Appendix S1: Accession numbers of organisms used in phylogenetic analyses
General tree
Acc number
DQ369018
DQ369015
AB045583
AB058347
AB058368
AB101540
AB101542
AB179735
AB183605
AB183618
AB193602
AB231617
AB246692
AB246697
AF045049
AF054890
AF091146
AF100940
AF107080
AF107081
AF107083
AF107085
AF107087
AF107088
AF107089
AF107577
AF123596
AF166377
AF168884
AF185053
AF290050
AF290063
AF290068
AF290069
AF290071
AF290072
AF290073
AF290077
AF290079
AF293895
AF293898
AF342748
AF472555
AF530525
AJ007284
AJ007286
AJ246269
AJ246271
AJ402329
AJ402330
AJ402331
genus
UEPAC33p4
UEPACLp3
Glaucosphaera
Isochrysis
Geminigera
Dictyocoryne
Spongaster
Eucyrtidium
Imantonia
Emiliania
Leucocryptos
Katablepharis
Pseudocubus
Pterocorys
Nannochloropsis
Lotharella
Collozoum
Monosiga
Helianthus
Bolidomonas
Zea
Symbiomonas
Echinamoeba
Leptomyxa
Compsopogon
Amoebophrya ex Scrippsiella
Hemiselmis
Rhodomonas
Prymnesium
Chrysochromulina
Species/strain/clone name
UEPAC33p4
UEPACLp3
vacuolata
sp. MBIC10464
cryophila MBIC10575
profunda
tetras
hexagonatum
sp. MBIC10497
sp. MBIC10582
marina
japonica
obeliscus
zancleus
salina CCMP537
vacuolata
pelagicum
brevicollis
OLI16029 (75m)
OLI16010 (75m)
OLI26017 (15m)
OLI26047 (15m)
OLI51033 (60m)
OLI51050 (15m)
OLI51059 (60m)
annuus
mediterranea
Prymnesiophyte symbiont
mays
scintillans
DH147-EKD21 (2,000m)
DH144-EKD10 (250m)
DH147-EKD6 (2,000m)
DH147-EKD3 (2,000m)
DH147-EKD16 (2,000m)
DH147-EKD17 (2,000m)
DH147-EKD18 (2,000m)
DH148-EKD27 (3,000m)
DH148-EKD14 (3,000m)
exundans
reticulata
caeruleus
sp.
AT4-94 (sediment 2,264m)
virescens CCMP 443
sp. M1480
parvum K081
kappa EN3
OLI11010 (75m)
OLI11012 (75m)
OLI11013 (75m)
References
Worden, A.Z. 2006
Worden, A.Z. 2006
Yokoyama et al 2004
Unpublished
Unpublished
Takahashi et al 2004
Takahashi et al 2004
Yuasa et al 2005
Unpublished
Unpublished
Okamoto,N. and Inouye,I.
Okamoto,N. and Inouye,I.
Kunitomo et al 2006
Kunitomo et al 2006
Andersen et al 1998
Van de Peer et al 1996
Amaral Zettler et al 1999
Collins,A.G. 1998
Moon-van der Staay et al. 2000
Moon-van der Staay et al. 2000
Moon-van der Staay et al. 2000
Moon-van der Staay et al. 2000
Moon-van der Staay et al. 2000
Moon-van der Staay et al. 2000
Moon-van der Staay et al. 2000
Unpublished
Guillou et al 1999
Gast et al 2000
Unpublished
Guillou et al 1999
Lopez-Garcia et al. 2001
Lopez-Garcia et al. 2001
Lopez-Garcia et al. 2001
Lopez-Garcia et al. 2001
Lopez-Garcia et al. 2001
Lopez-Garcia et al. 2001
Lopez-Garcia et al. 2001
Lopez-Garcia et al. 2001
Lopez-Garcia et al. 2001
Amaral Zettler et al 2000
Amaral Zettler et al 2000
Mueller et al 2001
Gunderson et al 2002
Lopez-Garcia et al. 2003
Marin et al 1998
Marin et al 1998
Unpublished
Unpublished
Moon-van der Staay et al. 2001
Moon-van der Staay et al. 2001
Moon-van der Staay et al. 2001
AJ402334
AJ402339
AJ402341
AJ402342
AJ402343
AJ402350
AJ402356
AJ402357
AJ632204
AY083224
AY129031
AY129038
AY129039
AY129051
AY129055
AY129060
AY129065
AY129066
AY129068
AY129069
AY266292
AY266294
AY294144
AY295689
AY381171
AY381204
AY425310
AY425316
AY426835
AY635830
AY635841
J01353
L07375
Saccharomyces
Perkinsus
OLI11019 (75m)
OLI11026 (75m)
OLI11030 (75m)
OLI11032 (75m)
OLI11511 (75m)
OLI11008 (75m)
OLI11066 (75m)
OLI11006 (75m)
grethae CCAP1077-3
bacillisporus
UEPAC05Ap2 (Surface coastal)
UEPACEp3 (Surface coastal)
UEPACAQp3 (Surface coastal)
UEPAC46p4 (Surface coastal)
UEPACFp5 (Surface coastal)
UEPAC05Cp2 (Surface coastal)
UEPAC37p4 (Surface coastal)
UEPACCp4 (Surface coastal)
UEPACOp5 (Surface coastal)
UEPACRp5 (Surface coastal)
trigonopa
scolymantha
stenopodia
RA010613.144 (Surface coastal)
HE001005.112 (Surface coastal)
BL001221.26 (Surface coastal)
sp. RCC 143
pusilla
BL000921.8 (Surface coastal)
sp. JEL342 AFTOL-ID 47
ranarum AFTOL-ID 301
N414.27/WS (50m)
cerevisiae
sp.
L37415
M88521
Toxoplasma
Symbiodinium
gondii
microadriaticum
U03479
U07403
U14386
U21338
U37107
U42381
X53904
X68483
X81811
Y16234
Y19155
Z15105
Chlorarachnion
Acanthamoeba
Pelagococcus
Labyrinthuloides
Developayella
Ochromonas
Volvox
Cyanophora
Paulinella
Prorocentrum
Amoebidium
Babesia
CCMP242
castellanii
subviridis
haliotidis
elegans
CCMP584
carteri
paradoxa
chromatophora
arenarium
Parasiticum ATCC 32708
equi
Skeletonema
Cryptococcus
Aulosphaera
Aulacantha
Platyamoeba
Ostreococcus
Micromonas
Catenomyces
Basidiobolus
DQ060524
Moon-van der Staay et al. 2001
Moon-van der Staay et al. 2001
Moon-van der Staay et al. 2001
Moon-van der Staay et al. 2001
Moon-van der Staay et al. 2001
Moon-van der Staay et al. 2001
Moon-van der Staay et al. 2001
Moon-van der Staay et al. 2001
Sarno et al 2005
Unpublished
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Polet et al 2004
Polet et al 2004
Fahrni et al 2004
Romari & Vaulot 2004
Massana et al. 2004
Massana et al. 2004
Guillou et al 2004
Guillou et al 2004
Massana et al. 2004
Unpublished
Unpublished
Lovejoy et al 2006
Mankin et al 1986
Goggin,C.L. and Barker,S.C.
2003
Luton et al 1995
Rowan,R. and Powers,D.A.
1992
Mc Fadden et al 1994
Gast et al 1996
Saunders et al 1995
Leipe et al 1996
Leipe et al 1996
Andersen et al 1999
Rausch et al 1989
Steinkotter et al 1994
Bhattacharya et al 1995
Grzebyk et al 1998
Ustinova et al 2000
Allsopp et al 1994
Alveolate tree
Acc number
AF022156
AF022191
AF022192
AF022193
AF022195
AF022198
AF022202
AF069516
AF093502
AF239260
AF245279
AF290050
AF290064
AF290068
AF290069
AF290071
AF290073
AF290074
AF290075
AF290077
AF290078
AF290079
AF324218
AF472554
AF472555
AF530539
AJ402326
AJ402327
AJ402328
AJ402329
AJ402330
AJ402335
AJ402338
AJ402340
AJ402343
AJ402344
AJ402348
AJ402352
AJ402354
AY004773
AY046599
AY046614
AY046624
AY046674
AY046798
AY046800
AY129029
AY129030
AY129031
AY129032
AY129036
AY129037
AY129038
AY129039
Genus
Pyrocystis
Alexandrium
Ceratium
Gymnodinium
Gymnodinium
Heterocapsa
Peridinium
Amoebophrya
Cryptosporidium
Amoebophrya
Theileria
Perkinsus
Amoebophrya ex
Gymnodinium instriatum
Amoebophrya ex Scrippsiella
Diophrys
Species/strain/clone name
noctiluca
tamarense
tenue
catenatum
mikimotoi
triquetra
sp.
sp.
