Department of Biochemistry and Molecular Biology

Dalhousie University

Andrew J. Roger

Professor

roger
Department of Biochemistry and Molecular Biology

Email: andrew.roger@dal.ca
Phone: 902-494-2620
Phone: 902-494-2881
Mailing Address: 
5850 College Street, Room 8-C1
Sir Charles Tupper Medical Building
PO Box 15000
Halifax, Nova Scotia, Canada B3H 4R2
 

Education

  • PhD, Dalhousie University

Academic Positions

Research Topics

Genome, Organelle and Protein Evolution

Research

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

Current Lab Members

Tugba Nur Atalay Grad Student (MSc)
Min Cho Grad Student (MSc)
Marlena Dlutek Lab Manager/Technician
Katherine Dunn Research Associate (co-supervised with J. Archibald)
Marycolette Ezediokpu Postdoctoral Fellow
Ryo Harada Postdoctoral Scholar
Joran Martijn Research Associate
Charley McCarthy Postdoctoral Fellow
Greg Seaton
 Grad Student (PhD)
Jason Shao Grad Student (MSc)
Kelsey Williamson Grad Student (PhD)
Dandan Zhao Bioinformatician

 

Publications

  1. Muñoz-Gómez S.A., Cadena L.R., Gardiner A.T., Leger M.M., Sheikh S., Connell L.B., Bily T., Kopejtka K., Beatty J.T., Koblížek M., Roger, A.J., Slamovits C.H., Lukeš J. and Hashimi H. (2023) Intracytoplasmic-membrane development in alphaproteobacteria involves the homolog of the mitochondrial crista-developing protein Mic60. Curr. Biol. 33:1099-1111
  2. Higuera A., Salas-Leiva D.E., Curtis B.A., Patiño L.H., Zhao D., Jerlström-Hultqvist J, Dlutek M., Muñoz M., Roger A.J., Ramírez J.D. (2023) Draft genomes of Blastocystis subtypes from human samples of Colombia. Parasites & Vectors 1:1-10.
  3. Hess S., Williams S.K., Busch A., Irisarri I., Delwiche C.F., de Vries S., Darienko T., Roger A.J., Archibald J.M., Buschmann H., von Schwartzenberg K. and de Vries J. (2022) A phylogenomically informed five-order system for the closest relatives of land plants. Curr. Biol. 32:4473-4482.e7
  4. Gerbracht J.V., Harding T., Simpson A.G.B., Roger A.J., Hess S. (2022) Comparative transcriptomics reveals the molecular toolkit used by an algivorous protist for cell wall perforation. Curr. Biol. 32:3374-3384. e5
  5. Mathavarajah S., Vergunst K.L., Williams, S.K., He R., Maliougina M., Habib E.B., Park M., Salsman J., Roy s., Braasch I. Roger A.J., Langelaan D.N. and Dellaire G. (2022) PML7 and PML-like exonucleases restrict retrotransposons in jawed vertebrates. bioRxiv 2022.07. 29.501749 [now ‘in press’ in Nucleic Acids Research]
  6. Baños, H., Susko E. and Roger A.J. (2022) Are profile mixture models overparameterized? bioRxiv https://doi.org/10.1101/2022.02.18.481053
  7. Youssef N., Susko E., Roger A.J. and Bielawski J.P. (2022) Evolution of amino acid propensities under stability-mediated epistasis. Mol. Biol. Evol. https://doi.org/10.1093/molbev/msac030
  8. Muñoz-Gómez S.A., Susko E., Williamson K., Eme L., Slamovits C.H., Moreira D., López-García P. and Roger A.J. (2022) Site-and-branch-heterogeneous analyses of an expanded dataset favors mitochondria as sister to known Alphaproteobacteria. Nat. Ecol. Evol. https://doi.org/10.1038/s41559-021-01638-2
  9. Salas-Leiva D.E., Tromer E.C., Curtis B.A., Jerlström-Hultqvist J., Kolisko M., Yi Z., Salas-Leiva J., Gallot-Lavallée L., Kops G.J.P.L., Archibald J.M., Simpson A.G.B., Roger A.J. (2021) A free-living protist that lacks canonical eukaryotic DNA replication and segregation systems. Nat. Commun. 12: 6003. https://doi.org/10.1038/s41467-021-26077-2
  10. Stairs C.W., Táborski P., Kolisko M., Pánek T., Eme L., Hradilová M., Vlček C., Jerlström-Hultqvist J., Roger A.J. and Čepička I. (2021) Anaeramoebae are a deeply divergent lineage of eukaryotes that clarify the transition from anaerobic mitochondria to hydrogenosomes. Curr. Biol. 31: 5605-5612
  11. Tice AK, Žihala D, Pánek T, Jones RE, Salomaki E, Nenarokov S, Burki F, Eliáš M, Eme L, Roger A.J., Rokas A, Shen X, Strassert JFH, Kolísko M, Brown MW. (2021). PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. PLoS Biol. https://doi.org/10.1371/journal.pbio.3001365
