Simpson Lab - Department of Biology, Dalhousie University, Canada

2011

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

Heiss, A.A., Walker, G. & Simpson A.G.B. (In press) The ultrastructure of Ancyromonas, a eukaryote without supergroup affinities. Protist.

2010

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. [link to paper]

Kolisko, M., Silberman, J.D., Cepicka, 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. [link to paper]

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. [link to paper]

Simpson A.G.B. & Cepicka, I. (2010) Amitochondriate protists (Diplomonads, Parabasalids and Oxymonads). update for online edition of Encyclopedia of Microbiology, 3rd Edition. Elsevier.

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. [link to paper]

Wilson, S., Simpson, A.G.B & Lynn, D.H. (2010) Maintaining journal figure quality. Journal of Eukaryotic Microbiology, 57: 221-222.

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. [link to paper]

2009

Lynn, D.H., & Simpson, A.G.B. (2009) Describing new taxa of unicellular protists. Journal of Eukaryotic Microbiology, 56: 403-405

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. [link to paper]

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. [link to paper]

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. [pubmed entry]

Simpson A.G.B. & Cepicka, I. (2009) Amitochondriate protists (Diplomonads, Parabasalids and Oxymonads).Pp. 545-557 in Encyclopedia of Microbiology, 3rd Edition. Elsevier.

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

2008

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.[pubmed entry]

Kolisko, M., Cepicka, 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, a-tubulin and HSP90 genes: implications for the evolutionary history of the double karyomastigont of diplomonads. BMC Evolutionary Biology, 8: art.205.[pubmed entry]

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.[pubmed entry]

Hampl, V. & Simpson, A.G.B. (2008) Possible mitochondria-related organelles in poorly-studied ‘amitochondriate’ eukaryotes. in Tachezy, J. (ed.) Hydrogenosomes and Mitosomes: mitochondria of anaerobic eukaryotes . Microbiology Monographs 9. Springer Verlag.

2007

Adl, S.M. & Simpson, A.G.B. (2007) Eukaryotic Microorganisms. Chapter 23 (p. 687-733) in Staley J.T., Gunsalus R.P., Lory S. & Perry J.J. Microbial Life, 2nd Edition. Sinauer Associates, Inc.

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.[pubmed entry]

2006

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.[pubmed entry]

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.[pubmed entry]

Simpson, A.G.B. & Patterson, D.J. (2006) Current perspectives on high-level groupings of protists. Pp. 7-30 in Katz, L. & Bhattacharya, D. (eds.) Genomics and Evolution of Microbial Eukaryotes. Oxford University Press.

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

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. [pubmed entry]

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. [pubmed entry]

2005

Lee, W.J., Simpson, A.G.B. & Patterson D.J. (2005) Free-living heterotrophic flagellates from freshwater sites in Tasmania (Australia), a field survey. Acta Protozoologica, 44: 321-350.

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. [pdf]

Simpson, A.G.B. (2005) Evolution downunder: Meeting report for the fifteenth meeting of the International Society for Evolutionary Protistology. Protist, 156: 143-147. [pubmed entry]

Miao, W., Simpson, A.G.B., Fu, C. & Lobban C.S. (2005) The giant zooxanthellae-bearing ciliate Maristentor dinoferus (Heterotrichea) is closely related to Folliculinidae. Journal of Eukaryotic Microbiology, 52: 11-16. [pubmed entry]

2004

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. [pubmed entry]

Simpson, A.G.B. & Roger, A.J. (2004) The real 'kingdoms' of eukaryotes. Current Biology 14: R693-696. [pubmed entry] [The True Tree]

Simpson A.G.B. & Roger A.J. (2004) Excavata and the origin of amitochondriate eukaryotes. Pp. 27-53 in Hirt, R.P. & Horner, D.S. (eds.) Organelles, Genomes, and Eukaroyote Phylogeny: An Evolutionary Synthesis in the Age of Genomics. CRC Press.

Baldauf, S.L., Bhattacharya, D., Cockrill, J., Hugenholtz, P., Pawlowski, J. & Simpson, A.G.B. (2004) The tree of life, an overview. Pp. 43-75 in Cracraft, J. & Donoghue, M.J. (eds.) Assembling the Tree of Life. Oxford University Press.

Inagaki, Y, Simpson A.G.B., Dacks J.B. & Roger A.J. (2004) Phylogenetic artifact can be caused by leucine, serine and arginine codon usage heterogeneity: dinoflagellate plastid origins as a case study. Systematic Biology 53: 582-593

Brugerolle G. & Simpson A.G.B. (2004) The flagellar apparatus of Heterolobosea. Journal of Eukaryotic Microbiology 51: 966-107.

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.

Prior publications by Alastair Simpson

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., MacQuarrie E.K., & Roger A.J. (2002) Early evolution of canonical introns. Nature 419: 270.

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

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.

Al-Qassab S., Lee W.J., Murray S., Simpson A.G.B. & Patterson D.J. (2002) Flagellates from stromatolites and surrounding sediments in Shark Bay, Western Australia. Acta Protozoologica 41: 91-144.