Serpentis CSP05
sp. 'Dinophysis'
youngi
DH147-EKD21 (2,000m)
DH144-EKD3 (250m)
DH147-EKD6 (2,000m)
DH147-EKD3 (2,000m)
DH147-EKD16 (2,000m)
DH147-EKD18 (2,000m)
DH147-EKD19 (2,000m)
DH147-EKD20 (2,000m)
DH148-EKD27 (3,000m)
DH148-EKD22 (3,000m)
DH148-EKD14 (3,000m)
marinus P-1
sp.
References
Saunders,G.W et al 1997
Saunders,G.W et al 1997
Saunders,G.W et al 1997
Saunders et al 1997
Saunders et al 1997
Saunders et al 1997
Saunders et al 1997
Gunderson et al 1999
Xiao et al 1999
Janson et al 2000
Unpublished
Lopez-Garcia,P. et al 2001
Lopez-Garcia,P. et al 2001
Lopez-Garcia,P. et al 2001
Lopez-Garcia,P. et al 2001
Lopez-Garcia,P. et al 2001
Lopez-Garcia,P. et al 2001
Lopez-Garcia,P. et al 2001
Lopez-Garcia,P. et al 2001
Lopez-Garcia,P. et al 2001
Lopez-Garcia,P. et al 2001
Lopez-Garcia,P. et al 2001
Unpublished
Gunderson et al 2002
sp.
AT4-47 (sediment 2,264m)
OLI11115 (75m)
OLI11001 (75m)
OLI11038 (75m)
OLI11010 (75m)
OLI11012 (75m)
OLI11023 (75m)
OLI11261 (75m)
OLI11027 (75m)
OLI11511 (75m)
OLI11055 (75m)
OLI11009 (75m)
OLI11029 (75m)
OLI11011 (75m)
appendiculata
CS_E001 (vent sediment)
C1_E010 (vent sediment)
C1_E023 (vent sediment)
A1_E007 (vent sediment)
C2_E007 (vent sediment)
C2_E009 (vent sediment)
UEPACCp1 (Surface coastal)
UEPACJp1 (Surface coastal)
UEPAC05Ap2 (Surface coastal)
UEPAC05Ep2 (Surface coastal)
UEPACCp3 (Surface coastal)
UEPACHp3 (Surface coastal)
UEPACEp3 (Surface coastal)
UEPACAQp3 (Surface coastal)
Gunderson et al 2002
Lopez-Garcia,P. et al 2003
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Chen,Z. and Song,W. 2001
Edgcomb,V.P. et al 2002
Edgcomb,V.P. et al 2002
Edgcomb,V.P. et al 2002
Edgcomb,V.P. et al 2002
Edgcomb,V.P. et al 2002
Edgcomb,V.P. et al 2002
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
AY129040
AY129041
AY129042
AY129044
AY129046
AY129048
AY129049
AY129050
AY129052
AY129053
AY129054
AY129055
AY129056
AY129057
AY129058
AY208892
AY208893
AY256303
AY295368
AY295373
AY295394
AY295397
AY295422
AY295430
AY295435
AY295438
AY295444
AY295446
AY295452
AY295467
AY295484
AY295491
AY295492
AY295494
AY295496
AY295500
AY295524
AY295532
AY295549
AY295564
AY295573
AY295574
AY295588
AY295591
AY295592
AY295607
AY295608
AY295639
AY295643
AY295680
AY295684
AY295690
AY295692
AY295693
AY295694
AY295696
Amoebophrya ex Ceratium
tripos
Amoebophrya. ex
Prorocentrum micans
UEPACFp3 (Surface coastal)
UEPACAPp3 (Surface coastal)
UEPAC41p3 (Surface coastal)
UEPAC15p4 (Surface coastal)
UEPACDp4 (Surface coastal)
UEPAC36p4 (Surface coastal)
UEPAC42p4 (Surface coastal)
UEPAC43p4 (Surface coastal)
UEPACEp5 (Surface coastal)
UEPACAIp5 (Surface coastal)
UEPACAPp5 (Surface coastal)
UEPACFp5 (Surface coastal)
UEPACQp5 (Surface coastal)
UEPACAFp5 (Surface coastal)
UEPACDp5 (Surface coastal)
sp.
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Unpublished
sp
Unpublished
D69 (270m, anoxic)
RA000412.123 (Surface coastal)
RA000412.134 (Surface coastal)
RA000412.20 (Surface coastal)
RA000412.25 (Surface coastal)
RA000412.80 (Surface coastal)
RA000412.90 (Surface coastal)
RA000412.95 (Surface coastal)
RA000609.10 (Surface coastal)
RA000609.17 (Surface coastal)
RA000609.2 (Surface coastal)
RA000609.26 (Surface coastal)
RA000609.43 (Surface coastal)
RA000907.12 (Surface coastal)
RA000907.2 (Surface coastal)
RA000907.20 (Surface coastal)
RA000907.22 (Surface coastal)
RA000907.24 (Surface coastal)
RA000907.29 (Surface coastal)
RA000907.61 (Surface coastal)
RA001219.11 (Surface coastal)
RA001219.36 (Surface coastal)
RA001219.54 (Surface coastal)
RA001219.67 (Surface coastal)
RA001219.8 (Surface coastal)
RA010412.21 (Surface coastal)
RA010412.29 (Surface coastal)
RA010412.3 (Surface coastal)
RA010412.49 (Surface coastal)
RA010412.5 (Surface coastal)
RA010516.31 (Surface coastal)
RA010516.37 (Surface coastal)
RA010613.126 (Surface coastal)
RA010613.135 (Surface coastal)
RA010613.15 (Surface coastal)
RA010613.17 (Surface coastal)
RA010613.18 (Surface coastal)
RA010613.19 (Surface coastal)
RA010613.20 (Surface coastal)
Stoeck et al 2003
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
AY295698
AY295714
AY295720
AY295727
AY295731
AY295733
AY295735
AY295755
AY426850
AY426861
AY426869
AY426870
AY426873
AY426886
AY426887
AY426891
AY426900
AY426903
AY426908
AY426911
AY426920
AY426937
AY937630
AY937647
AY937662
AY937682
AY937683
AY937783
AY937804
AY937838
AY937860
AY937888
AY937907
AY937956
AY937957
AY937977
AY937981
AY937996
AY938084
AY938085
AY938119
AY938127
AY938136
AY938138
AY938142
AY938211
AY938339
AY938413
AY938420
AY938421
L07375
L13716
L37415
M64244
M64245
M87328
U14385
U41087
Perkinsus
Gloeodinium
Toxoplasma
Sarcocystis
Crypthecodinium
Nannochloropsis
Dictyocha
Gymnodinium
RA010613.22 (Surface coastal)
RA010613.9 (Surface coastal)
RD010517.11 (Surface coastal)
RD010517.26 (Surface coastal)
RD010517.30 (Surface coastal)
RD010517.37 (Surface coastal)
RD010517.40 (Surface coastal)
RD010517.68 (Surface coastal)
BL000921.32 (Surface coastal)
BL001221.9 (Surface coastal)
BL001221.18 (Surface coastal)
BL001221.19 (Surface coastal)
BL001221.24 (Surface coastal)
BL001221.40 (Surface coastal)
BL001221.41 (Surface coastal)
BL010320.3 (Surface coastal)
BL010320.15 (Surface coastal)
BL010320.20 (Surface coastal)
BL010320.28 (Surface coastal)
BL010320.32 (Surface coastal)
BL010625.7 (Surface coastal)
BL010625.44 (Surface coastal)
ENI40076.00334 (Surface 30% Sol Irad)
ENI40076.00354 (Surface 30% Sol Irad)
ENI40076.00297 (Surface 30% Sol Irad)
ENI40076.00421 (Surface 30% Sol Irad)
ENI40076.00422 (Surface 30% Sol Irad)
ENI40076.00627 (Surface 30% Sol Irad)
ENI40076.00670 (Surface 30% Sol Irad)
ENI40076.00725 (Surface 30% Sol Irad)
ENI40076.00755 (Surface 30% Sol Irad)
ENI40076.00788 (Surface 30% Sol Irad)
ENI40076.00808 (Surface 30% Sol Irad)
ENI40076.00863 (Surface 30% Sol Irad)
ENI40076.00864 (Surface 30% Sol Irad)
ENI42482.00038 (Surface 30% Sol Irad)
ENI42482.00044 (Surface 30% Sol Irad)
ENI42482.00062 (Surface 30% Sol Irad)
ENI42482.00202 (Surface 30% Sol Irad)
ENI42482.00203 (Surface 30% Sol Irad)
ENI42482.00244 (Surface 30% Sol Irad)
ENI42482.00254 (Surface 30% Sol Irad)
ENI42482.00266 (Surface 30% Sol Irad)
ENI42482.00268 (Surface 30% Sol Irad)
ENI42482.00275 (Surface 30% Sol Irad)
ENI42482.00363 (Surface 30% Sol Irad)
ENI47296.00213 (Surface 30% Sol Irad)
ENI47296.00347 (Surface 30% Sol Irad)
ENI47296.00361 (Surface 30% Sol Irad)
ENI47296.00362 (Surface 30% Sol Irad)
sp.
