<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

mastigonemes; posterior cilium attached or free; phagotrophic or osmotrophic; cytostome, when present, anterolateral; free-living or commensal/parasitic. Node: *Cryptobia*, *Jarrellia*, *Parabodo*, *Procryptobia*, *Try-panoplasma*.

●●●●● Eubodonida Vickerman in Moreira et al. 2004 (R)

Eukinetoplast with kDNA not in a single network, but in parakinetosomal position; biciliated with anterior cilium with nontubular mastigonemes; phagotrophic; anterolateral cytostome surrounded by lappets; free-living *Bodo*.

●●●●●● Trypanosomatida Kent 1880, emend. Vickerman in Moreira et al. 2004

Eukinetoplastic with kDNA network associated with ciliary basal body; unciliated, lacking mastigonemes and emerging from anterior pocket, or emerging laterally and attached to body; phagotrophic or osmotrophic; cytos- tome, when present, simple and close to ciliary pocket; exclusively parasitic. Node: monoxenous (= single host) genera *Angomonas*, *Blechomonas*, *Leptomonas*, *Paratrypanosoma*, *Sergeia*, *Strigomonas*, *Wallaceina* and dixe- nous (= two hosts) genera *Phytonomas*, *Trypanosoma*.

●●●●●●● Leishmaniinae Maslov & Lukeš 2012 (R)

Group identified by SSU rRNA and GAPDH phylogenies, with relatively slow evolution of the gene sequences. Includes monoxenous genera *Borovskyia*, *Crithidia*, *Leptomonas*, *Lotmaria*, *Novymonas*, *Por- cisia*, *Zelonia*, and dixenous genera *Endotrypanum*, *Leishmania*.

● **Malawimonadidae** O’Kelly & Nerad 1999

Small free-living biciliated cells, superficially similar to *Carpediemonas* but not closely related, with a typical respiratory mitochondrion with discoidal cristae and genome; two kinetosomes, posterior cilium with a single ventral (*Malawimonas*) or two opposing (*Gefionella*) vanes; typically from freshwater or soil. *Gefionella*, *Malawimonas*.

● “CRuMs” (Brown et al. 2018) [Varisulca Cavalier-Smith 2012] (R)

This probable sister clade in Amorphea, informally referred to as CRuMs, includes at least Collodictyonidae, Rigifilida and *Mantamonas*.
All members exhibit some form of cellular plasticity, some with pseudopodia.
*Incertae sedis CRuMs: Glissandra*.

●● Collodictyonidae Brugerolle et al. 2002, emend. Adl et al. 2019 [Diphylleidae Cavalier-Smith 1993, Diphylleida Cavalier-Smith 1993, Diphyllatea Cavalier-Smith 2003, Sulcomonadidae Cavalier-Smith 2013]

Free-swimming 10–15 µm long cells with two or four equal apical cilia orthogonal to each other; ciliary transition zone long, with a two-part axosome; phagocytosis of other eukaryotic cells occurring through use of pseudopodia in a conspicuous longitudinal ventral groove that extends to posterior end, giving a double-lobed appearance. *Collodictyon*, *Diphylleia* (= *Aulacomonas*), *Sulcomonas*.

●● Rigifilida Cavalier-Smith in Yabuki et al. 2012

Cells rounded, 5–10 µm in diameter, approximately circular in dorsoventral aspect although somewhat plastic; pellicle underlies cell mem-
brane on dorsal and lateral surfaces; central circular depression on venter of cell, with collar-like margin of reflected pellicle; branching
fine pseudopodia arising from ventral depression, used to capture bacteria; flat mitochondrial cristae. *Micronuclearia*, *Rigifila*.

●● Mantamonas Cavalier-Smith and Glücksman in Glücksman et al. 2011 (M)

Gliding marine biciliated ~5-µm cell; body flattened, characteristically seen wider than long with left side of cell having angled shape or with short (~1 µm) rounded projection, and right side plastic; however, cell can also be longer than wide, with rounded anterior with posterior end tapering to point at posterior cilium, or any intermediate shape; long posteriorly directed cilium directed straight behind gliding cell; anterior cilium very short and thin, projecting stiffly forward and left. *Mantamonas plastica*.

● Ancyromonadida Cavalier-Smith 1998 [=Planomonadida Cavalier-Smith 2008]

Small (~5 µm) benthic gliding cells, dorsoventrally compressed, with leftward-oriented rostrum at anterior; two unequal cilia, each emerging in separate shallow pocket; short apical anterior cilium may be very thin or terminate at cell membrane; long posterior cilium inserts ventrally/left-laterally; rostrum contains extrusomes in rows; cell membrane supported by a thin single-layered theca; discoidal/ flat mitochondrial cristae; bacterivorous. This clade is the likely sister clade to the Amorphea and CRuMs. *Ancyromonas*, *Fabomonas*, *Nutomonas*, *Planomonas*.

● Hemimastigophora Foissner et al. 1988

Ellipsoid to vermiform cells, cilia typically 15–40 µm long, arranged in two lateral rows that may or may not run the whole length of the cell, with up to about a dozen cilia per row; submembranous thecal plates separate the cilia; thecal plates rotationally symmetrical, supported by microtubules; anterior differentiated into a capitulum, which is the site of phagocytosis; tubular and saccular mitochondrial cristae; with bottle-shaped extrusomes.

*Incertae sedis Hemimastigophora: Paramastix.*

(continued)
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

●● Spironemidae Doflein 1916
*Hemimastix, Spironema, Stereonema.*

● *Meteora* Hausmann et al. 2002 (M)
Gliding 3–4 µm round cell with long, thin, stiff anterior and posterior protrusions; two (rarely more) short paired lateral ‘arms’ that wave anteriorly and posteriorly as if rowing, generally at same frequency but varying between moving in same or opposite directions; ‘arms’ usually straight, ~cell diameter long, but may be branched; ‘arms’ often have linearly arranged nodules, nodules occasionally also found in anterior/posterior protrusions. *Meteora sporadica*.

<table><caption>**Table 3.** Genera *incertae sedis* in eukaryotes, with uncertain affiliation within protists</caption><tr><td>Acinetactis</td><td>Ectobiella</td><td>Ovicola</td></tr><tr><td>Actinastrum</td><td>Elaeorhanis</td><td>Palisporomonas</td></tr><tr><td>Actinocoma</td><td>Embryocola</td><td>Pansporella</td></tr><tr><td>Actinolophus</td><td>Endamoeba</td><td>Paradinemula</td></tr><tr><td>Adinomonas</td><td>Endemosarca</td><td>Paraluffisphaera</td></tr><tr><td>Aletium</td><td>Endobiella</td><td>Paramonas</td></tr><tr><td>Amphimonas</td><td>Endomonas</td><td>Paraplasma</td></tr><tr><td>Amylophagus</td><td>Endospora</td><td>Parastasia</td></tr><tr><td>Anaeramoeba</td><td>Enteromyxa</td><td>Parastasiella</td></tr><tr><td>Aphelidiopsis</td><td>Eperythrocytozoon</td><td>Peliainia</td></tr><tr><td>Asterocaelum</td><td>Errera</td><td>Peltomonas</td></tr><tr><td>Asthmatos</td><td>Fromentella</td><td>Petasaria</td></tr><tr><td>Aurospora</td><td>Gymnococcus</td><td>Phagodinium</td></tr><tr><td>Barbetia</td><td>Gymnophrydium</td><td>Phanerobia</td></tr><tr><td>Belaria</td><td>Haematotragidium</td><td>Phloxamoeba</td></tr><tr><td>Belonocystis</td><td>Hartmannina</td><td>Phyllomitus</td></tr><tr><td>Bertarellia</td><td>Heliobodo</td><td>Phyllomonas</td></tr><tr><td>Bertramia</td><td>Heliomonas</td><td>Physcosporidium</td></tr><tr><td>Bodopsis</td><td>Hermisenella</td><td>Piridium</td></tr><tr><td>Boekelovia</td><td>Heterogromia</td><td>Pleuophrys</td></tr><tr><td>Branchipocola</td><td>Hillea</td><td>Pleuromastix</td></tr><tr><td>Camptozyche</td><td>Hyalodakylethra</td><td>Protenterospora</td></tr><tr><td>Chalarodora</td><td>Immanoplasma<sup>b</sup></td><td>Protomonas</td></tr><tr><td>Cibdelia</td><td>Isoselmis</td><td>Pseudoactiniscus</td></tr><tr><td>Cichkovia</td><td>Janickina</td><td>Pseudosporopsis</td></tr><tr><td>Cinetidomyxa</td><td>Kamera</td><td>Rhizomonas</td></tr><tr><td>Cingula</td><td>Lagenidiopsis</td><td>Rhynchodinium</td></tr><tr><td>Cladomonas</td><td>Liegeosia</td><td>Rigidomastix</td></tr><tr><td>Clathrella</td><td>Luffisphaera<sup>c</sup></td><td>Schewiakoffia</td></tr><tr><td>Codonoeca</td><td>Lymphocytozoon</td><td>Sergentella</td></tr><tr><td>Coelosporidium<sup>a</sup></td><td>Lymphosporidium</td><td>Serpentoplasma</td></tr><tr><td>Copromonas</td><td>Macappella</td><td>Sphaerasuctans</td></tr><tr><td>Cyanomastix</td><td>Magosphaera</td><td>Spongastericus</td></tr><tr><td>Cyclomonas</td><td>Malpighiella</td><td>Spongocyclia</td></tr><tr><td>Cytamoeba</td><td>Martineziella</td><td>Stephanomonas</td></tr><tr><td>Dallingeria</td><td>Megamoebomyxa</td><td>Strobilomonas</td></tr><tr><td>Dictyomyxa</td><td>Meringosphaera</td><td>Tetradimorpha</td></tr><tr><td>Dimastigamoeba</td><td>Microcometes</td><td>Tetragonidium</td></tr><tr><td>Dinemula</td><td>Monochrysis</td><td>Thaulirens</td></tr><tr><td>Dinoasteromonas</td><td>Monodus</td><td>Topsentella</td></tr><tr><td>Diplocalium</td><td>Mononema</td><td>Toshiba</td></tr><tr><td>Diplomita</td><td>Myrmicisporidium</td><td>Trichonema</td></tr><tr><td>Diplophysalis</td><td>Naupliicola</td><td>Urbanella</td></tr><tr><td>Diploselmis</td><td>Nephrodinium</td><td></td></tr><tr><td>Dobellina</td><td>Neurosporidium</td><td></td></tr><tr><td>Ducelleria</td><td>Orbulinella</td><td></td></tr></table>

<footnote><sup>a</sup>Probably a junior synonym of *Nephridiophaga*, a Zygomycete.</footnote>

<footnote><sup>b</sup>Immanoplasma Neumann 1909 (see Kar 1990).</footnote>

<footnote><sup>c</sup>*Belonocystis* (*Amoebozoa incertae sedis*) and *Luffisphaera* may be the same genus.</footnote>
<table><caption>**Table 4.** Recommended primers for environmental samples</caption><thead><tr><th>Supergroup or highest rank</th><th>Clades</th><th>Primer pair codes</th><th>Sequence length (bp)</th><th>Forward primer (5'→3')</th><th>Reverse primer (5'→3')</th></tr></thead><tbody><tr><td rowspan="5">Amorphea<br>Amoebozoa</td><td>Apusomonadida¹</td><td>18S, EK-42F & APU-1R</td><td>1,500-2,200</td><td>CTCAARGAYTAAGCCATGCA</td><td>CTTCCTTTGGTTAAACAC</td></tr><tr><td>Tubulinea,</td><td>18S, RibA & RibB</td><td>Entire SSU molecule, variable</td><td>ACCTGGTTGATCCTDCCAGT</td><td>TGATCCATCTGCAGGTTCACCTAC</td></tr><tr><td>Discosea, Variosea</td><td>18S, RibA & S20R</td><td>-1,800</td><td>ACCTGGTTGATCCTDCCAGT</td><td>GACGGCGGTGTGTACAA</td></tr><tr><td>Tubulinea,</td><td>Cox-I, LCO1490 & HCO2198 (modified Folmer primers)</td><td>-660</td><td>GGTCAACAAATCATAAAGATATTGG</td><td>TAAACTTCAGGGTGACCAAAAAATCA</td></tr><tr><td>Discosea, Variosea</td><td>1st step, Euk 82F & Euk 1498 R, 2nd step, cloning</td><td>Variable</td><td>GAAACTGCGAATGGCTC</td><td>CYGCAGGTTCACCTA C</td></tr><tr><td rowspan="10">Opisthokonta<br>Porifera³</td><td>Arcellinida</td><td>18S, 42F & 1510R Cox-I (Folmer primers), LCO1490 & HCO2198</td><td>-1,750 658</td><td>CTCAARGAYTAAGCCATGCA GGTCAACAAATCATAAAGATATTGG</td><td>CCTTCYGAGGTTCACCTAC TAAACTTCAGGGTGACCAAAAAATCA</td></tr><tr><td rowspan="5">Homoscleromorpha:</td><td>28S, C1 & D2, universal primers</td><td>800-900</td><td>ACCCGCTGAATTTAAGCAT</td><td>TCCGTGTTTCAAGACGGG</td></tr><tr><td>28S D1-D2, Por28S-15F & Por28S-878R</td><td>790-830</td><td>GCGAGATCACCYGCTGAAT</td><td>CACTCCTTGGTCCGTGTTTC</td></tr><tr><td>28S D3-D5, Por28S-830F & Por28S-1520R</td><td>650-660</td><td>CATCCGACCCGTCTTGAA</td><td>GCTAGTTGATTCGGCAGGTG</td></tr><tr><td>28S D3-D5, NL4F & NL4R</td><td>650-660</td><td>GACCCGAAAGATGGTG AACTA</td><td>ACCTTGGAGACCTGA TGCG</td></tr><tr><td>28S C-region, C2 & D2, or C2 modified & D2</td><td>430-470</td><td>GAAAAGAACTTTGRARAGAGT or GAAA AGCACTTTGAAAAGAGA</td><td>TCCGTGTTTCAAGACGGG</td></tr><tr><td rowspan="2">Hexactinellida:</td><td>28S D3-D5, NL4F & NL4R</td><td>900-1,000</td><td>ACCCGAAAGATGGTG AACTA</td><td>ACCTTGGAGACCTGATGCG</td></tr><tr><td>16S partial primers, 16S1fw & 16SH modified</td><td>500</td><td>TCGACTGTTTACCAAAAAACATAGC</td><td>YRTAATTCAACATCGAGGTC</td></tr><tr><td rowspan="10">Fungi</td><td rowspan="10">Chytridiomycota⁴,⁵,⁶,⁷</td><td>18S, NS1 & NS4</td><td>-950-1,100</td><td rowspan="10"></td><td rowspan="10"></td></tr><tr><td>PolySSU1 & PolySSU1R</td><td>Variable</td></tr><tr><td>28S, LOR & LR5</td><td>-800-950</td></tr><tr><td>ITS1-5.8S-ITS2, ITS5 & ITS4</td><td>-614-987</td></tr><tr><td>EF-1a,* 983F & EF1aZ-1R</td><td>-1,150</td></tr><tr><td>EF-1a-like,** 983F & EFL-RS2R</td><td>--550-590</td></tr><tr><td>ITS (See citation 9, Table S1)</td><td>Variable</td></tr><tr><td>18S, AU2-F & AU4-R, & inner AUPH1</td><td>TTTCGATGGTAGG ATAGDGG</td><td>RTCTCACTAAGCCATTC, and inner AGAGCTMTCAATCTGTCAATCCT</td></tr><tr><td>1F & 1528R (or EukA & EukB)</td><td>1,800</td><td>AACCTGGTTGATCCTGCCAGT</td></tr><tr><td rowspan="5">Haptista</td><td>EukF & EukR</td><td>1,795</td><td>ACCTGGTTGATCCTGCCAG</td></tr><tr><td>TAReuk454FWD1 & TAReukREV3</td><td>830</td><td>GGGTTCGATTCGGAGAG</td></tr><tr><td>Hapto4 & Euk34r</td><td>1,000</td><td>CCAGCA(G)C/C(T)GCGGTAAATTCC</td></tr><tr><td>LSU1 (Lhapto8 & Lhapto20R_bis)</td><td>350-400</td><td>ATGGCGAATGAAGCGGGC GGTATCGGAGAAGGTGAGAATCCT</td></tr><tr><td></td><td></td><td></td><td>GCATCGCCAGTTCTGCTTACC TCAGACTCCTTGGTCCGTGTTTCT</td></tr></tbody></table>

(continued)
<table><caption>**Table 4.** (continued)</caption><thead><tr><th>Supergroup or highest rank</th><th>Clades</th><th>Primer pair codes</th><th>Sequence length (bp)</th><th>Forward primer (5'→3')</th><th>Reverse primer (5'→3')</th></tr></thead><tbody><tr><td rowspan="10">Centroplasthelida<sup>12</sup></td><td rowspan="10">Stramenopiles</td><td>Prym03-3 & Hapto1R</td><td>416</td><td>GTAAATTTGCCCGAATCCTG</td><td>CGAAACCAACAAAATAGCAC</td></tr><tr><td>528FLong & PRYM01 + 7</td><td>399</td><td>GCGGTAATTCCAGCTCCAA</td><td>GATCAGTGAAAACATCCTGG</td></tr><tr><td>Pavlova-V4F & 1528R</td><td>904</td><td>GTGAAATTCTTAGACCCACGGA</td><td>TGATCCTTCTGCAGGTTCCACCTAC</td></tr><tr><td>1F & Pavlova-V4F2R</td><td>593</td><td>See 1F above</td><td>GTGAAATCTTTAGACCCACGGA</td></tr><tr><td>Pry421F & Pry1572R</td><td>1,070</td><td>AGCAGCGCGGTAAATTTGCCG</td><td>TCAACGYRCGCTGATGACA</td></tr><tr><td>Hap220F & Pav1702R</td><td>1,400</td><td>ACCGTCTCCGGTTGCGTGC</td><td>TAGATGATAAGGTTTGGGTG</td></tr><tr><td>Helio1979R</td><td>Variable</td><td></td><td>CACACTTCWAGGAYTTCCTCG</td></tr><tr><td>18S-0024F & 18S-1757R</td><td>Variable</td><td>CTGGTTGATCCTGCCAGTAGT</td><td>TTSAAGACG</td></tr><tr><td>18S-33F & 18S-1768R</td><td>1,700-1,800</td><td>CCT GCC AGT AGT CAT AYG CTT</td><td>CAGGTTCCACCTACGGAAACCT</td></tr><tr><td rowspan="2">Euglyphid<sup>16</sup></td><td rowspan="2">1st step EuglySSUF & EuglyLSUR</td><td rowspan="2">Variable</td><td>TCGTCGGCAGCGTCAGATGTG</td><td>TGA TCC TTC YGC AGG TTC ACC</td></tr><tr><td>ATAAGAGACA</td><td>ATGTGTATAAGAGACAGRACT</td></tr><tr><td rowspan="2">Assulinidae<sup>17</sup></td><td>2nd step EuglySSUF & EuglySSUR</td><td>Variable</td><td>GCGTACAGCTCATTATATCAGCA</td><td>ACGAGCTTTTTAACTGC</td></tr><tr><td>1st step, COI: Eucox1F & Euglycox1R</td><td>Variable</td><td></td><td>GTTTGGCACCTTAACTCGCG</td></tr><tr><td rowspan="2">Amphitremida</td><td>2nd step, Assucox 1F & Assucox 1R</td><td>Variable</td><td>GCGTACAGCTCATTATATCAGCA</td><td></td></tr><tr><td>1st step, Euk 82F & Euk 1498</td><td>Variable</td><td>GAYATGGKCTTNNCCAAGATTAAA</td><td>GCACCACCACCCATAGAAT</td></tr><tr><td rowspan="2">Diatomea<sup>18,19</sup></td><td>R, 2nd step, cloning</td><td>Variable</td><td>AAYATGAGRGCYAGRGG</td><td>CWAGAAAGATC</td></tr><tr><td>rbcL, 646F& 998R</td><td>379</td><td>GAAACTGCGAATGGCTC</td><td>AGCACCCATTGAHAAAAACRTAATG</td></tr><tr><td rowspan="10">Alveolata</td><td rowspan="10">Syndiniales</td><td>Diat_rbcL_708F (mixture of 3 primers)<br/>& two reverse primers R3_1 & R3_2</td><td>312 (amplicon 263)</td><td>ATGCGTTGGAGAGARCGTTC</td><td>5ø-CGTAAATGAAARTGWCCYACC</td></tr><tr><td>18S V4,</td><td>Variable</td><td>1: AGGTGAAGTAAAGGTTWCWACTTAAA,<br/>and 2: AGGTGAAGTTAAAGGTTCWT</td><td></td></tr><tr><td>18S PF1 & R4</td><td>Variable</td><td>AYTTAAA and 3: AGGTGAAACTAA</td><td>1: CCTTCTAATTTACCWACW</td></tr><tr><td>18S V4 TAReuk454FWD1 & TAReukREV3</td><td>Variable</td><td>AGGTTWCWACTTAAA</td><td>ACTG, and 2: CCTTCTAATTT</td></tr><tr><td>18S V4, 346Fmix & 785P-mix</td><td>Variable</td><td></td><td>ACCWACAACAG</td></tr><tr><td rowspan="2">Dinoflagellata****23,24</td><td rowspan="2">Syndiniales</td><td rowspan="2">Apicomplexa<sup>21,22</sup></td><td rowspan="2">Variable</td><td>CADCGACGGGTACGGGGAATTA;</td><td>GATCCTTCTGCAGGTTCCACCTAC</td></tr><tr><td>TCGTCGGCAGCGTCAGATGTGTAT</td><td>ACTTTCGTCTTGAT(C/T)(A/G)</td></tr><tr><td rowspan="2">Rhizaria</td><td rowspan="2">Cercozoa</td><td rowspan="2">18S V4, 528F & UnonMet</td><td rowspan="2">Variable</td><td>AAGAGACAG[C[CAGCASCYGCGGTAAATTCC]</td><td>IIITATCCATGCTGIAGTATTCA;</td></tr><tr><td>18S V4, 3NDF & 1256R</td><td>~500</td><td>IIITATCCATGCTGAAATCTTCA</td></tr><tr><td></td><td></td><td></td><td></td><td></td><td>GTCTCGTGGGCTCGGAGATGT</td></tr><tr><td></td><td></td><td></td><td></td><td></td><td>GTATAAGAGACAG[ACTTTCGTTC</td></tr><tr><td></td><td></td><td></td><td></td><td></td><td>TTGATYRATGA]</td></tr></tbody></table>

(continued)
<table><caption>**Table 4.** (continued)</caption><thead><tr><th>Supergroup or highest rank</th><th>Clades</th><th>Primer pair codes</th><th>Sequence length (bp)</th><th>Forward primer (5'→3')</th><th>Reverse primer (5'→3')</th></tr></thead><tbody><tr><td rowspan="10">Excavates</td><td>Cyphoderiidae<sup>25</sup></td><td>18S V4***, 25F &amp; 1256R</td><td>1,200</td><td>CATATGCTTGTCTCAAGATTAAGCCA</td><td>GCACCACCACCAYAGAATCAAG AAAGAWCTTC</td></tr><tr><td>Foraminifera<sup>26</sup></td><td>Cox-I, Eucox1F &amp; Euglycox1R</td><td>Variable</td><td>GAYATGGCKTTNCCAAGATTAA</td><td>GCACCACCACCAYAGAATCAAG AAAGAWCTTC</td></tr><tr><td>Fornicata<sup>27</sup></td><td>18S, 14F1 &amp; s17</td><td>300-400</td><td>AAGGGCACCACACAAGAACGC</td><td>AGCACCCATTGAHAAAAACRTAATG</td></tr><tr><td>Parabasalia</td><td>EukA &amp; EukB*</td><td>Variable</td><td>TACTTGGTTGATCCTGCC</td><td>CGGTCACGTTCGTTGC</td></tr><tr><td rowspan="2">Jakobida</td><td>16S1 &amp; 16S RR (or EukA &amp; B)</td><td>Variable</td><td>TTCAGTTCAGCGGGTCTTCC</td><td>TCACCCTACCGTTACCCTTG</td></tr><tr><td>ITS-F &amp; ITS-R</td><td>Variable</td><td></td><td>GTAGGTGAACCTGCCGTTGG</td></tr><tr><td rowspan="2">Heterologobea</td><td>EukA - EukB</td><td>Variable</td><td>GTCTTCGTAGGTGAACCTGC</td><td>CCGCTTACTGATATGCTTAA</td></tr><tr><td>ITS1-5.8S &amp; ITS2, ITS-F &amp; JITS-R, (or EukA &amp; EukB)</td><td>Variable</td><td></td><td></td></tr><tr><td>Preaxostyla:</td><td>Mon-F &amp; Mon-R</td><td>Variable</td><td>GAAGTCATATGCTGTCTCAA,</td><td>TCACCTACGGAAACCTT</td></tr><tr><td>Oxymonadida</td><td rowspan="2">EukA &amp; EukB</td><td rowspan="2">1,800-3,100</td><td rowspan="2">CTGGTTGATCCTGCCAG</td><td rowspan="2">TGATCCTTCTGCAGGTTCACCTAC</td></tr><tr><td>Preaxostyla:</td></tr><tr><td>Paratrimastigida, Trimastigida</td><td>See citation</td><td>Varies with the primer pairs</td><td></td><td></td></tr><tr><td>Euglenida Heterotrophs<sup>28</sup></td><td>See citation</td><td>Varies with the primer pair</td><td></td><td></td></tr><tr><td rowspan="2">Protist, general<sup>*27</sup></td><td>General Medlin primers</td><td>EukA-F &amp; EukB-R</td><td>Variable</td><td>CTGGTTGATCCTGCCAG</td><td>TGATCCTTCTGCAGGTTCACCTAC</td></tr><tr><td>General Stoeck primers</td><td>See citation</td><td>Variable</td><td></td><td></td></tr></tbody></table>

*Selective amplification of species, some clades missed.

