Roger Lab

Refereed papers (published):

2018:

Roger, A.J. and Susko, E. (2018) Molecular clocks provide little information to date methanogenic archaea. Nature Ecol. Evol. 2: 1676-1677.

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.

Pyrihová, E., Motycková, A., Voleman, L., Wandyszewska, N., Fišer, R., Seydlová, G., Roger, A., 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.

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.

Roger, A.J. (2018) Q & A. Curr. Biol. 28: R1233-R1234.

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.

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., 5: 171707.

Leger, M.M., Eme, L., Stairs, C.W. and Roger, A.J. (2018) Demystifying eukaryote lateral gene transfer (Response to Martin 2017 DOI: 10.1002/bies.201700115). Bioessays 40: e1700242.

Roger, A.J. (2018) Reply to ‘Eukaryote lateral gene transfer is Lamarckian.’ Nature Ecol. Evol. 2: 755.

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 Apr. 26; 7. pii: e34292. doi: 10.7554/ eLife. 34292. [Epub ahead of print]

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.

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.

2017:

Gentekaki, E., Curtis, B.A., Stairs, C.W., Klimes, V., Elias, 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.

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.

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.

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., May 16 [epub ahead of print].

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.

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.

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.

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 Biology 15: 8.

Munoz-Gomez, S.A., Wideman, J.G., Roger, A.J. and Slamovits, C.H. (2017) The origin of mitochondrial cristae from alphaproteobacteria. Mol. Biol. Evol. 34: 943-956.

Roger, A.J., Munoz-Gomez, S.A. and Kamikawa, R. (2017) The origin and diversification of mitochondria. Curr. Biol., 27: R1177-R1192.

2016:

Wang, H., Susko, E. and Roger A.J. (2016) Split-specific bootstrap measures for quantifying phylogenetic stability and the influence of taxon selection. Mol. Phylogenet. Evol. 105:114-25.

Gawryluk, R., Kamikawa, R., Stairs, C.W., Brown, M.W., Silberman, J.D. and Roger, A.J. (2016) The earliest stages of mitochondrial adaptation to low oxygen revealed in a novel rhizarian. Curr. Biol. 24;26(20):2729-2738.

Xu, F., Jerlström-Hultqvist, J., Kolisko, M., Simpson, A.G., Roger, A.J., Svärd, S.G. and Andersson, J.O. (2016) On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1. BMC Biol. 14: 62.

Leger, M.M., Eme, L., Hug, L.A. and Roger, A.J. (2016) Novel hydrogenosomes in the microaerophilic jakobid Stygiella incarcerata. Mol. Biol. Evol. doi: 10.1093/molbev/msw103

Pyrih, J., Martincova, E., Kolísko, M., Stojanovová, D., Basu, S., Harant, K., Haindrich, A.C., Lukeš, J., Roger, A.J. and Tachezy, J. (2016) Cytosolic and mitosomal localization of the cytosolic iron sulfur cluster assembly system in the anaerobic protist Giardia intestinalis. Mol. Microbiol. 102: 701-714

Dacks, J., Field, M., Buick, R., Eme, L., Gribaldo, S., Roger, A.J., Brochier, C. and Devos, D.P. (2016) The changing view of eukaryogenesis: Fossils, cells, lineages and fusions. J. Cell Sci. 129, 3695-3703

Hamann, E., Gruber-Vodicka, H., Kleiner, M., Tegetmeyer, H., Riedel, D., Littmann, S., Chen, J., Milucka, J., Viehweger, B., Becker, K., Dong, X., Stairs, C.W., Hinrichs, K., Brown, M.W., Roger, A.J. and Strous, M. (2016) Environmental Breviatea harbor mutualistic Arcobacter epibionts. Nature 534: 254-258.

Karnkowska, A., Vacek, V., Zubáčová, Z., Treitli, S.C., Petrželková, R., Eme, L., Novák, L., Žárský, V., Barlow, L.D., Herman, E.K., Soukal, P., Hroudová, M., Doležal, P., Stairs, C.W., Roger, A.J., Eliáš, M., Dacks, J.B., Vlček, Č. and Hampl V. (2016) A eukaryote without a mitochondrial organelle. Curr. Biol. 26: 1274-1284.

