2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | pre-2015


Salas-Leiva, D.E., Tromer, E., Curtis, B., Jerlström Hultqvist, J., Kolisko, M., Yi, Z., Salas-Leiva, J., Gallot-Lavallee, L., Williams, S., Kops, G., Archibald, J.M, Simpson, A.G.B & Roger, A.J. (2021) Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist. Nature Communications. 12: 6003. doi.org/10.1038/s41467-021-26077-2

More, K. Simpson, A.G.B. & Hess, S. (2021) Description of the marine predator Sericomyxa perlucida gen. et sp. nov., a cultivated representative of the deepest branching lineage of vampyrellid amoebae (Vampyrellida, Rhizaria). Journal of Eukaryotic Microbiology. 68: e12864. doi:10.1111/jeu.12864

Rybarski, A.E., Nitsche, F., Park, J.S., Filz, P., Schmidt, P., Kondo, R., Simpson, A.G.B., Arndt, H. (2021) Revision of the phylogeny of Placididea (Stramenopiles): Molecular and morphological diversity of novel placidid protists from extreme aquatic environments. European Journal of Protistology. 81: 125809. doi:10.1016/j.ejop.2021.125809

Lax, G., Kolisko, M., Eglit, Y., Lee, W.J., Yubuki, N., Karnkowska, A., Leander, B.S., Burger, G., Keeling, P.J., Simpson, A.G.B. (2021). Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs. Molecular Phylogenetics and Evolution. 159: 107088 doi:10.1016/j.ympev.2021.107088

Ettahi, K., Lhee, D.H., Sung, J.Y., Simpson, A.G.B., Park, J.S. & Yoon, H.S. (2021) Evolutionary history of mitochondrial genomes in Discoba, including the extreme halophile Pleurostomum flabellatum (Heterolobosea). Genome Biology and Evolution. 13: evaa241 doi:10.1093/gbe/evaa241

Heiss, A.A., Warring, S.D., Lukacs, K., Favate, J., Yang, A., Gyaltshen, Y., Filardi, C., Simpson, A.G.B., Kim, E. (2021) Imasa heleensis gen. nov. sp. nov., a deep-branching marine malawimonad and possible key taxon in understanding early eukaryotic evolution. Journal of Eukaryotic Microbiology. 68: e12837 doi:10.1111/jeu.12837


Lax, G., Simpson, A.G.B. (2020) The molecular diversity of phagotrophic euglenids examined using single-cell methods. Protist. 171: 125757. doi:10.1016/j.protis.2020.125757

Yazaki, E., Kume, K., Shiratori, T., Eglit, Y., Tanifuji, G., Harada, R., Simpson, A.G.B., Ishida, K., Hashimoto, T., Inagaki, Y. (2020) Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP. Proceedings of the Royal Society, Series B. 287: 20201538. doi:10.1098/rspb.2020.1538

Kolisko, M. Flegontova, O., Karnkowska, A., Lax, G., Maritz, J.M., Pánek, T., Táborský, P. Carlton, J.M., Čepička, I., Horák, A., Lukeš, J., Simpson, A.G.B., Tai, V. (2020) EukRef-Excavates: Seven curated SSU ribosomal RNA gene databases. Database 2020: baaa80. doi:10.1093/database/baaa080

Burki F.*, Roger A.J., Brown M.W., Simpson A.G.B.* (2020) The new tree of eukaryotes. Trends in Ecology and Evolution. 35: 43-55. doi:10.1016/j.tree.2019.08.008


Hess S., Eme L., Roger A.J., Simpson A.G.B. (2019) A natural toroidal microswimmer with a rotary eukaryotic flagellum. Nature Microbiology. 4: 1620-1626. doi:10.1038/s41564-019-0478-6

Galindo L.J., Torruella G., Moreira D., Eglit Y., Simpson A.G.B., Völcker E., Clauß S., López-García P. (2019) Combined cultivation and single-cell approaches to the phylogenomics of nucleariid amoebae, close relatives of Fungi. Philosophical Transactions of the Royal Society, Series B. 374: 20190094. doi:10.1098/rstb.2019.0094

Wideman J.G.*, Lax G.*, Leonard G., Milner D., Simpson A.G.B., Richards T.A. (2019) A single-cell genome reveals diplonemid-like ancestry of kinetoplastid mitochondrial gene structure. Philosophical Transactions of the Royal Society, Series B. 374: 20190100. doi:10.1098/rstb.2019.0100