Simpson A.G.B., Radek R., Dacks J.B. & O'Kelly, C.J. (2002) How oxymonads lost their groove: An ultrastructural comparison of Monocercomonoides and excavate taxa. Journal of Eukaryotic Microbiology.49: 239-248.

Edgcomb V.P., Simpson A.G.B., Amaral Zettler L., Nerad T.A., Patterson D.J., Holder M.E. & Sogin M.L.(2002) Pelobionts are degenerate protists: insights from molecules and morphology. Molecular Biology and Evolution.19: 978-982.

Silberman J.D., Simpson A.G.B., KuldaJ., Cepicka I., Hampl V., Johnson P.J. & Roger A.J. (2002) Retortamonad flagellates are closely related to diplomonads: implications for the history of mitochondrial function in eukaryote evolution. Molecular Biology and Evolution19: 777-786.

Lobban C.S. Schefter M., Simpson A.G.B., Pochon X., Pawlowski J. & Foissner W. (2002) Maristentor dinoferus nov. gen., nov. spec., a giant heterotrich ciliate (Protozoa, Ciliophora) with zooxanthellae, from Pacific coral reefs. Marine Biology, 140: 411-423.

Simpson A.G.B. & Patterson D.J. (2001) On core jakobids and excavate taxa: The ultrastructure of Jakoba incarcerata. Journal of Eukaryotic Microbiology 48: 480-492.

Dacks J.B., Silberman J.D., Simpson A.G.B., Moriya S., Kudo T., Ohkuma M. & Redfield R.J. (2001) Oxymonads are closely related to the excavate taxon Trimastix. Molecular Biology and Evolution 18: 1034-1044.

Edgcomb V.P., Roger A.J., Simpson A.G.B., Kysela D.T., & Sogin M.L. (2001) Evolutionary relationships among “jakobid” flagellates as indicated by alpha- and beta- tubulin phylogenies. Molecular Biology and Evolution 18: 514-522.

Walker G., Simpson A.G.B., Edgcomb, V.P., Sogin M.L. & Patterson D.J. (2001) Ultrastructural identities of Mastigamoeba punctachora, Mastigamoeba simplex and Mastigella commutans and assessment of hypotheses of relatedness of the pelobionts (Protista). European Journal of Protistology37: 25-49.

Simpson A.G.B., Bernard C. & Patterson D.J. (2000) The ultrastructure of Trimastix marina Kent, 1880 (Eukaryota), an excavate flagellate. European Journal of Protistology36: 229-252.

Buck K.R., Barry J.P. & Simpson A.G.B. (2000) Monterey Bay cold seep infauna: Euglenozoans with hydrogen sulphide oxidizing bacterial epibionts. European Journal of Protistology 36: 117-126.

Bernard C., Simpson A.G.B. & Patterson D.J. (2000) Some free-living flagellates from anoxic sediments. Ophelia 52: 113-142.

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.

Weerakoon N.D., Harper J.D.I., Simpson A.G.B. & Patterson D.J. (1999) Centrin in the groove: Immunolocalisation of centrin and microtubules in the putatively primitive protist, Chilomastix cuspidata (Retortamonadida). Protoplasma 210: 75-84.

Patterson, D.J., Simpson A.G.B. & Weerakoon, N. (1999) Free-living flagellates from anoxic habitats and the assembly of the eukaryotic cell. Biological Bulletin 196: 381-384.

Edgcomb V.P., Viscogliosi E., Simpson A.G.B., Delgado-Viscogliosi P., Roger A.J. & Sogin M.L. (1998) New insights into the phylogeny of trichomonads inferred from small subunit rRNA sequences. Protist 149: 359-366.

Heep T., Rohozinski J., Simpson A.G.B.& Patterson D.J. (1998) Stentor amethystinus (Protista, Ciliophora, Heterotrichida), a common protozoan member of fresh-water plankton in Australia. Records of the Australian Museum 50: 211-216.

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

Bernard C., Simpson A.G.B. & Patterson D.J. (1997) An ultrastructural study of a free-living retortamonad, Chilomastix cuspidata (Larsen & Patterson, 1990) n. comb. (Retortamonadida, Protista). European Journal of Protistology 33: 254-265.

Simpson A.G.B., van den Hoff J., Bernard C., Burton H. & Patterson D.J. (1997) The ultrastructure and systematic position of the Euglenozoon Postgaardi mariagerensis, Fenchel et al. Archiv für Protistenkunde 147: 213-225.

Simpson A.G.B., Bernard C., Fenchel T. & Patterson D.J. (1997) The organisation of Mastigamoeba schizophrenia n. sp.: More evidence of ultrastructural idiosyncrasy and simplicity in pelobiont protists. European Journal of Protistology 33: 87-98.

Patterson D.J. & Simpson A.G.B. (1996) Heterotrophic flagellates from coastal marine and hypersaline sediments in Western Australia.  European Journal of Protistology 32: 423-448.

Simpson A.G.B. & Patterson D.J., (1996) Ultrastructure and identification of the predatory flagellate Colpodella pugnax Cienkowski (Apicomplexa) with a description of Colpodella turpis (n. sp.) and a review of the genus. Systematic Parasitology 33: 187-198.