viscum
gondii
muris
cohnii
salina
speculum
beii
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Massana, R. et al 2004
Massana, R. et al 2004
Massana, R. et al 2004
Massana, R. et al 2004
Massana, R. et al 2004
Massana, R. et al 2004
Massana, R. et al 2004
Massana, R. et al 2004
Massana, R. et al 2004
Massana, R. et al 2004
Massana, R. et al 2004
Massana, R. et al 2004
Massana, R. et al 2004
Massana, R. et al 2004
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Countway, P.D. et al 2005
Goggin,C.L. and Barker,S.C 1993
Unpublished
Luton,K. et al 1995
Gajadhar,A.A. et al 1991
Gajadhar,A.A. et al 1991
Unpublished
Saunders et al 1995
Gast et Caron 1996
U52352
U52355
U52356
U97112
X03772
X03947
X03948
X65150
X80344
Y16234
Z15105
Unidentified symbiotic
dinoflagellate
Unidentified symbiotic
dinoflagellate from
Spongostaurus sp.
Unidentified symbiotic
dinoflagellate
Strombidium
Paramecium
Stylonychia
Oxytricha
Furgasonia
Hyphochytrium
Prorocentrum
Babesia
BBSR 153
Gast and Caron 1996
Gast and Caron 1996
BBSR 323
Gast and Caron 1996
purpureum
tetraurelia
pustulata
nova
blochmanni
catenoides
arenarium
equi
Hirt,R.P. et al unpublished
Sogin,M.L. and Elwood,H.J. 1986
Elwood,H.J. et al 1985
Elwood,H.J. et al 1985
Bernhard,D. et al 1995
Van der Auwera et al 1995
Grzebyk,D et al 1998
Allsopp et al 1994
Stramenopiles tree
Acc number
AB022104
AB022111
AB023499
AF045045
AF072883
AF109323
AF123298
AF167157
AF185051
AF185053
AF257316
AF290063
AF290083
AF363185
AF363186
AF363187
AF363189
AF363190
AF363191
AF363193
AF363194
AF363196
AF363197
AF363203
AF363204
AF363206
AF363207
AF363208
AJ402337
AJ402339
AJ402341
AJ402350
AJ402355
AJ402356
AJ402357
AJ421145
AJ880418
AY032607
AY129059
AY129060
AY129061
AY129063
AY129064
AY129065
AY129066
AY129067
AY129068
AY129069
AY254857
AY295674
AY295683
AY295685
AY295703
AY295745
AY307399
genus
Japonochytrium
Thraustochytrium
Blastocystis
Nannochloropsis
Siluania
Paraphysomonas
Epipyxis
Bolidomonas
Picophagus
Symbiomonas
Thraustochytriidae
Porphyridium
Porphyridium
Eurychasma
Florenciella
Ectocarpus
Species/strain/clone name
sp. ATCC 28207
multirudimentale
hominis
oculata CCMP533
monomastiga
imperforata
pulchra
pacifica
flagellatus
scintillans RCC 25
sp.
DH144-EKD10 (250m)
DH148-5-EKD53 (3,000m)
ANT37-30 (surface)
ME1-17 (surface)
ME1-18 (surface)
ME1-20 (surface)
ME1-21 (surface)
ME1-22 (surface)
ANT12-7 (surface)
ANT12-24 (surface)
ANT12-10 (surface)
ANT12-11 (surface)
NA11-4 (surface)
NA11-5 (surface)
ANT37-16 (surface)
ME1-24 (surface)
ANT12-8 (surface)
OLI11025 (75m)
OLI11026 (75m)
OLI11030 (75m)
OLI11008 (75m)
OLI11150 (75m)
OLI11066 (75m)
OLI11006 (75m)
aerugineum
purpureum
dicksonii
UEPACDDp1 (surface coastal)
UEPAC05Cp2 (surface coastal)
UEPAC30Cp2 (surface coastal)
UEPAC48p3 (surface coastal)
UEPAC45p4 (surface coastal)
UEPAC37p4 (surface coastal)
UEPACCp4 (surface coastal)
UEPACLp5 (surface coastal)
UEPACOp5 (surface coastal)
UEPACRp5 (surface coastal)
parvula
RA010613.114 (surface coastal)
RA010613.134 (surface coastal)
RA010613.136 (surface coastal)
RA010613.38 (surface coastal)
RD010517.56
sp.