Tommy Harding; Matthew W. Brown; Alastair G.B. Simpson; Andrew J. Roger (2016) Osmoadaptative strategy and its molecular signature in obligately halophilic heterotrophic protistss. Genome Biol. Evol. doi: 10.1093/gbe/evw152

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

Wu, J., Susko, E., Roger, A. J. (2007) An independent heterotachy model and its implications for phylogeny and divergence time estimation. Mol. Phylogenet. Evol. 46: 801-806

Susko, E., Roger, A. J. (2007) On reduced amino acid alphabets for phylogenetic inference. Mol. Biol. Evol. 24(9): 2139-50.

Hug, L. A., Roger, A. J. (2007) The impact of fossils and taxon sampling on ancient molecular dating analyses. Mol. Biol. Evol. 24(8): 1889-97.

Rodriguez-Ezpeleta, N., Brinkmann, H., Burger, G., Roger, A. J., Gray, M. W., Philippe, H., Lang, B. F. (2007) Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans. Curr Biol. 17(16): 1420-5.

Andersson, J. O., Sjogren, A. M., Horner, D. S., Murphy, C. A., Dyal, P. L., Svard, S. G., Logsdon, J. M. Jr., Ragan, M. A., Hirt, R. P., Roger, A. J. (2007) A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryotic genome evolution. BMC Genomics, 8:51.

Ruiz-Trillo, I., Burger, G., Holland, P. W., King, N., Lang, B. F., Roger, A. J., Gray, M. W.(2007) The origins of multicellularity: a multi-taxon genome initiative. Trends Genet. 23(3):113-8.

Pepke, S. L., Butt, D., Nadeau, I., Roger, A. J., Blouin, C. (2007) Using confidence set heuristics during topology search improves the robustness of phylogenetic inference. J. Mol. Evol. 64(1):80-9.

Wang, H. C., Spencer, M., Susko, E., Roger, A. J. (2007) Testing for covarion-like evolution in protein sequences. Mol. Biol. Evol. 24(1): 294-305.

2006:

Goddard, M. R., Leigh, J., Roger, A. J., Pemberton, A. J. (2006) Invasion and persistence of a selfish gene in the cnidaria. PLoS ONE, 1:e3.

Stechmann, A., Baumgartner, M., Silberman, J. D., Roger, A. J. (2006) The glycolytic pathway of Trimastix pyriformis is an evolutionary mosaic. BMC Evol. Biol. 6:101.

Ruiz-Trillo, I., Lane, C. E., Archibald, J. M., Roger, A. J. (2006) Insights into the evolutionary origin and genome architecture of the unicellular opisthokonts Capsaspora owczarzaki and Sphaeroforma arctica. J. Eukaryot. Microbiol. 53(5): 379-84.

Roger, A. J., Hug, L. A., (2006) The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation. Philos Trans R Soc Lond B Biol Sci, 361(1470), 1039-54.

Inagaki, Y., Roger, A. J. (2006) Phylogenetic estimation under codon models can be biased by codon usage heterogeneity. Mol Phylogenet Evol 40(2), 428-34.

Andersson, J. O., Hirt, R. P., Foster, P. G., Roger, A. J. (2006) Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes. BMC Evol Biol, Mar 21, 6, 27.

Inagaki, Y., Susko, E., Roger, A. J. (2006) Recombination between elongation factor 1alpha genes from distantly related archaeal lineages. PNAS 103(12), 4528-4533.

Wang, H. C., Susko, E., 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(3), 681-684.

Simpson, A. G., Inagaki, Y., Roger, A. J. (2006) Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes. Mol Biol Evol 23(3), 615-625.

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.

Susko, E., Spencer, M., Roger, A. J. (2005) Biases in phylogenetic estimation can be caused by random sequence segments. J Mol Evol 61(3), 351-359.