Frail-Gauthier, J.L., Mudie, P.J., Simpson, A.G.B., Scott, D.B. (2019) Mesocosm and microcosm experiments on the feeding of temperate salt marsh foraminifera. Journal of Foraminiferal Research. 49: 259-274. doi.org/10.2113/gsjfr.49.3.259

Lax G., Lee W.J., Eglit Y., Simpson A.G.B. (2019) Ploeotids represent much of the phylogenetic diversity of euglenids. Protist. 170:233–257. doi.org/10.1016/j.protis.2019.03.001

More, K., Simpson, A.G.B., Hess, S. (2019) Two new marine species of Placopus (Vampyrellida, Rhizaria) that perforate the theca of Tetraselmis (Chlorodendrales, Viridiplantae). Journal of Eukaryotic Microbiology. 66: 560–573. doi:10.1111/jeu.12698


Lax, G.*, Eglit, Y.*, Eme, L.*, Roger, A.J., Simpson, A.G.B. (2018) Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes. Nature. 564:410–414. doi.org/10.1038/s41586-018-0708-8

Buchwald, R., Scheibling, R.E., Simpson, A.G.B. (2018) Detection and quantification of a keystone pathogen in a coastal marine ecosystem. Marine Ecology Progress Series. 606:79–90.

Goodwin, J.D., Lee, T.F., Kugrens, P., Simpson, A.G.B. (2018) Allobodo chlorophagus n. gen n. sp, a kinetoplastid that infiltrates and feeds on the invasive alga Codium fragile. Protist. 169:911–925.

Harding, T., Simpson, A.G.B. (2018) Recent advances in halophilic protozoa research. Journal of Eukaryotic Microbiology. 65:556–570.

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. Royal Society Open Science, 10:171707.

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 as deep sisters to Amorphea and identifies a novel eukaryotic super-group. Genome Biology and Evolution, 10:427–433.


Yang, J., Harding, T., Kamikawa, R., Simpson, A.G.B., Roger A.J. (2017) Mitochondrial genome evolution and a novel RNA editing system in deep-branching heteroloboseids. Genome Biology and Evolution, 9:1161–1174.

Harding, T., Roger, A.J., Simpson, A.G.B. (2017) Adaptations to high salt in a halophilic protist: Differential expression and gene acquisitions through duplications and gene transfers. Frontiers in Microbiology, 8:944.

Leger, M.M.*, Kolisko, M.*, Kamikawa, R.*, Stairs, C.W., Kume, K., Čepicka, I., Silberman, J.D., Andersson, J.O., Xu, F. Yabuki, A., Eme, L., Zhang, Q., Takishita, K., Inagaki, Y., Simpson, A.G.B., Hashimoto, T., Roger, A.J. (2017) Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes. Nature Ecology and Evolution, 1:0092.

Simpson, A.G.B., Slamovits, C., Archibald, J.M. (2017) Protist diversity and eukaryote phylogeny. in Archibald, J.M., Simpson, A.G.B. & Slamovits C. (eds.) Handbook of the Protists, 2nd edition. Springer

Simpson, A.G.B. (2017) Jakobida. in Archibald, J.M., Simpson, A.G.B. & Slamovits C. (eds.) Handbook of the Protists, 2nd edition. Springer

Heiss, A.A., Brown, M.W., Simpson, A.G.B. (2017) Apusomonadida. in Archibald, J.M., Simpson, A.G.B. & Slamovits C. (eds.) Handbook of the Protists, 2nd edition. Springer

Panek, T., Simpson, A.G.B., Brown, M.W., Dexter Dyer B. (2017) Heterolobosea. in Archibald, J.M., Simpson, A.G.B. & Slamovits C. (eds.) Handbook of the Protists, 2nd edition. Springer

Leander, B.S., Lax, G., Karnkowska, A., Simpson, A.G.B., (2017) Euglenida. in Archibald, J.M., Simpson, A.G.B. & Slamovits C. (eds.) Handbook of the Protists, 2nd edition. Springer


Novák, L., Zubáčová, Z., Karnkowska, A. Kolisko, M., Hroudová, M., Stairs, C.W., Simpson, A.G.B., Keeling, P.J., Roger, A.J., Čepička, I., Hampl, V. (2016) Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes. BMC Evolutionary Biology, 16:197.