References
Honda et al 1999
Honda et al 1999
Arisue et al 2002
Andersen et al 1998
Karpov et al 1998
Caron et al 1999
Andersen et al 1999
Guillou et al 1999
Guillou et al 1999
Guillou et al 1999
Mo et al 2002
Lopez-Garcia et al 2001
Lopez-Garcia et al 2001
Diez et al. 2001
Diez et al. 2001
Diez et al. 2001
Diez et al. 2001
Diez et al. 2001
Diez et al. 2001
Diez et al. 2001
Diez et al. 2001
Diez et al. 2001
Diez et al. 2001
Diez et al. 2001
Diez et al. 2001
Diez et al. 2001
Diez et al. 2001
Diez et al. 2001
Moon-van der Staay et al. 2001
Moon-van der Staay et al. 2001
Moon-van der Staay et al. 2001
Moon-van der Staay et al. 2001
Moon-van der Staay et al. 2001
Moon-van der Staay et al. 2001
Moon-van der Staay et al. 2001
Unpublished
Hoef-Emden et al 2005
Unpublished
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Worden, A.Z. 2006
Eikrem et al 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Romari,K. and Vaulot,D. 2004
Unpublished
AY381157
AY381160
AY381161
AY381162
AY381163
AY381170
AY381171
AY381172
AY381174
AY381175
AY381177
AY381181
AY381183
AY381187
AY381190
AY381191
AY381194
AY381198
AY381200
AY381201
AY381203
AY381204
AY381206
AY381211
AY381212
AY381216
AY381218
AY381219
AY485452
AY485473
AY520449
AY788936
AY827849
AY919688
AY937842
DQ019446
DQ062463
DQ062464
DQ062471
DQ062475
DQ062476
DQ062481
DQ062485
DQ062486
DQ062487
DQ062489
DQ337349
DQ337350
DQ337351
DQ337353
DQ337354
DQ337356
DQ337358
DQ337359
DQ337360
DQ666484
L27634
Thalassiosira
Skeletonema
Cafeteria
Heterosigma
Cafeteria
Cylindrotheca
Sargassum
Labyrinthuloides
HE000427.21 (surface coastal)
HE000427.182 (surface coastal)
HE000427.196 (surface coastal)
HE000803.3 (surface coastal)
HE000803.35 (surface coastal)
HE001005.47 (surface coastal)
HE001005.112 (surface coastal)
HE001206.6 (surface coastal)
HE001206.17 (surface coastal)
HE001206.37 (surface coastal)
HE010218.8 (surface coastal)
OR000415.17 (surface)
OR000415.39 (surface)
OR000415.127 (surface)
BL000921.9 (surface coastal)
BL000921.11 (surface coastal)
BL000921.22 (surface coastal)
BL000921.33 (surface coastal)
BL000921.38 (surface coastal)
BL000921.40 (surface coastal)
BL001221.23 (surface coastal)
BL001221.26 (surface coastal)
BL010320.2 (surface coastal)
BL010320.22 (surface coastal)
BL010625.8 (surface coastal)
BL010625.31 (surface coastal)
BL010625.33 (surface coastal)
BL010625.35 (surface coastal)
Pseudonana CCMP1335
costatum
minima
akashiwo CCMP 1870
roenbergensis HFCC32
LG03-12 (20m FW lake)
ENI40076.00734 (surface 30% sol Ira)
closterium
MD65.10 (5m)
NW414.28 (50m)
MD65.09 (5m)
NW414.05 (50m)
NW414.26 (50m)
MD65.30
NW414.07 (50m)
MD65.13 (5m)
MD65.32 (5m)
NW614.11 (50m)
IND31.4
IND31.15
IND31.46
IND31.95
IND31.115
IND58.11
IND58.31
IND60.24
IND70.02
thunbergii
minuta
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Massana et al. 2004
Damste et al. 2004
Damste et al. 2004
Cavalier-Smith,T. and
Chao,E.E. 2006
Bowers et al 2006
Scheckenbach et al 2005
Richards et al. 2005
Countway et al. 2005
Unpublished
Lovejoy et al 2006
Lovejoy et al 2006
Lovejoy et al 2006
Lovejoy et al 2006
Lovejoy et al 2006
Lovejoy et al 2006
Lovejoy et al 2006
Lovejoy et al 2006
Lovejoy et al 2006
Lovejoy et al 2006
Massana et al 2006
Massana et al 2006
Massana et al 2006
Massana et al 2006
Massana et al 2006
Massana et al 2006
Massana et al 2006
Massana et al 2006
Massana et al 2006
Unpublished
Leipe et al 1994
L34054
L37205
M32705
M87325
U14385
U14386
U14388
U18240
U21338
U40927
U41052
U51152
U73220
U73228
U73230
X54266
Ulkenia
Ciliophrys
Achlya
Bacillaria
Dictyocha
Pelagococcus
Rhizochromulina
Pseudo-nitzschia
Labyrinthuloides
Coccoid pelagophyte
Pseudocharaciopsis
Blastocystis
Synura
Mallomonas
Mallomonas
Lagenidium
profunda
infusionum
bisexualis
paxillifer
speculum
subviridis
cf. marina
pungens
haliotidis
CCMP1395
minuta
sp.
mammillosa
caudata
annulata
giganteum
Cavalier-Smith et al 1994
Unpublished
Gunderson et al 1987
unpublished
Saunders et al 1995
Saunders et al 1995
Saunders et al 1995
Manhart et al 1995
Leipe et al 1996
Potter et al 1997
Andersen et al 1998
Silberman et al 1996
Lavau et al 1997
Lavau et al 1997
Lavau et al 1997
Forster et al 1990
Radiolaria tree
Acc number
AB101540
AB101541
AB101542
AB179732
AB179733
AB179734
AB179735
AB179736
AB193605
AF018158
AF018159
AF018161
AF018162
AF018163
AF057743
AF057744
AF063239
AF063240
AF063241
AF063242
AF091146
AF091147
AF091148
AF174369
AF290072
AF382824
AF382825
AF426157
AF530524
AF530525
AJ402332
AJ402333
AJ402342
AY266292
AY266293
AY266294
AY266295
AY266297
AY268045
U07413
X81811
genus
Dictyocoryne
Dictyocoryne
Spongaster
Euchitonia
Dicranastrum
Triastrum
Eucyrtidium
Pterocorys
Didymocyrtis
Chaunacanthid
Haliommatidium
Sphaerozoum
Collozoum
Collosphaera
Thalassicolla
Thalassicolla
Arthracanthid
Acanthometra
Chaunacanthid
Symphyacanthid
Collozoum
Rhaphidozoum
Acrosphaera
Massisteria
Hartmannella
Aulosphaera
Coelodendrum
Aulacantha
Collozoum
Thalassicolla
Sticholonche
Acanthamoeba
Paulinella
Species/strain/clone name
profunda
truncatum
tetras
elegans
furcatum
aurivillii
hexagonatum
zancleus
tetrathalamus
sp. 218
sp.
punctatum
serpentinum
globularis-huxleyi
nucleata strain W10.74
nucleata strain W10.79
sp. 206
sp.
sp. 217
sp. 211
pelagicum
acuferum
sp. CR6A
marina strain ATCC50266
DH147-EKD17
DH145-HA2
DH145-KW16
vermiformis
AT8-54
AT4-94
OLI11015
OLI11016
OLI11032
trigonopa
ramosissimum
scolymantha
inerme
pellucida
sp.
castellanii ATCC 50374
chromatophora
Reference
Takahashi,O. et al 2004
Takahashi,O. et al 2004
Takahashi,O. et al 2004
Yuasa,T. et al 2005
Yuasa,T. et al 2005
Yuasa,T. et al 2005
Yuasa,T. et al 2005
Yuasa,T. et al 2005
Yuasa,T. et al 2004
Zettler,L.A. et al 1997
Zettler,L.A. et al 1997
Zettler,L.A. et al 1997
Zettler,L.A. et al 1997
Zettler,L.A. et al 1997
Zettler,L.A. et al 1998
Zettler,L.A. et al 1998
Amaral Zettler,L.A. and Caron,D.A. 2000
Amaral Zettler,L.A. and Caron,D.A. 2000
Amaral Zettler,L.A. and Caron,D.A. 2000
Amaral Zettler,L.A. and Caron,D.A. 2000
Amaral Zettler,L.A. et al 1999
Amaral Zettler,L.A. et al 1999
Amaral Zettler,L.A. et al 1999
Atkins, M.S et al 2000
Lopez-Garcia,P. et al 2001
Lopez-Garcia,P. et al 2002
Lopez-Garcia,P. et al 2002
Unpublished
Lopez-Garcia,P. et al 2003
Lopez-Garcia,P. et al 2003
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Polet,S. et al 2004
Polet,S. et al 2004
Polet,S. et al 2004
Polet,S. et al 2004
Polet,S. et al 2004
Nikolaev,S.I. et al 2004
Gast,R.J. et al 1996
Bhattacharya,D. et al 1995
Radiolaria partial – Fig 4C
Acc number
AACY01111334
AB101540
AB101541
AB101542
AB179732
AB179733
AB179734
AB179735
AB179736
AB193605
AF018158
AF018159
AF018161
AF018162
AF018163
AF057743
AF057744
AF063239
AF063240
AF063241
AF063242
AF091146
AF091147
AF091148
AF174369
AF290072
AF382824
AF382825
AF530524
AF530525
AJ402332
AJ402333
AJ402342
AY046601
AY046642
AY046647
AY046664
AY046714
AY046840
AY046843
AY046858
AY256248
AY256264
AY256275
AY256277
AY256279
AY256283
AY266292
AY266293
AY266294
AY266295
AY266297
AY268045
AY882481
AY882482
genus
Dictyocoryne
Dictyocoryne
Spongaster
Euchitonia
Dicranastrum
Triastrum
Eucyrtidium
Pterocorys
Didymocyrtis
Chaunacanthid
Haliommatidium
Sphaerozoum
Collozoum
Collosphaera
Thalassicolla
Thalassicolla
Arthracanthid
Acanthometra
Chaunacanthid
Symphyacanthid
Collozoum
Rhaphidozoum
Acrosphaera
Massisteria
Aulosphaera
Coelodendrum
Aulacantha
Collozoum
Thalassicolla
Sticholonche
Species/strain/clone name
IBEA_CTG_2022727
profunda
truncatum
tetras
elegans
furcatum
aurivillii
hexagonatum
zancleus
tetrathalamus
sp. 218
sp.
