Department of Biology

Faculty of Science

Alastair Simpson

PROFESSOR
BSc (Sydney, 1994)
PhD (Sydney, 2000)

  • Teaching & Research
  • Publications
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    Teaching & Research
    origin and early evolution of eukaryotes, Protistan biodiversity, phylogenetics and systematics, Protistan ultrastructure, and molecular evolution


    was born, raised and educated in Sydney, Australia. I finished a PhD in Biology at the University of Sydney in 2000, having also spent several months at the Marine Biology Laboratory at Woods Hole (USA). I came to Dalhousie University in 2000 as a postdoctoral fellow in the Biochemistry Department, and joined the Biology Faculty in July 2003.

    Classes in which Alastair currently teaches:
    My research examines the origin and evolutionary history of eukaryotic cells. I work with 'protists', that is, all those eukaryotes that are NOT animals, plants or fungi. Most protists are inconspicuous single cells, but they comprise the vast bulk of eukaryote biodiversity. They are therefore key to understanding the course of eukaryotic evolution and are of huge ecological importance. However, most protists are very poorly studied. I examine the evolutionary history and diversity of several major protist groups (think 'phyla' and 'kingdoms'), using molecular phlyogenetics / phylogenomics and sub-cellular morphology. See the lab website for more details.

    My particular interests are:

    1) Understanding eukaryote diversity at the broadest scale: How many major groups (~"kingdoms") of eukaryotes are there on earth? How different from one another are they? How much can we infer about the last eukaryote common ancestor (LECA) from living forms?  Our principal contributions have included i) the discovery or rediscovery of several 'mystery' lineages that represent distinct major groups, ii) phylogenetics/phylogenomic studies that focus on these and other 'difficult-to-place' eukaryote groups, and iii) detailed studies of the flagellar apparatus cytoskeleton, a sub-cellular system that shows remarkable conservation across much of eukaryote diversity, such that parts it can be traced back to LECA.

    2) The biodiversity, evolutionary history and broadest-scale adaptations of heterotrophic protists (protozoa) that live in extremely high salt environments (i.e. halophiles and extreme halophiles).  We have documented through cultivation-based methods that halophilic protozoa have a evolved a large number of times independently.   Transcriptome-based studies  of the exemplar taxa Halocafeteria and Pharyngomonas reveal possible 'signals' of halophily in the inferred amino-acid composition of the proteome, and suites of genes that are up-regulated under high salt conditions.  Much of our work has examined bacterivorous protists, but we also study species that (obligately) feed on other unicellular protists, which tend to come from completely different phylogenetic groups.

    3) The biodiversity and evolutionary history of the taxon Euglenozoa. Euglenozoa includes the agents of sleeping sickness, Chagas' disease and kala azar, as well as the laboratory alga Euglena, and a very wide diversity of ecologically important free-living forms.  Most our recent work focuses on the molecular phylogenetics of phagotrophic euglenids, which are the diverse but poorly studied assemblage from which algal euglenids evolved.  We are exploiting single-cell molecular methods, includng single-cell transcriptomics, to avoid the bottle-neck of having to cultivate these organisms.  We have also studied a parasite or necrotroph of the invasive alga Codium fragile, which represents a new family-level grouping within kinetoplastid Euglenozoa.

    4) Green sea urchins (Strongylocentrotus droebachiensis) are an ecologically important species in coastal Nova Scotia, where their abundance determines whether luxuriant kelp beds will form, or whether the bottom will be an ecosystem-services-poor 'urchin barrens'.  A major control of green sea urchin abundance are mass mortality events caused by an amoeba, Paramoeba invadens.  In collaboration with the Robert Scheibling's group, we have been using molecular tools to characterise P. invadens (confirming, unexpectedly, that it is truly a separate species), and to develop methods to detect the organism at low abundance in sea urchin tissues and environmental samples.  The ultimate goal is to determine the reservoir of the pathogen, and the mechanism by which it is introduced to uninfected sea urchin populations.

    I am also interested in eukaryote (protist) genome evolution, including lateral gene transfer, in species concepts and autecology in protists, and in the procedures governing protist taxonomy and systematics.

    Selected Publications

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

    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.

    Lax G.*, Eglit Y.*, Eme L.*, Bertrand E. Roger A.J. & Simpson A.G.B (2018) Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes. Nature, 564, 410-414.

    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.

    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.

    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.

    Harding, T. & Simpson, A.G.B. 2018. Recent advances in halophilic protozoa research. Journal of Eukaryotic Microbiology, in press.

    Archibald, J.M., Simpson, A.G.B. & Slamovits C. (eds.) 2017. Handbook of the Protists, 2nd edition. Springer. 1657 pp.

    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.

    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.

    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

    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.

    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.

    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.

    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.

    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.

    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.

    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.

    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, 3859-64.

    Roger, A.J. & Simpson, A.G.B. 2009. Evolution: Revisiting the Root of the Eukaryote Tree. Current Biology, 19, R165-167.

    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.

    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.

    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.

    Park J.S., Cho B.C., and 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., Stevens, J.R. & Lukes J. 2006. The evolution and diversity of kinetoplastid flagellates. Trends in Parasitology, 22, 168-174.

    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.

    Adl, S.M., Simpson, A.G.B., Farmer, M., & 25 others 2005.The new higher-level classification of eukaryotes with emphasis on the taxonomy of protists. Journal of Eukaryotic Microbiology, 52, 399-451.

    Simpson A.G.B., Gill E.E., Callahan H.A., Litaker R.W. & Roger A.J. 2004. Early evolution within kinetoplastids (Euglenozoa), and the late emergence of trypanosomatids. Protist 155, 407-422.

    Simpson, A.G.B. & Roger, A.J. 2004.The real 'kingdoms' of eukaryotes. Current Biology 14, R693-696.

    Simpson A.G.B. & Roger A.J. 2004. Protein phylogenies robustly resolve the deep-level relationships within Euglenozoa. Molecular Phylogenetics and Evolution, 30: 201-212.

    Simpson A.G.B. 2003. Cytoskeletal organisation, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota). International Journal of Systematic and Evolutionary Microbiology, 53: 1759-1777.

    Simpson A.G.B., Lukes J. & Roger A.J. 2002. Evolutionary history of kinetoplastids, and their kinetoplasts. Molecular Biology and Evolution 19: 2071-2083.

    Simpson A.G.B., and Roger A.J. 2002. Eukaryotic evolution: Getting to the root of the problem. Current Biology, 12: 691-693.

    Simpson A.G.B., MacQuarrie E.K., & Roger A.J. 2002. Early evolution of canonical introns. Nature 419: 270.

    Simpson A.G.B., Roger A.J., Silberman J.D., Leipe, D.D., Edgcomb V.P., Jermiin, L.S., Patterson, D.J. & Sogin M.L. 2002. Evolutionary history of 'early diverging' eukaryotes: The excavate taxon Carpediemonas is a close relative of Giardia. Molecular Biology and Evolution 19: 1782-1791.

    Simpson A.G.B. & Patterson, D.J. 1999. The ultrastructure of Carpediemonas membranifera: (Eukaryota), with reference to the 'excavate hypothesis'. European Journal of Protistology 35: 353-370.

    Simpson A.G.B. 1997. The identity and composition of the Euglenozoa. Archiv für Protistenkunde 148: 318-328.

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