Simpson, A.G.B., Eglit, Y. (2016) Protist Diversification. Pp 344–360 in Kliman, R.M. (ed.) Encyclopedia of Evolutionary Biology, Volume 3. Elsevier.

Xu, F., Jerlström-Hultqvist, J., Kolisko, M., Simpson, A.G.B., Roger, A.J., Svärd, S.G., Andersson, J.O. (2016) On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1. BMC Biology, 14:62.

Harding, T., Brown, M., Simpson, A.G.B., Roger, A.J. (2016) Osmoadaptive strategy and its molecular signature in obligately halophilic heterotrophic protists. Genome Biology and Evolution, 8:2241–2258.

Park, J.S., Simpson, A.G.B. (2016) Characterization of a deep-branching heterolobosean, Pharyngomonas turkanaensis n. sp., isolated from a non-hypersaline habitat, and ultrastructural comparison of cysts and amoebae among Pharyngomonas strains. Journal of Eukaryotic Microbiology, 63:100–111.


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 lineage within Preaxostyla, separate from other known trimastigids (Paratrimastix n. gen.). Protist, 166:468–491.

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.). Journal of Eukaryotic Microbiology, 62:637–649.

Park, J.S., Simpson, A.G.B (2015) Diversity of heterotrophic protists from extremely hypersaline habitats. Protist, 166:422–437.

Buchwald, R.T., Feehan, C.J., Scheibling, R.E., Simpson, A.G.B. (2015) Low temperature tolerance of a sea urchin pathogen: implications for benthic community dynamics in a warming ocean. Journal of Experimental Marine Biology and Ecology, 469:1–9.

Kirby, W.A., Tikhonenkov, D.V., Mylnikov, A.P., Janouškovec, J., Lax, G., Simpson, A.G.B. (2015) Characterisation of Tulamoeba bucina n. sp., an extremely halotolerant amoeboflagellate heterolobosean belonging to the Tulamoeba-Pleurostomum clade (Tulamoebidae n. fam.). Journal of Eukaryotic Microbiology, 62:227–238.


Lee, W.J. & Simpson, A.G.B. (2014) Morphological and molecular characterisation of Notosolenus urceolatus Larsen and Patterson 1990, a member of an understudied deep-branching euglenid group (petalomonads). Journal of Eukaryotic Microbiology, 61:463–479.

Keeling, P.J., … Simpson, A.G.B., … & Worden, A.Z. (81 authors) (2014) The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biology, 12:e1001889.

Pánek, T., Simpson, A.G.B., Hampl, V. & Čepička, I. (2014) Creneis carolina gen. et sp. nov. (Heterolobosea), a novel marine anaerobic protist with strikingly derived morphology and life cycle. Protist, 165:542–567.

Lee, W.J. & Simpson, A.G.B. (2014) Ultrastructure and molecular phylogenetic position of Neometanema parovale sp. nov. (Neometanema gen. nov.), a marine phagotrophic euglenid with skidding motility. Protist, 165:452–472.

Lee, W.J., Miller, K. & Simpson, A.G.B. (2014) Morphological and molecular characterisation of a new species of Stephanopogon, Stephanopogon pattersoni n. sp. Journal of Eukaryotic Microbiology, 61:389–398.


Lax, G. & Simpson, A.G.B. (2013) Combining molecular data with classical morphology for uncultured phagotrophic euglenids (Excavata); A single-cell approach. Journal of Eukaryotic Microbiology, 60:615–625.

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. Proceedings of the Royal Society, series B 280:20131755.

Kamikawa, R., Brown, M.W., Nishimura Y., Sako, Y., Heiss, A.A., Yubuki, N., Gawryluk, R., Simpson, A.G.B., Roger, A.J., Hashimoto, T., Inagaki, Y. (2013) Parallel re-modeling of EF-1α function: Divergent EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes. BMC Evolutionary Biology, 13:e131.

Heiss, A.A., Walker, G. & Simpson, A.G.B. (2013) The microtubular cytoskeleton of the apusomonad Thecamonas, a sister lineage to the opisthokonts. Protist, 164:598–621.

Yubuki, N., Simpson, A.G.B. & Leander, B.S. (2013) Comprehensive ultrastructure of Kipferlia bialata provides evidence for character evolution within the Fornicata. Protist, 164:423–439.

