Faculty of Medicine
Department of Biochemistry & Molecular Biology
HALIFAX, NOVA SCOTIA | CANADA B3H 4R2 | 1 (902) 494-2480

Dr. Andrew Roger, Ph.D. (Dalhousie)


Professor
Director, Centre for Comparative Genomics and Evolutionary Bioinformatics (CGEB)
Fellow, CIFAR Program in Integrated Microbial Biodiversity

8-B1 Tupper
(902) 494-2620
(902) 494-2881
Email
Lab Homepage

Research Areas

Determining the "super-kingdoms" of eukaryotic organisms by phylogenomics.

Using genomic surveys and molecular genetic methods, we isolate genes coding for multiple highly conserved proteins (ribosomal proteins, cpn60, hsp70 and hsp90, elongation factors, tubulins, RNA polymerases etc.) from diverse aerobic and anaerobic, parasitic and free-living protists. We do computer-based phylogenetic analyses of these sequences to: reconstruct ancient relationships amongst the unicellular protistan eukaryotes and other major eukaryotic groups. In particular we are investigating a hypothetical eukaryote super-kingdom called the 'Excavata' that is proposed to contain organisms such as Giardia, Trichomonas, trypanosomes and a variety of aerobic and anaerobic flagellates and amoebae.

Comparative genomics of unicellular eukaryotes
Through EST surveys, we characterize the highly expressed genes from a wide variety of protistan genomes. We are specifically interested in the gene content of anaerobic protists, that have acquired genes by lateral gene transfer (LGT) from Eubacteria, Archaebacteria and Eukaryotes. By studying LGT in these organisms we are gaining an understanding of how both parasitic and free-living unicellular eukaryotic genomes change over time.

The biology and evolution of mitochondria, hydrogenosomes and mitosomes
Mitochondria are derived from an ancient endosymbiosis of a eubacterium in eukaryotic cells. Although all known eukaryotes appear to have diverged from each other since this event, many unicellular eukaryotes that live in oxygen-poor habitats (e.g. the human gut or anoxic fresh-water environments) lack aerobic mitochondrial functions and instead have transformed their mitochondria into hydrogen-producing 'hydrogenosomes or reduced mitosomes. We are interested in characterizing the functional biodiversity of these alternatives to mitochondria and understanding the mechanisms by which they have evolved.

Modeling the evolution of genes and genomes
We collaborate extensively with statisticians and computer scientists to develop stochastic models of gene, protein and genome evolution. We are particularly interested in creating models that capture the dynamic nature of molecular evolution over the 3.5 billion years of divergence in the tree of life.

Keywords:
DNA-sequencing, phylogenetic methods, bioinformatics, computational biology, immunofluorescence, comparative genomics

Graduate Students


Javier Alfaro Masters Program
Daniel Gaston PhD Program
Tommy Harding PhD (co-supervised by A. Simpson, Biology) Program
Michelle Leger PhD Program
Susan Sharpe MSc Program
Courtney Stairs PhD Program

Postdoctoral Fellows


Matthew Brown University of Arkansas
Laura Eme CNRS, Marseilles, France
Ryan Gawryluk Dalhousie University
Eleni Gentekaki University of Guelph
Martin Kolisko Czech Republic
Anastasios Tsaousis Newcastle University, UK
Huaichun Wang University of Ottawa