  12. Pipaliya S., Santos R., Salas-Leiva D., Balmer E.A., Wirdnam C.D., Roger A.J., Hehl A.B., Faso, C. and Dacks J.B. (2021) Unexpected organellar locations of ESCRT machinery in Giardia intestinalis and complex evolutionary dynamics spanning the transition to parasitism in the lineage Fornicata. BMC Biol. https://doi.org/10.1101/2021.02.11.430673
  13. Susko E., Steel, M. and Roger, A.J. (2021) Conditions under which distributions of edge length ratios on phylogenetic trees can be used to order evolutionary events. J. Theor. Biol. 526:110788
  14. Zhang, T., Li C., Zhang Z., Wang C., Roger A.J. and Gao F. (2021) Characterization and comparative analyses of mitochondrial genomes in single-celled eukaryotes to shed light on the diversity and evolution of linear molecular architecture. Int. J. Mol. Sci. 22:2546
  15. Susko E. and Roger, A.J. (2021) Long branch attraction biases in phylogenetics. Syst. Biol. 70:838-843
  16. Žárský V., Klimeš V., Pačes J., Vlček C., Hradilová M., Beneš V., Nývltová E., Hrdý I., Pyrih J., Mach J., Barlow L., Stairs C.W., Eme L., Hall N., Eliáš M., Dacks J.B., Roger, A.J. and Tachezy J. (2021) The Mastigamoeba balamuthi genome and the nature of the free-living ancestor of Entamoeba. Mol. Biol. Evol. (in press) https://doi.org/10.1093/molbev/msab020
  17. Roger A.J. (2021) Thomas Cavalier-Smith (1942-2021) Curr. Biol. 31: R977-R981 (Obituary)
  18. Youssef N., Susko E., Roger A.J. and Bielawski J.P. (2021) Shifts in amino acid preferences as proteins evolve: a synthesis of experimental and theoretical work. Protein Sci. https://doi.org/10.1002/pro.4161
  19. Gray M.W., Burger, G, Derelle R., Klimeš V, Leger M.M., Sarrasin M., Vlček C., Roger A.J., Eliáš M., Lang B.F. (2020) The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome. BMC Biology 18: 22 https://doi.org/10.1186/s12915-020-0741-6
  20. Roger A.J., Susko E. and Leger M.M. (2021) Evolution: Reconstructing the timeline of eukaryogenesis (Dispatch). Curr. Biol. 31: R193-R196
  21. Sibbald S.J., Eme L., Archibald J.M. and Roger A.J. (2020) Lateral gene transfer mechanisms and pan-genomes in eukaryotes. Trends Parasitol. 36:927-941
  22. Burki, F., Roger, A.J., Brown, M.W. and Simpson, A.G.B. (2020) The New Tree of Eukaryotes. Trends Ecol. Evol. 35: 43-55.
  23. Susko E. and Roger, A.J. (2020) On the use of information criteria for model selection in phylogenetics. Mol. Biol. Evol. 37:549-562, doi: 10.1093/molbev/msz228.
  24. Karnkowska A., Treitli S.C., Brzoň O., Novák L., Vacek V., Soukal P., Barlow L.D., Herman E.K., Pipaliya S., Pánek T., Žihala D., Petrželková R., Butenko A., Eme L., Stairs C.W., Roger A.J., Eliáš M., Dacks J.B. and Hampl V. (2019) The oxymonad genome displays canonical eukaryotic complexity in the absence of a mitochondrion. Mol. Biol. Evol. 36: 2292-2312
  25. Hess, S., Eme, L., Roger, A.J. and Simpson, A.G.B. (2019) A natural toroidal microswimmer propelled by a rotary eukaryotic flagellum. Nature Microbiol. 4:1620-1626.
  26. Wang, H.-C., Susko, E. and Roger, A.J. (2019) The relative importance of modeling site pattern heterogeneity versus partition-wise heterotachy in phylogenomic inference. Syst. Biol. 68: 1003-1019.
  27. Muñoz-Gómez, S.A., Hess, S., Burger, G., Lang, B.F., Susko, E., Slamovits, C.H. and Roger, A.J. (2019) An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins. eLife, Feb. 25; 8. pii: e42535.
  28. Cenci, U., Sibbald, S.J., Curtis, B.A., Kamikawa, R., Eme, L., Moog, D., Henrissat, B., Maréchal, E., Chabi, M., Djemiel, C., Roger, A.J., Kim, E. and Archibald, J.M. (2018) Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights in the evolution of secondary plastids. BMC Biol. 16: 137.
  29. Pyrihová, E., Motycková, A., Voleman, L., Wandyszewska, N., Fišer, R., Seydlová, G., Roger, A.J., Kolísko, M. and Doležal, P. (2018) A single tim translocase in the mitosomes of Giardia intestinalis illustrates convergence of protein import machines in anaerobic eukaryotes. Genome Biol. Evol. 10: 2813-2822.