**Spizellomycetales.

***Chytridiomycota except Spizellomycetales.

****See citations for DINOREF in PR2 v.4.9.0.

¹Torruella, G., Moreira, D. & López-García, P. 2017. Phylogenetic and ecological diversity of apusomonads, a lineage of deep-branching eukaryotes *Env. Microbiol. Rep.* 9:113-119. doi.org/10.1111/1758-2229.12507.

²Amaral-Zettler, L.A., McCliment, E.A., Ducklow, H.W. & Huse, S.M. 2009. A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes. *PLOS one* 4 (12): https://doi.org/10.1371/journal.pone.0006372.

³Morrow, C.C., Picton, B.E., Erpenbeck, D., Boury-Esnault, N., Maggs, C.A. & Alcock, A.L. 2012. Congruence between nuclear and mitochondrial genes in Demospongiae: A new hypothesis for relationships within the G4 clade (Porifera: Demospongiae). *Molecular Phylogenetics and Evolution* 62: 174–190.

⁴White, M.M., James, T.Y., O'Donnell, K., Cafaro, M.J., Tanabe, Y. & Sugiyama, J. 2006. Phylogeny of the Zygomycota based on nuclear ribosomal sequence data. *Mycologia*, 98(6): 872-884. https://doi.org/10.1080/15572536.2006.11832617.

⁵Simmons, D.R. 2011. Phylogeny of Powellomycesaceae fam. nov. and description of *Geranomyces variabilis* gen. et comb. Nov. *Mycologia* 103(6):1411-1420.

⁶Vilgalys, R. & Hester, M. 1990. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. *J. Bacteriology* 172(8):4238-4246.

⁷James, T.Y., Letcher, P.M., Longcore, J.E., Mozley-Standridge, S.E., Porter, D., Powell, M.J., Griffith, G.W. & Vilgalys, R. 2006. A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota). *Mycologia* 98(6):860-871.

⁸Schoch, C.I., Seifert, K.A, Huhndorf, S., Robert, V., Spouge, J.L., Levesque, C.A., Chen, W. & Fungal Barcoding Consortium. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. *PNAS* 109 (16): 6241-6246; https://doi.org/10.1073/pnas.1117018109.
⁹Vandenkoornhuyse, P., Baldauf, S.L., Leyval, C., Straczek, J. & Young, J.P.W. 2002. Extensive Fungal Diversity in Plant Roots Science 295 (5562): 2051 https://doi.org/10.1126/science.295.5562.2051.

¹⁰Egge, E., Bittner, L., Andersen, T., Audic, S. de Vargas, C. 2013. 454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes. *PLoS ONE* 8(9): e74371. https://doi.org/10.1371/journal.pone.0074371

¹¹Edvardsen, B., Egge, E.S. & Vaulot, D. 2016. Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review. *Perspectives in Phycology* 3(2): 77–91.

¹²Cavalier-Smith, T. & von der Heyden, S. 2007. Molecular phylogeny, scale evolution and taxonomy of centrohelid heliozoan. *Molecular Phylogenetics and Evolution* 44(3): 1186–1203. https://doi.org/10.1016/j.mpev.2007.04.019.

¹³Kim, E., Simpson, A.G.B. & Graham, L.E. 2006. Evolutionary relationships of apusomonads inferred from taxon-rich analyses of 6 nuclear encoded genes. *Molec. Biol. Evol.* 23(12):2455–2466.

¹⁴Kim, E. & Archibald, J. 2013. Ultrastructure and molecular phylogeny of the Cryptomonad *Gonimonas avonlea* sp. Nov. *Protist* 164(2):160–182.

¹⁵Sisson, C., Gulla-Devaney, B., Katz, L.A. & Grattepanche, J-D. 2018. Seed bank and seasonal patterns of eukaryotic SAR (Stramenopila, Alveolata, Rhizaria) clade in a New England vernal pool. *J. Plankton Res.* 00(00): 1–15. https://doi.org/10.1093/plankt/fby020.

¹⁶Lara, E., Simpson, A.G.B. & Graham, L.E. 2006. Evolutionary relationships of apusomonads inferred from taxon-rich analyses of 6 nuclear encoded genes. *Molec. Biol. Evol.* 23(12):2455–2466.

¹⁷Lara, E., Heger, T.J., Scheihing, R. & Mitchell, E.A.D. 2011. COI gene and ecological data suggest size-dependent high dispersal and low intra-specific diversity in free-living terrestrial protists (Euglyphida: Assulinal). *Journal of Biogeography* 38(4): 640–650.

¹⁸Kelly, M., Boonham, N., Juggins, S., Kille, P., Mann, D., Pass, D., Sapp, M., Sato, S. & Glover, R. 2018. A DNA based diatom metabarcoding approach for Water Framework Directive classification of rivers. *SCIENCE* 359(6382): 111–114. https://doi.org/10.1073/pnas.1755-0998.1146.

¹⁹Vasselon, V., Rimet, F., Tapolczai, K. & Bouchez, A. 2017. Assessing ecological status with diatoms DNA metabarcoding: scaling up on a WFD monitoring network (Mayotte island, France). *Ecol. Indicators* 82: 1–12.

²⁰Lara, E., Berney, C., Harms, H. & Chatzinotas, A. 2007. Cultivation-independent analysis reveals a shift in ciliate 18S rRNA gene diversity in a polycyclic aromatic hydrocarbon-polluted soil. *FEMS Microbiol. Ecol.* 62:365–373.

²¹Stoeck, T., Bass, D., Nebel, Christen, R., Jones, M.C.M., Breiner, H-W. & Richards, T. 2010. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. *Mol. Ecol.* 19(1), 21–31.

²²Janouškovec, J., Tikhonenkov, D.V., Burki, F., Howe, A.T., Kolisko, M., Mylnikov, A.P., & Keeling, P. 2015. Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives. *PNAS* 112(33), 10200–10207.

²³Piredda R., Tomasino, M.P., D'Erchia, A.M., Manzari, C., Pesole, G., Montresor, M., Kooistra, W.H.C F., Sarno, D. & Zingone, A. 2017. Diversity and temporal patterns of planktonic protist assemblages at a Mediterranean Long Term Ecological Research site *FEMS Microbiology Ecology*, 93(1), fiv200, doi.org/10.1093/femsec/fiv200.

²⁴Mordret, S., Piredda, R., Vaulot, D., Montresor, M., Koostra, W.H.C.F. & Sarno. D. DINOREF: A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene. *Mol Ecol Resour.* 2018;1–14. https://doi.org/10.1111/1755-0998.12781.

²⁵Heger, T., Pawlowski, J., Lara, E., Leander, B.S., Todorov, M., Golemansky, V. & Mitchell, E.A.D. 2011. Comparing potential COI and SSU rDNA barcodes for assessing the diversity and phylogenetic relationships of cyphoderiid testate amoebae (Rhizaria: Euglyphida). *Protist* 162(1):131–141.

²⁶Pawlowski, J. & Lecroq, B. 2010. Short rDNA barcodes for species identification in foraminifera. *J. Eukaryot. Microbiol.* 57(2):197–205.

²⁷Medlin, L., Elwood, H.J., Stickel, S. & Sogin, M.L. 1988. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. *Gene* 71(2): 491–499. https://doi.org/10.1016/0378-1119(88)90066-2.

²⁸Lax, G. & Simpson, AGB. 2013. Combining molecular data with classical morphology for uncultured phagotrophic euglenids (Excavata): a single cell approach. *J. Eukaryot. Microbiol.* 60(6):615–625. https://doi.org/10.1111/jeu.12068.
LITERATURE CITED

Adl, M. S., Leander, B. S., Simpson, A. G. B., Archibald, J. M., Anderson, O. R., Barta, J. R., Bass, D., Bowser, S. S., Brugerolle, G., Farmer, M. A., Karpov, S., Kolisko, M., Lane, C. E., Lodge, J., Lynn, D. H., Mann, D. G., Meisterfeld, R., Mendoza, L., Moestrup, Ø., Mozley-Standridge, S. E., Smirnov, A. V. & Spiegel, F. W. 2007. Diversity, nomenclature and taxonomy of protists. *Syst. Biol.*, 56(4):684–689.

Adl, M. S., Simpson, A. G. B., Farmer, M. A., Andersen, R. A., Anderson, O. R., Barta, J. R., Bowser, S. S., Brugerolle, G., Fensome, R. A., Fredericq, S., James, T. Y., Karpov, S., Kugrens, P., Krug, J., Lane, C. E., Lewis, L. A., Lodge, J., Lynn, D. H., Mann, D. G., McCourt, R. M., Mendoza, L., Moestrup, Ø., Mozley-Standridge, S. E., Nerad, T. A., Shearer, C. A., Smirnov, A. V., Spiegel, F. W. & Taylor, F. J. R. 2005. The new classification of eukaryotes with emphasis on the taxonomy of protists. *J. Eukaryot. Microbiol.*, 52(5):399–451.

Adl, S. M., Simpson, A. G., Lane, C. E., Lukeš, J., Bass, D., Bowser, S. S., Brown, M. W., Burki, F., Dunthorn, M., Hampl, V., Heiss, A., Hoppenrath, M., Lara, E., Le Gall, L., Lynn, D. H., McManus, H., Mitchell, E. A. D., Mozley-Standridge, S. E., Parfrey, L. W., Pawlowski, J., Rueckert, S., Shadwick, L., Schoch, C., Smirnov, A. & Spiegel, F. W. 2012. The revised classification of eukaryotes. *J. Eukaryot. Microbiol.*, 59:429–493.

Bass, D., Czech, L., Williams, B. A. P., Berney, C., Dunthorn, M., Mahé, F., Torruella, G., Stentiford, G. D. & Williams, T. A. 2018. Clarifying the relationships between microsporidia and cryptomycota. *J. Euk. Microbiol.*, 65(6):773–782.

Berney, C., Ciuprina, A., Bender, S., Brodie, J., Edgcomb, V., Kim, E., Rajan, J., Wegener Parfrey, L., Adl, S., Audic, S., Bass, D., Caron, D. A., Cochrane, G., Czech, L., Dunthorn, M., Geisen, S., Oliver Glückner, F., Mahé, F., Quast, C., Kaye, J. Z., Simpson, A. G. B., Stamatakis, A., del Campo, J., Yilmaz, P. & de Vargas, C. 2017. UniEuk: time to speak a common language in protistology! *J. Eukaryot. Microbiol.*, 64:407–411. https://doi.org/10.1111/jeu.12414

Berney, C., Geisen, S., Van Wichelen, J., Nitsche, F., Vanormelingen, P., Bonkowski, M. & Bass, D. 2015. Expansion of the "reticulosphere": diversity of novel branching and network-forming amoebae helps to define Variosea (Amoebozoa). *Protist*, 166:271–295.

Blandenier, Q., Seppey, C. V. W., Singer, D., Vlimant, M., Simon, A., Duckert, C. & Lara, E. 2017. *Mycamoeba gemmipara* nov. gen., nov. sp., the first cultured member of the environmental Dermamoebidae Clade LKM74 and its unusual life cycle. *J. Eukaryot. Microbiol.*, 64:257–265.

Brown, M. W., Heiss, A. A., Kamikawa, R., Inagaki, Y., Yabuki, A., Tice, A. K., Shiratori, T., Ishida, K., Hashimoto, T., Simpson, A. G. B. & Roger, A. J. 2018. Phylogenomics places orphan protistan lineages in a novel eukaryotic super-group. *Genome Biol. Evol.*, 10:427–433.

del Campo, J., Kolisko, M., Boscaro, V., Santoferrara, L. F., Masana, R., Guillou, L., Simpson, A. G. B., Berney, C., de Vargas, C., Brown, M., Keeling, P. & Parfrey, L. W. 2018. EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. *PLOS Biol.* 2018;16:e2005849.

Cantino, P. D. 1998. Binomials, hyphenated uninomials, and phylogenetic nomenclature. *Taxon* 47:425–429.

Cavalier-Smith, T., Chao, E. E. & Lewis, R. 2016. 187-Gene phylogeny of protozoan phylum Amoebozoa reveals a new class (Cutosea) of deep-branching, ultrastructurally unique, enveloped marine Lobosa and clarifies amoeba evolution. *Mol. Phylogenet. Evol.*, 99:275–296.

De Vargas, C., Audic, S., Henry, N., Decelle, J., Mahé, F., Logares, R., Lara, E., Berney, Č., Le Bescot, N., Probert, I., Carmichael, M., Poulain, J., Romac, S., Colin, S., Aury, J.-M., Bittner, L., Chaffron, S., Dunthorn, M., Engelen, S., Flegontova, O., Guidi, L., Horák, A., Jaillon, O., Lima-Mendez, G., Lukeš, J., Malviya, S., Morard, R., Mulot, M., Scalco, E., Siano, R., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Acinas, S. G., Bork, P., Bowler, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Raes, J., Sieracki, M. E., Speich, S., Stemmann, L., Sunagawa, S., Weissenbach, J., Wincker, P., Karsenti, E., Boss, E., Follows, M., Karp-Boss, L., Krzic, U., Reynaud, E. G., Sardet, C., Sullivan, M. B. & Velayoudon, D. 2015. Eukaryotic plankton diversity in the sunlit ocean. *Science*, 348 (6237):1261605. https://doi.org/10.1126/science.1261605

Dutrochet, R. J. H. 1824. Recherches anatomiques et physiologiques sur la structure intime des animaux et des végétaux. Baillière, Paris.

Ehrenberg, C. G. 1838. Über das Massenverhältniss der jetzt lebenden Kiesel-Infusorien und über ein neues Infusorien-Conglomerat als Polierschiefer von Jastraba in Ungarn. Königlich Akademie der Wissenschaften zu Berlin, Abhandlungen. Vol. 1: p. 109–135, pl.1-2.

Fenchel, T. 1986. Protozoan filter feeding. *Prog. Protistol.*, 1:65–114. Eds. Corliss, J.O. & Patterson, D.J. Biopress Ltd.

Grassi, B. 1881. Intorno ai chetognati. *Reale Ist. Lombardo Sci. Lett.*, 2:185-224.

Hibberd, D. J. 1983. Ultrastructure of the colonial colouless flagellates *Phalansterium digitatum* Stein (Phalansteriida ord. nov.) and *Spongomonas uvella* (Spongomonadida ord. nov.). *Protistologica*, 19:523-535.

Karpov, S. A., Torruella, G., Moreira, D., Mamkaeva, M. A. & López-García, P. 2017a. Molec. Phylogeny of *Paraphelidium letcheri* sp. nov. (Aphelida, Opisthosporidia) *J. Euk. Micro.* 64 (5): 573-578.

Karpov, S. A., Tcvetkova, V. S., Mamkaeva, M. A., Torruella, G., Timpano, H., Moreira, D., Mamanazarova, K. S. & López-García, P. 2017b. Morphological and genetic diversity of opisthosporidia: New aphelid *Paraphelidium tribonemae* gen. et sp. nov. *J. Euk. Micro.* 64(2):204–212.

Kang, S., Tice, A. K., Spiegel, F. W., Silberman, J. D., Pánek, T., Cepička, I., Kostka, M., Kosakyan, A., Alcántara, D. M., Roger, A. J., Shadwick, L. L., Smirnov, A., Kudryavstev, A., Lahr, D. J. & Brown, M. W. 2017. Between a pod and a hard test: the deep evolution of amoebae. *Mol. Biol. Evol.*, 34:2258–2270. https://doi.org/10.1093/molbev/msx162

Kar, D. 1990. A pirhemocyton-like parasite of the blenny, *Blennius pholis* L. (Teleostei: Blennidae) and its relationship to *immuneplasma* Neumann 1909. *Int. J. Parasitol.*, 3:235e241.

Lahr, D. J. G., Grant, J. R. & Katz, L. A. 2013. Multigene phylogenetic reconstruction of the Tubulinea (Amoebozoa) corroborates four of the six major lineages, while additionally revealing that shell composition does not predict phylogeny in the Arcellinida. *Protist*, 164:323–339.

Lahr, D. J. G., Grant, J., Nguyen, T., Lin, J. H. & Katz, L. A. 2011. Comprehensive phylogenetic reconstruction of Amoebozoa based on concatenated analyses of SSU-rDNA and actin genes. *PLoS ONE*, 6:e22780. https://doi.org/10.1371/journal.pone.0022780

Lahr, J. G., Lara, E. & Mitchell, E. A. D. 2012. Time to regulate microbial eukaryote nomenclature. *Biol. J. Linn. Soc.*, 107 (3):469–476. https://doi.org/10.1111/j.1095-8312.2012.01962.x.

Lara, E., Heger, T. J., Ekelund, F., Lamentowicz, M. & Mitchell, E. A. D. 2008. Ribosomal RNA genes challenge the monophyly
of the Hyalospheniidae (Amoebozoa: Arcellinida). *Protist*, 159:165-176.

Letcher, P. M., Longcore, J. E., Quandt, C. A., Leite, D. D. S., James, T. Y. & Powell, M. J. 2017. Morphological, molecular, and ultrastructural characterization of *Rozella rhizoclosmatii*, a new species in Cryptomycota. *Fungal Biol.*, 121(1):1-10.

López-Escardó, D., López-García, P., Moreira, D., Ruiz-Trillo, I. & Torruella, G. 2018. *Parvularia atlantis* gen. et sp. nov., a Nucleariid Filose Amoeba (Holomycota, Opisthokonta). *J. of Euk. Microbiol.* 65(2): 170-179.

Meisterfeld, R. 2002. Order Arcellinida Kent 1880. In: Lee, J. J., Leedale, G. F. & Bradbury, P. (ed.), An Illustrated Guide to the Protozoa, 2nd ed. Society of Protozoologists, Lawrence, KS (Year 2000). p. 827-860.

Mikryukov, K. A. & Mylnikov, A. P. 1998. The fine structure of a carnivorous multiflagellar protist, *Multicilia marina* Cienkowski, 1881 (Flagellata incertae sedis). *Eur. J. Protist*, 34:391-401.

Nguyen, N. H., Song, Z., Bates, S. T., Branco, S., Tedersoo, L., Menke, J., Schilling, J. S. & Kennedy, P. G. 2016. FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild. *Fungal Ecol.*, 20:241-248.

Pánek, T., Zadrobiłková, E., Walker, G., Brown, M. W., Gentekaki, E., Hroudrová, M., Kang, S., Roger, A. J., Tice, A. K., Vlček, Č. & Čepička, I. 2016. First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group. *Mol. Phylogenet. Evol.*, 98:41-51.

Pawlowski, J., Audic, S., Adl, S., Bass, D., Belbahri, L., Berney, C., Bowser, S. S., Cepicka, I., Decelle, J., Dunthorn, M., Fiore-Donno, A. M., Gile, G. H., Holzmann, M., Jahn, R., Jirkū, M., Keeling, P. J., Kostka, M., Kudryavtsev, A., Lara, E., Lukeš, J., Mann, D. G., Mitchell, E. A. D., Nitsche, F., Romeralo, M., Saunders, G. W., Simpson, A. G. B., Smirnov, A. V., Spouge, J. L., Stern, R. F., Stoeck, T., Zimmermann, J. & Schindel, D. 2012. CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. *PLoS Biol.*, 10(11):e1001419.

Powell, M. J., Letcher, P. M. & James, T. Y. 2017. Ultrastructural characterization of the host-parasite interface between *Allomyces anomalus* (Blastocladiomycota) and *Rozella allomycis* (Cryptomycota). *Fungal Biol.* 121(6-7): 561-572.

Pleijel, F., and G. W. Rouse. 2003. Ceci n'est pas une pipe: Clades and phylogenetic nomenclature. *J. Zool. Syst. Evol. Res.* 41:162-174.

Quandt, C. A., Beaudet, D., Corsaro, D., Wallochnik, J., Michel, R., Corradi, N., & James, T. Y. 2017. The genome of an intranuclear parasite, *Paramicrosporidium saccamoebae*, reveals alternative adaptations to obligate intracellular parasitism. *Elife*, 6.

Richards, T. A., Leonard, G. & Wideman, J. G. 2017. What defines the "Kingdom" Fungi? *Microbiol. Spectrum* 01 Jun 2017, 5(3) DOI: 10.1128/microbiolspec.FUNK-0044-2017

Ruggiero, M. A., Dennis, P. G., Orrell, T. M., Bailly, N., Bourgoin, T., Brusca, R. C., Cavalier-Smith, T., Guiry, M. D. & Kirk, P. 2015. A higher level classification of all living organisms. *PLoS ONE*, 10(6):e0130114. https://doi.org/10.1371/journal.pone.0119248.

Saint-Exupéry, A. 1943. Le petit prince. Reynal & Hitchcock, New York, NY.

Schaudinn, F. 1899. Untersuchungen über den Generationswechsel von *Trichosphaerium sieboldi*. Schn. Abh. K. Preuss. Akad. Wiss., Berlin, (Suppl.):1-93.

Schierwater, B. & DeSalle, R. 2018. Placozoa. *Curr. Biol.*, 28:R97-R98.

Schleiden, M. J. 1838. Beiträge zur phytogenesis. Veit et Comp, Berlin.

Schwann, T. 1839. Mikroskopische Untersuchungen über die Uebereinstimmung in der Struktur und dem Wachstum der Thiere und Pflanzen, Berlin.

Shadwick, J. D. L., Silberman, J. D. & Spiegel, F. W. 2017. Variation in the SSUrDNA of the genus *Protostelium* leads to a new phylogenetic understanding of the genus and of the species concept for *Protostelium mycophaga* (Protosteliida, Amoebozoa). *J. Eukaryot. Microbiol.*, 65:331-344. https://doi.org/10.1111/jeu.12476

Sheikh, S., MatsThulin Cavender, J. C., Escalante, R., Kawakami, S. I., Lado, C., Landolt, J. C., Nanjundiah, V., Queller, D. C., Strassmann, J. E., Spiegel, F. W., Stephenson, S. L., Vadell, S. M. & Baldauf, S. L. 2018. A new classification of the dicytostelids. *Protist*, 169:1-28.

Sibbald, S. J., Cenci, U., Colp, M., Eglit, Y., O'Kelly, C. J. & Archibald, J. M. 2017. Diversity and evolution of *Paramoeba* spp. and their kinetoplastid endosymbionts. *J. Eukaryot. Microbiol.*, 64:598-607. https://doi.org/10.1111/jeu.12394

Simpson, A. G. B. & Roger, A. J. 2004. The real "kingdoms" of eukaryotes. *Curr. Biol.*, 14:R693-R896. https://doi.org/10.1016/j.cub.2004.08.038.