Honours Students


Neil Mutsaers Biochemistry

Lab Personnel


Jacqueline de Mestral Lab Manager/Technician

Publications

  1. Stairs, C.W., Roger, A.J. and Hampl, V. , (2011) Eukaryotic pyruvate formate lyase and its activating enzyme were acquired laterally from a firmicute. Mol. Biol. Evol. 28:2087-2099
  2. Zou, L., Susko E., Field, C. and Roger, A.J., (2011) The Parameters of the Barry and Hartigan General Markov Model are Statistically Nonidentifiable. Syst. Biol. [Epub ahead of print]:
  3. Wang, H.-C., Susko, E. and Roger, A.J. , (2011) Fast statistical tests for detecting heterotachy in protein evolution. Mol. Biol. Evol. [Epub ahead of print]:
  4. Kamikawa, R., Inagaki, Y., Tokoro, M., Roger, A.J. and Hashimoto, T. , (2011) Split introns in the genome of a divergent eukaryote Giardia intestinalis are excised by spliceosome-mediated trans-splicing. Curr. Biol. 21:311-315
  5. Tsaousis, A.D., Gaston, D., Stechmann, A., Walker, P.B., Lithgow, T. and Roger, A.J. , (2011) A functional Tom70 in the human parasite Blastocystis sp.: Implications for the evolution of the mitochondrial import apparatus. Mol. Biol. Evol. 28:781-791
  6. Hug, L.A., Stechmann, A. and Roger, A.J., (2010) Phylogenetic distributions and histories of proteins involved in anaerobic pyruvate metabolism in eukaryotes. Mol. Biol. Evol. 27:311-324
  7. Barberŕ, M.J., Ruiz-Trillo, I., Tufts, J.Y.A., Bery, A., Silberman, J.D. and Roger, A.J., (2010) Sawyeria marylandensis (Heterolobosea) has a hydrogenosome with novel metabolic properties. Euk. Cell 9:1913-1924
  8. Sebé-Pedros, A., Roger, A.J., Lang, F.B., King, N. and Ruiz-Trillo, I., (2010) From the cover: Ancient origin of the integrin-mediated adhesion and signaling machinery. Proc. Natl. Acad. Sci. USA 107:10142-10147
  9. Baurain, D., Brinkmann, H., Petersen, J., Rodríguez-Ezpeleta, N., Stechmann, A., Demoulin, V., Roger, A.J., Burger, G., Lang, B.F. and Philippe, H., (2010) Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes and stramenopiles. Mol. Biol. Evol. 27:1698-1709
  10. Kolisko M., Silberman, J.D., Cepicka, I., Yubuki, N., Takishita, K., Yabuki, A., Leander, B.S., Inouye, I., Inagaki, Y., Roger, A.J. and Simpson, A.G.B. , (2010) A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitats. Env. Microbiol. 12:2700-2710
  11. Susko, E. and Roger, A.J. , (2009) Statistical analysis of expressed sequence tags. Expressed Sequence Tags (ESTs): Generation and Analysis, Vol. 533, Humana Press Inc.:277-287
  12. Gaston, D., Tsaousis, A.D. and Roger A.J., (2009) Predicting proteomes of mitochondria and related organelles from genomic and expressed sequence tag data. Methods Enzymol. 457:21-41 [PubMed]
  13. Wang, H.-C., Susko, E. and Roger, A.J., (2009) PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specfic covarion pattern analysis. BMC Evol. Biol. 9:225-237
  14. Kamikawa, R., Sanchez-Pérez, G.F., Sako, Y., Roger, A.J. and Inagaki, Y. , (2009) Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes. Mol. Phylogenet. Evol. 53:565-570
  15. Hampl, V., Hug, L.A., Leigh, J.W., Dacks, J.B., Lang, B.F., Simpson, A.G.B. and Roger, A.J. , (2009) Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups". Proc. Natl. Acad. Sci. USA 106:3859-3864
  16. Blouin, C., Perry, S., Lavell, A., Susko, E., Roger, A.J., (2009) Reproducing the manual annotation of multiple sequence alignments using a SVM classifier. Bioinformatics 23(25):3093-8 [PubMed]