  30. Lax, G., Eglit, Y., Eme, L., Bertrand, E.M., Roger, A.J. and Simpson, A.G.B. (2018) Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes. Nature 564: 410-414. 
  31. Roger, A.J. and Susko, E. (2018) Molecular clocks provide little information to date methanogenic archaea. Nature Ecol. Evol. 2: 1676-1677.
  32. Brown, M.W., Heiss, A.A., Kamikawa, R., Inagaki, Y., Yabuki, A., Tice, A.K., Shiratori, T., Ishida, K.I., Hashimoto, T., Simpson, A.G.B. and Roger, A.J., (2018) Phylogenomics places orphan protistan lineages in a novel eukaryotic super-group. Genome Biol. Evol. 10:427-433
  33. Heiss, A., Kolisko, M., Ekelund, F., Brown, M.W., Roger, A.J. and Simpson, A.G. , (2018) Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes. Roy. Soc. Open Sci. :
  34. Leger, M.M., Eme, L., Stairs, C.W. and Roger, A.J., (2018) Demystifying eukaryote lateral gene transfer. Bioessays 40:e1700242
  35. Roger, A.J. , (2018) Reply to ‘Eukaryote lateral gene transfer is Lamarckian.’ Nature Ecol. Evol. 2:755
  36. Stairs, C.W., Eme, L., Muñoz-Gómez, S., Cohen, A., Dellaire, G., Shepherd, J.N., Fawcett, J.P. and Roger, AJ., (2018) Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis. Elife 7:e34292
  37. Susko, E., Lincker, L. and Roger, A.J., (2018) Accelerated estimation of frequency classes in site-heterogeneous profile mixture models. Mol. Biol. Evol. 35:1266-1283
  38. Wang, H.-C., Minh, B.Q., Susko, E. and Roger, A.J., (2018) Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst. Biol. 67:216- 235
  39. Stairs, C., Eme, L., Muñoz-Gómez, S.A., Cohen, A., Dellaire, G., Shepherd, J., Fawcett, J., and Roger, A.J., (2018) Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis. eLife e34292:
  40. Muñoz-Gómez, S.A., Wideman, J.G., Roger, A.J., and Slamovits, C.H., (2017) The origin of mitochondrial cristae from alphaproteobacteria. Mol. Biol. Evol. 34(4):943-956: [PubMed] [Article]
  41. Roger, A.J., Muñoz-Gómez, S.A., and Kamikawa, R., (2017) The Origin and Diversification of Mitochondria. Curr. Biol. 27(21):R1177-R1192 [Article]
  42. Eme, L., Gentekaki, E., Curtis, B., Archibald, J.M. and Roger A.J., (2017) Lateral gene transfer in the adaptation of the anaerobic parasite Blastocystis to the gut. Curr. Biol. 27:807-820
  43. Gentekaki, E., Curtis, B.A., Stairs, C.W., Klimeš, V., Eliáš, M., Salas-Leiva, D.E., Herman, E.K., Eme, L., Arias, M.C., Henrissat, B., Hilliou, F., Klute, M.J., Suga, H., Malik, S.B., Pightling, A.W., Kolisko, M., Rachubinski, R.A., Schlacht, A., Soanes, D.M., Tsaousis, A.D., Archibald, J.M., Ball, S.G., Dacks, J.B., Clark, C.G., van der Giezen, M. and Roger, A.J., (2017) Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis. PLoS Biol. 15:e2003769
  44. Harding, T., Roger, A.J. and Simpson, A.G.B., (2017) Adaptations to high salt in a halophilic protist: differential expression and gene acquisitions through duplications and gene transfers. Front Microbiol. 8:944
  45. Kang, S., Tice, A.K., Spiegel, F.W., Silberman, J.D., Pánek, T., Cepicka, I., Kostka, M., Kosakyan, A., Alcântara, D.M., Roger, A.J., Shadwick L.L., Smirnov A., Kudryavstev A., Lahr D.J.G. and Brown, M.W., (2017) Between a pod and a hard test: the deep evolution of amoebae. Mol. Biol. Evol. 34:2258-2270
  46. 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. and Roger, A.J. (, (2017) Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes. Nature Ecol. Evol. 1:0092
  47. Pánek, T., Žihala, D., Sokol, M., Derelle, R., Klimeš, V., Hradilová, M., Zadrobílková, E., Susko, E., Roger, A.J., Cepǐcka, I. and Eliáš, M. (, (2017) Nuclear genetic codes with a different meaning of the UAG and the UAA condon. BMC Biol. 15:8
  48. Takishita, K., Chikaraishi, Y.,Tanifuji, G., Ohkouchi, N., Hashimoto, T., Fujikura, K. and Roger, A.J., (2017) Microbial eukaryotes that lack sterols. J. Eukaryot. Microbiol. 64:897-900
  49. Yang, J., Harding, T., Kamikawa, R., Simpson, A.G.B. and Roger, A.J., (2017) Mitochondrial genome evolution and a novel RNA editing system in deep-branching heteroloboseids. Genome Biol. Evol. 9:1161-1174