Smirnov, A. 2008. Amoebas, Lobose. In: Schaechter, M. (ed.), Encyclopedia of Microbiology. Elsevier Science Publishers, Oxford. p. 558-577.

Spiegel, F. W., Shadwick, L. L., Ndiritu, G. G., Brown, M. W., Aguilar, M. & Shadwick, J. D. L. 2017. Protosteloid Amoebozoa (Protosteliids, Protosporangiida, Cavostellida, Schizoplasmodiida, Fractoviteliida, and sporcarpic members of Vanellida, Centramoebida, and Pellitida). In: Archibald, J. M., Simpson, A. G. B. & Slamovits, C. (ed.), Handbook of the Protists (Second Edition of the Handbook of Protoctista by Margulis et al.). Springer Reference Works (e-book). https://doi.org/10.1007/978-3-319-32669-6_12-1

Srivastava, M., Begovic, E., Chapman, J., Putnam, N. H., Hellsten, U., Kawashima, T., Kuo, A., Mitros, T., Salamov, A., Carpenter, M. L., Signorovitch, A. Y., Moreno, M. A., Kamm, K., Grimwood, J., Schmutz, J., Shapiro, H., Grigoriev, I. V., Buss, L. W., Schierwater, B., Dellaporta, S. L. & Rokhsar, D. S. 2008. The *Trichoplax* genome and the nature of placzoans. *Nature*, 454 (7207):955-960. https://doi.org/10.1038/nature07191.

Tekle, Y. I., Anderson, O. R., Katz, L. A., Maurer-Alcala, X. X., Romero, M. A. & Molestina, R. 2016. Phylogenomics of 'Diseosea': A new molecular phylogenetic perspective on Amoebozoa with flat body forms. *Mol. Phylogenet. Evol.*, 99:144-154.

Tekle, Y. I. & Wood, F. C. 2017. Longamoebia is not monophyletic: phylogenomic and cytoskeleton analyses provide novel and well-resolved relationships of amoebozoa subclades. *Mol. Phylogenet. Evol.*, 114:249-260. https://doi.org/10.1016/j.ympev.2017.06.019

Tice, A. K., Shadwick, L. L., Fiore-Donno, A. M., Geisen, S., Kang, S., Schuler, G. A., Spiegel, F. W., Wilkinson, K. A., Bonkowski, M., Dumack, K., Lahr, D. J. G., Voelcker, E., Clauß, S., Zhang, J. & Brown, M. W. 2016. Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group. *Biol. Direct*, 11:69. https://doi.org/10.1186/s13062-016-0171-0.

Torruella, G., Grau-Bové, X., Moreira, D., Karpov, S. A., & Burns, J. A., Sebé-Pedrós, A., Völcker, E. & López-García, P. 2019. Global transcriptome analysis of the aphelid *Paraphelidium tribonemae* supports the phagotrophic origin of fungi. *Communications Biology*. In press. https://doi.org/10.1038/s42003-018-0235-z
Van Tieghem, M. P. 1884. *Cænonia*, genre nouveau de Myxomycètes a plasmode agrégé. *Bull. Soc. Bot. France*, 31:303–306. https://doi.org/10.1080/00378941.1884.10828252.

Van Vichelen, J., D'Hondt, S., Claeys, M., Vyverman, W., Berney, C., Bass, D. & Vanormelingen, P. 2016. A hotspot of amoebae diversity: 8 new naked amoebae associated with the planktonic bloom-forming cyanobacterium *Microcystis*. *Acta Protozool.*, 55:61–87.

## APPENDICES

**Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes** by Sina M. Adl, David Bass, Christopher E. Lane, Julius Lukeš, Conrad L. Schoch, Alexey Smirnov, Sabine Agatha, Cedric Berney, Matthew W. Brown, Fabien Burki, Paco Cárdenas, Ivan Čepička, Ludmila Chistyakova, Javier del Campo, Micah Dunthorn, Bente Edvardsen, Yana Eglit, Laure Guillou, Vladimír Hampl, Aaron A. Heiss, Mona Hoppenrath, Timothy Y. James, Anna Karnkowska, Sergey Karpov, Eunsoo Kim, Martin Kolisko, Alexander Kudryavtsev, Daniel J. G. Lahr, Enrique Lara, Line Le Gall, Denis H. Lynn, David G. Mann, Ramon Massana i Molera, Edward A. D. Mitchell, Christine Morrow, Jong Soo Park, Jan W. Pawlowski, Martha J. Powell, Daniel J. Richter, Sonja Rueckert, Lora Shadwick, Satoshi Shimano, Frederick W. Spiegel, Guifré Torruella i Cortes, Noha Youssef, Vasily Zlatogursky, Qianqian Zhang.

Appendix S1. Supplementary references.

Appendix S2. Functional group assignments.

Appendix S3. Translation guide for East Asian users.

## APPENDIX S1. SELECTED LITERATURE MOSTLY SINCE 2012.

### AMORPHEA

Berney, C., Geisen, S., Van Wichelen, J., Nitsche, F., Vanormelingen, P., Bonkowski, M. & Bass, D. 2015. Expansion of the "reticulosphere": diversity of novel branching and network-forming amoebae helps to define Variosea (Amoebozoa). *Protist*, **166**, 271–295.

Brown, M. W., Sharpe, S. C., Silberman, J. D., Heiss, A. A., Lang, B. F., Simpson, A. G. B. & Roger, A. J. 2013. Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads. *Proc. R. Soc. Lond. B*, **280**:1769.

Cavalier-Smith, T., Chao, E., E., & Lewis, R. 2016. 187-Gene phylogeny of protozoan phylum Amoebozoa reveals a new class (Cutosea) of deep-branching, ultrastructurally unique, enveloped marine Lobosa and clarifies amoeba evolution. *Mol. Phylogenet. Evol.*, **99**: 275–296.

Hamann, E., Gruber-Vodicka, H., Kleiner, M., Tegetmeyer, H. E., Riedel, D., Littmann, S., Chen, J., Milucka, J., Viehweger, B., Becker, K. W., Dong, X., Stairs, C. W., Hinrichs, K.-U., Brown, M. W., Roger, A. J. & Strous, M. 2016. Environmental Breviatea harbor mutualistic Acrobacter epibionts. *Nature*, **534**:254–258.

Heiss, A. A., Lee, W. J., Ishida, K. & Simpson, A. G. B. 2015. Cultivation and characterisation of new species of

apusomonads (the sister group to opisthokonts), including close relatives of *Thecamonas* (*Chelonemonas* n. gen.). *J. Eukaryot. Microbiol.*, **62**:637-649.

Kang, S., Tice, A.K., Spiegel, F. W., Silberman, J. D., Pánek, T., Čepička, I., Kostka, M., Kosakyan, A., Alcântara, D. M., Roger, A. J., Shadwick, L. L., Smirnov, A., Kudryavstev, A., Lahr, D. J., & Brown, M. W. 2017. Between a pod and a hard test: the deep evolution of amoebae. *Mol Biol Evol* msx162. https://doi.org/10.1093/molbev/msx162.

Pánek, T, Zadrobílková, Walker, G., Brown, M. W., Gen tekaki, E., Hroudrová, M., Kang, S. Roger, A. J., Tice, A. K., Vlček, Č., & Čepička, I. 2016. First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group. *Molec. Phylogen. Evol.*, **98**:41-51.

Schaap, P., Winckler, T., Nelson, M., Alvarez-Curto, E., Elgie, B., Hagiwara, H., Cavender, J., Milano-Curto, A., Rozen, D. E., Dingermann, T., Mutzel, R. & Baldauf, S. 2006. Molecular phylogeny and evolution of morphology in the social amoebas. *Science*, 314: 661–663.

Spiegel, F. W., Shadwick, L. L., Ndiritu, G. G., Brown, M. W., Aguilar, M., & Shadwick, J. D. L. 2017. Protosteloid Amoeboazoa (Protosteliids, Protosporangiida, Cavostellida, Schizoplasmodiida, Fractoviteliida, and sporcarpic members of Vanellida, Centramoebida, and Pellitida). In: Archibald, J. M., Simpson, A. G. B., and Slamovits, C., eds. Handbook of the Protists (Second Edition of the Handbook of Protoctista by Margulis et al.) Springer Reference Works (e-book) https://doi.org/10.1007/978-3-319-32669-6_12-1

Sheikh, S., MatsThulin Cavender, J.C., Escalante, R., Kawakami, S.I., Lado, C., Landolt, J.C., Nanjundiah, V., Queller, D.C., Strassmann, J.E., Spiegel, F.W., Stephenson, S.L., Vadell, S.M., & Baldauf, S.L. 2018. A new classification of the dictyostelids. *Protist* **169**: 1-28.

Wilkinson, D. M. & Mitchell, E. A. D. 2010. Testate amoebae and nutrient cycling with particular reference to soils. *Geomicrobiol J.*, 27(6):520-533. https://doi.org/10.1080/01490451 003702925.

Walker, G., Zadrobílková, E., Čepička., I. (2017) Archamoebae In: Archibald, J. M., Simpson, A. G. B., & Slamovits, C., eds. Handbook of the Protists (Second Edition of the Handbook of Protoctista by Margulis et al.) Springer Reference Works (e-book) https://doi.org/10.1007/978-3-319-28149-0_11

### AMOEBOZOA

Berney, C., Geisen, S., Van Wichelen, J., Nitsche, F., Vanormelingen, P., Bonkowski, M. & Bass, D. 2015. Expansion of the "reticulosphere": diversity of novel branching and network-forming amoebae helps to define Variosea (Amoebozoa). *Protist*, **166**, 271–295.

Cavalier-Smith, T., Chao, E., E., & Lewis, R. 2016. 187-Gene phylogeny of protozoan phylum Amoebozoa reveals a new class (Cutosea) of deep-branching, ultrastructurally unique, enveloped marine Lobosa and clarifies amoeba evolution. *Mol. Phylogenet. Evol.*, **99**: 275–296.
Kang, S., Tice, A.K., Spiegel, F. W., Silberman, J. D., Pánek, T., Čepička, I., Kostka, M., Kosakyan, A., Alcântara, D. M., Roger, A. J., Shadwick, L. L., Smirnov, A., Kudryavstev, A., Lahr, D. J. & Brown, M. W. 2017. Between a pod and a hard test: the deep evolution of amoebae. *Mol Biol Evol* msx162. https://doi.org/10.1093/molbev/msx162.

Pánek, T., Zadrobílková, Walker, G., Brown, M. W., Gen-
tekaki, E., Hroudrová, M., Kang, S. Roger, A. J., Tice, A. K.,
Vlček, Č., & Čepička, I. 2016. First multigene analysis of
Archamoebae (Amoebozoa: Conosa) robustly reveals its
phylogeny and shows that Entamoebidae represents a deep
lineage of the group. *Molec. Phylogenet. Evol.*, **98**:41-51.

Schaap, P., Winckler, T., Nelson, M., Alvarez-Curto, E., Elgie, B., Hagiwara, H., Cavender, J., Milano-Curto, A., Rozen, D. E., Dingermann, T., Mutzel, R. & Baldauf, S. 2006. Molecular phylogeny and evolution of morphology in the social amoebas. *Science*, **314**: 661-663.

Spiegel, F. W., Shadwick, L. L., Ndiritu, G. G., Brown, M. W., Aguilar, M. & Shadwick, J. D. L. 2017. Protosteloid Amoeboazoa (Protosteliids, Protosporangiida, Cavostellida, Schizoplasmodiida, Fractoviteliida, and sporcarpic members of Vanellida, Centramoebida, and Pellitida). In: Archibald, J. M., Simpson, A. G. B., and Slamovits, C., eds. Handbook of the Protists (Second Edition of the Handbook of Protoctista by Margulis et al.) Springer Reference Works (e-book) https://doi.org/10.1007/978-3-319-32669-6_12-1

Sheikh, S., MatsThulin Cavender, J.C., Escalante, R., Kawakami, S.I., Lado, C., Landolt, J.C., Nanjundiah, V., Queller, D.C., Strassmann, J.E., Spiegel, F.W., Stephenson, S.L., Vadell, S.M. & Baldauf, S.L. 2018. A new classification of the dictyostelids. *Protist* **169**: 1-28.

Smirnov, A., V., Brown, S., 2004. Guide to the methods
of study and identification of soil gymnamoebae. *Protistol-
ogy* **3**, 148–190.

Wilkinson, D. M. & Mitchell, E. A. D. 2010. Testate amoebae and nutrient cycling with particular reference to soils. Geomicrobiol J., 27(6):520-533. https://doi.org/10.1080/01490451003702925.

Walker, G., Zadrobílková, E. & Čepička., I. 2017
Archamoebae In: Archibald, J. M., Simpson, A. G. B. &
Slamovits, C., eds. Handbook of the Protists (Second Edi-
tion of the Handbook of Protoctista by Margulis et al.)
Springer Reference Works (e-book) https://doi.org/10.
1007/978-3-319-28149-0_11

OPISTHOKONTA

Holozoa

Grau-Bové, X., Torruella, G., Donachie, S., Suga, H., Leonard, G., Richards, T.A. & Ruiz-Trillo, I. 2017. Dynamics of genomic innovation in the unicellular ancestry of animals. *eLife* 6, e26036.

Hehenberger, E., Tikhonenkov, D.V., Kolisko, M., del Campo, J., Esaulov, A.S., Mylnikov, A.P., & Keeling, P.J., 2017. Novel predators reshape holozoa phylogeny and

reveal the presence of a two-component signaling sys-
tem in the ancestor of animals. *Curr. Biol.*, **27**: 2043-
2050.

Toruella, G., Mendoza, A., Grau Bauvé, X., Anto, M., Chaplin, M., del Campo, J., Eme, L., Perez Cordon, G., Whipps, C.M., Nichols, K.M., Paley, R., Roger, A.J., Sitja-Bobadillas, A., Donachie, S., & Ruiz-Trillo, I. 2015. Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi. *Curr. Biol.*, **25**: 2404-2410. https://doi.org/10.1016/j.cub.2015.07.053

Choanoflagellata

Brunet, T. & King, N. 2017 The origin of animal multicellu-
larity and cell differentiation. *Developmental Cell*, **43**: 124-
140. https://doi.org/10.1016/j.devcel.2017.09.016

Budd, G.E. & Jensen, S. 2017. The origin of the animals and a "Savannah" hypothesis for early bilaterian evolution *Biol. Rev. Camb Philos. Soc.*, **92**: 446-473.

Carr, M., Richter, D.J., Fozouni, P., Smith, T.J., Jeuck, A., Leadbeater, B.S.C. & Nitsche, F., 2017. A six-gene phylogeny provides new insights into choanoflagellate evolution. *Mol. Phylogenetics Evol.*, **107**: 166-178.

Nitsche, F., Carr, M., Arndt, H. & Leadbeater, B. S. C. 2011. Higher level taxonomy and molecular phylogenetics of the Choanoflagellatea. *J.Eukaryot. Microbiol.*, **58**: 452-462. https://doi.org/10.1111/j.1550-7408.2011.00572.x

Richter, D.J. & Nitsche, F., 2017. Choanoflagellatea. In: Archibald, J.M., Simpson, A.G.B. & Slamovits, C.H. (Eds.) Handbook of the Protists. Springer International Publishing, pp. 1479-1496.

Porifera

Cárdenas, P., Pérez, T. & Boury-Esnault, N. 2012. Sponge Systematics facing new challenges. *Adv.Marine Biol.*, **61**: 79-209.

Dohrmann, M., Kelley, C., Kelly, M., Pisera, A., Hooper,
J. N. A. & Reiswig, H. M. 2017. An integrative systematic
framework helps to reconstruct skeletal evolution of glass
sponges (Porifera, Hexactinellida). *Frontiers Zool.*, **14**: 18.

Morrow, C. & Cárdenas, P. 2015. Proposal for a revised classification of the Demospongiae (Porifera). *Frontiers Zool.*, **12**: 1-27.

Redmond, N. E., Morrow, C. C., Thacker, R. W., Diaz, M. C., Boury-Esnault, N., Cárdenas, P., et al. 2013. Phylogeny and Systematics of Demospongiae in Light of New Small Subunit Ribosomal DNA (18S) Sequences. *Integr. Comparat. Biol.*, **53**: 388-415.

Ruiz, C., Muricy, G., Lage, A., Domingos, C., Cheneseau, S. & Pérez, T. 2017. Descriptions of new sponge species and genus, including aspiculate Plakinidae, overturn the Homoscleromorpha classification. *Zool. J. Linn. Soc.*, **179**: 707-724.

Voigt, O., Wülfing, E. & Wörheide, G. 2012. Molecular Phylogenetic Evaluation of Classification and Scenarios of Character Evolution in Calcareous Sponges (Porifera, Class Calcarea). PLoS ONE, 7, e33417.
## Metazoa

Cannon, J.T., Vellutini, B.C., Smith, J., Ronquist, F., Jondelius, U. & Hejnol, A. 2016. Xenacoelomorpha is the sister group to Nephrozoa. *Nature*, **530**: 89-93.

Laumer, C.E., Bekkouche, N., Kerbl, A., Goetz, F., Neves, R.C., Sørenson, M.V., Kristensen, R.M., Hejnol, A., Dunn, C.W., Giribet, G. & Worsaae, K. 2015. Spiralian phylogeny informs the evolution of microscopic lineages. *Curr. Biol.*, **25**: 2000-2006.

Simion, P., Philippe, H., Baurain, D., Jager, M., Richter, D.J., Di Franco, A., Roure, B., Satoh, N., Queinnec, E., Ereskovsky, A., Lapebie, P., Corre, E., Delsuc, F., King, N., Wörheide, G. & Manuel, M. 2017. A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals. *Curr. Biol.*, **27**: 958-967.

Whelan, N.V., Kocot, K.M., Moroz, T.P., Mukherjee, K., Williams, P., Paulay, G., Moroz, L.L. & Halanych, K.M. 2017. Ctenophore relationships and their placement as the sister group to all other animals. *Nat. Ecol. Evol.*, **1**: 1737-1746.

## Holomycota

Bass, D., Czech, L., Williams, B.A.P., Berney, C., Dunthorn, M., Mahé, F., Torruella, G., Stentiford, G.D., Williams, T.A. 2018. Clarifying the Relationships between Microsporidia and Cryptomycota. *J. Euk. Microbiol.*, **65**: 773-782. https://doi.org/10.1111/jeu.12519

Jones, M. D. M., Richards, T. A., Hawksworth, D. L. & Bass, D. 2011. Validation and justification of the phylum name Cryptomycota. *IMA Fungus*, **2**:173-175.

Karpov, S. A., Mamkaeva, M. A., Aleoshin, V. V., Nassonova, E., Lilje, O. & Gleason, F. H. 2014. Morphology, phylogeny, and ecology of the aphelids (Aphelidea, Opisthokonta) and proposal for the new superphylum Opisthosporidia. *Front. Microbiol.*, **5**:112.

Lara, E., Moriera, D. & Lopez-Garcia, P. 2010. The environmental clade LKM11 and *Rozella* form the deepest branching clade of fungi. *Protist*, **161**:116-121.

Liu, Y., Steenkamp, E.T., Brinkmann, H., Forget, L., Philippe, H. & Lang, F.B. 2009. Phylogenomic analyses predict sistergroup relationship of nucleariids and Fungi and phyly of zygomycetes with significant support. *BMC Evol. Biol.*, **20099**:272, https://doi.org/10.1186/1471-2148-9-272.

## Fungi

Bauer, R., Garnica, S., Oberwinkler, F., Riess, K., Weiss, M. & Begerow, D. 2015. Entorrhizomycota: A New Fungal Phylum Reveals New Perspectives on the Evolution of Fungi. *PLoS One*, **10:e0128183.

Chang, Y., Wang, S. S., Sekimoto, S., Aerts, A. L., Choi, C., Clum, A., LaButti, K. M., Lindquist, E. A., Ngan, C. Y., Ohm, R. A., Salamov, A. A., Grigoriev, I. V., Spatafora, J. W. & Berbee, M. L. 2015. Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants. *Genome Biol. Evol.*, **7**:1590-1601.

Edlind, T. D., Li, J., Visvesvara, G. S., Vodkin, M. H., McLaughlin, G. L. & Katiyar, S. K. 1996. Phylogenetic analysis of beta-tubulin sequences from amitochondrial protozoa. *Mol. Phylogenet. Evol.*, **5**:359-67.

Hibbett, D. S., Binder, M., Bischoff, J. F., Blackwell, M., Cannon, P. F., Eriksson, O. E., Huhndorf, S., James, T., Kirk, P. M., Lücking, R., Lumbsch, T., Lutzoni, F., Matheny, P. B., Mclaughlin, D. J., Powell, M. J., Redhead, S., Schoch, C. L., Spatafora, J. W., Stalpers, J. A., Vilgalys, R., Aime, M. C., Aptroot, A., Bauer, R., Begerow, D., Benny, G. L., Castlebury, L. A., Crous, P. W., Dai, Y.-C., Gams, W., Geiser, D. M., Griffith, G. W., Gueidan, C., Hawksworth, D. L., Hestmark, G., Hosaka, K., Humber, R. A., Hyde, K., Ironside, J. E., Köljalg, U., Kurtzman, C. P., Larsson, K.-H., Lichtwardt, R., Longcore, J., Miadlikowska, J., Miller, A., Moncalvo, J.-M., Mozley-Standridge, S., Oberwinkler, F., Parmasto, E., Reeb, V., Rogers, J. D., Roux, C., Ryvarden, L., Sampaio, J. P., Schüßler, A., Sugiyama, J., Thorn, R. G., Tibell, L., Untereiner, W. A., Walker, C., Wang, Z., Weir, A., Weiß, M., White, M. M., Winka, K., Yao, Y.-J. & Zhang, N. 2007. A higher-level phylogenetic classification of the Fungi. *Mycological Res.*, **111**:509-547.

Hibbett, D. S., Blackwell, M., James, T. Y., Spatafora, J. W., Taylor, J. W. & Vilgalys, R. 2018. Phylogenetic taxon definitions for Fungi, Dikarya, Ascomycota and Basidiomycota. *IMA Fungus*, **9**: 291-298.

James, T. Y., Kauff, F., Schoch, C. L., Matheny, P. B., Hofstetter, V., Cox, C. J., Celio, G., Gueidan, C., Fraker, E., Miadlikowska, J., Lumbsch, H. T., Rauhut, A., Reeb, V., Arnold, A. E., Amtoft, A., Stajich, J. E., Hosaka, K., Sung, G.-H., Johnson, D., O'Rourke, B., Crockett, M., Binder, M., Curtis, J. M., Slot, J. C., Wang, Z., Wilson, A. W., Schuszler, A., Longcore, J. E., O'Donnell, K., Mozley-Standridge, S., Porter, D., Letcher, P. M., Powell, M. J., Taylor, J. W., White, M. M., Griffith, G. W., Davies, D. R., Humber, R. A., Morton, J. B., Sugiyama, J., Rossman, A. Y., Rogers, J. D., Pfister, D. H., Hewitt, D., Hansen, K., Hambleton, S., Shoemaker, R. A., Kohlmeyer, J., Volkmann-Kohlmeyer, B., Spotts, R. A., Serdani, M., Crous, P. W., Hughes, K. W., Matsuura, K., Langer, E., Langer, G., Untereiner, W. A., Lucking, R., Budel, B., Geiser, D. M., Aptroot, A., Diederich, P., Schmitt, I., Schultz, M., Yahr, R., Hibbett, D. S., Lutzoni, F., McLaughlin, D. J., Spatafora, J. W. & Vilgalys, R. 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. *Nature*, **443**:818-822.

Jones, M. D. M., Richards, T. A., Hawksworth, D. L. & Bass, D. 2011. Validation and justification of the phylum name Cryptomycota phyl. nov. *IMA Fungus*, **2**:173-175.

Jones, M. D. M., Forn, I., Gadelha, C., Egan, M. J., Bass, D., Massana, R. & Richards, T. A. 2011. Discovery of novel intermediate forms redefines the fungal tree of life. *Nature*, **474**:200-203.

Karpov, S. A., Mamkaeva, M. A., Aleoshin, V. V., Nassonova, E., Lilje, O. & Gleason, F. H. 2014. Morphology, phylogeny, and ecology of the aphelids (Aphelidea, Opisthokonta) and proposal for the new superphylum Opisthosporidia. *Front. Microbiol.*, **5**:112.
Keeling, P. J. 2003. Congruent evidence from alpha-tubulin and beta-tubulin gene phylogenies for a zygomycete origin of microsporidia. *Fungal Genet Biol*, **38**:298-309.

