Refereed papers (published):


2016:


  • Kamikawa, R., Shiratori, T., Ishida, K., Miyashita, H. and Roger, A.J. (2016) Group II intron-mediated trans-splicing in the gene-rich mitochondrial genome of an enigmatic eukaryote, Diphylleia rotans. Genome Biol. Evol. 8(2): 458-466.
  • Pánek, T., Zadrobílková, E., Walker, G., Brown, M.W., Gentekaki, E., Hroudová, M., Kang, S., Roger, A.J., Tice, A.K., Vlček, Č. and Čepička I. (2016) First multigene analysis of Archamoebae robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group. Mol Phylogenet Evol. 98: 41-51.

2015:


  • Torruella, G., de Mendoza, A., Grau-Bové, X., Antó, M., Chaplin, M.A., Del Campo, J., Eme, L., Pérez-Cordón, G., Whipps, C.M., Nichols, K.M., Paley, R., Roger, A.J., Sitjà-Bobadilla, A., Donachie, S. and Ruiz-Trillo, I. (2015) Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi. Curr Biol. 25: 2404-2410.
  • Stairs, C.W., Leger, M.M., and Roger, A.J. (2015) Diversity and origins of anaerobic metabolism in mitochondria and related organelles. Phil Trans R Soc Lond B Biol Sci 370(1678).
  • Gawryluk, R., Eme, L. and Roger, A.J. (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.
  • Leger, M.M., Petrů, M., Žárský, V., Eme, L., Vlček, Č., Harding, T., Lang, B.F., Eliáš, M., Doležal, P. and Roger, A.J. (2015) An ancestral bacterial division system is widespread in eukaryotic mitochondria. Proc. Natl. Acad. Sci. USA [Mar. 23, epub ahead of print].
  • Nývltová, E., Stairs, C.W., Hrdý, I., Rídl, J., Mach, J., Pačes, J., Roger, A.J. and Tachezy, J. (2015) Lateral gene transfer and gene duplication played a key role in the evolution of Mastigamoeba balamuthi hydrogenosomes. Mol. Biol. Evol. 32: 1039-55.

2014:


  • Eme, L., Sharpe, S.C., Brown, M.W. and Roger, A.J. (2014) On the age of eukaryotes: evaluating evidence from fossils and molecular clocks. Cold Spring Harb. Perspect. Biol. 6: pii: a016139.
  • Klimeš, V., Gentekaki, E., Roger AJ., and Eliáš, M. (2014) A large number of nuclear genes in the human parasite Blastocystis require mRNA polyadenylation to create functional termination codons. Genome Biol. Evol. 6: 1956-1961.
  • Tanifuji, G., Onodera N.T., Brown, M.W., Curtis, B.A., Roger A.J., Wong G., Melkonian M. and Archibald, J.M. (2014) Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae. BMC Genomics 15: 374.
  • 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.
  • Stairs, C.W., Eme, L, Brown, M.W., Mutsaers, C, Susko, E. Dellaire, G., Soanes, D.M., van der Giezen, M. and Roger, A.J. (2014) A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia. Curr. Biol. 24: 1176-1186.
  • Wang, H.C., Susko, E. and Roger A.J. (2014) An amino acid substitution-selection model adjusts residue fitness to improve phylogenetic estimation. Mol. Biol. Evol. 31: 779-792.
  • Kamikawa, R., Kolisko, M., Nishimura, Y., Yabuki, A., Brown, M.W., Ishikawa, S.A., Ishida, K., Roger, A.J., Hashimoto, T. and Inagaki, Y. (2014) Gene content evolution in discobid mitochondria deduced from the phylogenetic position and complete mitochondrial genome of Tsukubamonas globosa. Genome Biol. Evol. 6:306-15.
  • Tsaousis, A.D., Gentekaki, E., Eme, L., Gaston, D. and Roger, A.J. (2014) Evolution of the cytosolic iron-sulfur cluster assembly machinery in Blastocystis sp. and other microbial eukaryotes. Eukaryot. Cell 13: 143-153.