Heiss, A.A., Walker, G. & Simpson, A.G.B. (2013) The flagellar apparatus of Breviata anathema, a eukaryote without a clear supergroup affinity. European Journal of Protistology, 49:354–372.

Feehan, C.J., Johnson-Mackinnon, J., Scheibling, R.E., Lauzon-Guay, J.-S. & Simpson, A.G.B. (2013) Validating the identity of Paramoeba invadens, the causative agent of recurrent mass mortality of sea urchins in Nova Scotia. Diseases of Aquatic Organisms, 103:209–227.

O’Malley, M., Simpson, A.G.B. & Roger, A.J. (2013) The other eukaryotes in light of evolutionary protistology. Biology and Philosophy, 28:299–330.

Harding, T., Brown, M.W., Plotnikov, A., Selivanova, E., Park, J.S., Gunderson, J.H., Baumgartner, M., Silberman, J.D., Roger, A.J. & Simpson, A.G.B. (2013) Amoeba stages in the deepest branching heteroloboseans, including Pharyngomonas: Evolutionary and systematic implications. Protist, 164:272–286.

Yubuki, N., Simpson, A.G.B. & Leander, B.S. (2013) Reconstruction of the feeding apparatus in Postgaardi mariagerensis provides evidence for character evolution within the Symbiontida. European Journal of Protistology, 49:32–39.


Pawlowski, J. and 32 others (2012) CBOL Protist working group: Barcoding eukaryotic richness beyond the animal, plant and fungal kingdoms. PLoS Biology, 10:e1001419.

Park, J.S., DeJonckheere, J.F. & Simpson, A.G.B. (2012) Characterization of Selenaion koniopes n. gen., n. sp., an amoeba that represents a new major lineage within Heterolobosea, isolated from the Wieliczka salt mine. Journal of Eukaryotic Microbiology, 59:601–613.

Adl, S.M., Simpson, A.G.B., & 23 others (2012) The revised classification of eukaryotes. Journal of Eukaryotic Microbiology, 59:429–514.

Zhang, Q., Simpson, A.G.B. & Song, W. (2012) Insights into the phylogeny of systematically controversial haptorian ciliates (Ciliophora, Litostomatea) based on multigene analyses. Proceedings of the Royal Society, series B 279:2625–2635.

Takishita, K., Kolisko, M., Komatsuzaki, H., Yabuki, A., Inagaki, Y., Čepička, I., Smejkalová, P., Silberman, J.D., Hashimoto, T., Roger, A.J. & Simpson, A.G.B. (2012) Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest relatives of ‘amitochondriate’ diplomonads and retortamonads. Protist, 163:344–355.


Park, J.S. & Simpson, A.G.B. (2011) Characterization of Pharyngomonas kirbyi (= “Macropharyngomonas halophila” nomen nudum), a very deep-branching, obligately halophilic heterolobosean flagellate. Protist, 162:691–709.

Mora, C., Tittensor, D.P., Adl, S., Simpson, A.G.B., Worm, B. (2011) How many species are there on Earth and in the Ocean? PLoS Biology, 9:e1001127.

Heiss, A.A., Walker, G. & Simpson, A.G.B. (2011) The ultrastructure of Ancyromonas, a eukaryote without supergroup affinities. Protist, 162:373–393.

Tong, J., Dolezal, P., Selkrig, J., Crawford, S., Simpson, A.G.B., Noinaj, N., Buchanan, S.K., Gabriel, K. & Lithgow, T. (2011) Ancestral and derived protein import pathways in the mitochondrion of Reclinomonas americana. Molecular Biology and Evolution, 28:1581–1591.


Park, J.S., Kolisko, M. & Simpson, A.G.B. (2010) Cell morphology and formal description of Ergobibamus cyprinoides n. gen., n. sp., another Carpediemonas-like relative of diplomonads. Journal of Eukaryotic Microbiology, 57:520–528.

Kolisko, M., Silberman, J.D., Čepička, I., Yubuki, N., Takishita, K., Yabuki, A., Leander, B.S., Inouye, I., Inagaki, Y., Roger, A.J. & Simpson, A.G.B. (2010) A wide diversity of previously undetected relatives of diplomonads isolated from marine/saline habitats. Environmental Microbiology, 12:2700–2710.

Kim, E., Park, J.S., Simpson, A.G.B., Matsunaga, S., Watanabe, M., Murakami, A., Sommerfeld, K., Onodera, N.T., & Archibald, J.M. (2010) Complex array of endobionts in Petalomonas sphagnophila, a large heterotrophic euglenid protist from sphagnum-dominated peatlands. The ISME Journal, 4:1108–1120.