Kirk, P. M., Cannon, P. F., Minter, D. W. & Stalpers, J. A. 2008. Ainsworth and Bisby's dictionary of the Fungi, 10th ed. CAB International., Wallingford, UK p. 771.

Lara, E., Moreira, D. & Lopez-Garcia, P. 2010. The Environmental Clade LKM11 and *Rozella* Form the Deepest Branching Clade of Fungi. *Protist*, **161**:116-121.

Lee, S. C., Corradi, N., Doan, S., Dietrich, F. S., Keeling, P. J. & Heitman, J. 2010. Evolution of the sex-related locus and genomic features shared in Microsporidia and Fungi. *Plos ONE*, **5**:e10539.

Liu, Y., Steenkamp, E. T., Brinkmann, H., Forget, L., Philippe, H. & Lang, B. F. 2009. Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support. *BMC Evol. Biol.*, **9**:272.

Ren, R., Sun, Y., Zhao, Y., Geiser, D., Ma, H. & Zhou, X. 2016. Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes. *Genome Biol. Evol.*, **8**:2683-701.

Spatafora, J. W., Chang, Y., Benny, G. L., Lazarus, K., Smith, M. E., Berbee, M. L., Bonito, G., Corradi, N., Grigoriev, I., Gryganskyi, A., James, T. Y., O'Donnell, K., Roberson, R. W., Taylor, T. N., Uehling, J., Vilgalys, R., White, M. M. & Stajich, J. E. 2016. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. *Mycologia*, **108**:1028-1046.

Tedersoo, L., Sanchez-Ramirez, S., Koljalg, U., Bahram, M., Doring, M., D., S., May, T., Ryberg, M. & Abarenkov, K. 2018. High-level classification of the Fungi and a tool for evolutionary ecological analyses. *Fungal Diversity*, **90**:135-159.

## Chytridiomycota

Barr, D. J. S. 1980. An outline for the reclassification of the Chytridiales, and for a new order, the Spizellomycetales. *Can. J. Bot.*, **58**:2380-2394.

Karpov, S. A., Kobseva, A. A., Mamkaeva, M. A., Mamkaeva, K. A., Mikhailov, K. V., Mirzaeva, G. S. & Aleoshin, V. V. 2014. *Gromochytrium mamkaevae* gen. & sp. nov. and two new orders: Gromochytriales and Mesochytriales (Chytridiomycetes). *Personia*, **32**:115-126.

Letcher, P. M., Powell, M. J., Churchill, P. F. & Chambers, J. G. 2018. Ultrastructural and molecular phylogenetic delineation of a new order, the Rhizophydiales (Chytridiomycota). *Mycol. Res.*, **110**:898-915.

Letcher P. M., Powell, M. J., Barr, D. J. S., Churchill, P. F., Wakefield, W. S. & Picard, K. T. 2008. Rhizophyctidales-a new order in Chytridiomycota. *Mycol. Res.*, **112**:1031-1048.

Longcore, J. E. & Simmons, D. R. 2012. The Polychytriales ord. nov. contains chitinophilic members of the rhizophyctoid alliance. *Mycologia*, **104**: 276-294.

Longcore, J. E., Simmons, D. R. & Letcher, P. M. 2016. *Synchytrium microbalum* sp. nov. is a saprobic species in a lineage of parasites. *Fungal Biol.*, **120**:1156-1164.

Mozley-Standridge, S. E., Letcher, P. M., Longcore, J. E., Porter, D. & Simmons, D. R. 2009. Cladochytriales-a new order in the Chytridiomycota. *Mycol. Res.*, **113**:498-507.

Simmons, D. R., James, T. Y., Meyer, A. F. & Longcore, J. E. 2009. Lobulomycetales, a new order in the Chytridiomycota. *Mycol. Res.*, **113**:450-460.

Smith, D.S., Rocheleau, H., Chapados, J. T., Abbott, C., Ribero, S., Redhead, S. A., Lévesque, C. A., & De Boer, S. H., 2014. Phylogeny of the genus *Synchytrium* and the development of TaqMan PCR assay for sensitive detection of *Synchytrium endobioticum* in soil. *Phytopath.*, **104**:422-432.

Torruella, G., Grau-Bové, X., Moreira, D., Karpov, S. A., Burns, J. A., Sebé-Pedrós, A., Völcker E. & López-García, P. 2019. Global transcriptome analysis of the aphelid Para-phelidium tribonemae supports the phagotrophic origin of fungi. *Communications Biology.* **1**: 231, https://doi.org/10.1038/s42003-018-0235-z

Vélez, C. G., Letcher, P. M., Schultz, S., Powell, M. J. & Churchill, P. F. 2011. Molecular phylogenetic and zoospore ultrastructural analyses of *Chytridium olla* establish the limits of a monophyletic Chytridiales. *Mycologia*, **103**:118-130.

## DIAPHORETICKES ARCHAЕPLASTIDA

### Chloroplastida

Fawley, M.V., Yun, Y., & Qin, M. 2000. Phylogenetic analyses of 18S rDNA sequences reveal a new coccoid lineage of the Prasinophyceae (Chlorophyta). *J. Phycol.*, **36**:387-393.

Fucikova, K., Leliaert, F., Cooper, E.D., Skaloud, P., D'Hondt, S., De Clerk, O., Gurgel, C.F.D., Lewis, L.A., Lewis, P.O., Lopez-Bautista, J.M., Delwiche, C.F., Verbruggen, H. 2014. New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data. *Frontiers Ecol. Evol.*, **2**:67, https://doi.org/10.3389/fevo.2014.00063

Leliaert, F., Tronholm, A., Lemieux, C., Bhattacharya, D., Karol, K.G., Fredericq, S. 2016. Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov. *Sci. Rep.*, **6**:25367, https://doi.org/10.1038/srep25367

Lopes Dos Santos, A., Pollina, T., Gourvil, P., Corre, E., Marie, D., Garrido J.L., Rodríguez, F., Noël, M.H. & Vaulot, D., Eikrem W. 2017. Chloropicophyceae, a new class of picophytoplanktonic prasinophytes. *Sci. Rep.*, **25**:14019, https://doi.org/10.1038/s41598-017-12412-5

Nakayama, T., Marin, B., Kranz, H.D., Surek, B., Huss, V.A., Inouye, I. & Melkonian, M. 1998. The basal position of scaly green flagellates among the green algae (Chlorophyta) is revealed by analyses of nuclear-encoded SSU rRNA sequences. *Protist*, **149**:378-380.

### Rhodophyceae and Glaucophyta

Muñoz-Gómez, S.A., Mejía-Franco, F.G., Durnin, K., Colp, M., Grisdale, C.J., Archibald, J.M. & Slamovits C.H. 2017. The New Red Algal Subphylum Proteorhodophytina
Comprises the Largest and Most Divergent Plastid Genomes Known. *Curr. Biol.*, **27**: 1677–1684.

Chong, J., Jackson, C., Kim, J. I., Yoon, H. S. & Reyes-Prieto, A. 2014. Molecular markers from different genomic compartments reveal cryptic diversity within glaucophyte species. *Mol. Phylogenet. Evol.*, **76**:181–188.

Jackson, C., Clayden, S. & Reyes-Prieto, A. 2015. The Glaucophyta: The blue-green plants in a nutshell. *Acta Soc. Bot. Pol.*, **84**:149–165.

Jackson C.J., Reyes-Prieto A. 2014. The Mitochondrial Genomes of the Glaucophytes *Gloeochaete wittrockiana* and *Cyanopyche gloeocystis*: Multilocus Phylogenetics Suggests a Monophyletic Archaeplastida. *Gen. Biol. Evol.*, **6**: 2774–2785.

Price, D.C., Chan, C.X., Yoon, H.S., Yang, E.C., Qiu, H., Weber, A.P.M., Schwacke, R., Gross, J., Blouin, N.A., Lane, C., Reyes-Prieto, A., Durnford, D.G., Neilson, J.A.D., Lang, B.F., Burger, G., Steiner, J.M., Loffelhardt, W., Meuser, J.E., Posewitz, M.C., Ball, S., Arias, M.C., Henris-sat, B., Coutinho, P.M., Rensing, S.A., Symeonidi, A., Doddapaneni, H., Green, B.R., Rajah, V.D., Boore, J. & Bhattacharya, D. 2012. *Cyanophora paradoxa* genome elucidates origin of photosynthesis in algae and plants. *Science*, **335**:843–847.

Takahashi, T., Sato, M., Toyooka, K., Matsuzaki, R., Kawafune, K., Kawamura, M., Okuda, K. & Nozaki, H. 2014. Five *Cyanophora* (Cyanophorales, Glaucophyta) species delineated based on morphological and molecular data. *J. Phycol.*, **50**:1058–1069.

Takahashi, T., Nishida, T., Tuji, A., Saito, C., Matsuzaki, R., Sato, M., Toyooka, K., Yasuda, H. & Nozaki, H. 2016. Delineation of six species of the primitive algal genus *Glaucocystis* based on in situ ultrastructural characteristics. *Sci. Rep.*, **6**:29209.

## Sar

Burki, F., Shalchian-Tabrizi, K., Minge, M., Skjaeveland, A., Nikolaev, S. I., Jakobsen, K. S., & Pawlowski, J. 2007. Phylogenomics reshuffles the eukaryotic supergroups. *PLoS ONE*, **2**(8), e790. https://doi.org/10.1371/journal.pone.0000790

Hackett, J. D., Yoon, H. S., Li, S., Reyes-Prieto, A., Rümmele, S. E., & Bhattacharya, D. 2007. Phylogenomic analysis supports the monophyly of cryptophytes and haptopytes and the association of rhizaria with chromalveolates. *Molec. Biol. Evol.*, **24**(8), 1702–1713. https://doi.org/10.1093/molbev/msm089

Rodriguez-Ezpeleta, N., Brinkmann, H., Burger, G., Roger, A. J., Gray, M. W., Philippe, H., & Lang, B. F. 2007. Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans. *Current Biol.*, **17**(16): 1420–1425. https://doi.org/10.1016/j.cub.2007.07.036

## Stramenopiles

Aleoshin, V. V., A. P. Mylnikov, G. S. Mirzaeva, K. V. Mikhailov, and S. A. Karpov. 2016. Heterokont Predator

*Develorapax marinus* gen. et sp. nov. - A Model of the Ochrophyte Ancestor. *Front. Microbiol.*, **7**:1194.

Cavalier-Smith, T. 2018. Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences. *Protoplasma*, **255**:297-357.

Cavalier-Smith, T., and J. M. Scoble. 2013. Phylogeny of Heterokonta: *Incisomonas marina*, a uniciliate gliding opalozoan related to *Solenicola* (Nanomonadea), and evidence that Actinophryida evolved from raphidophytes. *Eur. J. Protistol.*, **49**:328-353.

Chang, F. H., J. Sutherland, and J. Bradford-Grieve. 2017. Taxonomic revision of Dictyochales (Dictyochophyceae) based on morphological, ultrastructural, biochemical and molecular data. *Phycol. Res.* **65**:235-347.

Derelle, R., P. Lopez-Garcia, H. Timpano, and D. Moraire. 2016. A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts). *Mol. Biol. Evol.*, **33**:2890-2898.

Lin, Y. C., T. Campbell, C. C. Chung, G. C. Gong, K. P. Chiang, and A. Z. Worden. 2012. Distribution patterns and phylogeny of marine stramenopiles in the north pacific ocean. *Appl. Environ. Microbiol.* **78**:3387-3399.

Massana, R., J. del Campo, M. E. Sieracki, S. Audic, and R. Logares. 2014. Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles. *ISME J.*, **8**:545-566.

McCarthy, C. G. P., and D. A. Fitzpatrick. 2017. Phylogenomic Reconstruction of the Oomycete Phylogeny Derived from 37 Genomes. *mSphere*, **2**.

Shiratori, T., T. Nakayama, and K. Ishida. 2015. A New Deep-branching Stramenopile, *Platysulcus tardus* gen. nov., sp. nov. *Protist*, **166**:337-348.

Yang, E. C., G. H. Boo, H. J. Kim, S. M. Cho, S. M. Boo, R. A. Andersen, and H. S. Yoon. 2012. Supermatrix data highlight the phylogenetic relationships of photosynthetic stramenopiles. *Protist*, **163**:217-231.

Yubuki, N., T. Panek, A. Yabuki, I. Cepicka, K. Takishita, Y. Inagaki, and B. S. Leander. 2015. Morphological Identities of Two Different Marine Stramenopile Environmental Sequence Clades: *Bicosoeca kenaiensis* (Hilliard, 1971) and Cantina marsupialis (Larsen and Patterson, 1990) gen. nov., comb. nov. *J. Eukaryot. Microbiol.*, **62**:532-542.

## Diatomea

Ashworth, M. P., Nakov, T. & Theriot, E. C. 2013. Revisiting Ross and Sims (1971): toward a molecular phylogeny of the Biddulphiaceae and Eupodiscaceae (Bacillariophyceae). *J. Phycol.* **49**:1207–1222.

Ichinomiya, M., Yoshikawa, S., Kamiya, M., Ohki, K., Takaichi, S. & Kuwata, A. 2011. Isolation and characterization of Parmales (Heterokonta/Heterokontophyta/Stramenopiles) from the Oyahio region, western North Pacific. *J. Phycol.* **47**:144–151.

Ichinomiya, M., Lopes dos Santos, A., Gourvil, P., Yoshikawa, S., Kamiya, M., Ohki, K., Audic, S., Vargas, C. de, Noël, M.-H., Vaulot, D. & Kuwata, A. 2016. Diversity and oceanic distribution of the Parmales (Bolidophyceae), a
picoplanktonic group closely related to diatoms. *ISME J.* **10**:2419-2434.

Mann, D.G., Crawford, R.M. & Round, F.E. 2017. Bacillariophyta. In: *Handbook of the Protists* (Archibald, J.M., Simpson, A.G.B. & Slamovits, C.H., eds), 62 pp. Springer, Cham. https://doi.org/10.1007/978-3-319-32669-6_29-1.

Medlin, L. K. 2016. Opinion: can coalescent models explain deep divergences in the diatoms and argue for the acceptance of paraphyletic taxa at all taxonomic hierarchies? *Nova Hedwigia* **102**:107-128.

Medlin, L. K. & Kaczmarska, I. 2004. Evolution of the diatoms: V. Morphological and cytological support for the major clades and a taxonomic revision. *Phycologia* **43**:245-270.

Nakov, T., Beaulieu, J. M. & Alverson, A. J. 2018. Accelerated diversification is related to life history and locomotion in hyperdiverse lineage of microbial eukaryotes (diatoms, Bacillariophyta). *New Phytol.*, https://doi.org/10.1111/nph.15137

Parks, M. B., Wickett, N. J. & Alverson, A. J. 2017. Signal, uncertainty, and conflict in phylogenomic data for a diverse lineage of microbial eukaryotes (diatoms, Bacillariophyta). *Mol. Biol. Evol.*, **35**:80-93.

Theriot, E. C., Ashworth, M. P., Nakov, T., Ruck, E. C. & Jansen, R. K. 2015. Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling. *Mol. Phylogenet. Evol.* **89**:28-36.

Round, F. E., Crawford, R. M. & Mann, D. G. 1990. The diatoms. Biology and morphology of the genera. Cambridge: Cambridge University Press. 747 pp.

## ALVEOLATA

Cumbo, V. R., Baird, A. H., Moore, R. B., Negri, A. P., Neilan, B. A., Salih, A., et al. 2013. *Chromera velia* is endosymbiotic in larvae of the reef corals *Acropora digitifera* and *A. tenuis*. *Protist* **164**: 237-244.

Freeman, M. A., Fuss, J., Kristmundsson, A., Bjorbaekmo, M. F. M., Mangot, J. F., del Campo, J., Keeling, P. J., Shalchian-Tabrizi, K. & Bass, D. 2017. X-cells are globally distributed, genetically divergent fish parasites related to perkinsids and dinoflagellates. *Curr. Biol.*, **27**: 1645-1651. https://doi.org/10.1016/j.cub.2017.04.045

Gile, G. H. & Slamovits, C. H. 2014 Transcriptomic analysis reveals evidence for a cryptic plastid in the colpodellid *Voromonas pontica*, a close relative of chromerids and apicomplexan parasites. *PLoS ONE*. **9**: e96258. https://doi.org/10.1371/journal.pone.0096258

Mathur, V., del Campo, J., Kolisko, M. & Keeling, P. J. 2018. Global diversity and distribution of close relatives of apicomplexan parasites. *Environ. Microbiol.* **20**: 2824-2833. https://doi.org/10.1111/1462-2920.14134

Oborník, M., Kručinská, J. & Esson, H. 2016. Life cycles of chromerids resemble those of colpodellids and apicomplexan parasites. *Perspect. Phycol.* **3**: 21-27. https://doi.org/10.1127/pip/2016/0038

Oborník M., Lukeš J. 2015. The organellar genomes of *Chromera* and *Vitrella*, the phototrophic relatives of

apicomplexan parasites. *Annu. Rev. Microbiol.* **69**: 129-144. https://doi.org/10.1146/annurev-micro-091014-104449

Okamoto, N., & Keeling, P. J. 2014. A comparative overview of the flagellar apparatus of dinoflagellate, perkinsids and colpodellids. *Microorganisms*, **2**: 73-91. https://doi.org/10.3390/microorganisms2010073

Reñé, A., Alacid, E., Ferrera, I., & Garcés, E. 2017. Evolutionary trends of Perkinsozoa (Alveolata) characters based on observations of two new genera of parasitoids of dinoflagellates, *Dinovorax* gen. nov. and *Snorkelia* gen. nov. *Front. Microbiol.* **8**: 1594. https://doi.org/10.3389/fmicb.2017.01594

Tikhonenkov, D. V., Janouškovec, J., Mylnikov, A. P., Mikhailov, K. V., Simdyanov, T. G., Aleoshin, V. V. & Keeling, P. J. 2014. Description of *Colponema vietnamicasp*. n. and *Acavomonas peruvianan*. gen. n. sp., two new Alveolate phyla (Colponemidia nom. nov. and Acavomonidia nom. nov.) and their contributions to reconstructing the ancestral state of alveolates and eukaryotes. *PLoS ONE*, **9**: e95467. https://doi.org/10.1371/journal.pone.0095467

Woo, Y.H., Ansari, H., Otto, T.D., Klinger, C.M., Kolisko, M., Michalek, J., et al. 2015. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. *eLife*. **4**:1-41.

Yuan, C. L., Keeling, P. J., Krause, P. J., Horak, A., Bent, S., Rollend, L. & Hua, X. G. 2012. *Colpodella* spp.-like Parasite infection in woman, China. *Emerg. Infect. Dis.* **18**: 125-127. https://doi.org/10.3201/eid1801.110716.

## Apicomplexa

Arisue, N. & Hashimoto, T. 2015. Phylogeny and evolution of apicoplasts and apicomplexan parasites. *Parasitol. Int.* **64**: 254-259.

Cavalier-Smith, T. 2018. Kingdom Chromista and its eight phyla: A new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences. *Protoplasma*. **1**: 297-357. https://doi.org/10.1007/s00709-017-1147-3

Cavalier-Smith, T. 2014. Gregarine site-heterogeneous 18S rDNA trees, revision of gregarine higher classification, and the evolutionary diversification of Sporozoa. *Europ. J. Protistol.* **50**: 472-495. https://doi.org/10.1016/j.ejop.2014.07.002

Desportes, I. & Schrével, J. 2013. Treatise on Zoology - Anatomy, Taxonomy, Biology. The Gregarines, Vol 1 & 2. Brill, Leiden.

Flegontov, P. Michálek, J., Tomčala, A., Janouškovec, J., Jirků, M., Lai, D. H., Hajdušková, E., Otto, T. D., Keeling, P. J., Pain, A., Oborník, M. & Lukeš, J. 2015. Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites. *Mol. Biol. Evol.* **32**: 1115-1131. https://doi.org/10.1093/molbev/msv021

Ghazy, A. A., Abdel-Shafy, S. & Shaapan, R. M. 2015. Cryptosporidiosis in animals and man: 1. taxonomic classification, life cycle, epidemiology and zoonotic importance. *Asian J. Epidemiol.* **8**: 48-63. https://doi.org/10.3923/aje.2015.48.63

Heintzelman, M. B. 2015. Gliding motility in apicomplexan parasites. *Semin. Cell. Dev. Biol.* **46**:135-142. https://doi.org/10.1016/j.semcdb.2015.09.020
Iritani, D., Wakeman, K. & Leander, B.S. 2018. Molecular phylogenetic positions of two new marine gregarines (Apicomplexa) from the intestines of *Lumbrineris inflata* (Polychaeta) show patterns of co-evolution: *Paralecudina anankea* nov. sp. and *Lecudina caspera* nov. sp. *J. Eukaryot. Microbiol.* **65**:211-219. https://doi.org/10.1111/jeu.12462

Janouškovec, J., Tikhonenkov, D. V., Burki, F., Howe, A. T., Kolisko, M., Mylnikov, A. P., et al. 2015. Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives. *Proc. Natl. Acad. Sci. USA* **112**: 10200-10207. https://doi.org/10.1111/1462-2920.14134

Janouškovec, J. Horák, A., Barrot, K. L., Rohwer, F. L. & Keeling, P. J. 2012. Global analysis of plastid diversity reveals new apicomplexan-related lineages associated with coral reefs. *Curr. Biol.* **22**: R518-9. https://doi.org/10.1016/j.cub.2012.04.047

Karadjian, G., Chavatte, J.-M., & Landau, I. 2015. Systematic revision of the adeleid haemogregarines, with creation of *Bartazoon* n. g., reassignment of *Hepatozoon argantis* Garnham, 1954 to *Hemolivia*, and molecular data on *Hemolivia stellata*. *Parasite*. **22**: 31. https://doi.org/10.1051/parasite/2015031

Megía-Palma, R., Martínez, J., Nasri, I., Cuervo, J. J., Martín, J., Acevedo, I., Belliure, J., Ortega, J., García-Roa, R., Selmi, S. & Merino, S. 2016. Phylogenetic relationships of *Isospora*, *Lankesterella*, and *Caryospora* species (Apicomplexa: Eimeriidae) infecting lizards. *Org. Divers. Evol.* **16**: 275-288. https://doi.org/10.1007/s13127-015-0253-3

Muñoz-Gómez S. A. & Slamovits C. H. 2018. Chapter Three - Plastid Genomes in the Myzozoa. In: Chaw, S.-M. & Jansen, R. K. *Adv. Bot. Res.* **85**: 55-94. https://doi.org/10.1016/bs.abr.2017.11.015.

Ogedengbe, M. E., El-Sherry, S., Ogedengbe, J. D., Chapman, H. D. & Barta, J. R. 2018. Phylogenies based on combined mitochondrial and nuclear sequences conflict with morphologically defined genera in the eimeriid coccidia (Apicomplexa). *Int. J. Parasitol.* **48**: 59-69. https://doi.org/10.1016/j.ijpara.2017.07.008.

Ogedengbe, J. D., Ogedengbe, M. E., Hafeez, M. A. & Barta, J. R. 2015. Molecular phylogenetics of eimeriid coccidia (Eimeriidae, Eimeriorina, Apicomplexa, Alveolata): A preliminary multi-gene and multi-genome approach. *Parasitol. Res.* **114**: 4149-4160. https://doi.org/10.1007/s00436-015-4646-1

Rueckert, S. & Horák, A. 2017. Archigregarines of the English Channel revisited: New molecular data on *Selenidium* species including early described and new species and the uncertainties of phylogenetic relationships. *PLoS ONE* **12**: e0187430. https://doi.org/10.1371/journal.pone.0187430

Rueckert, S., Wakeman, K.C. & Leander, B.S. 2013. Discovery of a diverse clade of gregarine apicomplexans (Apicomplexa: Eugregarinorida) from Pacific eunicid and onuphid polychaetes, including descriptions of *Paralecudina* n. gen., *Trichotokara japonica* n. sp., and *T. eunicae* n. sp. *J. Eukaryot. Microbiol.* **60**:121-136. https://doi.org/10.1111/jeu.12015

Ryan, U., Fayer, R. & Xiao, L. (2014) *Cryptosporidium* species in humans and animals: Current understanding and research needs. *Parasitol.*, **141**: 1667-1685. https://doi.org/10.1017/s0031182014001085

Schrével, J., Valigurová, A., Prensier, G., Chambouvet, A., Florent, I. & Guillou, L. 2016. Ultrastructure of *Selenidium pendula*, the type species of archigregarines, and phylogenetic relations to other marine Apicomplexa. *Protist*, **167**: 339-368. https://doi.org/10.1016/j.protis.2016.06.001.