punctatum
serpentinum
globularis-huxleyi
nucleata strain W10.74
nucleata strain W10.79
sp. 206
sp.
sp. 217
sp. 211
pelagicum
acuferum
sp. CR6A
marina strain ATCC50266
DH147-EKD17
DH145-HA2
DH145-KW16
AT8-54
AT4-94
OLI11015
OLI11016
OLI11032
CS_E004 (vent sediment)
C1_E045 (vent sediment)
CS_E020 (vent sediment)
CS_E043 (vent sediment)
A2_E002 (vent sediment)
C3_E010 (vent sediment)
C3_E013 (vent sediment)
C3_E029 (vent sediment)
E16 (340m)
E107 (340m)
E187 (340m)
E191 (340m)
E196 (340m)
E215 (340m)
trigonopa
ramosissimum
scolymantha
inerme
pellucida
sp.
T45B2 (340m)
T37C4 (340m)
Reference
Venter et al 2004
Takahashi,O. et al 2004
Takahashi,O. et al 2004
Takahashi,O. et al 2004
Yuasa,T. et al 2005
Yuasa,T. et al 2005
Yuasa,T. et al 2005
Yuasa,T. et al 2005
Yuasa,T. et al 2005
Yuasa,T. et al 2004
Zettler,L.A. et al 1997
Zettler,L.A. et al 1997
Zettler,L.A. et al 1997
Zettler,L.A. et al 1997
Zettler,L.A. et al 1997
Zettler,L.A. et al 1998
Zettler,L.A. et al 1998
Amaral Zettler,L.A. and Caron,D.A. 2000
Amaral Zettler,L.A. and Caron,D.A. 2000
Amaral Zettler,L.A. and Caron,D.A. 2000
Amaral Zettler,L.A. and Caron,D.A. 2000
Amaral Zettler,L.A. et al 1999
Amaral Zettler,L.A. et al 1999
Amaral Zettler,L.A. et al 1999
Atkins, M.S et al 2000
Lopez-Garcia,P. et al 2001
Lopez-Garcia,P. et al 2002
Lopez-Garcia,P. et al 2002
Lopez-Garcia,P. et al 2003
Lopez-Garcia,P. et al 2003
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Edgcomb et al 2002
Edgcomb et al 2002
Edgcomb et al 2002
Edgcomb et al 2002
Edgcomb et al 2002
Edgcomb et al 2002
Edgcomb et al 2002
Edgcomb et al 2002
Stoeck et al 2003
Stoeck et al 2003
Stoeck et al 2003
Stoeck et al 2003
Stoeck et al 2003
Stoeck et al 2003
Polet,S. et al 2004
Polet,S. et al 2004
Polet,S. et al 2004
Polet,S. et al 2004
Polet,S. et al 2004
Nikolaev,S.I. et al 2004
Stoeck et al 2006
Stoeck et al 2006
AY882485
AY882486
AY882490
AY882491
AY882493
AY882494
AY882496
p15D07 (340m)
p15C2 (340m)
T41E10 (340m)
T41D11 (340m)
p14C4 (340m)
T41A2 (340m)
T41F3 (340m)
Stoeck et al 2006
Stoeck et al 2006
Stoeck et al 2006
Stoeck et al 2006
Stoeck et al 2006
Stoeck et al 2006
Stoeck et al 2006
Radiolaria partial – Fig 4B
Acc number
AB101540
AB101541
AB101542
AB179732
AB179733
AB179734
AB179735
AB179736
AB193605
AF018158
AF018159
AF018161
AF018162
AF018163
AF057743
AF057744
AF063239
AF063240
AF063241
AF063242
AF091146
AF091147
AF091148
AF174369
AF290072
AF382824
AF382825
AF530524
AF530525
AJ402332
AJ402333
AJ402342
AJ829783
AJ829787
AJ829788
AJ829791
AJ829800
AJ829811
AJ829813
AJ829823
AJ829833
AJ829834
AJ829837
AJ829842
AY266292
AY266293
AY266294
AY266295
AY266297
AY268045
DQ001480
DQ001483
DQ001518
genus
Dictyocoryne
Dictyocoryne
Spongaster
Euchitonia
Dicranastrum
Triastrum
Eucyrtidium
Pterocorys
Didymocyrtis
Chaunacanthid
Haliommatidium
Sphaerozoum
Collozoum
Collosphaera
Thalassicolla
Thalassicolla
Arthracanthid
Acanthometra
Chaunacanthid
Symphyacanthid
Collozoum
Rhaphidozoum
Acrosphaera
Massisteria
Aulosphaera
Coelodendrum
Aulacantha
Collozoum
Thalassicolla
Sticholonche
Species/strain/clone name
profunda
truncatum
tetras
elegans
furcatum
aurivillii
hexagonatum
zancleus
tetrathalamus
sp. 218
sp.
punctatum
serpentinum
globularis-huxleyi
nucleata strain W10.74
nucleata strain W10.79
sp. 206
sp.
sp. 217
sp. 211
pelagicum
acuferum
sp. CR6A
marina strain ATCC50266
DH147-EKD17 (2,000m)
DH145-HA2 (500m)
DH145-KW16 (500m)
AT8-54 (1,675m microcolonizer)
AT4-94 (2,264m sediments)
OLI11015 (75m)
OLI11016 (75m)
OLI11032 (75m)
NS371B04 (100m)
NS371B38 (100m)
NS371B39 (100m)
NS371C36 (100m)
NS371D25 (100m)
NS371A47 (100m)
NS51A161 (100m)
NS51B106 (100m)
NS51B282 (100m)
NS51B291 (100m)
NS51C262 (100m)
NS51D167 (100m)
trigonopa
ramosissimum
scolymantha
inerme
pellucida
sp.
