwin C (1859) On the origin of species by means of natural selection,
or the preservation of favoured races in the struggle for life. John
Murray, London
Daubin V, Gouy M, Perriere G (2001) Bacterial molecular phylogeny
using supertree approach. Genome Inform Ser Workshop Genome
Inform 12:155–164
Di Giulio M (2003) The universal ancestor and the ancestor of bacteria
were hyperthermophiles. J Mol Evol 57:721–730
Doolittle WF (1999) Phylogenetic classification and the universal tree.
Science 284:2124–2128
Dyall SD, Brown MT, Johnson PJ (2004) Ancient invasions: from
endosymbionts to organelles. Science 304:253–257
El Albani A, Bengston S, Canfield DE, Bekker A, Macchiarelli R,
Mazurier A, Hammarlund EU, Boulvais P, Dupuy JJ, Fontaine C,
Fu ¨rsich FT, Gauthier-Lafay F, Janvier P, Javaux E, Ossa Ossa F,
Pierson-Wickmann AC, Riboulleau A, Sardini P, Vachard D,
Whitehoute M, Meunier A (2010) Large colonial organisms with
coordinated growth in oxygenated environments 2.1 Gyr ago.
Nature 466:100–104
Embley TM, Martin W (2006) Eukaryotic evolution, changes and
challenges. Nature 440:623–630
Falkowski PG, Katz ME, Knoll AH, Quigg A, Raven JA, Schofield O,
Taylor FJR (2004) The evolution of modern eukaryotic phytoplankton. Science 305:354–360
Feldmann J, Feldmann G (1946) Recherches sur l’appareil conducteur
des Floride ´es. Rev Cytol 8:159–209
Fischer MG et al (2010) Giant virus with a remarkable complement of
genes infects marine zooplankton. Proc Natl Acad Sci U S A
107:19508–19513
Forterre P, Philippe H (1999) The last universal common ancestor
(LUCA): simple or complex? Biol Bull 196:373–375; discussion:
375–377
Fox GE, Stackbrandt E, Hespell RB, Gibson J, Maniloff J, Dyer TA,
Wolfe RS, Balch WE, Tanner RS, Magrum LJ, Zablen B,
Blakemore R, Gupta R, Bonen L, Lewis BJ, Stahl DA, Luehrsen
KR, Chen KN, Woese CR (1980) The phylogeny of prokaryotes.
Science 209:457–463
Galtier N, Tourasse N, Gouy M (1999) A nonhyperthermophilic common ancestor to extant life forms. Science 283:220–221
Germot A, Philippe H, Le Guyader H (1997) Evidence for loss of
mitochondria in Microsporidia from a mitochondrial-type HSP70
in Nosema locustae. Mol Biochem Parasit 87:159–168
Gorenflot R, Guern M (1989) Organisation et biologie des
Thallophytes. Doin Publishing, Paris
Green BR (2005) Lateral gene transfer in the cyanobacteria: chlorophylls,
proteins and scraps of ribosomal RNA. J Phycol 41:449–452
Haeckel E (1894) Systematische Phylogenie. Entwurf eines naturlichen
Systems der Organismen auf Grund ihrer Stammesgeschichte.
142
C.-F. Boudouresque et al.