Seeber, F. & Steinfelder, S. 2016. Recent advances in understanding apicomplexan parasites. *F1000Research.* **5**:1369. https://doi.org/10.12688/f1000research.7924.1

Simdyanov, T. G., Paskerova, G. G., Valigurová, A., Diakin, A., Kováčiková, M., Schrével, J., Guillou, L., Dobrovolskij, A. A. & Aleoshin, V. V. (2018) First ultrastructural and molecular phylogenetic evidence from the blastogregarines, an early branching lineage of plesiomorphic Apicomplexa. *Protist*, **169**: 697-726. https://doi.org/10.1016/j.protis.2018.04.006.

Votýpka, J., Modrý, D., Oborník, M., Šlapeta, J. & Lukeš, J. 2017. Apicomplexa. In: Archibald, J. M., Simpson, A. G. B., and Slamovits, C., eds. Handbook of the Protists (Second Edition of the Handbook of Protoctista by Margulis et al.) Springer Reference Works (e-book) https://doi.org/10.1007/978-3-319-32669-6_12-1.

Wakeman, K.C., Heintzelman, M.B. & Leander, B.S. 2014. Comparative ultrastructure and molecular phylogeny of *Selenidium melongena* n. sp. and *S. terebellae* Ray 1930 demonstrate niche partitioning in marine gregarine parasites (apicomplexa). *Protist.* **165**: 493-511. https://doi.org/10.1016/j.protis.2014.05.007

Wakeman, K., Reimer, J.D., Jenke-Kodama, H. & Leander, B.S. 2014. Molecular phylogeny and ultrastructure of *Caliculum glossobalani* n. gen. et sp. (Apicomplexa) from a Pacific *Glossobalanus minutus* (Hemichordata) confounds the relationships between marine and terrestrial gregarines. *J. Eukaryot. Microbiol.* **61**:343-353.

## Ciliophora

Antipa, G.A., Dolan, J.R., Lynn, D.H., Obolkina, L.A. & Strüder-Kypke, M.C. 2016. Molecular phylogeny and evolutionary relationships between the ciliate genera *Peniculistoma* and *Mytilophilus* (Peniculistomatidae, Pleuronematida). *J. Eukaryot. Microbiol.*, **63**:642-650.

Bourland, W., Rotterová, J. & Čepička, I. 2017. Morphologic and molecular characterization of seven species of the remarkably diverse and widely distributed metopid genus *Urostomides* Jankowski, 1964 (Armophorea, Ciliophora). *Eur. J. Protist.*, **61**:194-232.

Bourland, W.A., Hampikian, G. & Vďačný, P. 2012. Morphology and phylogeny of a new woodruffiid ciliate, *Etoschophrya inornata* sp. n. (Ciliophora, Colpodea, Platyophryida), with an account on evolution of platyophryids. *Zool. Scr.*, **41**:400-416.

Chen, X., Ma, H.-G., Al-Rasheidm, K. A. S. & Miao, M. 2015. Molecular data suggests the ciliate *Mesodinium*
(Protista: Ciliophora) might represent an undescribed taxon at class level. *Zool. Syst.*, **40**:31-40.

Dunthorn, M., Otto, J., Berger, S. A., Stamatakis, A., Mahé, F., Romac, S., de Vargas, C., Audic, S., BioMarKs Consortium, Stock, A., Kauff, F. & Stoeck, T. 2014. Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context. *Mol. Biol. Evol.*, **31**:993-1009.

Fan, X., Pan, H., Li, L., Jiang, J., Al-Rasheid, K.A.S. & Gu, F. 2014. Phylogeny of the poorly known ciliates, Microthoracida, a systematically confused taxon (Ciliophora), with morphological reports of three species. *J. Eukaryot. Microbiol.*, **61**:227-237.

Feng, J.-M., Jiang, C.-Q., Warren, A., Tian, M., Cheng, J., Liu, G.-L., Xiong, J. & Miao, W. 2015. Phylogenomic analyses reveal subclass Scuticociliatia as the sister group of subclass Hymenostomatia within class Oligohy-menophorea. *Mol. Phylogenet. Evol.*, **90**:104-111.

Fernandes, N.M., Vizzoni, V.F., Borges, B.d.N., Soares, C.A.G., da Silva-Neto, I.D. & Paiva, T.d.S. 2018. Molecular phylogeny and comparative morphology indicate that odontostomatids (Alveolata, Ciliophora) form a distinct class-level taxon related to Armophorea. *Mol. Phylogenet. Evol.*, **126**:382-389.

Foissner, W., Stoeck, T., Agatha, S. & Dunthorn, M. 2011. Intraclass evolution and classification of the Colpo-dea (Ciliophora). *J. Eukaryot. Microbiol.*, **58**:397-415.

Foissner, W., Bourland, W.A., Wolf, K.W., Stoeck, T. & Dunthorn, M. 2014. New SSU-rDNA sequences for eleven colpodeans (Ciliophora, Colpodea) and description of *Apocyrtolophosis* nov. gen. *Eur. J. Protistol.*, **50**:40-46.

Gao, F., Katz, L.A. & Song, W. 2012. Insights into the phylogenetic and taxonomy of philasterid ciliates (Protozoa, Ciliophora, Scuticociliatia) based on analyses of multiple molecular markers. *Mol. Phylogenet. Evol.*, **64**:308-317.

Gao, F., Katz, L.A. & Song, W. 2013. Multigene-based analyses on evolutionary phylogeny of two controversial ciliate orders: Pleuronematida and Loxocephalida (Protista, Ciliophora, Oligohymenophorea). *Mol. Phylogenet. Evol.*, **68**:55-63.

Gao, F., Warren, A., Zhang, Q., Gong, J., Miao, M., Sun, P., Xu, D., Huang, J., Yi, Z. & Song, W. 2016. The all-data-based evolutionary hypothesis of ciliated protists with a revised classification of the Phylum Ciliophora (Eukaryota, Alveolata). *Sci. Rep.*, **6**:24874.

Gentekaki, E., Kolisko, M., Gong, Y. & Lynn, D. 2017. Phylogenomics solves a long-standing evolutionary puzzle in the ciliate world: the subclass Peritrichia is monophyletic. *Mol. Phylogenet. Evol.*, **106**:1-5.

Gentekaki, E., Kolisko, M., Boscaro, V., Bright, K. J., Dini, F., Di Giuseppe, G., Gong, Y., Miceli, C., Modeo, L., Molestina, R.E., Petroni, G., Pucciarelli, S., Roger, A.J., Strom, S.L. & Lynn, D.H. 2014. Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon *Protocruzia* and unravels the deep phylogenetic affinities of the ciliate lineages. *Mol. Phylogenet. Evol.*, **78**:36-42.

Gong, J., Stoeck, T., Yi, Z., Miao, M., Zhang, Q., Roberts, D. M., Warren, A. & Song, W. 2009. Small subunit rRNA phylogenies show that the class Nassophorea is not monophyletic (Phylum Ciliophora). *J. Eukaryot. Microbiol.*, **56**:339-347.

Johnson, M. D., Tengs, T., Oldach, D. W., Delwiche, C. F. & Stoecker, D. K. 2004. Highly divergent SSU rRNA genes found in the marine ciliates *Myrionecta rubra* and *Mesodinium pulex*. *Protist*, **155**:347-359.

Kittelmann, S., Devente, S.R., Kirk, M.R., Seedorf, H., Dehority, B.A. & Janssen, P.H. 2015. Phylogeny of intestinal ciliates, including *Charonina ventriculi*, and comparison of microscopy and 18S rRNA gene pyrosequencing for rumen ciliate community structure analysis. *Appl. Environ. Microbiol.*, **81**:2433-2444.

Liu, A., Yi, Z., Lin, X., Hu, X., Al-Farraj, S. A. & Al-Rasheid, K. A. S. 2015. Molecular phylogenetic lineage of *Plagiopogon* and *Askenasia* (Protozoa, Ciliophora) revealed by their gene sequences. *J. Ocean Univ. China*, **14**:724-730.

Lynn, D. H. 2008. The ciliated protozoa: characterization, classification, and guide to the literature, 3rd edition. Springer, Dordrecht.

Lynn, D.H., Kolisko, M. & Bourland, W. 2018. Phylogenomic analysis of *Nassula variabilis* n. sp., *Furgasonia blochmanni*, and *Pseudomicrothorax dubius* confirms a nassophorean clade. *Protist*, **169**:180-189.

Orsi, W., Edgcomb, V., Faria, J., Foissner, W., Fowle, W. H., Hohman, T., Suarez, P., Taylor, C., Taylor, G. T., Vďačný, P. & Epstein, S. 2012. Class *Cariacotrichea*, a novel ciliate taxon from the anoxic Cariaco Basin, Venezuela. *Int. J. Syst. Evol. Microbiol.*, **62**:1425-1433.

Pan, H., Stoeck, T. 2017. Redescription of the halophile ciliate, *Blepharisma halophilum* Ruinen, 1938 (Ciliophora, Heterotrichea, Heterotrichida) shows that the genus *Blepharisma* is non-monophyletic. *Eur. J. Protistol.*, **61**:20-28.

Santoferrara, L. F., Alder, V.V. & McManus, G.B. 2017. Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea). *Mol. Phylogenet. Evol.*, **112**:12-22.

Sauvadet, A.-L., Lynn, D.H., Roussel, E. G., Le Panse, S., Bigeard, E., Schrével, J. & Guillou, L. 2017. Redescription and phylogenetic analyses of *Durchoniella* spp. (Ciliophora, Astomatida) associated with the polychaete *Cirriformia ten-taculata* (Montagu, 1808). *Eur. J. Protistol.*, **61**:265-277.

Shin, M. K., Hwang, U. W., Kim, W., Wright, A.-D. G., Krawczyk, C. & Lynn, D. H. 2000. Phylogenetic position of the ciliates *Phacodinium* (Order Phacodiniida) and *Protocruzia* (Subclass Protocruziida) and systematics of the spirotrich ciliates examined by small subunit ribosomal RNA gene sequences. *Europ. J. Protistol.*, **36**:293-302.

Vďačný, P. & Rataj, M. 2017. Evaluation of systematic position of helicoprorodontids and chaeneids (Ciliophora, Litostomatea): an attempt to break long branches in 18S rRNA gene phylogenies. *J. Eukaryot. Microbiol.*, **64**:608-621.

Wang, P., Wang, Y., Wang, C., Zhang, T., Al-Farraj, S.A. & Gao, F. 2017. Further consideration on the phylogeny of the Ciliophora: analyses using both mitochondrial and nuclear data with focus on the extremely
confused class Phyllopharyngea. *Mol. Phylogenet. Evol.*, **112**:96-106.

Xu, Y., Shao, C., Miao, M. & Song, W. 2013. Redescrip-
tion of *Parasonderia vestita* (Kahl, 1928) comb. nov. (Cilio-
phora, Plagiopylida), with notes on its phylogeny based on
SSU rRNA gene. *Eur. J. Protistol.*, **49**:106-113.

Yan, Y., Xu, Y., Al-Farraj, S.A., Al-Rasheid, K.A.S. & Song, W. 2016. Morphology and phylogeny of three tracheocerids (Protozoa, Ciliophora, Karyorelictea), with description of two new species and insight into the evolution of the family Trachelocercidae. *Zool. J. Linn. Soc.-Lond.*, **177**:306-319.

Zhan, Z., Xu, K. & Dunthorn, M. 2013. Evaluating molecular support for and against the monophyly of the Peritrichia and phylogenetic relationships within the Mobilida (Ciliophora, Oligohymenophorea) Zool. Scripta, **42**:213-226.

Zhan, Z., Xu, K., Warren, A. & Gong, Y. 2009. Reconsideration of phylogenetic relationships of the subclass Peritrichia (Ciliophora, Oligohymenophorea) based on small subunit ribosomal RNA gene sequences, with the establishment of a new subclass Mobilia Kahl, 1933. *J. Eukaryot. Microbiol.*, **56**:552-558.

Zhang, Q., Fan, X., Clamp, J.C., Al-Rasheid, K.A.S. & Song, W. 2010. Description of *Paratetrahymena parawassi* n. sp. using morphological and molecular evidence and a phylogenetic analysis of *Paratetrahymena* and other taxonomically ambiguous genera in the order Loxocephalida (Ciliophora, Oligohymenophorea). *J. Eukaryot. Microbiol.*, **57**:483-493.

Zhang, Q., Miao, M., Strüder-Kypke, M.C., Al-Rasheid, K.A.S., Al-Farraj, S.A. & Song, W. 2011. Molecular evolution of *Cinetochilum* and *Sathrophilus* (Protozoa, Ciliophora, Oligohymenophorea), two genera of ciliates with morphological affinities to scuticociliates. *Zool. Scr.*, **40**:317-325.

Zhang, Q., Yi, Z., Fan, X., Warren, A., Gong, J. & Song, W. 2014. Further insights into the phylogeny of two ciliate classes Nassophorea and Prostomatea (Protista, Ciliophora). *Mol. Phylogenet. Evol.*, **70**:162-170.

Zhang, X., Ji, D., Zhang, Q. & Li, C. 2015. Description and phylogeny of a new prostomatid, *Metacystis similis* nov. spec. (Protista, Ciliophora) from the East China Sea. *Zootaxa*, **4033**:584-592.

Zhao, X., Miao, M., Chen, X., Ma, H. & Al-Rasheid, K.A.S. 2014. A phylogenetic reconsideration of suctorian ciliates (Protista, Ciliophora, Phyllopharyngea) based on small sub-unit rRNA gene sequences. *Zool. Scr.*, **43**:206-216.

Dinoflagellata

Bachvaroff, T. R., Gornik, S. G., Concepcion, G. T., Waller,
R. F., Mendez, G. S., Lippmeier, J. C. & Delwiche, C. F.
2014. Dinoflagellate phylogeny revisited: using ribosomal
proteins to resolve deep branching dinoflagellate clades.
*Mol. Phylogen. Evol.*, **70**: 314-322.

Boutrup, P. V., Moestrup, Ø., Tillmann, U. & Daugbjerg, N. 2016. *Katodinium glaucum* (Dinophyceae) revisited: proposal of new genus, family and order based on ultrastructure and phylogeny. *Phycologia*, **55**(2): 147-164.

Hoppenrath, M. 2017. Dinoflagellate taxonomy - a
review and proposal of a revised classification. *Mar. Bio-
div.*, **47**: 381-403.

Janouskovec, J., Gavelis, G. S., Burki, F., Dinh, D., Bachvaroff, T. R., Gornik, S. G., Bright, K. J., Imanian, B., Strom, S. L., Delwiche, C. F., Waller, R. F., Fensome, R. A., Leander, B. S., Rohwer, F. L. & Saldarriaga, J.F. 2017. Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics. *PNAS, USA*, **114**: E171-E180.

Orr, R. J. S., Murray, S. A., Stüken, A., Rhodes, L. & Jakobsen, K. S. 2012. When naked became armored: an eight-gene phylogeny reveals monophyletic origin of theca in dinoflagellates. *PLoS ONE*, **7**(11): e50004.

Takano, Y., Yamaguchi, H., Inouye, I., Moestrup, Ø. & Horiguchi, T. 2014. Phylogeny of five species of *Nusutto-dinium* gen. nov. (Dinophyceae), a genus of unarmoured kleptoplastidic dinoflagellates. *Protist*, **165**(6): 759-778.

RHIZARIA

Bass, D., Tikhonenkov, D.V., Foster, R., Dyal, P., Janous-
kovec, J., Keeling, P.J., Gardner, M., Neuhauser, S., Har-
tikainen, H., Mylnikov, A.P., & Berney, C. 2018. Rhizarian
'Novel Clade 10' revealed as abundant and diverse plank-
tonic and terrestrial flagellates, including *Aquavolon* n.
gen. *J. Eukaryot. Microbiol.* **65**: 828–842. https://doi.org/
10.1111/jeu.12524.

Cavalier-Smith, T., Chao, E.E., & Lewis, R. 2018. Multi-
gene phylogeny and cell evolution of chromist infraking-
dom Rhizaria: contrasting cell organisation of sister phyla
Cercozoa and Retaria. *Protoplasma*, **255**: 1517-1574.
https://doi.org/10.1007/s00709-018-1241-1.

Krabberød, A.K., Orr, R.J., Bråte, J., Kristensen, T., Bjørlklund, K.R., & Shalchian-Tabrizi, K. 2017. Single cell transcriptomics, mega-phylogeny, and the genetic basis of morphological innovations in Rhizaria. *Mol. Biol. Evol.* **34**:1557-1573. https://doi.org/10.1093/molbev/msx075.

Sierra, R., Cañas-Duarte, S.J., Burki, F., Schwelm, A., Fogelqvist, J., Dixelius, C., González-García, L.N., Gile, G.H., Slamovits, C.H., Köpp, C., Restrepo, S., Arzul, I., & Pawlowski, J. 2016. Evolutionary origins of Rhizarian parasites. *Mol. Biol. Evol.* **33**:980-983. https://doi.org/10.1093/molbev/msv340.

Cercozoa

Bass, D., Silberman, J.D., Brown, M.W., Pearce, R.A., Tice, A.T., Jousset, A., Geisen, S., & Hartikainen, H. 2016. Coprophilic amoebae and flagellates, including *Guttulinop-sis*, *Rosculus* and *Helkesimastix*, characterise a divergent and diverse rhizarian radiation and contribute to a large diversity of faecal-associated protists. *Env. Microbiol.* **18**:1604-1619. https://doi.org/10.1111/1462-2920.13235.

Bass, D., Yabuki, A., Santini, S., Romac, S., & Berney, C. 2012. *Reticulamoeba* is a long-branched Granofilosean (Cercozoa) that is missing from sequence databases. *PLoS One* **7**:e49090. https://doi.org/10.1371/journal.pone.0049090.
Bugge Harder, C., Rønn, R., Brejnrod, A., Bass, D., Al-Soud, W.A. & Ekelund, F. 2016. Local diversity of heathland Cercozoa explored by in-depth sequencing. *ISME J.* **10**: 2488-97.

Cavalier-Smith, T. & Oates, B. (2012). Ultrastructure of *Allapsa vibrans* and the Body Plan of Glissomonadida (Cercozoa). *Protist*, **163**: 165-187.

Cavalier-Smith, T. & Karpov, S.A. 2012. *Paraceromonas* Kinetid Ultrastructure, Origins of the Body Plan of Cercomonadida, and Cytoskeleton Evolution in Cercozoa. *Protist*, **163**, 47-75.

Chatelain, A.P., Meisterfeld, R., Roussel-Delif, L., & Lara, E. 2013. Sphenoderiidae (fam. nov.), a new clade of euglyphid testate amoebae characterized by small, round scales surrounding the aperture. *Protist* **164**:782-792.
https://doi.org/10.1016/j.protis.2013.08.001.

Dumack, K., Baumann, C. & Bonkowski, M. 2016. A Bowl with Marbles: Revision of the Thecate Amoeba Genus *Lecythium* (Chlamydophryidae, Tectofilosida, Cercozoa, Rhizaria) Including a Description of Four New Species and an Identification Key. *Protist*, **167**: 440–459.

Dumack, K., Schuster, J., Bass, D., & Bonkowski, M. 2016. A novel lineage of 'naked filose amoebae'; *Kraken carinae* gen. nov. sp. nov. (Cercozoa) with a remarkable locomotion by disassembly of its cell body. *Protist* **167**:268-278. https://doi.org/10.1016/j.protis.2016.04.002.

Dumack, K., Flues, S., Hermanns, K. & Bonkowski, M. 2017. Rhogostomidae (Cercozoa) from soils, roots and plant leaves (*Arabidopsis thaliana*): Description of *Rhogostoma epiphylla* sp. nov. and *R. cylindrica* sp. nov. *Europ. J. Protistol.*, **60**, 76–86.

Dumack, K., Mausbach, P., Hegmann, M. & Bonkowski, M. 2017. Polyphyly in the Thecate Amoeba Genus *Lecythium* (Chlamydophryidae, Tectofilosida, Cercozoa), Redescription of its Type Species *L. hyalinum*, Description of *L. jennyae* sp. nov. and the Establishment of *Fisculla* gen. nov. and Fiscullidae fam. nov. *Protist*, **168**: 294–310.

Dumack, K., Mylnikov, A.P. & Bonkowski, M. 2017. Evolutionary Relationship of the Scale-Bearing *Kraken* (incertae sedis, Monadofilosa, Cercozoa, Rhizaria): Combining Ultrastructure Data and a Two- Gene Phylogeny. *Protist*, **168**: 362–373.

Dumack, K., Öztoprak, H., Rüger, J. & Bonkowski, M. 2017. Shedding Light on the Polyphyletic Thecate Amoeba Genus *Plagiophrys*: Transition of Some of its Species to *Rhizaspis* (Tectofilosida, Thecofilosea, Cercozoa) and the Establishment of *Sacciforma* gen. nov. and Rhogostomidae fam. nov. (Cryomonadida, Thecofilosea, Cercozoa). *Protist*, **168**: 92–108.

Dumack, K., Bonkowski, M., Clauss, S. & Völcker, E. 2018. Phylogeny and redescription of the testate amoeba *Diaphoropodon archeri* (Chlamydophryidae, Thecofilosea, Cercozoa), De Saedeleer 1934, and annotations on the polyphyly of testate amoebae with agglutinated tests in the Cercozoa. *J. Eukaryot. Microbiol.* [Epub ahead of print] https://doi.org/10.1111/jeu.12474.

Dumack, K., Siemensma, F. & Bonkowski, M. 2018. Rediscovery of the testate amoeba genus Penardeugenia

(Thaumatomonadida, Imbricatea). *Protist*, **169**:29-42.
https://doi.org/10.1016/j.protis.2017.12.002.

Hess, S. & Melkonian, M. 2013. The mystery of clade X: *Orciraptor* gen. nov. and *Viridiraptor* gen. nov. are highly specialised, algivorous amoeboflagellates (Glissomonadida, Cercozoa). *Protist*, **164**:706-747. https://doi.org/10.1016/j.protis.2013.07.003.

Kosakyan, A., Gomaa, F., Lara, E. & Lahr, D.J.G. 2016. Current and future perspectives on the systematics, taxonomy and nomenclature of testate amoebae. *Eur. J. Protistol.*, **55**:105-117. https://doi.org/10.1016/j.ejop.2016.02.001.

Lee, W.J. & Park, J.S. 2016. Placement of the unclassified *Cyranomonas australis* Lee 2002 within a novel clade of Cercozoa. *Eur. J. Protistol.*, **56**:60-66. https://doi.org/10.1016/j.ejop.2016.06.004.

Ngo, C.N., Braithwaite, K.S., Bass, D., Young, A.J. & Croft, B.J. 2018. *Phytoceromonas venanatans*, a new species of Cercozoa associated with chlorotic streak of sugarcane. *Phytopathology*, **108**:479-486. https://doi.org/10.1094/phyto-07-17-0237-r.

Nicholls, K.H. 2012. *Zoelucasa sablensis* n. gen. et n. sp. (Cercozoa, Incertae sedis), a new scale-covered flagellate from marine sandy shores. *Acta Protozoologica*, **51**(2): 113-117.

Scoble, J.M. & Cavalier-Smith, T. 2014 Scale evolution, sequence phylogeny, and taxonomy of thaumatomonad Cercozoa: 11 new species and new genera *Scutellomonas*, *Cowlomonas*, *Thaumatospina* and *Ovaloplaca*. *Europ. J. Protistol.*, **50**: 270–313.