2013:


  • 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. and Inagaki, Y. (2013) Parallel re-modeling of EF-1a function: divergent EF-1a genes co-occur with EFL genes in diverse distantly related eukaryotes. BMC Evol. Biol. 13:131.
  • O'Malley, M.A., Simpson, A.G.B. and Roger, A.J. (2013) The other eukaryotes in light of evolutionary protistology. Biol. Philos. 28: 299-330.
  • Wang, H.-C., Susko, E. and Roger, A.J. (2013) The site-wise log-likelihood score is a good predictor of genes under positive selection. J. Mol. Evol. 76: 280-294.
  • Harding, T., Brown, M.W., Plotnikov, A., Selivanova, E., Park, J.S., Gunderson, J.H., Baumgartner, M., Silberman, J.D., Roger, A.J. and Simpson, A.G.B. (2013) Amoeba stages in the deepest branching heteroloboseans, including Pharyngomonas: Evolutionary and systematic implications. Protist 164: 272-286.
  • Susko, E. and Roger, A.J. (2013) Problems with estimation of ancestral frequencies under stationary models. Syst. Biol. 62: 330-338.
  • Gaston, D. and Roger, A.J. (2013) Functional divergence and convergent evolution in the plastid-targeted glyceraldehyde-3-phosphate dehydrogenases of diverse eukaryotic algae. PLOS ONE (in press)
  • Leger, M.M., Gawryluk, R.M., Gray, M.W. and Roger, A.J. (2013) The mitochondrion of Acanthamoeba castellanii has a hydrogenosomal type anaerobic ATP generation pathway. PLOS ONE (in press)
  • Suga, H., Chen, Z., de Mendoza, A., Sebe-Pedros, A., Brown, M.W., Kramer, E., Carr, M., Kerner, P., Vervoort, M., Sanchez-Pons, N., Torruella, G., Derelle, R., Manning, G., Lang, B.F., Russ, C., Haas, B.J., Roger, A.J., Nusbaum, C. and Ruiz-Trillo, I. (2013) The genome of Capsaspora reveals a complex unicellular prehistory of animals. Nature Communications (in press)
  • Brown, M.W., Sharpe, S., Silberman, J.D., Heiss, A., Lang, B. F., Simpson, A.G.B. and Roger, A.J. (2013) Phylogenomics demonstrates that breviate flagellates are related to opisthokonts: implications for the origin of genes involved in multicellularity. Submitted to Proc. Roy. Soc. B. (under revision)

2012:


  • Tsaousis, A.D., Ollagnier de Choudens, S., Gentekaki, E., Long, S., Gaston, D., Stechmann, A., Vinella D., Py, B., Fontecave, M., Barras, F., Lukeš, J. and Roger A.J. (2012) Evolution of Fe/S cluster biogenesis in the anaerobic parasite Blastocystis. Proc. Natl. Acad. Sci. USA 109: 10426-10431.
  • Brown, M.W., Kolisko, M., Silberman, J.D. and Roger, A.J. (2012) Aggregative multicellularity evolved independently in the eukaryotic supergroup Rhizaria. Curr. Biol. 22:1123-1127.
  • Liberles, D., Teichmann, S., Bahar, I., Bastolla, U., Bloom, J., Bornberg-Bauer, E., Colwell, L., de Koning, J., Dokholyan, N., Echave, J., Elofsson, A., Gerloff, D.,Goldstein, R., Grahnen, J., Holder, M., Lakner, C., Lartillot, N., Lovell, S., Naylor, G., Perica, T., Pollock, D., Pupko, T., Regan, L., Roger, A., Rubin0stein, N., Shakhnovich, E., Sjölander, K., Sunyaev, S., Teufel, A., Thorne, J., Thornton, J., Weinreich, D., Whelan, S. (2012) The interface of protein structure, protein biophysics, and molecular evolution. Protein Science 21:769-785.
  • Zou, L., Susko, E., Field, C. and Roger, A.J. (2012) Fitting nonstationary general-time-reversible models to obtain edge-lengths and frequencies for the Barry-Hartigan Model. Syst. Biol. 61: 927-40.
  • Takishita, K., Kolisko, M., Komatsuzaki, H., Yabuki, A., Inagaki, Y., Cepicka, I., Smejkalová, P., Silberman, J.D., Hashimoto, T., Roger, A.J. and Simpson, A.G. (2012) Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest relatives of 'Amitochondriate' Diplomonads and Retortamonads. Protist. 163:344-355.
  • Susko E, Roger A.J. (2012) The probability of correctly resolving a split as an experimental design criterion in phylogenetics. Syst. Biol. 61:811-821.
  • Takishita, K., Chikaraishi, Y., Leger, M.L., Kim, E., Yabuki, A., Ohkouchi, N. and Roger, A.J. (2012) Lateral transfer of tetrahymenol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen. Biology Direct 7: 5.
  • Torruella, G., Derelle, R., Paps, J., Lang, B.F., Roger, A.J., Shalchian-Tabrizi, K. and Ruiz-Trillo, I. (2012) Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single copy protein domains. Mol. Biol. Evol. 29: 531-544.
  • Tsaousis, A.D., Leger, M.L., 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. In Anoxia, Vol. 21: Cellular Origin, Life in Extreme Habitats and Astrobiology, pp. 51-81, A.V. Altenbach, J.M. Bernhard & J. Seckbach (Eds.), Springer.
  • Roger, A.J., Kolisko, M. and Simpson, A.G.B. (2012) Phylogenomic analysis. In Evolution of Virulence in Eukaryotic Microbes, pp. 44-69, L.D. Sibley, B.J. Howlett, and J. Heitman (Eds.), Wiley-Blackwell.

