Schaap P et al (2006) Molecular phylogeny and evolution of morphology in the social amoebas. Science 314:661–663
Schmidt AR, Do ¨rfelt H, Perrichot V (2007) Carnivorous Fungi from
Cretaceous amber. Science 318:1743
Schnepf E, Ku ¨hn SF, Bulman S (2000) Phagomyxa bellerocheae sp.
nov. and Phagomyxa odontellae sp. nov., Plasmodiophoromycetes
feeding on marine diatoms. Helgol Mar Res 54:237–241
Schoenwaelder MEA (2002) The occurrence and cellular significance
of physodes in brown algae. Phycologia 41:125–139
Scott JL, Baca B, Ott FD, West JA (2006) Light and electron microscopic
observations on Erythrolobus coxiae gen. et sp. nov. (Porphyridiophyceae, Rhodophyta) from Texas U.S.A. Algae 21:407–416
Selosse MA, Le Tacon F (1998) The land flora: a phototroph- fungus
partnership? Trends Ecol Evol 13:15–20
Seo KS, Fritz L (2002) Diel changes in pyrenoid and starch reserves in
dinoflagellates. Phycologia 41:22–28
Shalchian-Tabrizi K et al (2006) Telonemia, a new protest phylum with
affinity to chromist lineages. Proc Roy Soc B 273:1833–1842
Silberman JD, Collins AG, Gershwin LA, Johnson PJ, Roger AJ (2004)
Ellobiopsids of the genus Thalassomyces are Alveolates. J Eukaryot
Microbiol 51:246–252
Simpson AGB (2003) Cytoskeletal organization, phylogenetic
affinities and systematic in the contentious taxon Excavata
(Eukaryota). Int J Syst Evol Microbiol 53:1759–1777
Sims PA, Mann DG, Medlin LK (2006) Evolution of the diatoms: insights
from fossil, biological and molecular data. Phycologia 45:361–402
Sinninghe-Damste ´ JS et al (2004) The rise of rhizosolenid diatoms.
Science 304:584–587
Six C, Worden AZ, Rodrı ´guez F, Moreau H, Partensky F (2005) New
insights into the nature and phylogeny of Prasinophyte antenna
proteins: Ostreococcus tauri, a case study. Mol Biol Evol
22:2217–2230
S ˇ lapeta J, Lo ´pez-Garcı ´a P, Moreira D (2005a) Global dispersal and
ancient cryptic species in the smallest marine eukaryotes. Mol Biol
Evol 23:23–29
S ˇ lapeta J, Moreira D, Lo ´pez-Garcı ´a P (2005b) The extent of protist
diversity: insights from molecular ecology of freshwater
eukaryotes. Proc Roy Soc B 272:2073–2081
Smirnov A, Berney C, Nikolaev S, Pochon X, Pawlowski J (2009)
Molecular phylogeny of amoeboid protists. www.biani.unige.ch/
msg/Amoeboids/Amoebozoa/html
Smith M, Hansen J (2007) Interaction between Mesodinium rubrum
and its prey: importance of prey concentration, irradiance and pH.
Mar Ecol Prog Ser 338:61–70
Steenkamp ET, Wright J, Baldauf SL (2006) The protistan origin of
animal and fungi. Mol Biol Evol 23:93–106
Stevenson RN, South GR (1974) Coccomyxa parasitica sp. nov.
(Coccomyxaceae, Chlorococcales), a parasite of giant scallops in
Newfounland. Br Phycol Bull 9:319–329
Stevenson RN, South GR (1976) Observations on phagocytosis of
Coccomyxa parasitica (Coccomyxaceae: Chlorococcales) in
Placopecten magellanicus. J Invertebr Pathol 25:307–311
Swanberg NR, Anderson OR (1981) Collozoum caudatum sp. nov.: a
giant colonial radiolarian from equatorial and Gulf Stream waters.
Deep Sea Res 28A(9):1033–1047
Takahashi F, Okabe Y, Nakada T, Sekimoto H, Ito M, Kataoka H,
Nozaki H (2007) Origins of the secondary plastids of Euglenophyta
and Chlorarachniophyta as revealed by an analysis of the plastidtargeting, nuclear-encoded gene psbO. J Phycol 43:1302–1309
Tanifuji G, Onodera NT, Wheeler TJ, Dlutek M, Donaher N, Archibald
JM (2011) Complete nucleomorph genome sequence of the
nonphotosynthetic alga Cryptomonas paramecium reveals a core
nucleomorph gene set. Genome Biol Evol 3:44–54
Thu ¨s H, Muggia L, Pe ´rez-Ortega S, Favero-Longo SE, Joneson S,
O’Brien H, Nelsen MP, Duque-Thu ¨s R, Grube M, Friedl T,
Brodie J, Andrew CJ, Lu ¨cking R, Lutzoni F, Gueidan C (2011)
Revisiting photobiont diversity inthe lichen family Verrucariaceae
(Ascomycota). Eur J Phycol 46(4):399–415
Todd JD, Rogers R, Li YG, Wexler M, Bond PL, Sun L, Curson ARJ,
Malin G, Steinke M, Johnston AWB (2007) Structural and regulatory genes required to make the gas dimethyl sulfide in bacteria.