  17. Wu, J. Susko, E. and Roger, A.J. , (2008) An independent heterotachy model and its implications for phylogeny and divergence time estimation. Mol. Phylogenet. Evol. 46:801-806
  18. Leigh, J., Susko, E., Baumgartner, M. and Roger, A.J. , (2008) Testing congruence in phylogenomic analysis. Syst. Biol. 57:104-115
  19. Wang, H.-C., Susko, E., Spencer, M. and Roger, A.J. , (2008) Topological estimation biases with covarion evolution. J.Mol.Evol. 66:50-60
  20. Ruiz-Trillo, I., Roger, A.J., Burger, G., Gray, M.W. and Lang, B.F. , (2008) A phylogenomic investigation into the origin of Metazoa. Mol.Biol.Evol. 25:664-672
  21. Hampl, V., Silberman, J.D., Stechmann, A., Diaz-Triviño, S., Johnson, P.J. and Roger, A.J. , (2008) Genetic evidence for a mitochondriate ancestry in the amitochondriate flagellate Trimastix pyriformis. PLoS ONE 3:e1383 [PubMed]
  22. Kolisko, M., Cepicka, I., Hampl, V., Leigh, J., Roger, A.J., Kulda, J., Simpson, A.G.B. and Flegr, J., (2008) Molecular phylogeny of diplomonads and enteromonads based on SSU rRNA, (alpha)-tubulin and HSP90 genes: implications for the evolutionary history of the double karyomastigont of diplomonads. BMC Evol.Biol. 8:205
  23. Stechmann, A., Hamblin, K., Pérez-Brocal, V., Gaston, D., Richmond, G.S., van der Giezen, M., Clark, C.G. and Roger, A.J., (2008) Organelles in Blastocystis that blur the distinction between mitochondria and Hydrogenosomes. Curr. Biol. 18:580-585
  24. Wang, H.-C., Li, K.M., Susko, E. and Roger A.J., (2008) A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny. BMC Evol. Biol. 8:331
  25. Sanchez-Pérez, G., Hampl, V., Simpson, A.G.B. and Roger, A.J. , (2008) A new divergent type of eukaryotic methionine adenosyltransferase that has spread by gene transfer between secondary algae. J. Euk. Microbiol. 55:374-381
  26. Pepke, S., Butt, D., Nadeau, I., Roger, A.J. and Blouin C. , (2007) Using confidence set heuristics during topology search improves the robustness of phylogenetic inference. J.Mol.Evol. 64:80-89
  27. Andersson, J.O., Sjogren, Å., Horner D.S., Murphy, C.A., Dyal, P., Svärd S., Logsdon J.M., Ragan, M.A., Hirt, R.P., and Roger, A.J. , (2007) A genomic survey of the fish parasite Spironucleus salmonidia indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution. BMC Genomics 8:51
  28. Hug, L.A. and Roger, A.J. , (2007) The impact of fossils and taxon sampling on ancient molecular dating analyses. Mol. Biol. Evol. 24:1889-1897
  29. Susko, E. and Roger, A.J. , (2007) On reduced amino acid alphabets for phylogenetic inference. Mol. Biol. Evol. 24:2139-2150
  30. Rodríguez-Ezpeleta, N., Brinkmann, H., Burger, G., Roger, A.J., Gray M.W., Philippe H. and Lang, B.F. , (2007) Toward resolving the eukaryotic tree: the phylogenetic position of jakobids and cercozoans. Curr. Biol. 17:1420-1425
  31. Gill, E.E., Diaz-Triviño, S., Barberà, M.J., Silberman, J.D., Stechmann, A., Gaston, D., Tamas, I. and Roger, A.J. , (2007) Novel mitochondrion-related organelles with a unique array of functions in the anaerobic amoeba Mastigamoeba balamuthi. Mol. Microbiol. 66:1306-1320 [PubMed]
  32. Ruiz-Trillo, I., Burger, G., Holland, P., King, N., Lang, B.F., Roger, A.J. and Gray, M.W. , (2007) The origins of multicellularity: a multi-taxon genome initiative. Trends Genet. 23:113-118