Schuler, G.A., Tice, A.K., Pearce, R.A., Foreman, E., Stone, J., Gammill, S., Wilson, J.D., Reading, C., Silberman, J.D., Brown, M.W., Phylogeny and Classification of Novel Diversity in Sainouroidea (Cercozoa, Rhizaria) Sheds Light on a Highly Diverse and Divergent Clade. *Protist* https://doi.org/10.1016/j.protis.2018.08.002

Shiratori, T. & Ishida, K-I. 2016. *Trachyrhizium urniformis* n. g., n. sp., a Novel Marine Filose Thecate Amoeba Related to a Cercozoan Environmental Clade (Novel Clade 4) *J. Euk. Microbiol.*, **63**:722-731.

Shiratori, T., Yabuki, A. & Ishida, K-I. 2012. *Esquamula lacrimiformis* n. g., n. sp., a New Member of Thaumatomonads that Lacks Siliceous Scales. *J. Eukaryot. Microbiol.*, **59**(6): 527–536.

Shiratori, T., Yokoyama, A. & Ishida, K-I. 2014. Phylogeny, Ultrastructure, and Flagellar Apparatus of a New Marimonad Flagellate *Abollifer globosa* sp. nov. (Imbricatea, Cercozoa). *Protist*, **165**: 808-824.

Shiratori, T., Fujita, S., Shimizu, T., Nakayama, T. & Ishida, K. 2017. *Viridiuvalis adhaerens* gen. et sp. nov., a novel colony-forming chlorarachniophyte. *J. Plant Res.*, **130**:999-1012. https://doi.org/10.1007/s10265-017-0961-1.

Yabuki, A. & Ishida, K. 2018. An orphan protist *Quadricilia rotundata* finally finds its phylogenetic home in Cercozoa. *J. Eukaryot. Microbiol.* [Epub ahead of print] https://doi.org/10.1111/jeu.12502.

Yabuki, A. & Ishida, K-I. 2011. *Mataza hastifera* n. g., n. sp.: A Possible New Lineage in the Thecofilosea (Cercozoa). *J. Eukaryot. Microbiol.*, **58**(2): 94–102.
## Endomyxa

Berney, C., Romac, S., Mahé, F., Santini, S., Siano, R. & Bass, D. 2013. Vampires in the oceans: predatory cercozoan amoebae in marine habitats. *ISME J.*, **7**:2387-2399.
https://doi.org/10.1038/ismej.2013.116.

Gong, Y., Patterson, D.J., Li, Y., Hu, Z., Sommerfeld, M., Chen, Y. & Hu, Q. 2015 *Vernalophrys algivore* gen. nov., sp. nov. (Rhizaria: Cercozoa: Vampyrellida), a new algal predator isolated from outdoor mass culture of Scedesmus dimorphus. *Appl. Environ. Microbiol.*, **81**:3900 – 3913. https://doi.org/10.1128/aem.00160-15.

Hartikainen, H., Stentiford, G.D., Bateman, K.S., Berney, C., Feist, S.W., Longshaw, M., Okamura, B., Stone, D., Ward, G., Wood, C. & Bass, D. 2014. Mikrocytids are a broadly distributed and divergent radiation of parasites in aquatic invertebrates. *Curr. Biol.*, **24**:807-812. https://doi.org/10.1016/j.cub.2014.02.033.

Hartikainen, H., Ashford, O.S., Berney, C., Okamura, B., Feist, S.W., Baker-Austin, C., Stentiford, G.D. & Bass, D. 2014. Lineage-specific molecular probing reveals novel diversity and ecological partitioning of haplosporidians. *ISME J.*, **8**: 177-86.

Hess, S. 2017. Description of *Hyalodiscus flabellus* sp. nov. (Vampyrellida, Rhizaria) and identification of its bacterial endosymbiont, "Candidatus *Megaira polyxenophila*" (Rickettsiales, Alphaproteobacteria). *Protist*, **168**:109-133.
https://doi.org/10.1016/j.protis.2016.11.003.

Hess, S., Sausen, N. & Melkonian, M. 2012. Shedding Light on Vampires: The Phylogeny of Vampyrellid Amoebae Revisited. *PLoS ONE*, **7**(2): e31165. https://doi.org/10.1371/journal.pone.0031165

Neuhauser, S., Kirchmair, M., Bulman, S. & Bass, D. 2014. Cross-kingdom host shifts of phytomyxid parasites. *BMC Evol. Biol.*, **14**:33. https://doi.org/10.1186/1471-2148-14-33.

Ward, G.M., Bennett, M., Bateman, K., Stentiford, G.D., Kerr, R., Feist, S.W., Williams, S.T., Berney, C. & Bass, D. 2016. A new phylogeny and environmental DNA insight into paramyxids: an increasingly important but enigmatic clade of protistan parasites of marine invertebrates. *Int. J. Parasitol.*, **46**:605-619. https://doi.org/10.1016/j.ijpara.2016.04.010.

Ward, G.M., Neuhauser, S., Groben, R., Ciaghi, S., Berney, C., Romac, S. & Bass, D. 2018. Environmental sequencing fills the gap between parasitic haplosporidians and free-living giant amoebae. *J. Eukaryot. Microbiol.*, **65**: 574–586.
https://doi.org/10.1111/jeu.12501.

## Retaria

Biard, T., Pillet, L., Decelle, J., Poirier, C., Suzuki, N. & Not, F. 2015. Towards an integrative morpho-molecular classification of the Collodaria (Polycystinea, Radiolaria). *Protist*, **166**:374-388. https://doi.org/10.1016/j.protis.2015.05.002.

Decelle, J., Martin, P., Paborstava, K., Pond, D.W., Talling, G., Mahé, F., de Vargas, C., Lampitt, R. & Not, F. 2013. Diversity, ecology and biogeochemistry of cyst-

forming Acantharia (Radiolaria) in the oceans. *PLoS ONE*, **8:e53598**. https://doi.org/10.1371/journal.pone.0053598.

Gooday, A.J., Holzmann, M., Caulle, C., Goineau, A., Kamenskaya, O., Weber, A.A.T. & Pawlowski, J. 2017. Giant protists (xenophyophores, Foraminifera) are exceptionally diverse in parts of the abyssal eastern Pacific licensed for polymetallic nodule exploration. *Biological Conservation*, **207**:106-116. https://doi.org/10.1016/j.biocon.2017.01.006.

Holzmann, M. & Pawlowski, J. 2017. An updated classification of rotaliid foraminifera based on ribosomal DNA phylogeny. *Mar. Micropal.*, **132**:18-34. https://doi.org/10.1016/j.marmicro.2017.04.002.

Pawlowski, J., Holzmann, M. & Tyszka, J. 2013. New supraordinal classification of Foraminifera: Molecules meet morphology. *Mar. Micropal.*, **100**:1-10. https://doi.org/10.1016/j.marmicro.2013.04.002.

Siemensma, F., Apothéloz-Perret-Gentil, L., Holzmann, M., Clauss, S., Völcker, E. & Pawlowski, J. 2017. Taxonomic revision of freshwater foraminifera with the description of two new agglutinated species and genera. *Eur. J. Protistol.*, **60**:28-44. https://doi.org/10.1016/j.ejop.2017.05.006.

## Cryptista

Burki, F., Okamoto, N., Pombert, J.-F. & Keeling, P. J. 2012. The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins. *Proc. Roy. Soc. B: Biol. Sci.*, **279**(1736): 2246–2254. https://doi.org/10.1098/rspb.2011.2301

Yabuki, A., Kamikawa, R., Ishikawa, S. A., Kolisko, M., Kim, E., Tanabe, A. S., et al. 2014. *Palpitomonas bilix* represents a basal cryptist lineage: insight into the character evolution in Cryptista. *Sci. Reports*, **4**: 4641. https://doi.org/10.1038/srep04641

Cavalier-Smith, T., Chao, E. E. & Lewis, R. 2015. Multiple origins of Heliozoa from flagellate ancestors: New cryptist subphylum Corbihelia, superclass Corbistoma, and monophyly of Haptista, Cryptista, Hacrobia and Chromista. *Mol. Phylogenet. Evol.*, **93**: 331–362. https://doi.org/10.1016/j.ympev.2015.07.004

## Haptista

Edvardsen, B., Egge, E.S. & Vaulot, D. 2016. Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review. *Perspectives in Phycology*, **3**, Issue 2, p. 77–91.

Burki, F., Kaplan, M., Tikhonenkov, D. V., Zlatogursky, V., Minh, B. Q., Radaykina, L. V., et al. 2016. Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista. *Proc. Royal Soc. B: Biol. Sci.*, **283**(1823). https://doi.org/10.1098/rspb.2015.2802

Cavalier-Smith, T., Chao, E. E. & Lewis, R. 2015. Multiple origins of Heliozoa from flagellate ancestors: New cryptist subphylum Corbihelia, superclass Corbistoma, and monophyly of Haptista, Cryptista, Hacrobia and Chromista. *Mol. Phylogenet. Evol.*, **93**, 331–362. https://doi.org/10.1016/j.ympev.2015.07.004.
Egge, E.S., Bittner, L., Andersen, T., Audic, S., de Var-
gas, C. & Edvardsen, B. 2013. 454 Pyrosequencing to
Describe Microbial Eukaryotic Community Composition,
Diversity and Relative Abundance: A Test for Marine Hap-
tophytes. PLOS ONE, 8 e74371.

Centroplasthelida

Bass, D., Chao, E. E., Nikolaev, S., Yabuki, A., Ishida, K. I.,
Berney, C., Pakzad, U., Wylezich, C. & Cavalier-Smith, T.
2009. Phylogeny of novel naked filose and reticulose Cer-
cozoa: Granofilosea cl. n. and Proteomyxidea revised. Pro-
tist, **160**: 75-109.

Cavalier-Smith, T. & Chao, E. E. 2012. *Oxnerella micra* sp. n. (Oxnerellidae fam. n.), a tiny naked centrohelid, and the diversity and evolution of heliozoa. *Protist*, **163**: 574-601.

Cavalier-Smith, T. & Scoble J. M. 2013. Phylogeny of Heterokonta: *Incisomonas marina*, a uniciliate gliding opalozoa related to *Solenicola* (Nanomonadea), and evidence that Actinophryida evolved from raphidophytes. *Europ. J. Protistol.*, **49**: 328-353.

Febvre-Chevalier, C., & Febvre, J. 1984. Axonemal micro-
tubule pattern of *Cienkowska mereschkovskyi* and a revis-
sion of heliozoan taxonomy. *Origins of life*, **13**: 315-338.

Krabberød, A. K., Orr, R. J., Bråte, J., Kristensen, T.,
Bjørklund, K. R. & Shalchian-Tabrizi, K. 2017. Single Cell
Transcriptomics, Mega-Phylogeny, and the Genetic Basis
of Morphological Innovations in Rhizaria. *Mol. Biol. Evol.,*
**34**: 1557-1573.

Mikrjukov, K. A. 1996. Revision of Genera and Species
Composition of Lower Centroheliozoa. II. Family Raphidio-
phryidae n. fam. *Archiv. Protistenkd.*, **147**: 205-212.

Mikrjukov, K. A. 2000. Taxonomy and phylogeny of heliozoa. I. The order Desmothoracida Hertwig et Lesser, 1874. *Acta Protozool.*, **39**: 81-97.

Mikrjukov, K. A. 2002. Centrohelid heliozoans (Centrohe-
liozoa). KMK Scientific, Moscow. Sekiguchi, H., Kawachi,
M., Nakayama, T. & Inouye I. 2003. A taxonomic re-eva-
luation of the Pedinellales (Dictyochophyceae), based on
morphological, behavioural and molecular data. *Phycologia*,
**42**: 165-182.

Shishkin, Y., Drachko, D., Klimov, V. I. & Zlatogursky, V.
V. 2018. *Yogsothoth knorrus* gen. n., sp. n. and *Y. carteri*
sp. n. (*Yogsothothidae* fam. n., Haptista, Centroplasthe-
lida), with notes on Evolution and Systematics of Centro-
helids. *Protist*, https://doi.org/10.1016/j.protis.2018.06.003.

Zlatogursky, V. V. 2016. There and back again: parallel evolution of cell coverings in centrohelid heliozoans. *Protist*, **167**, 51-66.

Zlatogursky, V. V., Drachko, D., Klimov, V. I. & Shishkin, Y. 2018. On the phylogenetic position of the genus *Raphidocystis* (Haptista: Centroplasthelida) with notes on the dimorphism in centrohelid life cycle. *Europ. J. Protistol.*, **64**: 82-90.

Excavates

Bennett, M. S. & Triemer, R. E. 2012 A new method for obtaining nuclear gene sequences from field samples and taxonomic revisions of photosynthetic euglenoids

Lepocinclis (Euglena) helicoideus and Lepocinclis (Phacus) horridus (Euglenophyta). *J. Phycol.*, **48**: 254-60.

Bennett, M. S., Triemer R. E. 2014 The genus *Cyclidiopsis*: an obituary. *J. Eukaryot. Microbiol.*, **61**:166-72.

Bennett, M. S., Wiegert, K. E. & Triemer, R.E. 2014
Characterization of *Euglenaformis* gen. nov. and the
chloroplast genome of *Euglenaformis* [*Euglena*] proxima
(Euglenophyta). *Phycologia*, **53**: 66–73.

Breglia, S. A., Yubuki, N. & Leander, B. S., 2013
Ultrastructure and molecular phylogenetic position of *Het-
ronema scaphurum*: a eukaryovorous euglenid with a
cytoproct. *J. Eukaryot. Microbiol.*, **60**: 107-20.

Cavalier-Smith, T. 2013 Early evolution of eukaryote feeding modes, cell structural diversity, and classification of the protozoan phyla Loukozoa, Sulcozoa, and Choanozoa. *Eur. J. Protistol.*, **49**: 115-178.

Cavalier-Smith, T. 2016 Higher classification and phylogeny of Euglenozoa. *Eur. J. Protistol.*, **56**: 250-276.

Cavalier-Smith, T., Chao, E. E. & Vickerman, K. 2016
New phagotrophic euglenoid species (new genus Decas-
tava; *Scytomonas saepesedens*; *Entosiphon oblongum*),
Hsp90 introns, and putative euglenoid Hsp90 pre-mRNA
insertional editing. *Eur. J. Protistol.*, **56**: 147-170.

Čepička, I., Dolan, M. F. & Gile, H. F. 2017. Parabasalia. In: Archibald, J. M., Simpson, A. G. B., and Slamovits, C., eds. Handbook of the Protists (Second Edition of the Handbook of Protoctista by Margulis et al.) Springer Reference Works (e-book) https://doi.org/10.1007/978-3-319-32669-6_12-1.

Čepička, I., Hampl, V. & Kulda, J. 2010 Critical taxonomic revision of parabasalids with description of one new genus and three new species. *Protist*, **161**: 400-433.

Chan, Y.-F., Moestrup, Ø. & Chang, J. 2013 On *Keelun-
gia pulex* nov. gen. et nov. sp., a heterotrophic euglenoid
flagellate that lacks pellicular plates (Euglenophyceae,
Euglenida). *Eur. J. Protistol.*, **49**: 15-31.

Gibson, W. 2017 Kinetoplastea. In: Archibald, J. M., Simpson, A. G. B. & Slamovits, C., eds. Handbook of the Protists (Second Edition of the Handbook of Protoctista by Margulis et al.) Springer Reference Works (e-book) https://doi.org/10.1007/978-3-319-32669-6_12-1

Hampl, V. 2017 Preaxostyla. In: Archibald, J. M., Simpson, G. B., and Slamovits, C., eds. Handbook of the Protists (Second Edition of the Handbook of Protoctista by Margulis et al.) Springer Reference Works (e-book) https://doi.org/10.1007/978-3-319-32669-6_12-1

Hanousková, P., Táborský, P. & Čepička, I. 2018 *Dactylomonas* gen. nov., a novel lineage of heterolobosean flagellates with unique ultrastructure, closely related to the amoeba *Selenaion koniopes* Park, de Jonckheere & Simpson, 2012. *J. Eukaryot. Microbiol.*, in press.

Heiss, A. A., Kolisko, M., Ekelund, F., Brown, M. W., Roger, A. J. & Simpson, A. G. B. 2018. Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes. *R. Soc. Open Sci.*, **5**:171707. https://doi.org/10.1098/rsos.171707.

Kamikawa, R., Kolisko, M., Nishimura, Y., Yabuki, A.,
Brown, M. W., Ishikawa, S. A., Ishida, K., Roger, A. J.,
Hashimoto, T. & Inagaki, Y. 2014 Gene content evolution
in discobid mitochondria deduced from the phylogenetic
position and complete mitochondrial genome of *Tsukuba-
monas globosa*. *Genome Biol. Evol.*, **6**: 306-315.

Karnkowska, A., Bennett, M. S., Watza, D., Kim, J. I.,
Zakryś, B. & Triemer, R. E. 2015 Phylogenetic relation-
ships and morphological character evolution of photosyn-
thetic euglenids (Excavata) inferred from taxon-rich
analyses of five genes. *J. Eukaryot. Microbiol.*, **62**: 362-73.

Kaufer, A., Ellis, J., Stark, D. & Barratt, J. 2017 The evo-
lution of trypanosomatid taxonomy. *Parasites & Vectors,
10*: 287.

Kostygov, A.Y. & Yurchenko, V. 2017 Revised classifica-
tion of the subfamily Leishmaniinae (Trypanosomatidae).
*Folia Parasitol.*, **64**: 020.

Kulda, J., Nohýnková, E. & Čepička, I. 2017 Retorta-
monadida (with notes on *Carpediemonas*-like organisms
and Caviomonadidae). In: Archibald, J. M., Simpson, A. G.
B., and Slamovits, C., eds. Handbook of the Protists (Sec-
ond Edition of the Handbook of Protoctista by Margulis
et al.) Springer Reference Works (e-book) https://doi.org/
10.1007/978-3-319-32669-6_12-1.

Lax, G. & Simpson, A. G. B. 2013 Combining molecular
data with classical morphology for uncultured phagotrophic
euglenids (Excavata): a single-cell approach. *J. Eukaryot.
Microbiol.*, **60**: 615-25.

Leander, B. S., Lax, G., Karnkowska, A. & Simpson, A.
G. B. 2017 Euglenida. In: Archibald, J. M., Simpson, A. G.
B., and Slamovits, C., eds. Handbook of the Protists (Sec-
ond Edition of the Handbook of Protoctista by Margulis
et al.) Springer Reference Works (e-book) https://doi.org/
10.1007/978-3-319-32669-6_12-1

Lee, W. J. & Simpson, A. G. 2014 Ultrastructure and
molecular phylogenetic position of *Neometanema parovale*
sp. nov. (*Neometanema* gen. nov.), a marine phagotrophic
euglenid with skidding motility. *Protist*, **165**: 452-72.

Lee, W. J. & Simpson, A. G. 2014 Morphological and
molecular characterisation of *Notosolenus urceolatus* Lar-
sen and Patterson 1990, a member of an understudied
deep-branching euglenid group (petalomonads). *J. Eukar-
yot. Microbiol.*, **61**: 463-79.

Lukeš, J., Butenko, A., Hashimi, H., Maslov, D.A.,
Votýpka, J. & Yurchenko, V. 2018 Trypanosomatids are
much more than just trypanosomes: clues from the
expanded family tree. *Trends Parasitol.*, **34**: 466-480.

Pánek, T., Simpson, A. G. B., Brown, M. W. & Dyer, B.
D. 2017 Heterolobosea. In: Archibald, J. M., Simpson, A.
G. B., and Slamovits, C., eds. Handbook of the Protists
(Second Edition of the Handbook of Protoctista by Mar-
gulis et al.) Springer Reference Works (e-book) https://doi.
org/10.1007/978-3-319-32669-6_12-1.

Pánek T., Táborský P., Pachiadaki, M. G., Hroudová, M.,
Vlček, Č., Edgcomb, V. P. & Čepička, I. 2017 Combined
culture-based and culture-independent approaches provide
insights into diversity of jakobids, an extremely plesiomor-
phic eukaryotic lineage. *Front. Microbiol.*, **6**: 1288.

Okamoto, N., Gawryluk, R.M.R., del Campo, J., Stras-
sert, J.F.H., Lukeš, J., Richards, T.A., Worden, A.Z., San-
toro, A.E. & Keeling, P.J. 2018 A revised taxonomy of
diplonemids including the Eupelagonemidae n. fam. and a

type species, *Eupelagonema oceanica* n. gen. & sp. *J.*
*Euk. Microbiol.*, (in press)

Radek, R., Strassert, J. F., Krüger, J., Meuser, K., Schef-
frahn, R. H. & Brune, A. 2014 Phylogeny and ultrastructure
of *Oxymonas jouteli*, a rostellum-free species, and
*Opisthomitus longiflagellatus* sp. nov., *oxymonad* flagel-
lates from the gut of *Neotermes jouteli*. *Protist*, **165**: 384-99.

Simpson, A. G. B. 2017. Jakobida. In: Archibald, J. M.,
Simpson, A. G. B., & Slamovits, C., eds. Handbook of the
Protists (Second Edition of the Handbook of Protoctista by
Margulis et al.) Springer Reference Works (e-book)
https://doi.org/10.1007/978-3-319-32669-6_12-1.

Strassert, J. F. H., Tikhonenkov, D. V., Pombert, J. F.,
Kolisko, M., Tai, V., Mylnikov, A. P. & Keeling, P. J. 2016.
*Moramonas marocensis* gen. nov., sp. nov.: a jakobid flagel-
late isolated from desert soil with a bacteria-like, but bloated
mitochondrial genome. *Open Biol.*, **6**: 150239.

Tashyreva, D., Prokopchuk, G., Yabuki, A., Kaur, B., Fak-
torová, D., Votýpka, J., Kusaka, C., Fujikura, K., Shiratori,
T., Ishida, K.-I., Horák, A. & Lukeš, J. 2018. Phylogeny and
morphology of new diplonemids from Japan. *Protist*, **169**:
158-179.

Treitli, S. C., Kotyk, M., Yubuki, N., Jirounková, E.,
Vlasáková, J., Smejkalová, P., Šípek, P., Čepička, I. &
Hampl, V. 2018. Molecular and morphological diversity of
the *oxymonad* genera *Monocercomonoides* and *Blatta-
monas* gen. nov. *Protist*. **169**:744–783. https://doi.org/10.
1016/j.protis.2018.06.005

Yamaguchi, A., Yubuki, N. & Leander, B. S. 2012. Mor-
phostasis in a novel eukaryote illuminates the evolutionary
transition from phagotrophy to phototrophy: description of
*Rapaza viridis* n. gen. et sp. (Euglenozoa, Euglenida). *BMC
Evol. Biol.*, **12**: 29.

Yubuki, N., Zadrobílková, E. & Čepička, I. 2017.
Ultrastructure and molecular phylogeny of *lotanema spi-
rale* gen. nov. et sp. nov., a new lineage of endobiotic For-
nicata with strikingly simplified ultrastructure. *J. Eukaryot.
Microbiol.*, **64**: 422-433.

Zhang, Q., Táborský, P., Silberman, J. D., Pánek, T.,
Čepička, I. & Simpson, A. G. B. 2015. Marine isolates of
*Trimastix marina* form a plesiomorphic deep-branching lin-
eage within Preaxostyla, separate from other known tri-
mastigids (*Paratrimastix* n. gen.). *Protist*, **166**: 468-91.

Incertae sedis Eukarya

Foissner, I. & Foissner, W. (1993): Revision of the family
Spironemidae Doflein (Protista, Hemimastigophora), with
description of two new species, *Spironema terricola* n. sp.
and *Stereonema geiseri* n. g., n. sp. *J. Eukaryot. Micro-
biol.*, **40**:422-438.

Glücksman, E., Snell, E. A. & Cavalier-Smith, T. (2013)
Phylogeny and evolution of Planomonadida (Sulcozoa):
eight new species and new genera *Fabomonas* and *Nuto-
monas*. *Europ. J. Protistol.*, **49**:179–200.

Hausmann, K., Weitere, M., Wolf, M. & Arndt, H. 2002.
*Meteora sporadica* gen. et sp. nov. (Protista incertae sedis)
— an extraordinary free-living protist from the Mediter-
ranean deep sea. *Europ. J. Protistol.*, **38**:171–177.
Janouškovec, J., Tikhonenkov, D. V., Burki, F., Howe, A. T., Rohwer, F. L., Mylnikov, A. P. & Keeling, P. J. (2017). A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction. Curr. Biol., **27**(23), 3717-3724.e5. https://doi.org/10.1016/j.cub.2017.10.051

## CRuMs

Brown, M. W., Heiss, A. A., Kamikawa, R., Inagaki, Y., Yabuki, A., Tice A. K., Shiratori, T., Ishida, K., Hashimoto, T., Simpson, A. G. B. & Roger, A. J. 2018. Phylogenomics places orphan protistan lineages in a novel eukaryotic super-group. *Genome Biol. Evol.*, **10**:427-433.