Science 315:666–669
Todo Y, Kitazato H, Hashimoto J, Gooday AJ (2005) Simple foraminifera flourish at the ocean deepest point. Science 307:689
Tregouboff G (1953a) Classe des Radiolaires. In: Grasse ´ PP (ed) Traite ´
de zoologie. Anatomie, syste ´matique, biologie, Tome I. Protozoaires:
Rhizopodes, Actinopodes, Sporozoaires, Cnidosporidies. Fasicule II.
Masson & Cie, Paris, pp 321–436
Tregouboff G (1953b) Classe des He ´liozoaires. In: Grasse ´ PP (ed) Traite ´
de zoologie. Anatomie, syste ´matique, biologie. Tome I. Protozoaires:
Rhizopodes, Actinopodes, Sporozoaires, Cnidosporidies. Fasicule II.
Masson & Cie, Paris, pp 437–489
Tre ´guer P (2002) Les algues et le souffle d’Eole. La Recherche
355:52–53
Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RHY, Aerts A et al
(2006) Phytophtora genome sequences uncover evolutionary
origins and mechanisms of pathogenesis. Science 313:1261–1266
Valiela I (1991) Ecology of coastal ecosystems. In: Barnes RSK, Mann
KH (eds) Fundamentals of aquatic ecology. Blackwell Scientific
Publications, Oxford, pp 57–76
van den Hoek C, Mann DG, Jahns HM (1998) Algae. An introduction to
phycology. Cambridge University Press, Cambridge
Van De Vijver B, Kopalova K (2008) Orthoseira gremmenii sp. nov., a
new aerophylic diatom from Gouth Island (southern Atlantic
Ocean). Cryptogamie Algol 29(2):105–118
Verbruggen H, Maggs CA, Saunders GW, Le Gall L, Yoon HS, De
Clerck O (2010) Data mining approach identifies research priorities
and data requirements for resolving the red algal tree of life. BMC
Evol Biol 10(16):1–15
Versteegh GJM, Blokker P, Wood GD, Collinson ME, Damste ´ JSS, de
Leeuw JW (2004) An example of oxidative polymerization of
unsaturated fatty acids as a preservation pathway for dinoflagellate
organic matter. Org Geochem 35:1129–1139
Viprey M, Guillou L, Ferre ´ol M, Vaulot D (2008) Wide genetic diversity of picoplanktonic green algae (Chloroplastida) in the Mediterranean Sea uncovered by a phylumbiased PCR approach. Environ
Microbiol 10:1804–1822
Vogelbein WK, Lovko VJ, Shields JD, Reece KS, Mason PL, Haas
LW, Walker CC (2002) Pfiesteria shumwayae kills fish by
micropredation not by exotoxin secretion. Nature 418:967–970
Webster JP (2001) Rats, cats, people and parasites: the impact of latent
toxoplasmosis on behaviour. Microbes Infect 3:1037–1045
Wellman CH, Osterloff PL, Mohiuddin U (2003) Fragments of the
earliest land plants. Nature 425:282–285
Williams BAP, Hirt RP, Lucocq JM, Embley TM (2002) A mitochondrial remnant in the microsporidian Trachipleistophora hominis.
Nature 418:865–869
Yabuki A, Inagaki Y, Ishida KI (2010) Palpitomonas bilix gen. et sp.
nov.: a novel deep-branching heterotroph possibly related to
Archaeplastida or Hacrobia. Protist 161:523–538
Yoon HS, Ciniglia C, Wu M, Comeron JM, Pinto G, Pollio A,
Bhattacharya D (2006a) Establishment of endolithic populations
of extremophilic Cyanidiales (Rhodophyta). BMC Evol Biol
6:78
Yoon HS, Mu ¨ller KM, Sheath RG, Ott FD, Bhattacharya D (2006b)
Defining the major lineages of red algae (Rhodophyta). J Phycol
42:482–492
Yuan X, Xiao S, Taylor TN (2005) Lichen-like symbiosis 600 million
years ago. Science 308:1017–1020
Zhao S, Burki F, Bra ˚te J, Keeling PJ, Klaveness D, Salchian-Tabrizi K
(2012) Collodictyon – an ancient lineage in the tree of Eukaryotes.