  50. Muñoz-Gómez, S.A., and Roger, A.J., (2016) Leaving negative ancestors behind. eLife. 5:e20061 [Article]
  51. Gawryluk RM, Eme L, Roger AJ., (2015) Gene fusion, fission, lateral transfer, and loss: Not-so-rare events in the evolution of eukaryotic ATP citrate lyase. Mol Phylogenet Evol. 91:12-16 [PubMed]
  52. Leger MM, Petrů M, Žárský V, Eme L, Vlček Č, Harding T, Lang BF, EliᚠM, Doležal P, Roger AJ., (2015) An ancestral bacterial division system is widespread in eukaryotic mitochondria. Proc Natl Acad Sci U S A. pii: 201421392: [PubMed]
  53. Nývltová E, Stairs CW, Hrdý I, Rídl J, Mach J, Pačes J, Roger AJ, Tachezy J., (2015) Lateral gene transfer and gene duplication played a key role in the evolution of Mastigamoeba balamuthi hydrogenosomes. Mol Biol Evol. 2(4):1039-55 [PubMed]
  54. Sharpe, S.C., Eme, L., Brown, M.W. and Roger, A.J. , (2015) Timing the origins of multicellular eukaryotes through phylogenomics and relaxed molecular clock analyses. Evolutionary Transitions to Multicellular Life, Advances in Marine Genomics 2, I. Ruiz-Trillo and A.M. Nedelcu (Eds.) Springer Science:In Press
  55. Stairs CW, Eme L, Brown MW, Mutsaers C, Susko E, Dellaire G, Soanes DM, van der Giezen M, Roger AJ., (2014) A SUF Fe-S Cluster Biogenesis System in the Mitochondrion-Related Organelles of the Anaerobic Protist Pygsuia Curr. Biol 24(11):1176-1186 [PubMed] [Article]
  56. Eme L, Sharpe SC, Brown MW, Roger AJ., (2014) On the age of eukaryotes: evaluating evidence from fossils and molecular clocks. Cold Spring Harb Perspect Biol. 1;6(8): [PubMed]
  57. Klimeš V, Gentekaki E, Roger AJ, EliᚠM., (2014) A large number of nuclear genes in the human parasite blastocystis require mRNA polyadenylation to create functional termination codons. Genome Biol Evol. 6(8):1956-61 [PubMed]
  58. Tanifuji G, Onodera NT, Brown MW, Curtis BA, Roger AJ, Ka-Shu Wong G, Melkonian M, Archibald JM., (2014) Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae. BMC Genomics. 15(1):374 [PubMed]
  59. Kamikawa R, Kolisko M, Nishimura Y, Yabuki A, Brown MW, Ishikawa SA, Ishida K, Roger AJ, Hashimoto T, Inagaki Y., (2014) Gene content evolution in Discobid mitochondria deduced from the phylogenetic position and complete mitochondrial genome of Tsukubamonas globosa. Genome Biol Evol. 6(2):306-15 [PubMed]
  60. Wang HC, Susko E, Roger AJ., (2014) An amino acid substitution-selection model adjusts residue fitness to improve phylogenetic estimation. Mol Biol Evol. 31(4):779-92 [PubMed]
  61. Tsaousis AD, Gentekaki E, Eme L, Gaston D, Roger AJ., (2014) Evolution of the cytosolic iron-sulfur cluster assembly machinery in Blastocystis species and other microbial eukaryotes. Eukaryot Cell. 13(1):143-53 [PubMed]
  62. 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. and Lynn, DH. , (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. 78C:36-42
  63. Leger MM, Gawryluk RM, Gray MW, Roger AJ., (2013) Evidence for a hydrogenosomal-type anaerobic ATP generation pathway in Acanthamoeba castellanii. PLoS One. 8(9):e69532 [PubMed] [Article]
  64. Brown MW, Sharpe SC, Silberman JD, Heiss AA, Lang BF, Simpson AG, Roger AJ., (2013) Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads. Proc Biol Sci. 280(1769):20131755 [PubMed]
  65. Suga H1, Chen Z, de Mendoza A, Sebé-Pedrós A, Brown MW, Kramer E, Carr M, Kerner P, Vervoort M, Sánchez-Pons N, Torruella G, Derelle R, Manning G, Lang BF, Russ C, Haas BJ, Roger AJ, Nusbaum C, Ruiz-Trillo I., (2013) The Capsaspora genome reveals a complex unicellular prehistory of animals. Nat Commun. 4:2325 [PubMed]
  66. Gaston D, Roger AJ., (2013) Functional divergence and convergent evolution in the plastid-targeted glyceraldehyde-3-phosphate dehydrogenases of diverse eukaryotic algae. PLoS One. 8(7):70396 [PubMed]
  67. Kamikawa R, Brown MW, Nishimura Y, Sako Y, Heiss AA, Yubuki N, Gawryluk R, Simpson AG, Roger AJ, 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 Evol Biol. 13:131 [PubMed]