Brugerolle, G. 2006. Description of a new freshwater heterotrophic flagellate *Sulcomonas lacustris* affiliated to the collodictyonids. *Acta Protozool.*, **45**:175-182.

Brugerolle, G., Bricheux, G., Philippe, H. & Coffe, G. 2002. *Collodictyon triciliatum* and *Diphylleia rotans* ( = *Aulacomonas submarina*) form a new family of flagellates (Collodictyonidae) with tubular mitochondrial cristae that is phylogenetically distant from other flagellate groups. *Protist*, **153**:59-70.

Glücksman, E., Snell, E. A., Berney, C., Chao, E. E., Bass, D. & Cavalier-Smith, T. 2011. The novel marine gliding zooflagellate genus *Mantamonas* (Mantamonadida ord. n.: Apusozoa). *Protist*, **162**:207-221.

Yabuki, A., Ishida, K. & Cavalier-Smith, T. 2013. *Rigifila ramosa* n. gen., n. sp. a filose apusozoan with a distinctive pellicle, is related to *Micronuclearia*. *Protist*, **164**:75-88.

## APPENDIX S2. TROPHIC FUNCTIONAL GROUPS ACROSS PROTIST DIVERSITY.

Trophic functional group assignments facilitate interpretation of community structure and food web assembly from DNA sequence information identification of "operational taxonomic unit" (OTU). Here we tried to provide details of trends in eating habits of non-parasitic protists. Many genera have never been cultured so their feeding preferences are unknown. For definition of terms, please refer to the main text, page 6.

Across protists, in most cases it is safe to assume that species within a genus are most likely to have the same trophic function, with rare exceptions. However, it is not the case in some taxa, where there can be considerable variation between species within a genus. That is the case, for example, in Dinoflagellata, Arcellinida, and Euglyphida.

In the **Amnoebozoa**, genera can be assumed to ingest bacteria by phagocytosis with the following exceptions: *Amphizonella* (Corycida) and *Dermamoeba* also ingest Cyanobacteria; the Euamoebida genera *Amoeba*, *Cashia*, *Chaos*, *Polychaos*, *Trichamoeba* and *Deuteramoeba* are also cytotrophic; amoebae of the genera *Polychaos* and *Pseudothecamoeba* ingest diatoms. Some species or genera have a preference for heterotrophic bacteria over

of photosynthetic ones, or even discriminate against Cyanobacteria such as *Copromyxa* and *Copromyxella*. In Protosteliida, *Protostelium* spp. prefer yeasts but some will also eat bacteria, and several can eat coccoid green algae, except *P. nocturnum* which only eats bacteria; they can be cannibalistic in culture as can Cavosteliida and some Protosporangiidae. In Schizoplasmodiidae, all do best in culture on a mixture of yeast and bacteria, though some will survive on bacteria alone; when they eat yeasts, they puncture the cell wall and ingest only the protoplast. *Multicilia* (Holomastigida) is cytotrophic on other amoebae. Dictyostelia are primarily bacterivorous but they will eat yeasts in culture, and can also be cannibalistic in culture; zygotes are cannibalistic exclusively. Myxogastria ciliated stage is bacterivorous, their plasmodia are omnivorous and often cannibalistic when they first form. The Entamoebae are mostly commensal or parasitic and can eat bacteria by phagotrophy. A few strains of *Sappinia* and *Acanthamoeba* can be parasitic. Some *Archamoebae*, *Tricholimax*, *Thecamoeba*, *Korotnevella*, *Gocevia*, *Paragocevia*, *Leptomyxa* and *Mayorella* species are omnivores. There are some diatom specialists as in *Diffugia* and *Phryganella*. The ability to feed on yeast might be more widespread than reported. Similarly, in their habitat some soil amoebae probably ingest small Cercozoa such as Glissomonads. In the Arcellinida, at least species of *Nebela* and *Cryptodiflugia* are known to prey on nematodes. The tendency to cannibalism amongst some amoebae may be due to crowding in culture.

In Arcellinida certain species of *Cucurbitella*, *Diffugia*, *Heleopera*, *Hyalosphenia* and *Netzelia* form symbiosis with *Trebouxiophyta* species and can be considered mixotrophic.

Free-living basal genera of **Holozoa** and **Nucletmycea** are amoeboid, phagotrophic on bacteria. Parasitic ones, including *Microsporidia*, are intracellular parasites. The *Choanoflagellata* feed on bacteria by filtration through the collar. The Fungi are saprotrophic on external substrate, obtaining their nutrient by osmotrophy through a chitinous cell wall. Lichenous fungi are capable of photosynthesis. Mycorrhizal fungi receive most or all of their organic molecules from the host plant. Many Fungi are parasitic (see table 2). For details of substrate preference the reader is referred to FUNGuild (Nguyen et al., 2016, https://github.com/UMNFuN/FUNGuild).

In the **Archaeplastida**, ignoring the Embryophyta, all Chloroplastida are photosynthetic with *chl a*, *b*, with the exception of *Helicosporidium* (insect gut parasite), *Polytomella*, *Polytoma*, *Prototheca* which have 2º lost photosynthesis and are strictly osmotrophic. Among the **Rhodophyceae**, some Cyanidiales are facultative heterotrophs. Among the red algae certain species in several genera have lost photosynthesis and are parasites of other red algae. For example: *Gracilariophila oryzoides*, *Haveyella mirabilis*, *Choreocolax polysiphoniae*, *Janczewskia gardneri*, *Faucheocolax attenuata*, *Bostrychiocolax australis*, *Dawsoniocolax bostrychiae*, *Coccotylus hartzii*, *Epulo*
*multipedes* (see Blouin and Lane, 2012, Table S1). Nearly all of the parasitic genera end with the term “colax” to indicate the lifestyle. Most parasites are sister species with the hosts, and many of these genera need to be merged with the genus of their hosts, as they were described separately. This is in progress but obviously correcting the taxonomy is a slow process.

The **Cryptista** ingest bacteria prey by phagocytosis, and the photosynthetic ones are mixotrophic. In **Haptophyta**, Coccolithales are autotrophic, while genera without scales can be mixotrophic or heterotrophic on bacteria, with or without haptonema contributing to bacteria capture. The Centroplasthelida are typically cytotrophic.

In the **Apicomplexa**, all species are historically treated as parasites. Recent observation suggest some may be endobionts as commensals or at least not as parasites, especially among some invertebrate hosts. However, there are no free-living species known. The presence of a relic plastid genome in the Apicomplexa, and apicoplast in some, provides useful metabolic targets for drug treatment development. In contrast, both Dinoflagellata and Ciliophora provide a wide diversity of trophic functional groups.

The **Dinoflagellata** functional assignments vary between closely related genera, and are shown in Appendix 2, Table 2.1.

The **Ciliophora** are to be assumed to ingest bacteria by filtration except as noted below. Some genera of Karyorelictea (eg. Kentrophoridae) can be considered grazers as they live on sand surfaces covered in bacteria, and often harbour symbiotic bacteria. We discriminate between surface-feeding and water-column filtration feeding. Surface-feeding ciliophores spend most of their time gathering food particles from surfaces rather than by swimming in a volume of water. Thus clearing rates are calculated by surface area rather than volume of liquid. Most ciliophores (with exceptions noted in table 2.2) ingest bacteria, and many also ingest small protists (labelled omnivorous), while others can ingest larger protists by predation. Many omnivores can also ingest some detritus if the cytostome permits. In Ciliophora one should not assume that a small cell or a small cytostome implies a bacteria diet. There are parasites, histophagous species, endocommensals, and epibionts. The Stichotrichida contain species that can ingest larger protists and even small ciliophores for example in some species of Oxytrichidae. The Litostomatea are redoubtable predatory cytotrophs, and some can ingest prey larger than themselves. Entodiniomorphida are often (or typically) commensals in rumen. Among the Colpodea a small number of genera are cytotrophic, for example Bursaria (and maybe other Bursariomorphida). In the Nassulida, *Nassula* is phycotrophic by swallowing and can ingest cyanobacteria filaments. In the Prorodontida several genera, eg. *Coleps*, are attracted to dead or wounded invertebrates to the leaking tissues. The Astomatia can be found as symbionts in Oligochaetae gut. Some Tetrahymenida genera are parasitic or histophagous. The Suctoria (Phyllopharyngea) use specialised tentacles to capture and manipulate prey, typically other

ciliophores or small invertebrates; they are cytotrophic predators and 3° consumers as predators of invertebrates. The Rhynchodia (Phyllopharyngea) are parasites of bivalves. Among the Scuticociliatia the Philasterida contain cytotrophic genera, for example *Uronema*. See Appendix table 2.2 for more details.

Also in the **Alveolates**, the colpodellids, *Colponema*, *Acavomonas*, and *Oxyrrhis* are cytotrophic predators, while the Perkinsidae are parasitic as trophozoites.

Stramenopiles in the Ochrophyta are almost all photosynthetic. The Actinophryidae are cytotrophic. The Opali-nata, Bicosoecida, and Placididae are phagotrophic on bacteria, with the exception of the Proteromonada and *Blastocystis* (osmotrophic) which are intestinal commen-sals or parasites. The Hyphochytriales and Peronospor-mycetes are saprotrophs, but the latter contains numerous plant parasites. The Pirsoniales are parasites on diatoms.

**Rhizaria.** The Cercomonadida, Paracercomonadida, and Glissomonadida can be assumed to be phagotrophic predators on bacteria, with the notable exception of the Viridiraptoridae which are phycotrophic (mycotrophy not known) by penetration. The Vampyrellidae are mycotrophic or phycotrophic. The Euglyphida show some variation, although most are phagotrophic on bacteria. Observations indicate that the larger the cell the more likely it is to be cytotrophic; in fact the larger species cannot survive on bacteria alone. Many Hyalospheniidae need to prey at least partly on Euglyphida and use the scales to build their own test. Symbiosis occurs between Trebouxiophyta (pho-tosynthetic) with several genera of Rhizaria. This impli-cates at least some species of *Placocista* (Euglyphida), *Amphitrema* and *Archerella* (Labyrinthulomycetes). Chlo-rarachnea are photosynthetic but some species are mixo-trophic on bacteria. In the Endomyxa, the Phytomyxea are plant root parasites, while the Ascetosporea are parasites of invertebrates.

The Foraminifera are primarily bacteria eaters, but can ingest detritus, other protists, and larger forms can prey on small invertebrates.

Among the **Discoba** (Excavates) Heterolobosea graze bacteria by phagocytosis, except *Stephanopogon* and *Cre-neis* which are cytotrophic. Some strains of *Naegleria fow-leri* can cause primary amoebic meningoencephalitis, penetrating through the nose. The Jakobida and *Tsukubo-monas* are predatory on bacteria which are ingested by phagocytosis. The Diplonema are cytotrophic by phagocy-tosis and have an important role in aphotic marine waters; some species are parasitic or symbiotic with animals. Among the Euglenida (Discoba) the Aphagea (*Rhabdomo-nas*, *Gyropaigne*, *Menoidium*, *Parmidium* and *Rhabdos-pira*), *Astasia* and *Distigma* are osmotrophic; Euglenophyceae (except *Rapaza*) are photosynthetic with *chl a*, *b* in plastids, or secondarily osmotrophic, and *Rapaza* is cytotrophic; the Peranemids, Anisonemids, Pleo-tiids, and Petalomonadida are phagotrophic. Certain clades graze on bacteria by phagotrophy or are cytotrophic preda-tors. Among the Kinetoplastea (Discoba) all except the Trypanosomatida are predatory phagotrophs on bacteria.
The Trypanosomatida are animal blood and tissue para-
sites, except *Phytonomas* which lives in plant latex ves-
sels, and all are transferred by insect vectors.

The **Metamonada** (Fornicata, Parabasalia, and Preaxostyla Excavates) are predatory or grazers on bacteria, ingested by phagocytosis. The Preaxostyla are endosymbiont detritivores that phagocytose wood microchips, and acquire many nutrients by osmotrophy from syntrophic bacteria; some genera may also ingest bacteria by phagocytosis. *GIardia* (Diplomonadida) are osmotrophic gut parasites. Several genera have species that can be parasitic in humans and other animals.

**Human parasites.** For protists that are human para-
sites, see Adl and Matheson (2019) in ASM-Manual of
Clinical Microbiology chapter 132 (Taxonomy and Classifi-
cation of Human Eukaryotic Parasites), 12th edn.

**Definitions.** We further provide descriptions and clarifications for symbisois, microbiome, holobiont, intra- cellular and extracellular locations, that relate to interactions between organisms.

**Symbiosis** is a sustained relationship between at least two individuals (same or different species), living in direct contact or close enough one to the other, during part or the whole live cycle of the two partners. This interaction is transmitted either vertically (from one generation to the other) or horizontally (acquired de novo at each generation). Symbiosis is the antonym of transitory interactions (predatory). A symbiosis can be beneficial for both partners (mutualism) or at the other extreme, deleterious for one of these partners (parasite or parasitoid). In general, the larger species of this association is called the host, the smallest one is the symbiont. Examples of symbiosis: photosymbiosis (corals and *Symbiodinium*, kleptoplast), mycorrhizae, lichens, parasitism and hyperparasitism (parasite of parasite). Some specialist predators may also be considered as symbionts (example: *Helcion* living exclusively on laminarian). A virus is a parasitic symbiont.

The **microbiome** is a microbial community living in, on or at the close vicinity of an individual. Examples: gut community, biosphere of phytoplanktonic cells, microbes living on the skin/cuticule of metazoan, in the rhizopshere, microbes living in specialized tissues, or part of the cell. Unicellular symbionts are part of the microbiome of their host.

**Holobiont.** Ecoevolutionary concept considering an indi-
vidual together with its microbiome as the true unit on
which evolutionary processes will act.

**Intracellular (endocellular) versus extracellular.** Intra-
cellular symbionts are those where the parasite cytoplasm
and nucleus enter inside the host and reside inside the
host cell. In some extracellular symbionts, part of the cyto-
plasm (including the mitochondrion) may penetrate inside
the host cell, but never the parasite nucleus. Endobionts
penetrate the host tissue between cells, or inside a
matrix, but do not reside inside host cells. Mycorrhizae
are symbiotic endobionts.

APPENDIX 2, TABLE 2.1. TROPHIC FUNCTIONAL ASSIGNMENTS FOR DINOFLAGELLATES WHERE KNOWN

L = photosynthetic, M = mixotrophic (photosynthesis and phagotrophy), B = phagotrophic on bacteria, C = cytotrophic (phagotrophic on protists), H = heterotrophic. In general, few dinoflagellates nutritional strategy is really investigated, documented, and understood. For most of the taxa we can only indirectly judge and it is more or less a guess. Some genera are difficult to assign because some species are mixotrophic, and for other species we do not know whether they feed in addition to phototrophy. In *Amphidinium* s.s. for example we have pure heterotrophic but also photosynthetic and mixotrophic species. For these genera there is species level variation in trophic functions. Heterotrophic taxa are the species that have to feed on something, because they are not photosynthetic but we do not know what they feed on (only food bodies or vacuoles are visible but the content cannot be identified and the feeding process has not been recorded).

● Alveolata

●● Dinoflagellata

●●● Noctilucales

Abedinium *H*, Cachonodinium *H*, Craspedotella *H*, Cymbodinium *H*, Kofoidinium *C*, Leptodiscus *H*, Noctiluca *M C*, Petalodinium *H*, Pomatodinium *H*, Scaphodinium *H*, Spatulodinium *M H*.

●●● Dinophyceae

●●●● Gymnodiniphycidae

●●●●● Gymnodinium

Barrufeta **M C**, Dissodinium **L M C**, Erythropsidinium **C**,
Greuetodinium **C?**, Gymnodinium **L M**, Lepidodinium **L**,
Nematodinium **M C**, Nusuttodinium **M C**, Pellucidodinium **C**,
Polykrikos **C M**, Proterythropsis **C**, Warnowia **C**.

●●●●●● Amphidinium **L M C**.

●●●●● Gyrodinium C.

●●●●● Kareniaceae

Brachidinium *M*, Karenia *M B C*, Karlodinium *M B C*, Takayama *M C*.

●●●●●● Ceratoperidiniaceae

Ceratoperidinium *L*, Kirithra *L*.

●●●●●● Torodiniales

Kapelodinium *C*, Torodinium *M*.

●●●●●● Levanderina

Levanderina **M C**.

●●●●●● Margalefidinium

Margalefidinium **M C**.

●●●●●● Cochladinium

Cochladinium *strangulatum* *M*?

●●●●●● Ptychodiscales

Achradina *B*, Amphitolus, Balechina *H C?*, Ptychodiscus *L*,
Sclerodinium.

●●●●●● Borghiellaceae.

Baldinia **M C**, Borghiella *L*.

●●●●●● Tovelliaceae.

Bernardinium, Esopotrodinium **M C**, Jadwigia **L**, Tovellia **L M**.

●●●●●● Suessiaceae

(continued)
Ansanella L, Asulcocephalium L, Biecheleria M C, Biecheleriopsis L M, Leiocephalium L, Pelagodinium L, Polarella L, Prosoaulax M C, Protodinium, Symbiodinium L M B, Yihiella L M.

●●●●● Peridiniphycidae

●●●●●● Gonyaulacales

Alexandrium L M C, Amylax L M C, Ceratium L M C, Ceratocorys L, Coolia L, Fukuyoa L, Fragilidium

L M C, Gambierdiscus L M, Goniodoma L, Gonyaulax L M C,

Lingulodinium L M C, Ostreopsis L M,

Pentaplacodinium L, Peridiniella L, Protoceratium L M, Pyrocystis L,

Pyrodinium L, Pyrophacus L, Tripos L M C.

●●●●●● Peridiniales

Amphidiniopsis H C?, Archaeperidinium C, Blastodinium M, Diplopelta C, Diplopsalis C, Diplopsalopsis C, Herdmania H C?, Niea C, Oblea C, Palatinus L, Parvodinium L, Peridinium L, Peridiniopsis L C, Preperidinium C, Protoperidinium C, Qia C, Vulcanodinium L.

●●●●●● Thoracosphaeraceae

Aduncodinium C, Amyloodinium, Apocalathium, Blastodinium, Chimonodinium, Cryptoperidiniopsis M C, Duboscquodinium C, Ensiculifera L, Leonella, Luciella C, Naiadinium L M?, Paulsenella C, Pentapharsodinium L, Pfiesteria M C, Scrippsia L M C, Stoeckeria C, Theleodinium L M?, Thoracosphaera L, Tintinnophagus C, Tyrannodinium C.

●●●●●● Podolampadaceae

Blepharocysta C?, Gaarderiella, Heterobractum, Lissodinium, Mysticella, Podolampas M C.

●●●●●● Kryptoperidiniaceae

Blixaea L M, Durinskia L M, Galeidinium L M, Kryptoperidinium L M, Unruhdinium L.

●●●●●● Heterocapsaceae

Heterocapsa L M C.

●●●●●● Amphidomataceae

Amphidoma L, Azadinium L.

●●●●●● Oxytoxaceae.

Corythodinium M C?, Oxytoxum L M?

●●●●●● Centrodiniaceae

Centrodinium L

●●●●● Dinophysales

Amphisolenia L M, Citharistes M B, Dinofurcula H, Dinophysysis M C, Histioneis M B, Latifascia H, Metadinophysis L, Metaphalacroma H, Ornithocercus M B, Oxyphysis C, Parahistioneis M B, Phalacroma (M) C, Pseudophalacroma H, Sinophysysis H M?, B, Triposolenia M.

●●●●● Prorocentrales

Mesoporus L, Prorocentrum L M C.

●●●● Incertae sedis Dinoflagellata:

e.g., Adenoides L, Akashiwo M C, Amphidiniella L M, Ankistrodinium C, Apicoporus M C, Bispinodinium L M, Bysmatrum L M C, Cabra H C?, Cladopyxis, Crypthecodinium C, Cucumeridinium H, Dactylodinium L M, Dicroerisma H, Gloeodinium, Grammatodinium L M, Gynogonadinium, Gyrodiniellum C, Halostylodinium L, Heterodinium L?, Moestrupia L, Paragymnodinium M C, Phytodinium, Pileidinium L, Plagiodinium L, Planodinium H C?, Pseudadenoides L, Pseudothecadinium L, Pyramidodinium L, Roscoffia H C?, Rhinodinium H C?, Sabulodinium H, Sphaerodinium L, Spiniferodinium L M, Testudodinium L M, Thecadinium L M, Thecadiniopsis L, Togula L.

●●●● Incertae sedis Dinoflagellata [Blastodiniales Chatton 1906, no longer valid]. Amyloodinium*, Apodinium*, Cachonella, Crepidoodinium M, Haplozoon, Oodinium M, Piscinodinium M, Protoodinium M. *ectoparasites

APPENDIX 2, TABLE 2.2. TROPHIC FUNCTIONAL ASSIGNMENTS IN CILIOPPHORES

All genera feed on bacteria by filtration (B) except where noted. Omnivorous genera (O) ingest small protists in addition to bacteria. Those that are labelled cytrophic (C) need to ingest protists for growth, in addition to bacteria that are co-ingested. Many omnivores can occasionally ingest detritus (D). Those that feed on fungi (F) do so by digesting a small hole, while those that feed on other filaments (f) (Cyanobacteria and algae) do so by swallowing. Predators (P) are distinguished from those that obtain their food particles by filtration (the default state in ciliophores) or by grazing where noted. Histrophagous genera (P*) are distinguished from parasites (X) and commensals (*). Osmotrophic (S) genera feed extensively, or exclusively, by pinocytosis and other membrane transport mechanisms.