DGGE.190503_11 (80m)
DGGE.190503_27 (25m)
DGGE.190503_12 (80m)
Reference
Takahashi,O. et al 2004
Takahashi,O. et al 2004
Takahashi,O. et al 2004
Yuasa,T. et al 2005
Yuasa,T. et al 2005
Yuasa,T. et al 2005
Yuasa,T. et al 2005
Yuasa,T. et al 2005
Yuasa,T. et al 2004
Zettler,L.A. et al 1997
Zettler,L.A. et al 1997
Zettler,L.A. et al 1997
Zettler,L.A. et al 1997
Zettler,L.A. et al 1997
Zettler,L.A. et al 1998
Zettler,L.A. et al 1998
Amaral Zettler,L.A. and Caron,D.A. 2000
Amaral Zettler,L.A. and Caron,D.A. 2000
Amaral Zettler,L.A. and Caron,D.A. 2000
Amaral Zettler,L.A. and Caron,D.A. 2000
Amaral Zettler,L.A. et al 1999
Amaral Zettler,L.A. et al 1999
Amaral Zettler,L.A. et al 1999
Atkins, M.S et al 2000
Lopez-Garcia,P. et al 2001
Lopez-Garcia,P. et al 2002
Lopez-Garcia,P. et al 2002
Lopez-Garcia,P. et al 2003
Lopez-Garcia,P. et al 2003
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Moon-van der Staay,S.Y. et al 2001
Yuan et al. 2004
Yuan et al. 2004
Yuan et al. 2004
Yuan et al. 2004
Yuan et al. 2004
Yuan et al. 2004
Yuan et al. 2004
Yuan et al. 2004
Yuan et al. 2004
Yuan et al. 2004
Yuan et al. 2004
Yuan et al. 2004
Polet,S. et al 2004
Polet,S. et al 2004
Polet,S. et al 2004
Polet,S. et al 2004
Polet,S. et al 2004
Nikolaev,S.I. et al 2004
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
DQ001515
DQ001516
DQ001482
DQ001492
DQ001517
DQ001519
DQ001493
DQ001490
DQ001489
DQ001479
DQ001495
DQ001484
DQ001488
DQ001486
DQ001487
DQ001485
DQ001491
DQ001494
DQ001496
DGGE.190503_1 (5m)
DGGE.190503_1b (5m)
DGGE.250803_10 (80m)
DGGE.250803_20 (80m)
TTGE.231203_25 (5m)
TTGE.231203_34 (80m)
TTGE.141203_19 (95m)
TTGE.231203_47 (80m)
TTGE.141203_22 (80m)
TTGE.231203_30 (30m)
TTGE.231203_57 (50m)
TTGE.231203_37 (25m)
TTGE.231203_43 (25m)
TTGE.231203_41 (25m)
TTGE.231203_42 (25m)
TTGE.231203_38 (25m)
TTGE.231203_48 (80m)
TTGE.241203_71 (95m)
TTGE.241203_77 (5m)
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
Marie et al. 2006
References
Allsopp, M.T., Cavalier-Smith, T., De Waal, D.T. and Allsopp, B.A. (1994) Phylogeny and
evolution of the piroplasms. Parasitology 108 (Pt 2), 147-152
Amaral Zettler, L.A., Anderson, O.R. and Caron, D.A. (1999) Towards a Molecular Phylogeny
of Colonial Spumellarian Radiolaria. Mar. Micropaleontol. 36, 67-79
Amaral Zettler, L.A. and Caron, D.A. (2000) New Insights into the Phylogeny of the
Acantharea based on SSU rRNA Gene Sequencing. Eur. J. Protistol. 36, 34-39
Amaral Zettler, L.A., Nerad, T.A., O'Kelly, C.J., Peglar, M.T., Gillevet, P.M., Silberman, J.D.
and Sogin, M.L. (2000) A molecular reassessment of the Leptomyxid amoebae. Protist 151 (3),
275-282
Andersen, R.A., Van de Peer, Y., Potter, D., Sexton, J.P., Kawachi, M. and LaJeunesse, T.
(1999) Phylogenetic analysis of the SSU rRNA from members of the Chrysophyceae. Protist
150 (1), 71-84
Andersen, R.A., Brett, R.W., Potter, D. and Sexton, J.P. (1998) Phylogeny of the
Eustigmatophyceae based upon 18S rRNA, with emphasis on Nannochloropsis. Protist 149, 6174
Arisue, N., Hashimoto, T., Yoshikawa, H., Nakamura, Y., Nakamura, G., Nakamura, F., Yano,
T.A. and Hasegawa, M. (2002) Phylogenetic position of Blastocystis hominis and of
stramenopiles inferred from multiple molecular sequence data. J. Eukaryot. Microbiol. 49 (1),
42-53
Atkins, M.S., Teske, A.P. and Anderson, O.R. (2000) A survey of flagellate diversity at four
deep-sea hydrothermal vents in the Eastern Pacific Ocean using structural and molecular
approaches. J. Eukaryot. Microbiol. 47 (4), 400-411
Bernhard,D., Leipe,D.D., Sogin,M.L. and Schlegel,K.M. (1995) Phylogenetic relationships of
the Nassulida within the phylum Ciliophora inferred from the complete small subunit rRNA
gene sequences of Furgasonia blochmanni, Obertrumia georgiana, and Pseudomicrothorax
dubius. J. Eukaryot. Microbiol. 42 (2), 126-131
Bhattacharya,D., Helmchen,T. and Melkonian,M. (1995) Molecular evolutionary analyses of
nuclear-encoded small subunit ribosomal RNA identify an independent rhizopod lineage
containing the Euglyphina and the Chlorarachniophyta. J. Eukaryot. Microbiol. 42 (1), 65-69
Bowers, H.A., Tomas, C., Tengs, T., Kempton, J.W., Lewitus, A.J. and Oldach, D.W. (2006)
Raphidophyceae [Chadefaud ex Silva] systematics and rapid identification: sequence analyses
and real-time PCR assays. J. Phycol. 42 (6), 1333-1348
Caron, D.A., Lim, E.L., Dennett, M.R., Gast, R.J., Kosman, C. and Delong, E.F. (1999)
Molecular phylogenetic analysis of the heterotrophic chrysophyte genus Paraphysomonas
(Chrysophyceae), and the design of rRNA-targeted oligonucleotide probes for two species. J.
Phycol. 35 (4), 824-837
Cavalier-Smith, T. and Chao, E.E. (2006) Phylogeny and megasystematics of phagotrophic
heterokonts (kingdom chromista). J. Mol. Evol. 62 (4), 388-420
Cavalier-Smith, T., Allsopp, M.T.E.P. and Chao, E.E. (1994) Thraustochytrids are chromists,
not fungi: 18s rRNA signatures of heterokonta. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 346
(1318), 387-397
Chen, Z. and Song, W. (2001) Phylogenetic positions of Uronychia transfuga and Diophrys
appendiculata (Euplotida, Hypotrichia, Ciliophora) within hypotrichous ciliates inferred from
the small subunit ribosomal RNA sequences. Eur. J. Protistol. 37, 291-301
Collins, A.G. (1998) Evaluating multiple alternative hypotheses for the origin of Bilateria: an
analysis of 18S rRNA molecular evidence. Proc. Natl. Acad. Sci. U.S.A. 95 (26), 15458-15463
Countway, P.D., Gast, R.J., Savai, P. and Caron, D.A. (2005) Protistan Diversity Estimates
Based on 18S rDNA from Seawater Incubations in the Western North Atlantic. J. Eukaryot.
Microbiol. 52 (2), 95-106
Edgcomb,V.P., Kysela,D.T., Teske,A., de Vera Gomez,A. and Sogin,M.L. (2002) Benthic
eukaryotic diversity in the Guaymas Basin hydrothermal vent environment. Proc. Natl. Acad.
Sci. U.S.A. 99 (11), 7658-7662
Eikrem, W., Romari, K., Le Gall, F., Latasa, M., Throndsen, J. and Vaulot, D. (2004)
Florenciella parvula gen. and sp. nov. (Dictyochophyceae, Heterokontophyta) a small
flagellate isolated from the English Channel. Phycologia 43, 658-668
Elwood, H.J., Olsen, G.J. and Sogin, M.L. (1985) The small-subunit ribosomal RNA gene
sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Mol. Biol.
Evol. 2 (5), 399-410
Fahrni, J.F., Bolivar, I., Berney, C., Nassonova, E., Smirnov, A. and Pawlowski, J. (2003)
Phylogeny of lobose amoebae based on actin and small-subunit ribosomal RNA genes. Mol.
Biol. Evol. 20 (11), 1881-1886
Forster, H., Coffey, M.D., Elwood, H. and Sogin, M.L. (1990) Sequence analysis of the small
subunit ribosomal RNAs of three zoosporic fungi and implications for fungal evolution.
Mycologia 82, 306-312
Gajadhar,A.A., Marquardt,W.C., Hall,R., Gunderson,J., Ariztia-Carmona,E.V. and Sogin,M.L.
Ribosomal RNA sequences of Sarcocystis muris, Theileria annulata and Crypthecodinium
cohnii reveal evolutionary relationships among apicomplexans, dinoflagellates, and ciliates.