  68. Wang HC, Susko E, Roger AJ., (2013) The site-wise log-likelihood score is a good predictor of genes under positive selection. J Mol Evol. 6(5):280-94 [PubMed]
  69. Harding T, Brown MW, Plotnikov A, Selivanova E, Park JS, Gunderson JH, Baumgartner M, Silberman JD, Roger AJ, Simpson AG., (2013) Amoeba stages in the deepest branching heteroloboseans, including Pharyngomonas: evolutionary and systematic implications. Protist 164(2):272-86 [PubMed]
  70. Susko E, Roger AJ., (2013) Problems with estimation of ancestral frequencies under stationary models. Syst Biol. 62(2):330-8 [PubMed]
  71. Tsaousis, A.D, Leger, M. M., Stairs C.W., and Roger, A.J., (2012) The Biochemical Adaptations of Mitochondrion-Related Organelles of Parasitic and Free-Living Microbial Eukaryotes to Low Oxygen Environments Anoxia: Cellular Origin, Life in Extreme Habitats and Astrobiology 21(2):51-81
  72. Tsaousis AD, Ollagnier de Choudens S, Gentekaki E, Long S, Gaston D, Stechmann A, Vinella D, Py B, Fontecave M, Barras F, Lukeš J, Roger AJ., (2012) Evolution of Fe/S cluster biogenesis in the anaerobic parasite Blastocystis. Proc Natl Acad Sci U S A. 109(26):10426-31 [PubMed]
  73. Brown MW, Kolisko M, Silberman JD, Roger AJ., (2012) Aggregative multicellularity evolved independently in the eukaryotic supergroup Rhizaria. Curr Biol. 22(12):1123-7 [PubMed]
  74. Zou L, Susko E, Field C, Roger AJ., (2012) Fitting nonstationary general-time-reversible models to obtain edge-lengths and frequencies for the barry-hartigan model. Syst Biol. 61(6):927-40 [PubMed]
  75. Susko E1, Roger AJ, (2012) The probability of correctly resolving a split as an experimental design criterion in phylogenetics. Syst Biol. 61(5):811-21 [PubMed]
  76. Takishita K, Chikaraishi Y, Leger MM, Kim E, Yabuki A, Ohkouchi N, Roger AJ, (2012) Lateral transfer of tetrahymanol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen. Biol Direct. 7:5 [PubMed]
  77. 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
  78. 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]:
  79. 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]:
  80. 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
  81. 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
  82. 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
  83. Barberà, 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
  84. 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
  85. 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
  86. 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
  87. 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
  88. 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]
  89. 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
  90. 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
  91. 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
  92. 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]
  93. 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
  94. Leigh, J., Susko, E., Baumgartner, M. and Roger, A.J. , (2008) Testing congruence in phylogenomic analysis. Syst. Biol. 57:104-115
  95. Wang, H.-C., Susko, E., Spencer, M. and Roger, A.J. , (2008) Topological estimation biases with covarion evolution. J.Mol.Evol. 66:50-60
  96. 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
  97. 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]
  98. 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
  99. 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
  100. 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
  101. 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
  102. 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
  103. 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
  104. 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
  105. Susko, E. and Roger, A.J. , (2007) On reduced amino acid alphabets for phylogenetic inference. Mol. Biol. Evol. 24:2139-2150
  106. 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