Heiss, A.A., Walker, G., & Simpson, A.G.B. (2010) Clarifying the taxonomic identity of a phylogenetically important group of eukaryotes: Planomonas is a junior synonym of Ancyromonas. Journal of Eukaryotic Microbiology, 57:285–293.

Park, J.S. & Simpson, A.G.B. (2010) Characterisation of halotolerant Bicosoecida and Placididea (Stramenopila) that are distinct from marine forms, and the phylogenetic pattern of salinity preference in heterotrophic stramenopiles. Environmental Microbiology, 12:1173–1184.


Park, J.S., Kolisko, M., Heiss, A.A. & Simpson, A.G.B. (2009) Light microscopic observations, ultrastructure, and molecular phylogeny of Hicanonectes teleskopos n. gen., n. sp., a deep-branching relative of diplomonads. Journal of Eukaryotic Microbiology, 56:373–384.

Hampl, V., Hug, L., Leigh, J., Dacks, J.B., Lang, B.F., Simpson, A.G.B. & Roger, A.J. (2009) Phylogenomic analyses support the monophyly of Excavata and robustly resolve relationships among eukaryotic “supergroups”. Proceedings of the National Academy of Sciences USA, 106:3859–3864.

Park, J.S., Simpson, A.G.B., Brown, S. & Cho B.C. (2009) Ultrastructure and molecular phylogeny of two heterolobosean amoebae, Euplaesiobystra hypersalinica gen. et sp. nov. and Tulamoeba peronaphora gen. et sp. nov., isolated from an extremely hypersaline habitat. Protist, 160:265–283.


Sanchez-Perez, G.F., Hampl, V., Simpson, A.G.B. & Roger, A.J. (2008) A new divergent type of eukaryotic methionine adenosyltransferase spread by gene transfer between secondary algae. Journal of Eukaryotic Microbiology, 55:374–381.

Kolisko, M., Čepička, I., Hampl, V., Leigh, J., Roger, A.J., Kulda, J., Simpson, A.G.B. & Flegr, J. (2008) Molecular phylogeny of diplomonads and enteromonads based on SSU rRNA, α-tubulin and HSP90 genes: implications for the evolutionary history of the double karyomastigont of diplomonads. BMC Evolutionary Biology, 8:art.205.

Simpson, A.G.B., Perley, T. & Lara, E. (2008) Lateral transfer of the gene for a widely used marker, alpha tubulin, indicated by a multi-protein study of the phylogenetic position of Andalucia (Excavata). Molecular Phylogenetics and Evolution, 47:366–377.


Adl S.M., Leander B.S., & 18 others (2007) Diversity, nomenclature and taxonomy of protists. Systematic Biology, 56: 684-689.

Park J.S., Simpson A.G.B., Lee W.J. & Cho B.C. (2007) Ultrastructure and phylogenetic placement within Heterolobosea of the previously unclassified, extremely halophilic heterotrophic flagellate Pleurostomum flabellatum (Ruinen 1938). Protist, 158: 397-413.


Kim E., Simpson A.G.B. & Graham L.E. (2006) Evolutionary relationships of apusomonads inferred from taxon-rich analyses of six nuclear-encoded genes. Molecular Biology and Evolution, 23: 2455-2466.

Simpson A.G.B., Stevens J.R. & Lukes J. (2006) The evolution and diversity of kinetoplastid flagellates. Trends in Parasitology, 22: 168-174.

Park J.S., Cho B.C. & Simpson A.G.B. (2006) Halocafeteria seosinensis gen. et sp. nov. (Bicosoecida) A halophilic bacterivorous nanoflagellate isolated from a solar saltern. Extremophiles, 10:: 493-504.

Simpson A.G.B., Inagaki Y. & Roger A.J. (2006) Comprehensive multi-gene phylogenies of excavate protists reveal the evolutionary positions of ‘primitive’ eukaryotes. Molecular Biology and Evolution, 23: 615-625.

Lara E., Chatzinotas A. & Simpson A.G.B. (2006) Andalucia (gen. nov.): a new taxon for the deepest branch within jakobids (Jakobida; Excavata), based on morphological and molecular study of a new flagellate from soil. Journal of Eukaryotic Microbiology, 53: 112-120.