● Alveolata

●● Ciliophora

●●● Postodesmatophora

●●●● Karyorelictea

●●●●● Kentrophoridae(Kentrophoros) B

●●●●●● Loxodida

●●●●●●● Cryptopharyngidae (Cryptopharynx) O C

●●●●●●● Loxodidae (Loxodes) O C

●●●●● Geleiidae (Geleia) O C

●●●●● Heterotrichea

●●●●● Blepharismidae (Blepharisma) B

●●●●● Climacostomidae (Climacostomum) O

●●●●● Condylostomatidae (Chattonidium, Condylostoma) B

●●●●● Fabreidae (Fabrea) B

●●●●● Gruberiidae (Gruberia) B

●●●●● Coliphorina

●●●●●● Folliculinidae (Folliculina) B

●●●●●● Maristentoridae (Maristentor) O

●●●●●● Peritromidae (Peritromus) B

●●●●● Spirostomidae (Anigsteinia, Spirostomum) B

●●●●● Stentoridae (Stentor) O or C or P

●●● Intramacronucleata

●●●● SAL

Incertae sedis SAL: Mesodiniidae (Mesodinium)

Incertae sedis SAL: Phacodinium

●●●●●● Spirotrichea

●●●●●● Euplotia

●●●●●●● Euplotida

●●●●●●●● Aspidiscidae (Aspidisca) O

●●●●●●●● Certesiidae (Certesia) O

●●●●●●●● Euplotidae (Euplotes) O

●●●●●●●● Gastrocirrhidae (Gastrocirrhus) O

●●●●●●●● Uronychidae (Diophrys, Uronychia) O

●●●●●●●● Discocephalida

●●●●●●●● Discocephalidae(Discocephalus, Prodiscocephalus, Paradiscocephalus) O

●●●●●●●● Pseudoamphisiellidae (Leptoamphisiella, Pseudoamphisiella) O

●●●●●●●● Perilemmaphora

●●●●●●●● Hypotrichia

(continued)
●●●●●●●● Pseudogemmidae (Pseudogemma) C P
●●●●●●●● Rhynchetidae (Rhyncheta) C P
●●●●●●●● Solenophryidae (Solenophrya) C P
●●●●●●●● Tokophryidae (Tokophrya) C P
●●●●●●●● Trichophryidae (Trichophrya) C P
●●●●●●●● Evaginogenida
●●●●●●●● Cometodendridae (Cometodendron) C P
●●●●●●●● Cyathodiniidae (Cyathodinium) C P
●●●●●●●● Dendrocometidae (Dendrocometes) C P
●●●●●●●● Discophryidae (Discophrya) C P
●●●●●●●● Enchelyomorphidae (Enchelyomorpha) C P
●●●●●●●● Heliophryidae (Heliophrya) C P
●●●●●●●● Periacinetidae (Periacinetia) C P
●●●●●●●● Prodiscophryidae (Prodiscophrya) C P
●●●●●●●● Rhynchophryidae (Rhynchophrya) C P
●●●●●●●● Stylocometidae (Stylocometes) C P
●●●●●●●● Trypanococcidae (Trypanococcus) C P

●●●●● Colpodea

●●●●●●●● Bursariomorphida

●●●●●●●● Bryometopidae (Bryometopus, Thylakidium) P

●●●●●●●● Bursaridiidae (Bursaridium, Paracondylostoma) P

●●●●●●●● Bursariidae (Bursaria) P

●●●●●●●● Colpodida (smaller species <20 µm are probably ingesting primarily bacteria)

Incertae sedis Colpodida: Bardeliellidae, Hausmanniellidae, IIsiellidae, Marynidae, Pseudochlamydonellidae. O

●●●●●●●● Bryophryina

●●●●●●●● Bryophryidae (Bryophrya) O

●●●●●●●● Sandmanniellidae (Sandmanniella) O

●●●●●●●● Colpodina

●●●●●●●● Colpodidae (Colpoda) O

●●●●●●●● Grandoriidae (Grandoria) O

●●●●●●●● Tillinidae (Tillina) O

●●●●●●●● Grossglockneriidae (Grossglockneria, Pseudoplatyophrya) F

●●●●●●●● Cyrtolophosidida

●●●●●●●● Cyrtolophosididae (Cyrtolophosis) O

●●●●●●●● Kreyellidae (Kreyella) O

●●●●●●●● Platyophryida (C ingest small green algae)

●●●●●●●● Ottowphryidae (Ottowphrya, Platyophryides) C

●●●●●●●● Platyophryidae (Platyophrya) C

●●●●●●●● Sagittariidae (Sagittaria) C

●●●●●●●● Sorogenidae (Sorogenia) C

●●●●●●●● Woodruffiidae (Etoschophrya, Rostrophrya, Woodruffia) C

●●●●● Nassophorea

●●●●●●●● Colpodidiidae (Colpodidium) B

●●●●●●●● Nassulida (f, cyanobacteria)

●●●●●●●● Furgasoniidae (Furgasonia, Wolfkosia) f

●●●●●●●● Nassulidae (Nassula, Obertrumia) f

●●●●●●●● Microthoracida

●●●●●●●● Microthoracidae (Drepanomonas, Microthorax) f

●●●●●●●● Leptopharyngidae (Pseudomicrothorax, Leptopharynx) B) f

●●●●●●●● Prostomatea

●●●●●●●● Apsiktratidae (Apsikrata) O

●●●●●●●● Prorodontida

●●●●●●●● Balanionidae (Balanion) C D

●●●●●●●● Cryptocaryonidae (Cryptocaryon) C D

●●●●●●●● Colepidae (Coleps, Plagiopogon) C D

●●●●●●●● Holophryidae (Holophrya) C D

●●●●●●●● Lagynidae (Lagynus) C D

●●●●●●●● Metacystidae (Metacystis, Vasicola) C D

●●●●●●●● Placidae (Placus) C D

●●●●●●●● Plagiocampidae (Plagiocampa) C D

●●●●●●●● Prorodontidae (Prorodon) C D

●●●●●●●● Urotrichidae (Urotricha) C D

●●●●● Plagiopylea

●●●●● Plagiopylida

●●●●●●●● Epalxelliidae (Epalxella) B

●●●●●●●● Plagiopylidae (Plagiopyla) B

●●●●●●●● Sonderiidae (Sonderia) B

●●●●●●●● Trimyemidae (Trimyema) B

●●●●●●●● Oligohymenophorea

●●●●●●●● Apostomatia

●●●●●●●● Apostomatida

●●●●●●●● Colliniidae (Collinia, Metacollinia) S

●●●●●●●● Cyrtocaryidae (Cyrtocaryum) S

●●●●●●●● Foettingeriidae (Foettingeria) S

●●●●●●●● Pseudocolliniidae (Fusiforma, Pseudocollinia) S

●●●●●●●● Astomatophorida

●●●●●●●● Opalinopsidae (Opalinopsis) S

●●●●●●●● Pilisuctorida

●●●●●●●● Conidophryidae (Conidophrys) S

●●●●●●●● Astomatia

●●●●●●●● Anoplophryidae 910 (Anoplophrya) S

●●●●●●●● Buetschliellidae (Buetschliella) S

●●●●●●●● Clausilocolidae (Clausilocola) S

●●●●●●●● Contophryidae (Contophrya) S

●●●●●●●● Haptophryidae (Haptophrya) S

●●●●●●●● Hoplitophryidae (Hoplitophrya) S

●●●●●●●● Intoshellinidae (Intoshellina) S

●●●●●●●● Maupasellidae (Maupasella) S

●●●●●●●● Radiophryidae (Radiophrya) S

●●●●●●●● Hymenostomatia

●●●●●●●● Tetrahymenida (verify each species life cycle, macrostome stage is C)

Incertae sedis Tetrahymenida: Trichospiridae (Trichospira) B P*

●●●●●●●● Curimostomatidae (Curimostoma) B P*

●●●●●●●● Glaucomidae (Glaucoma) B P*

●●●●●●●● Spirozoniidae (Spirozona) B P*

●●●●●●●● Tetrahymenidae (Tetrahymena) B P*

●●●●●●●● Turaniellidae (Colpidium, Dexiostoma, Turaniella) B P*

●●●●●●●● Ophryoglenida

●●●●●●●● Ichthyophthiriidae (Ichthyophthirius) P* P

●●●●●●●● Ophryoglenidae (Ophryoglena) P* P

●●●●●●●● Peniculida

●●●●●●●● Peniculida

●●●●●●●● Clathrostomatidae (Clathrostoma) O

●●●●●●●● Frontoniidae (Disematostoma, Frontonia) O

●●●●●●●● Lembadionidae (Lembadion) O

●●●●●●●● Maritujiidae (Marituja) O

●●●●●●●● Neobursaridiidae (Neobursaridium) O

●●●●●●●● Parameciidae (Paramecium) O

●●●●●●●● Paranassulidae (Paranassula) O

●●●●●●●● Stokesiidae (Stokesia) O

●●●●●●●● Urocentriidae (Urocentrum) O

(continued)

(continued)
Peritrichia
Sessilida
Astylozoidae (Astylozoon, Hastatella) O
Ellobiophryidae (Ellobiophrya) O
Epistylididae (Epistylis) O
Lagenophryidae (Lagenophrys) O
Operculariidae (Opercularia) O
Rovinjellidae (Rovinjella) O
Scyphidiidae Kahl, 133 (Scyphidia) O
Termitophryidae (Termitophrya) O
Usconophryidae (Usconophrys) O
Vaginicolidae (Cothurnia, Pyxicola, Thuricola, Vaginicola) O
Vorticellidae (Carchesium, Vorticella) O
Zoothamniidae (Haplocaulus, Zoothamnium) O
Mobilida
Polycyclidae (Polycycla) O
Trichodinidae (Trichodina) O
Trichodinopsidae (Trichodinopsis) O
Urceolariidae (Leiotrocha, Urceolaria) O
Scuticociliatia
Philasterida
Cohnilembidae (Cohnilembus) O
Cryptochilidae (Cryptochilum.) O
Entodiscidae (Entodiscus) O
Entorhipidiidae (Entorhipidium) O
Orchitophryidae (Orchitophrya) O
Paralembidae (Anophrys, Paralembus) O

(continued)

Parauronematidae (Parauronema) O
Philasteridae (Kahlilembus, Philaster) O
Pseudocohnilembidae (Pseudocohnilembus) O
Schizocaryidae (Schizocaryum) O
Thigmophryidae (Thigmophrya) O
Thyrophylacidae (Thyrophylax) O
Uronematidae (Uronema) C
Urozonidae (Urozona) O
Pleuronematida
Calyptotrichidae (Calyptotricha) O
Conchophthiridae (Conchophthirus) O
Ctedoctematidae (Ctedoctema) O
Cyclidiidae (Cristigera, Cyclidium) O
Dragescoidae (Dragescoa) O
Eurystomatellidae (Eurystomatella) O
Histiobalantiidae (Histiobalantium) O
Peniculomatidae (Peniculistoma) O
Pleuronematidae (Pleuronema) O
Thigmocomidae (Thigmocoma) O
Thigmotrichida
Ancistridae (Ancistrum) B
Hemispeiridae (Hemispeira) B
Hysterocinetidae (Hysterocineta) B
Paraptychostomidae (Paraptychostomum) B
Loxocephalida
Cinetochilidae (Cinetochilum, Sathrophilus) B
Loxocephalidae (Cardiostomatella, Dexiotricha, Loxocephalus) B

APPENDIX 3. TABLE 3.1.

<table><caption>Protist names and common names for East Asian translations</caption><thead><tr><th>Higher level ranks and supergroups</th><th>Phylum</th><th>Important sub-divisions in Chinese characters</th><th>Common name translation</th></tr></thead><tbody><tr><td rowspan="5">Amoebozoa</td><td rowspan="3">Tubulinea</td><td>Corycida (皮殼葉狀根足綱) 皮壳管狀根足綱</td><td>Leathery-shell amoebae</td></tr><tr><td>Echinamoebida (多針葉狀根足綱) 多針管狀根足綱</td><td>Amoebae with spiny pseudopodia</td></tr><tr><td>Elardia (三組葉狀根足綱) 三組管狀根足綱</td><td>Amoeboid group including three groups (Euamoebida, Leptomyxida, Arcellinida)</td></tr><tr><td></td><td>Arcellinida (有殼葉狀變形綱) 有壳管狀根足綱</td><td>Testate amoebae partially enclosed in a simple shell</td></tr><tr><td>Evosea</td><td>Variosea (多圓錐型 根足綱) 多圓錐型根足綱</td><td>Amoebae with many conical-shaped pseudopodia</td></tr><tr><td rowspan="5">Incertae sedis Holozoa</td><td rowspan="5">Discosea</td><td>Eumycetozoa (真菌根足綱) 真粘菌根足綱</td><td>Genuine (mushroom) slime mold amoebae</td></tr><tr><td>Cutosea (真皮根足綱) 真皮根足綱</td><td>Amoebae with a discrete skin</td></tr><tr><td>Archamoebea (原始根足綱) 古变形綱</td><td>Ancient (first) amoebae</td></tr><tr><td>Stygamoebida (細片根足綱) 細片根足綱</td><td>Amoebae with pseudopodia resembling tooth-pick or splinters</td></tr><tr><td>Filasterea (星狀絲足綱) 星狀絲足綱</td><td>Centrosome-bearing amoebae</td></tr><tr><td></td><td></td><td></td><td>Rounded amoebae with pseudopodia like fingers</td></tr><tr><td rowspan="7">Nuclemycea</td><td rowspan="7">Opisthosporidia</td><td>Ichtyosporea (孢子型魚病根足綱) 孢子型魚病根足綱</td><td>Fish pathogenic amoebae forming a spore</td></tr><tr><td>Choanoflagellata (立襟鞭毛綱) 風鞭毛綱</td><td>Flagellates with a collar-like ring</td></tr><tr><td>Demospongiae (普通海綿綱) 普通海綿綱</td><td>Common sponges</td></tr><tr><td>Homoscleromorpha (同骨海綿綱) 同骨海綿綱</td><td>Sponge with undifferentiated cytoskeleton</td></tr><tr><td>Calcarea (石灰海綿綱) 石灰海綿綱</td><td>Chalk sponges</td></tr><tr><td>Hexactinellida (玻璃海綿綱) 玻璃海綿綱</td><td>Glass sponges</td></tr><tr><td>Aphelidea (藻寄生性根足綱) 藻寄生性根足綱</td><td>Amoeboid endobiotic parasitoids of algae</td></tr><tr><td></td><td></td><td></td><td>Primitive fungus-like parasite</td></tr><tr><td></td><td></td><td></td><td>Fungi having a thick-walled resting spore</td></tr></tbody></table>

(continued)
APPENDIX 3. (continued)

<table><thead><tr><th>Higher level ranks and supergroups</th><th>Phylum</th><th>Important sub-divisions in Chinese characters</th><th>Common name translation</th></tr></thead><tbody><tr><td rowspan="14">Bigyra</td><td rowspan="14">Rhodophyceae</td><td>Neocallimastigaceae (新多鞭毛菌綱) 新美鞭菌綱</td><td>New fungi having many/pretty flagella</td></tr><tr><td>Chytridiomycota (壺狀菌綱) 壶菌綱</td><td>Fungi resembling a broken-cracked egg</td></tr><tr><td>Mucoromycota (粘液菌綱) 粘液菌綱</td><td>Mucoid or sugar fungi</td></tr><tr><td>Zoopagomycota (動物生菌綱) 捕虫霉綱</td><td>Fungi growing on animals, Fungi able to catch bugs</td></tr><tr><td>Taphrinomycotina (外囊菌綱) 外囊菌綱</td><td>Fungi having an outer ascus</td></tr><tr><td>Saccharomycetales (酵母菌綱) 酵母菌綱</td><td>Fungi associated with fermentation</td></tr><tr><td>Pezizomycotina (周鉢菌綱) 盤菌綱</td><td>(Bowl-shaped fungi), plate-shaped fungi</td></tr><tr><td>Agaricomycotina (擔子菌綱) 担子菌綱</td><td>Fungi forming a stergma</td></tr><tr><td>Pucciniomycotina (銹菌綱) 柄锈菌綱</td><td>Fungi with stem and is associated with rust disease</td></tr><tr><td>Ustilaginomycotina (黑穗菌綱) 黑穗菌綱</td><td>Fungi associated with smut disease</td></tr><tr><td>Wallemiomy cotina (無子實體菌綱) 无子实体菌綱</td><td>Fungi without palisade of basidia</td></tr><tr><td>Proteorhodophytina (原始紅藻綱) 原始紅藻綱</td><td>Primitive red algae</td></tr><tr><td>Eurhodophytina (真正紅藻綱) 真红藻綱</td><td>Genuine red alage, which have two phases or three phases</td></tr><tr><td>Chloroplastida</td><td>Chlorophyta (綠藻綱) 绿藻綱</td><td>Green algae</td></tr><tr><td></td><td>Charophyta (輪藻綱) 轮藻綱</td><td>Wheel-shaped green algae</td></tr><tr><td></td><td>Nanomonadea (矮小鞭毛綱) 微小鞭毛綱</td><td>Tiny brown flagellates</td></tr><tr><td></td><td>Opalinat (皮下共生鞭毛綱) 蛙片虫綱</td><td>Animal endobionts; Flagellates mostly found in frog, with a flat shape like a slice</td></tr><tr><td></td><td>Placidida (小突起鞭毛綱) 小突起鞭毛綱</td><td>Flagellate having a papilla</td></tr><tr><td></td><td>Bicosoecida (毫髮鞭毛綱) 毫发鞭毛綱</td><td>Flagellates having tiny flagellar hairs</td></tr><tr><td></td><td>Labyrinthulomycetes (網形鞭毛綱) 网丝鞭毛綱</td><td>Gliding flagellates producing a network of filaments</td></tr><tr><td rowspan="14">Gyrista</td><td rowspan="14">Diatomeae</td><td>Pseudophyllomitidae (非附着鞭毛綱) 无附着鞭毛綱</td><td>Flagellates lacking the two adhering flagella</td></tr><tr><td>Developea (後固着鞭毛綱) 后附鞭毛綱</td><td>Flagellates with adhering posterior flagellum</td></tr><tr><td>Hyphochytriales (菌絲體鞭毛綱) 菌丝体鞭毛綱</td><td>Flagellates having hypha-like structures</td></tr><tr><td>Peronosporomycetes (植物病原體擬菌綱) 植病拟菌綱</td><td>Fungus-like plant pathogens</td></tr><tr><td>Pirsoniales (硅藻寄生綱) 硅藻寄生綱</td><td>Diatom parasites</td></tr><tr><td>Actinophryidae (太陽綱) 太阳綱</td><td>Sunlight (or star light)-shaped protozoa</td></tr><tr><td>Chrysophyceae (黃褐藻綱) 金藻綱</td><td>Golden brown algae</td></tr><tr><td>Eustigmatales (真眼點褐藻綱) 真眼点褐藻綱</td><td>Brown algae with a big eye spot</td></tr><tr><td>Phaeophyceae (大褐藻綱) 褐藻綱</td><td>The large brown algae</td></tr><tr><td>Phaeothamniophyceae (黄赤藻綱) 褐枝藻綱</td><td>Yellow-red algae with branches</td></tr><tr><td>Raphidophyceae (針鞭毛藻綱) 针胞藻綱</td><td>Algae with needle shaped flagellum</td></tr><tr><td>Xanthophyceae (黃綠藻綱) 黄绿藻綱</td><td>Yellow-green algae</td></tr><tr><td>Bolidomonas (迅游泳藻綱) 迅游藻綱</td><td>Diatom-like algae with rapid swimming</td></tr><tr><td>Diatomeae (硅褐藻綱) 硅褐藻綱</td><td>Brown algae like glass box with lid</td></tr><tr><td>Dictyochophyceae (硅質鞭毛藻綱) 硅鞭藻綱</td><td>Algae producing a siliceous skeleton</td></tr><tr><td>Pelagophyceae (浮生褐藻綱) 浮生褐藻綱</td><td>Filamentous brown algae living in the sea; brown algae living a planktonic habitat</td></tr><tr><td>Pinguiophyceae (脂褐藻綱) 脂褐藻綱</td><td>Brown algae containing (a high concentration of) fatty acids</td></tr><tr><td>Incertae sedis Alveolata</td><td>Colpodellida (捕食性鞭毛綱) 捕食鞭毛綱</td><td>Predatory flagellates</td></tr><tr><td rowspan="3">Dinoflagellata</td><td>Syndiniales (共生性渦鞭毛藻綱) 共生渦鞭藻綱</td><td>Parasitic dinoflagellates, symbiotic dinoflagellates</td></tr><tr><td>Noctilucales (夜光藻綱) 夜光藻綱</td><td>Algae with bioluminescence</td></tr><tr><td>Dinophyceae (渦鞭毛藻綱) 涡鞭藻綱</td><td>Algae with spiraling motility, algal flagellates with a spiral or girdle groove</td></tr><tr><td>Apicomplexa</td><td>Aconoidasida (無圓錐頂端複合體綱) 无圆锥体顶复纲</td><td>Apicomplexa lacking a conoid</td></tr><tr><td rowspan="4">Ciliophora</td><td>Conoidasida (圓錐頂端複合體綱) 圆锥体顶复纲</td><td>Apicomplexa possessing a conoid</td></tr><tr><td>Karyorelictea (核殘跡纖毛綱) 核残迹纤毛綱</td><td>Ciliophores having relict of parents' macronuclei</td></tr><tr><td>Heterotrichea (異毛纖毛綱) 异毛纤毛綱</td><td>Ciliophores with different length of flagella</td></tr><tr><td>Spirotrichea (型 旋纖毛綱) 旋唇纤毛綱</td><td></td></tr></tbody></table>

(continued)
APPENDIX 3. (continued)

<table><thead><tr><th>Higher level ranks and supergroups</th><th>Phylum</th><th>Important sub-divisions in Chinese characters</th><th>Common name translation</th></tr></thead><tbody><tr><td></td><td></td><td>Armophorea (鬚帽纖毛綱) 盎帽纤毛纲</td><td>Ciliophores with spiraling adoral zone of membranelles</td></tr><tr><td></td><td></td><td>Litostomatea (裂口纖毛綱) 裂口纤毛纲</td><td>Ciliophores having the appearance of military helmets</td></tr><tr><td></td><td></td><td>Phyllopharyngea (葉咽纖毛綱) 叶咽纤毛纲</td><td>Ciliophores with a cytostome with oral dome</td></tr><tr><td></td><td></td><td>Colpodea (腎形纖毛綱) 腎形纤毛纲</td><td>Ciliophores with a leaf-shaped cytopharynx</td></tr><tr><td></td><td></td><td>Prostomatea (前口纖毛綱) 前口纤毛纲</td><td>Ciliophores with a kidney shape</td></tr><tr><td></td><td></td><td>Plagiopylea (斜毛纖毛綱) 斜毛纤毛纲</td><td>Ciliophores with cytostome at the anterior pole</td></tr><tr><td></td><td></td><td>Oligohymenophorea (貧膜纖毛綱) 寡膜纤毛纲</td><td>Ciliophores with oblique slit flagella</td></tr><tr><td></td><td></td><td>Nassophorea (籃口纖毛綱) 篮口纤毛纲</td><td>Ciliophores with a small paroral membrane</td></tr><tr><td></td><td></td><td></td><td>Ciliophores showing a basket-shaped oral structure</td></tr><tr><td>Cercozoa</td><td></td><td>Silicofilosea (硅質絲狀根足綱) 硅质丝足纲</td><td>Filose amoebae covered by siliceous or glass scales, vase-shaped shell</td></tr><tr><td>Foraminifera</td><td></td><td>Monothalamea (單房室有孔綱) 单房室有孔纲</td><td>Foraminiferans with single chamber test</td></tr><tr><td></td><td></td><td>Tubothalamea (管狀有孔綱) 管狀有孔纲</td><td>Foraminiferans with tubular chamber test</td></tr><tr><td></td><td></td><td>Lagenida (單層有孔綱) 瓶狀有孔纲</td><td>Foraminiferans with monolamellar test</td></tr><tr><td>Radiolaria</td><td></td><td>Acantharia (放射棘綱) 等辐骨纲</td><td>Protozoa with axopods and filopodia; protist with radiated spicula of same length</td></tr><tr><td></td><td></td><td>Polycystinea (多孔囊綱) 多孔纲</td><td>Protozoa (with a sac) covered by many pores</td></tr><tr><td>Metamonada</td><td></td><td>Fornicata (拱門形纖維綱) 拱形纤维纲</td><td>Protozoa with an arched B-fiber</td></tr><tr><td></td><td></td><td>Parabasalia (副基体綱) 副基体纲</td><td>Protozoa with one or more parabasal apparatus</td></tr><tr><td></td><td></td><td>Preaxostyla (二重纖維綱) 二重纤维纲</td><td>Protozoa with I-fiber with double-cross matrix</td></tr><tr><td>Discoba</td><td></td><td>Jakobida (單背翼綱) 单背翼纲</td><td>Protozoa with a single dorsal vane in the posterior flagellum</td></tr><tr><td></td><td></td><td>Heterolobosea (噴出形根足綱) 异叶足纲</td><td>Amoebae with eruptive pseudopodia; amoebae with differentiated leaf-shaped pseudopodia</td></tr><tr><td>Euglenozoa</td><td></td><td>Kinetoplastid (運動核質鞭毛類) 动质体纲</td><td>Protozoa with kinetoplast</td></tr><tr><td></td><td></td><td>Euglenid (軟豆鞭毛類) 软豆鞭毛类</td><td>Yellow-green flagellates</td></tr><tr><td>Haptophyta</td><td></td><td>Prymnesiophyceae (碳酸鑛物化藻綱) 碳酸质鳞片藻纲</td><td>Algae with CO₂-mineralized scales</td></tr><tr><td></td><td></td><td>Coccolithophorid (圓石藻類) 颗石藻类</td><td>Haptophyte with calcareous (chalk) scales</td></tr><tr><td>Centroplasthelida</td><td></td><td>Pterocystida (無外骨格鞭毛綱) 无外骨骼鞭毛纲</td><td>Protozoa without any exoskeletal elements</td></tr><tr><td></td><td></td><td>Panacanthocystida (石鱗鞭毛綱) 石鱗鞭毛纲</td><td>Protozoa with siliceous scales or with organic spicules</td></tr><tr><td>Cryptista</td><td></td><td>Cryptophyceae (隱鞭毛藻型) 隐藻纲</td><td>New algae with prominent ejectisomes; cryptic algae</td></tr></tbody></table>