2011:


  • Gaston, D., Susko, E. and Roger, A.J. (2011) A phylogenetic mixture model for the identification of functionally divergent protein residues. Bioinformatics 27: 2655-2663.
  • Hampl, V., Stairs, C.W. and Roger A.J. (2011) The tangled past of eukaryotic enzymes involved in anaerobic metabolism. Mobile Genet. Elements 3: 71-74.
  • Kamikawa, R., Inagaki, Y., Roger, A.J. and Hashimoto, T. (2011) Splintrons in Giardia intestinalis: Spliceosomal introns in a split form. Commun. Integr. Biol. 4: 454-456.
  • Long, S., Changmai, P., Tsaousis, A.D., Skalický, T., Verner, Z., Wen, Y.Z., Roger, A.J. and Lukeš, J. (2011) Stage-specific requirement for Isa1 and Isa2 proteins in the mitochondrion of Trypanosoma brucei and heterologous rescue by human and Blastocystis orthologues. Mol. Microbiol. 81: 1403-1418.
  • 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.
  • 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. 60: 872-875.
  • Wang, H.-C., Susko, E. and Roger, A.J. (2011) Fast statistical tests for detecting heterotachy in protein evolution. Mol. Biol. Evol. 28: 2305-2315.
  • 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. Current Biol. 21: 311-315
  • 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

2010:


  • 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. Eukaryotic Cell 9: 1913-1924
  • 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
  • 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
  • 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
  • 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

2009:


  • Blouin C., Perry S., Lavell A., Susko E. and Roger A.J. (2009) Reproducing the manual annotation of multiple sequence alignment using a SVM classifier. Bioinformatics 25: 3093-3098
  • Wang, H.-C., Susko, E. and Roger, A.J. (2009) PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis. BMC Evol. Biol. 9:225
  • Kamikawa, R., Sanchez-Perez, 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
  • 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

2008:


  • 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
  • Sanchez-Perez, 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
  • Hamblin, K., Standley, D.M., Rogers, M.B., Stechmann, A., Roger, A.J., Maytum, R. and van der Giezen, M. (2008) Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase. Mol. Microbiol. 68: 1395-1405
  • 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, α-tubulin and HSP90 genes: implications for the evolutionary history of the double karyomastigont of diplomonads. BMC Evol. Biol. 8: 205
  • 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
  • Stechmann, A., Hamblin, K., Perez-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
  • 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
  • Wang, H.-C., Susko, E., Spencer, M. and Roger, A.J. (2008) Topological estimation biases with covarion evolution. J. Mol. Evol. 66: 50-60
  • Leigh, J., Susko, E., Baumgartner, M. and Roger, A.J. (2008) Testing congruence in phylogenomic analysis. Syst. Biol. 57: 104-115

2007:


  • 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

2006:


2005:


  • Keeling, P. J., Burger, G., Dumford, D. G., Lang, B. F., Lee, R. W., Pearlman, R. E., Roger, A. J., Gray, M. W. (2005) The tree of eukaryotes. Trends Ecol Evol. 20(12), 670-6.

2004:


2003:


2002:


2001:


2000:


1999:


1998:


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

1996:


1995:


1994:


1993:



Invited Review Articles, Commentaries/Book Chapters:


  • Roger, A.J. (1999) Reconstructing early events in eukaryotic evolution. American Naturalist 154: S146-S163. (refereed review article)
  • Roger, A.J. (1999) Changing views on the early evolution of eukaryotes. Proceedings of the DGHM Congress on Microbial Evolution & Infection (in press - accepted November, 1998)

Abstracts:


  • Roger, A.J., Svärd, S.G., Gillin, F.D. and Sogin, M.L. (1998) Protists without mitochondria: an update on the status of the Archezoa. J. Euk. Microbiol. 45:5A.