  107. 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]
  108. 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
  109. 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
  110. 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]
  111. 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
  112. Spencer, M., Susko, E. and Roger, A.J., (2006) Modeling prokaryote gene content. Evol. Bioinf. Online 2:165-186
  113. 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
  114. 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
  115. 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
  116. 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
  117. 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
  118. 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
  119. 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
  120. 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
  121. 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
  122. Roger, A. J., (2006) Telling evolutionary tales (book review). Nat.Rev.Genet. 38:1357
  123. 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]
  124. 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
  125. 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
  126. 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
  127. 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
  128. Spencer, M., Susko, E. and Roger, A.J., (2005) Likelihood, parsimony and heterogeneous evolution. Mol. Biol. Evol. 22:1161-1164
  129. 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]
  130. Simpson, A.G.B. and Roger, A. J., (2004) The real 'kingdoms' of eukaryotes. Curr. Biol. 14:R693-R696
  131. 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
  132. 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
  133. 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
  134. 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
  135. 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
  136. 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
  137. 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
  138. 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
  139. 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]
  140. 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]
  141. 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
  142. 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]
  143. 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
  144. 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
  145. 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
  146. 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
  147. 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
  148. 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]
  149. Simpson, A.G.B. and Roger, A.J., (2002) Eukaryote evolution: Getting to the root of the problem. Curr. Biol. 12:R691-R693
  150. Simpson, A.G.B., MacQuarrie, E. and Roger, A.J., (2002) Early origin of canonical introns. Nature 419:270
  151. Roger, A.J., and Silberman, J.D., (2002) Mitochondria in hiding. Nature 418:828-829
  152. 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
  153. 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
  154. 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
  155. 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
  156. 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]
  157. 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
  158. 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
  159. 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
  160. 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
  161. O'Malley, M.A., Roger, A.J. and Doolittle, W.F., (2002) Can commercial protection be good for research? Nature 419:111
  162. 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
  163. 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
  164. 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
  165. 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