Mol. Biochem. Parasitol. 45 (1), 147-154 (1991)
Gast, R.J., McDonnell, T.A. and Caron, D.A. (2000) srDNA-based Taxonomic affinities of
algal symbionts from a planktonic foraminifer and a solitary radiolarian. J. Phycol. 36, 172-177
Gast, R.J. and Caron, D.A. (1996) Molecular phylogeny of symbiotic dinoflagellates from
planktonic foraminifera and radiolaria. Mol. Biol. Evol. 13 (9), 1192-1197
Gast, R.J., Ledee, D.R., Fuerst, P.A. and Byers, T.J. (1996) Subgenus systematics of
Acanthamoeba: four nuclear 18S rDNA sequence types. J. Eukaryot. Microbiol. 43 (6), 498504
Goggin, C.L. and Barker, S.C. (1993) Phylogenetic position of the genus Perkinsus (Protista,
Apicomplexa) based on small subunit ribosomal RNA. Mol. Biochem. Parasitol. 60 (1), 65-70
Grzebyk, D., Sako, Y. and Berland, B. (1998) Phylogenetic analysis of nine species of
Prorocentrum (Dinophyceae) inferred from 18S ribosomal DNA sequences, morphological
comparisons and description of Prorocentrum panamensis sp. nov. J. Phycol. 34, 1055-1068
Guillou, L., Eikrem, W., Chretiennot-Dinet, M.-J., Le Gall, F., Massana, R., Romari, K.,
Pedros-Alio, C. and Vaulot, D. (2004) Diversity of picoplanktonic Prasinophytes assessed by
direct nuclear SSU rDNA sequencing of environmental samples and novel isolates retrieved
from oceanic and coastal marine ecosystems. Protist 155 (2), 193-214
Guillou, L., Moon-Van Der Staay, S.Y., Claustre, H., Partensky, F. and Vaulot, D. (1999)
Diversity and abundance of Bolidophyceae (Heterokonta) in two oceanic regions. Appl.
Environ. Microbiol. 65 (10), 4528-4536
Guillou, L., Chretiennot-Dinet, M.J., Boulben, S., Moon-van der Staay, S.Y. and Vaulot, D.
(1999) Symbiomonas scintillans gen. et sp. nov. and Picophagus flagellatus gen. et sp. nov.
(Heterokonta): two new heterotrophic flagellates of picoplanktonic size. Protist 150 (4), 383398
Gunderson, J.H., John, S.A., Boman, W.C. and Coats, D.W. (2002) Multiple strains of the
parasitic dinoflagellate Amoebophrya exist in Chesapeake Bay. J. Eukaryot. Microbiol. 49 (6),
469-474
Gunderson, J.H., Goss, S.H. and Coats, D.W. (1999) The phylogenetic position of
Amoebophrya sp. infecting Gymnodinium sanguineum. J. Eukaryot. Microbiol. 46 (2), 194-197
Gunderson, J.H., Elwood, H., Ingold, A., Kindle, K. and Sogin, M.L. (1987) Phylogenetic
relationships between chlorophytes, chrysophytes, and oomycetes. Proc. Natl. Acad. Sci.
U.S.A. 84 (16), 5823-5827
Grzebyk,D., Sako,Y. and Berland,B. (1998) Phylogenetic analysis of nine species of
Prorocentrum (Dinophyceae) inferred from 18S ribosomal DNA sequences, morphological
comparisons and description of Prorocentrum panamensis sp. Nov. J. Phycol. 34, 1055-1068
Hoef-Emden, K., Shrestha, R.P., Lapidot, M., Weinstein, Y., Melkonian, M. and Arad, S.M.
(2005) Actin phylogeny and intron distribution in bangiophyte red algae(rhodoplantae). J. Mol.
Evol. 61 (3), 360-371
Honda,D., Yokochi,T., Nakahara,T., Raghukumar,S., Nakagiri,A., Schaumann,K. and
Higashihara,T. (1999) Molecular phylogeny of labyrinthulids and thraustochytrids based on the
sequencing of 18S ribosomal RNA gene. J. Eukaryot. Microbiol. 46 (6), 637-647
Janson, S., Gisselson, L.A., Salomon, P.S. and Graneli, E. (2000) Evidence for multiple species
within the endoparasitic dinoflagellate Amoebophrya ceratii as based on 18S rRNA genesequence analysis. Parasitol. Res. 86 (11), 929-933
Karpov, S.A., Kersanach, R. and Williams, D.M. (1998) Ultrastructure and 18S rRNA gene
sequence of a small heterotrophic flagellate Siluania monomastiga gen. et sp. nov.
(Bicosoecida). Eur. J. Protistol. 34, 415–25
Kunitomo, Y., Sarashina, I., Iijima, M., Endo, K. and Sashida, K. (2006) Molecular phylogeny
of acantharian and polycystine radiolarians based on ribosomal DNA sequences, and some
comparisons with data from the fossil record. Eur. J. Protistol. 42, 143-153
Lavau, S., Wetherbee, R. and Saunders, G.W. (1997) A phylogenetic analysis of the
Synurophyceae using molecular data and scale case morphology. J. Phycol. 33, 135-151
Leipe, D.D., Tong, S.M., Goggin, C.L., Slemenda, S.B., Pieniazek, N.J. and Sogin, M.L.
(1996) 16S-like rDNA sequences from Developayella elegans, Labyrinthuloides haliotidis, and
Proteromonas lacertae confirm that the stramenopiles are a primarily heterotrophic group.
Europ. J. Protistol. 32, 449-458
Leipe,D.D., Wainright,P.O., Gunderson,J.H., Porter,D., Patterson,D.J., Valois,F., Himmerich,S.
and Sogin,M.L.
The stramenopiles from a molecular perspective: 16S-like rRNA sequences from
Labyrinthuloides minuta and Cafeteria roenbergensis. Phycologia 33 (55) 369-377 (1994)
Lopez-Garcia,P., Rodriguez-Valera,F., Pedros-Alio,C. and Moreira,D.
Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409 (6820),
603-607 (2001)
Lopez-Garcia, P., Philippe, H., Gail, F. and Moreira, D. (2003) Autochthonous eukaryotic
diversity in hydrothermal sediment and experimental microcolonizers at the Mid-Atlantic
Ridge. Proc. Natl. Acad. Sci. U.S.A. 100 (2), 697-702
Lopez-Garcia, P., Rodriguez-Valera, F. and Moreira, D. (2002) Toward the monophyly of
Haeckel's radiolaria: 18S rRNA environmental data support the sisterhood of polycystinea and
acantharea. Mol. Biol. Evol. 19 (1), 118-121
Luton, K., Gleeson, M. and Johnson, A.M. (1995) rRNA gene sequence heterogeneity among
Toxoplasma gondii strains. Parasitol. Res. 81 (4), 310-315
McFadden,G.I., Gilson,P.R., Hofmann,C.J., Adcock,G.J. and Maier,U.G. (1994) Evidence that
an amoeba acquired a chloroplast by retaining part of an engulfed eukaryotic alga. Proc. Natl.
Acad. Sci. U.S.A. 91 (9), 3690-3694
Manhart, J.R., Gryxell, G.A., Vilac, M.C. and Segura, L.Y. (1995) Pseudo-nitzschia pungens
and P. multiseries (Bacillariophyceae): nuclear ribosomal DNAs and species differences. J.
Phycol. 31, 421-427
Mankin, A.S., Skryabin, K.G. and Rubtsov, P.M. (1986) Identification of ten additional
nucleotides in the primary structure of yeast 18S rRNA. Gene 44 (1), 143-145
Marin, B., Klingberg, M. and Melkonian, M. (1998) Phylogenetic relationships among the
Cryptophyta: Analyses of nuclear-encoded SSU rRNA sequences support the monophyly of
extant plastid-containing lineages. Protist 149, 265-276
Massana, R., Balague, V., Guillou, L. and Pedros-Alio, C. (2004) Picoeukaryotic diversity in
an oligotrophic coastal site studied by molecular and culturing approaches. FEMS Microbiol.
Ecol. 50 (3), 231-243
Massana, R., Terrado, R., Forn, I., Lovejoy, C. and Pedros-Alio, C. (2006) Distribution and
abundance of uncultured heterotrophic flagellates in the world oceans. Environ. Microbiol. 8
(9), 1515-1522
Mo, C., Douek, J. and Rinkevich, B. (2002) Development of a PCR strategy for thraustochytrid
identification based on 18S rDNA sequence. Mar. Biol. 140, 883-889
Moon-van der Staay, S.Y., De Wachter, R. and Vaulot, D. (2001) Oceanic 18S rDNA
sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature 409 (6820), 607610
Mueller, K.M., Oliveira, M.C., Sheath, R.G. and Bhattacharya, D. (2001) Ribosomal DNA
phylogeny of the Bangiophycidae (Rhodophyta) and the origin of secondary plastids. Am. J.