Mol Biol Evol 29(6):1557–1568
7 Taxonomy and Phylogeny of Unicellular Eukaryotes
257
Schmidt AR, Do ¨rfelt H, Perrichot V (2007) Carnivorous Fungi from
Cretaceous amber. Science 318:1743
Schnepf E, Ku ¨hn SF, Bulman S (2000) Phagomyxa bellerocheae sp.
nov. and Phagomyxa odontellae sp. nov., Plasmodiophoromycetes
feeding on marine diatoms. Helgol Mar Res 54:237–241
Schoenwaelder MEA (2002) The occurrence and cellular significance
of physodes in brown algae. Phycologia 41:125–139
Scott JL, Baca B, Ott FD, West JA (2006) Light and electron microscopic
observations on Erythrolobus coxiae gen. et sp. nov. (Porphyridiophyceae, Rhodophyta) from Texas U.S.A. Algae 21:407–416
Selosse MA, Le Tacon F (1998) The land flora: a phototroph- fungus
partnership? Trends Ecol Evol 13:15–20
Seo KS, Fritz L (2002) Diel changes in pyrenoid and starch reserves in
dinoflagellates. Phycologia 41:22–28
Shalchian-Tabrizi K et al (2006) Telonemia, a new protest phylum with
affinity to chromist lineages. Proc Roy Soc B 273:1833–1842
Silberman JD, Collins AG, Gershwin LA, Johnson PJ, Roger AJ (2004)
Ellobiopsids of the genus Thalassomyces are Alveolates. J Eukaryot
Microbiol 51:246–252
Simpson AGB (2003) Cytoskeletal organization, phylogenetic
affinities and systematic in the contentious taxon Excavata
(Eukaryota). Int J Syst Evol Microbiol 53:1759–1777
Sims PA, Mann DG, Medlin LK (2006) Evolution of the diatoms: insights
from fossil, biological and molecular data. Phycologia 45:361–402
Sinninghe-Damste ´ JS et al (2004) The rise of rhizosolenid diatoms.
Science 304:584–587
Six C, Worden AZ, Rodrı ´guez F, Moreau H, Partensky F (2005) New
insights into the nature and phylogeny of Prasinophyte antenna
proteins: Ostreococcus tauri, a case study. Mol Biol Evol
22:2217–2230
S ˇ lapeta J, Lo ´pez-Garcı ´a P, Moreira D (2005a) Global dispersal and
ancient cryptic species in the smallest marine eukaryotes. Mol Biol
Evol 23:23–29
S ˇ lapeta J, Moreira D, Lo ´pez-Garcı ´a P (2005b) The extent of protist
diversity: insights from molecular ecology of freshwater
eukaryotes. Proc Roy Soc B 272:2073–2081
Smirnov A, Berney C, Nikolaev S, Pochon X, Pawlowski J (2009)
Molecular phylogeny of amoeboid protists. www.biani.unige.ch/
msg/Amoeboids/Amoebozoa/html
Smith M, Hansen J (2007) Interaction between Mesodinium rubrum
and its prey: importance of prey concentration, irradiance and pH.
Mar Ecol Prog Ser 338:61–70
Steenkamp ET, Wright J, Baldauf SL (2006) The protistan origin of
animal and fungi. Mol Biol Evol 23:93–106
Stevenson RN, South GR (1974) Coccomyxa parasitica sp. nov.
(Coccomyxaceae, Chlorococcales), a parasite of giant scallops in
Newfounland. Br Phycol Bull 9:319–329
Stevenson RN, South GR (1976) Observations on phagocytosis of
Coccomyxa parasitica (Coccomyxaceae: Chlorococcales) in
Placopecten magellanicus. J Invertebr Pathol 25:307–311
Swanberg NR, Anderson OR (1981) Collozoum caudatum sp. nov.: a
giant colonial radiolarian from equatorial and Gulf Stream waters.
Deep Sea Res 28A(9):1033–1047
Takahashi F, Okabe Y, Nakada T, Sekimoto H, Ito M, Kataoka H,
Nozaki H (2007) Origins of the secondary plastids of Euglenophyta
and Chlorarachniophyta as revealed by an analysis of the plastidtargeting, nuclear-encoded gene psbO. J Phycol 43:1302–1309
Tanifuji G, Onodera NT, Wheeler TJ, Dlutek M, Donaher N, Archibald
JM (2011) Complete nucleomorph genome sequence of the
nonphotosynthetic alga Cryptomonas paramecium reveals a core
nucleomorph gene set. Genome Biol Evol 3:44–54
Thu ¨s H, Muggia L, Pe ´rez-Ortega S, Favero-Longo SE, Joneson S,
O’Brien H, Nelsen MP, Duque-Thu ¨s R, Grube M, Friedl T,
Brodie J, Andrew CJ, Lu ¨cking R, Lutzoni F, Gueidan C (2011)
Revisiting photobiont diversity inthe lichen family Verrucariaceae
(Ascomycota). Eur J Phycol 46(4):399–415
Todd JD, Rogers R, Li YG, Wexler M, Bond PL, Sun L, Curson ARJ,
Malin G, Steinke M, Johnston AWB (2007) Structural and regulatory genes required to make the gas dimethyl sulfide in bacteria.