  33. Barberà, M. J., Ruiz-Trillo, I., Leigh, J. Hug, L.A. and Roger, A.J. , (2007) The diversity of mitochondrion-related organelles amongst eukaryotic microbes. Origins of Mitochondria and Hydrogenosomes, W.Martin and M. Müller (Eds.) Springer-Verlag:239-268
  34. Pepke, S.L., Butt, D., Nadeau, I., Roger, A.J. and Blouin C., (2007) Inferring Phylogenies by confidence set optimization. J Mol Evol 64(1):87-9 [PubMed]
  35. Roger, A.J. and Hug, L.A., (2006) The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation. Phil. Trans. R. Soc. B 361:1039-1054
  36. Spencer, M., Susko, E. and Roger, A.J., (2006) Modeling prokaryote gene content. Evol. Bioinf. Online 2:165-186
  37. Inagaki, Y. and Roger, A.J., (2006) Phylogenetic estimation under codon models can be biased by codon usage heterogeneity. Mol. Phylogenet. Evol. 40:428-434
  38. Andersson, J.O., Hirt, R.P., Foster, P.G. and Roger, A.J., (2006) Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes. BMC Evol. Biol. 6:27
  39. Wang, H.C., Susko, E. and Roger, A.J., (2006) On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: data quality and confounding factors. Biochem. Biophys. Res. Commun. 342:681-684
  40. Simpson, A.G.B., Inagaki, Y. and Roger, A.J., (2006) Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of 'primitive' eukaryotes. Mol. Biol. Evol. 23:615-625
  41. Inagaki, Y., Susko, E. and Roger, A.J., (2006) Recombination between elongation factor 1(alpha) genes from distantly-related archaeal linages. Proc. Natl. Acad. Sci. USA 103:4528-4533
  42. Ruiz-Trillo, I., Lane C., Archibald, J.M. and Roger, A.J. , (2006) Insights into the evolutionary origin and genome architecture of the unicellular opisthokonts Capsaspora owczarzaki and Sphaeroforma arctica. J. Euk. Microbiol. 53:379-384
  43. Wang, H.C., Spencer, M., Susko, E. and Roger, A.J., (2006) Testing for covarion-like evolution in protein sequences. Mol.Biol.Evol. 24:294-305
  44. Stechmann, A., Baumgartner, M., Silberman, J.D. and Roger, A.J. , (2006) The glycolytic pathway of Trimastix pyriformis is an evolutionary mosaic. BMC Evol. Biol 6:101
  45. Goddard, M., Leigh, J., Roger, A.J. and Pemberton, A.J. , (2006) Invasion and persistence of a selfish gene in the Cnidaria. PLoS ONE 1:e3
  46. Roger, A. J., (2006) Telling evolutionary tales (book review). Nat.Rev.Genet. 38:1357
  47. Blouin, C., Butt, D., Roger, A.J., (2005) The impact of taxon sampling on the estimatio nof rate of evolution at sites. Mol. Biol. Evol. 22(3):784-791 [PubMed]
  48. Keeling, P.J., Burger, G., Durford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J. and Gray, M.W. , (2005) The tree of eukaryotes. Trends Ecol. Evol. 20:670-676
  49. Andersson, J.O., Sarchfield, S. and Roger, A.J. , (2005) Gene transfers from Nanoarchaeota to an ancestor of diplomonads and parabasalids. Mol. Biol. Evol. 22:85-90
  50. Susko, E., Spencer, M. and Roger, A.J., (2005) Biases in phylogenetic estimation can be caused by random sequence segments. J. Mol. Evol. 61:351-359
  51. Butt, D., Roger, A.J. and Blouin, C., (2005) A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny. BMC Bioinformatics 6:138
  52. Spencer, M., Susko, E. and Roger, A.J., (2005) Likelihood, parsimony and heterogeneous evolution. Mol. Biol. Evol. 22:1161-1164
  53. Blouin, C. Butt, D. and Roger, A.J., (2004) Rapid evolution in conformational space: a study of loop regions in a ubiquitous GTP binding domain. Prot. Sci. 13(3):608-616 [PubMed]