Bot. 88 (8), 1390-1400
Nikolaev, S.I., Berney, C., Fahrni, J.F., Bolivar, I., Polet, S., Mylnikov, A.P., Aleshin, V.V.,
Petrov, N.B. and Pawlowski, J. (2004) The twilight of Heliozoa and rise of Rhizaria, an
emerging supergroup of amoeboid eukaryotes. Proc. Natl. Acad. Sci. U.S.A. 101 (21), 80668071
Okamoto, N. and Inouye, I. (2005) The katablepharids are a distant sister group of the
Cryptophyta: A proposal for Katablepharidophyta divisio nova/ Kathablepharida phylum
novum based on SSU rDNA and beta-tubulin phylogeny. Protist 156 (2), 163-179
Polet, S., Berney, C., Fahrni, J. and Pawlowski, J. (2004) Small-subunit ribosomal RNA gene
sequences of Phaeodarea challenge the monophyly of Haeckel's Radiolaria Protist 155 (1), 5363
Potter, D., LaJeunesse, T.C., Saunders, G.W. and Andersen, R.A. (1997) Convergent evolution
masks extensive biodiversity among marine coccoid picoplankton. Biodivers. Conserv. 6, 99107
Rausch, H., Larsen, N. and Schmitt, R. (1989) Phylogenetic relationships of the green alga
Volvox carteri deduced from small-subunit ribosomal RNA comparisons. J. Mol. Evol. 29 (3),
255-265
Romari, K. and Vaulot, D. (2004) Composition and temporal variability of picoeukaryote
communities at a coastal site of the English Channel from 18S rDNA sequences. Limnol.
Oceanogr. 49, 784-798
Rowan, R. and Powers, D.A. (1992) Ribosomal RNA sequences and the diversity of symbiotic
dinoflagellates (zooxanthellae). Proc. Natl. Acad. Sci. U.S.A. 89 (8), 3639-3643
Sarno, D., Wiebe, H.C., Kooistra, W.H.C.F., Medlin, L.K., Percopo, I. and Zingone, A. (2005)
Diversity in the genus skeletonema (bacillariophyceae). II. An assessment of the taxonomy of
S. costatum-like species with the description of four newspecies. J. Phycol. 41 (1), 151-176
Saunders, G.W., Potter, D., Paskind, M.P. and Andersen, R.A. (1995) Cladistic analyses of
combined traditional and molecular data sets reveal an algal lineage. Proc. Natl. Acad. Sci.
U.S.A. 92 (1), 244-248
Saunders, G.W., Hill, D.R., Sexton, J.P. and Andersen, R.A. (1997) Small-subunit ribosomal
RNA sequences from selected dinoflagellates: testing classical evolutionary hypotheses with
molecular systematic methods. (in) Bhattacharya, D. (Ed.); ORIGINS OF ALGAE AND
THEIR PLASTIDS: 237-259; Springer-Verlag Wein, New York
Scheckenbach, F., Wylezich, C., Weitere, M., Hausmann, K. and Arndt, H. (2005) Molecular
identity of strains of heterotrophic flagellates isolated from surface waters and deep-sea
sediments of the South Atlantic based on SSU rDNA. Aquat. Microb. Ecol. 38 (3), 239-247
Silberman, J.D., Sogin, M.L., Leipe, D.D. and Clark, C.G. (1996) Human parasite finds
taxonomic home. Nature 380 (6573), 398
Sogin, M.L. and Elwood, H.J. (1986) Primary structure of the Paramecium tetraurelia smallsubunit rRNA coding region: phylogenetic relationships within the Ciliophora. J. Mol. Evol. 23
(1), 53-60
Steinkotter, J., Bhattacharya, D., Semmelroth, I., Bibeau, C. and Melkonian, M. (1994)
Prasinophytes form independent lineages within the chlorophyta: evidence from ribosomal
RNA sequence comparisons. J. Phycol. 30, 340-345
Stoeck, T., Taylor, G.T. and Epstein, S.S. (2003) Novel Eukaryotes from the Permanently
Anoxic Cariaco Basin (Caribbean Sea). Appl. Environ. Microbiol. 69: 5656-5663
Stoeck, T., Hayward, B., Taylor, G.T., Varela, R. and Epstein, S.S. (2006) A Multiple PCRprimer Approach to Access the Microeukaryotic Diversity in Environmental Samples. Protist
157: 31-43
Takahashi, O., Yuasa, T., Honda, D. and Mayama, S. (2004) Molecular phylogeny of solitary
shell-bearing Polycystinea (Radiolaria). Rev. Micropaleontol. 47, 111-118
Ustinova, I., Krienitz, L. and Huss, V.A. (2000) Hyaloraphidium curvatum is not a green alga,
but a lower fungus; Amoebidium parasiticum is not a fungus, but a member of the DRIPs.
Protist 151 (3), 253-262
Van de Peer, Y., Rensing, S.A., Maier, U.G. and De Wachter, R. (1996) Substitution rate
calibration of small subunit ribosomal RNA identifies chlorarachniophyte endosymbionts as
remnants of green algae. Proc. Natl. Acad. Sci. U.S.A. 93 (15), 7732-7736
Van der Auwera, G., De Baere, R., Van de Peer, Y., De Rijk, P., Van den Broeck, I. and De
Wachter, R. (1995) The phylogeny of the Hyphochytriomycota as deduced from ribosomal
RNA sequences of Hyphochytrium catenoides. Mol. Biol. Evol. 12 (4), 671-678
Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., Wu, D.,
Paulsen, I., Nelson, K.E., Nelson, W., Fouts, D.E., Levy, S., Knap, A.H., Lomas, M.W.,
Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., Baden-Tillson, H., Pfannkoch,
C., Rogers,Y.H. and Smith, H.O. (2004) Environmental genome shotgun sequencing of the
Sargasso Sea. Science 304: 66-74
Worden, A.Z. (2006) Picoeukaryote diversity in coastal waters of the Pacific Ocean. Aquatic
Microbial Ecology 43: 165-175.
Xiao, L., Escalante, L., Yang, C., Sulaiman, I., Escalante, A.A., Montali, R.J., Fayer, R. and
Lal, A.A. (1999) Phylogenetic analysis of Cryptosporidium parasites based on the smallsubunit rRNA gene locus. Appl. Environ. Microbiol. 65 (4), 1578-1583
Yokoyama,A., Sato,K. and Hara,Y. (2004) The generic delimitation of Rhodella
(Porphyridiales, Rhodophyta) with emphasis on ultrastructure and molecular phylogeny.
Hydrobiologia 512, 177-183
Yuasa, T., Takahashi, O. and Mayama, S. (2004) PCR primers for the amplification of the
nuclear small subunit ribosomal DNA sequences from polycystine radiolarians. Gensei
Dobutsugaku Zasshi 37, 133-137
Yuasa, T., Takahashi, O., Honda, D. and Mayama, S. (2005) Phylogenetic analyses of the
polycystine Radiolaria based on the 18s rDNA sequences of the Spumellarida and the
Nassellarida. Eur. J. Protistol. 41, 287-298
Zettler, L.A., Sogin, M.L. and Caron, D.A. (1997) Phylogenetic relationships between the
Acantharea and the Polycystinea: a molecular perspective on Haeckel's Radiolaria. Proc. Natl.
Acad. Sci. U.S.A. 94 (21), 11411-11416
Zettler, L.A., Anderson, O.R. and Caron, D.A. (1998) Insights on the diversity within a
'species' of Thalassicolla (Spumellarida) based on 16S-like ribosomal RNA gene sequencing. J.
Eukaryot. Microbiol. 45 (5), 488-496