Science 315:666–669
Todo Y, Kitazato H, Hashimoto J, Gooday AJ (2005) Simple foraminifera flourish at the ocean deepest point. Science 307:689
Tregouboff G (1953a) Classe des Radiolaires. In: Grasse ´ PP (ed) Traite ´
de zoologie. Anatomie, syste ´matique, biologie, Tome I. Protozoaires:
Rhizopodes, Actinopodes, Sporozoaires, Cnidosporidies. Fasicule II.
Masson & Cie, Paris, pp 321–436
Tregouboff G (1953b) Classe des He ´liozoaires. In: Grasse ´ PP (ed) Traite ´
de zoologie. Anatomie, syste ´matique, biologie. Tome I. Protozoaires:
Rhizopodes, Actinopodes, Sporozoaires, Cnidosporidies. Fasicule II.
Masson & Cie, Paris, pp 437–489
Tre ´guer P (2002) Les algues et le souffle d’Eole. La Recherche
355:52–53
Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RHY, Aerts A et al
(2006) Phytophtora genome sequences uncover evolutionary
origins and mechanisms of pathogenesis. Science 313:1261–1266
Valiela I (1991) Ecology of coastal ecosystems. In: Barnes RSK, Mann
KH (eds) Fundamentals of aquatic ecology. Blackwell Scientific
Publications, Oxford, pp 57–76
van den Hoek C, Mann DG, Jahns HM (1998) Algae. An introduction to
phycology. Cambridge University Press, Cambridge
Van De Vijver B, Kopalova K (2008) Orthoseira gremmenii sp. nov., a
new aerophylic diatom from Gouth Island (southern Atlantic
Ocean). Cryptogamie Algol 29(2):105–118
Verbruggen H, Maggs CA, Saunders GW, Le Gall L, Yoon HS, De
Clerck O (2010) Data mining approach identifies research priorities
and data requirements for resolving the red algal tree of life. BMC
Evol Biol 10(16):1–15
Versteegh GJM, Blokker P, Wood GD, Collinson ME, Damste ´ JSS, de
Leeuw JW (2004) An example of oxidative polymerization of
unsaturated fatty acids as a preservation pathway for dinoflagellate
organic matter. Org Geochem 35:1129–1139
Viprey M, Guillou L, Ferre ´ol M, Vaulot D (2008) Wide genetic diversity of picoplanktonic green algae (Chloroplastida) in the Mediterranean Sea uncovered by a phylumbiased PCR approach. Environ
Microbiol 10:1804–1822
Vogelbein WK, Lovko VJ, Shields JD, Reece KS, Mason PL, Haas
LW, Walker CC (2002) Pfiesteria shumwayae kills fish by
micropredation not by exotoxin secretion. Nature 418:967–970
Webster JP (2001) Rats, cats, people and parasites: the impact of latent
toxoplasmosis on behaviour. Microbes Infect 3:1037–1045
Wellman CH, Osterloff PL, Mohiuddin U (2003) Fragments of the
earliest land plants. Nature 425:282–285
Williams BAP, Hirt RP, Lucocq JM, Embley TM (2002) A mitochondrial remnant in the microsporidian Trachipleistophora hominis.
Nature 418:865–869
Yabuki A, Inagaki Y, Ishida KI (2010) Palpitomonas bilix gen. et sp.
nov.: a novel deep-branching heterotroph possibly related to
Archaeplastida or Hacrobia. Protist 161:523–538
Yoon HS, Ciniglia C, Wu M, Comeron JM, Pinto G, Pollio A,
Bhattacharya D (2006a) Establishment of endolithic populations
of extremophilic Cyanidiales (Rhodophyta). BMC Evol Biol
6:78
Yoon HS, Mu ¨ller KM, Sheath RG, Ott FD, Bhattacharya D (2006b)
Defining the major lineages of red algae (Rhodophyta). J Phycol
42:482–492
Yuan X, Xiao S, Taylor TN (2005) Lichen-like symbiosis 600 million
years ago. Science 308:1017–1020
Zhao S, Burki F, Bra ˚te J, Keeling PJ, Klaveness D, Salchian-Tabrizi K
(2012) Collodictyon – an ancient lineage in the tree of Eukaryotes.
Mol Biol Evol 29(6):1557–1568
7 Taxonomy and Phylogeny of Unicellular Eukaryotes
257