  54. Simpson, A.G.B. and Roger, A. J., (2004) The real 'kingdoms' of eukaryotes. Curr. Biol. 14:R693-R696
  55. Inagaki, Y., Simpson, A.G.B., Dacks, J. and Roger, A.J., (2004) Phylogenetic artifacts can be caused by leucine, serine and arginine codon usage heterogeneity: dinoflagellate plastid origins as a case study. Syst. Biol. 53:582-593
  56. Silberman, J.D., Collins, A.G., Gershwin, L.-A., Johnson, P.J. and Roger, A.J. , (2004) Ellobiopsidae of the genus Thallasomyces are alveolates. J. Euk. Microbiol. 51:246-252
  57. Susko, E. and Roger, A. J., (2004) Estimating and comparing the rates of gene discovery and expressed sequence tag (EST) frequencies from EST surveys. Bioinformatics 20:2279-2287
  58. Inagaki, Y., Susko, E. Fast, N.M. and Roger, A.J. , (2004) Covarion shifts cause a long-branch attraction artifact that unites Microsporidia and Archaebacteria in EF-1alpha phylogenies. Mol. Biol. Evol. 21:1340-1349
  59. Susko, E., Inagaki, Y. and Roger, A.J. , (2004) On inconsistency of the neighbor-joining method, least squares and minimum evolution estimation when distances are incorrectly specified. Mol. Biol. Evol. 21:1629-1642
  60. Ruiz-Trillo, I., Inagaki, Y., Davis, L.A., Sperstad, S., Landfald, B. and Roger, A.J. , (2004) Capsaspora owczarzaki is an independent opisthokont lineage. Curr. Biol. 14:R946-R947
  61. Simpson, A.G.B., Gill, E.E., Callahan, H.A., Litaker, R.W. and Roger, A.J., (2004) Early evolutin within kinetoplastids (euglenozoa), and the late emergence of trypanosomatids. Protist 155:407-422
  62. Simpson, A.G.B. and Roger, A.J., (2004) Excavata and the origin of amitochondriate eukaryotes. Organelles, Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics, R.P. Hirt and D.S. Horner (eds.) CRC Press, Boca Raton, Florida:27-53
  63. Blouin, C., Boucher, Y., and Roger, A.J., (2003) Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information. Nucleic Acids Res. 31:790-797 [PubMed]
  64. Inagaki, Y., Blouin, C., Susko, E., and Roger, A.J., (2003) Assessing functional divergence in EF-1alpha and its paralogues in eukaryotes and archaebacteria. Nucleic Acids Res. 31:4227-4237 [PubMed]
  65. Simpson, A.G.B. and Roger, A.J., (2003) Protein phylogenies robustly resolve the deep-level evolutionary relationships amongst Euglenozoa. Mol. Phylogenet. Evol. 30:201-212
  66. Susko, E., Field, C., Blouin, C. and Roger, A.J., (2003) Estimation of rates-across-sites distributions in phylogenetic substitution models. Syst. Biol. 52(5):594-603 [PubMed]
  67. Andersson, J.O. and Roger, A.J., (2003) Evolution of glutamate dehydrogenase genes: lateral gene transfer within and between prokaryotes and eukaryotes. BMC Evolutionary Biology 3:14
  68. Andersson, J.O., Sjogren M., Davis, L.A.M., Embley, T.M. and Roger, A.J., (2003) Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes. Curr. Biol. 13:94-104
  69. Dacks, J.B., Davis, L.A.M., Sjogren, A.M., Andersson, J.O., Roger, A.J. and Doolittle, W.F., (2003) Evidence for Golgi bodies in proposed 'Golgi-lacking' lineages. Proc. R. Soc. Lond. B. Suppl. 2:S168-S171
  70. Shan, Y., Milios, E., Roger, A., Blouin, C. and Susko, E., (2003) Automatic recognition of regions of intrinsically poor multiple alignment. Proceedings of the 2003 IEEE Bioinformatics Conference (CSB2003):483-483
  71. Doolittle, W.F., Boucher, Y., Nesbo, C.L., Douady, C.J., Andersson, J.O. and Roger, A.J., (2003) How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Proc. Roy. Soc. Lond. Series B 358:39-58
  72. Archibald, J. M. and Roger, A. J., (2002) Gene conversion and the evolution of euryarchaeal chaperonins: a maximum likelihood-based method for detecting conflicting phylogenetic signal. J. Mol. Evol. 55:232-245 [PubMed]
  73. Simpson, A.G.B. and Roger, A.J., (2002) Eukaryote evolution: Getting to the root of the problem. Curr. Biol. 12:R691-R693
  74. Simpson, A.G.B., MacQuarrie, E. and Roger, A.J., (2002) Early origin of canonical introns. Nature 419:270
  75. Roger, A.J., and Silberman, J.D., (2002) Mitochondria in hiding. Nature 418:828-829
  76. Susko, E., Inagaki, Y., Field, C., Holder, M.E. and Roger, A.J., (2002) Testing for differences in rates across sites distributions in phylogenetic subtrees. Mol. Biol. Evol. 19:1514-1523
  77. Simpson, A.G.B., Roger, A.J., Silberman, J.D., Leipe, D., Edgcomb, V.E., Jermiin, L.S. Patterson, D.J. and Sogin, M.L., (2002) Molecular phylogenies reveal a novel close relative for diplomonads, the excavate taxon Carpediemonas. Mol. Biol. Evol. 19:1782-1791
  78. Silberman, J.D., Simpson, A.G.B., Kulda, J., Cepicka, I., Hampl, V., Johnson, P.J. and Roger, A.J., (2002) Retortamonad flagellates are closely related to diplomonads and endash, implications for the history of mitochondrial function in eukaryote evolution. Mol. Biol. Evol. 19:777-786
  79. Andersson, J. and Roger, A.J., (2002) Evolutionary analysis of the small subunit of glutamate synthase: Gene order conservation, gene fusions and prokaryote-to-eukaryote lateral gene transfers. Euk. Cell. 1:304-310
  80. Archibald, J. M. and Roger, A. J., (2002) Gene duplication and gene conversion shape the evolution of archaeal chaperonins. J. Mol. Biol. 316:1041-1050 [PubMed]
  81. Simpson, A.G.B., Lukes, J. and Roger, A.J., (2002) The evolutionary history of kinetoplastids and their kinetoplasts. Mol. Biol. Evol. 19:2071-2083
  82. Inagaki, Y., Doolittle, W.F., Baldauf, S.L. and Roger, A.J., (2002) Lateral transfer of an EF-1(alpha) gene: origin and evolution of the large subunit of ATP sulfurylase in eubacteria. Curr. Biol. 12:1-20
  83. Inagaki, Y., Blouin, C., Doolittle, W.F. and Roger, A.J., (2002) Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificity. Nucleic Acids Res. 30:532-544
  84. Andersson, J.A. and Roger, A.J., (2002) A cyanobacterial gene in non-photosynthetic protists - an early chloroplast acquisition in eukaryotes? Curr. Biol. 12:115-119
  85. O'Malley, M.A., Roger, A.J. and Doolittle, W.F., (2002) Can commercial protection be good for research? Nature 419:111
  86. Klein, M., Friedrich, M., Roger, A.J., Hugenholtz, P., Fishbain, S., Abicht, H., Blackall, L.L., Stahl, D.A. and Wagner, M., (2001) Multiple lateral transfer events of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. J. Bact. 183:6028-6035
  87. Morrison, H.G., Roger, A.J., Nystul, T.G., Gillin, F.D. and Sogin, M.L., (2001) Giardia lamblia expresses a proteobacterial-like3 DnaK homologue. Mol.Biol.Evol. 18:530-541
  88. Edgcomb, V.E., Roger, A.J., Simpson, A.G.B., Kysela, D.T. and Sogin, M.L., (2001) Evolutionary relationships among "jakobid" flagellates as indicated by alpha- and beta-tubulin phylogenies. Mol.Biol.Evol. 18:514-522
  89. Baldauf, S.L., Roger, A.J., Wenk-Siefert, I. and Doolittle, W.F., (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972-977
Last modified: 2011-07-29