Butt, D., Roger, A. J., Blouin, C. (2005) libcov: a C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny. BMC Bioinformatics 6(1), 138.

Spencer, M., Susko, E. and Roger, A. J. (2005). Likelihood, Parsimony, and Heterogeneous Evolution. Mol Biol Evol 22, 1161-1164.

Blouin, C., Butt, D. and Roger, A. J. (2005). Impact of taxon sampling on the estimation of rates of evolution at sites. Mol Biol Evol 22, 784-91.

Andersson, J. O., Sarchfield, S. W. and Roger, A. J. (2005). Gene transfers from nanoarchaeota to an ancestor of diplomonads and parabasalids. Mol Biol Evol 22, 85-90.

2004:

Susko, E., Inagaki, Y. and Roger, A. J. (2004). On inconsistency of the neighbor-joining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled. Mol Biol Evol 21, 1629-42.

Susko, E. and Roger, A. J. (2004). Estimating and comparing the rates of gene discovery and expressed sequence tag (EST) frequencies in EST surveys. Bioinformatics 20, 2279-87.

Simpson, A. G., Gill, E. E., Callahan, H. A., Litaker, R. W. and Roger, A. J. (2004). Early evolution within kinetoplastids (euglenozoa), and the late emergence of trypanosomatids. Protist 155, 407-22.

Simpson, A. G. and Roger, A. J. (2004). The real 'kingdoms' of eukaryotes. Curr Biol 14, R693-6.

Simpson, A. G. and Roger, A. J. (2004). Protein phylogenies robustly resolve the deep-level relationships within Euglenozoa. Mol Phylogenet Evol 30, 201-12.

Silberman, J. D., Collins, A. G., Gershwin, L. A., Johnson, P. J. and Roger, A. J. (2004). Ellobiopsids of the genus Thalassomyces are alveolates. J Eukaryot Microbiol 51, 246-52.

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, R946-7.

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, 1340-9.

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. Protein Sci 13, 608-16.

2003:

Susko, E., Field, C., Blouin, C. and Roger, A. J. (2003). Estimation of rates-across-sites distributions in phylogenetic substitution models. Syst Biol 52, 594-603.

Inagaki, Y., Blouin, C., Susko, E. and Roger, A. J. (2003). Assessing functional divergence in EF-1alpha and its paralogs in eukaryotes and archaebacteria. Nucleic Acids Res 31, 4227-37.

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? Philos Trans R Soc Lond B Biol Sci 358, 39-57; discussion 57-8.

Dacks, J. B., Davis, L. A., Sjogren, A. M., Andersson, J. O., Roger, A. J. and Doolittle, W. F. (2003). Evidence for Golgi bodies in proposed 'Golgi-lacking' lineages. Proc Biol Sci 270 Suppl 2, S168-71.

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, 790-7.

Andersson, J. O. and Roger, A. J. (2003). Evolution of glutamate dehydrogenase genes: evidence for lateral gene transfer within and between prokaryotes and eukaryotes. BMC Evol Biol 3, 14.

Andersson, J. O., Sjogren, A. M., Davis, L. A., 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.

2002:

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, 1514-23.

Simpson, A. G., Lukes, J. and Roger, A. J. (2002). The evolutionary history of kinetoplastids and their kinetoplasts. Mol Biol Evol 19, 2071-83.

Simpson, A. G. and Roger, A. J. (2002). Eukaryotic evolution: getting to the root of the problem. Curr Biol 12, R691-3.

Simpson, A. G., Roger, A. J., Silberman, J. D., Leipe, D. D., Edgcomb, V. P., Jermiin, L. S., Patterson, D. J. and Sogin, M. L. (2002). Evolutionary history of "early-diverging" eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia. Mol Biol Evol 19, 1782-91.

Simpson, A. G., MacQuarrie, E. K. and Roger, A. J. (2002). Eukaryotic evolution: early origin of canonical introns. Nature 419, 270.

Roger, A. J. and Silberman, J. D. (2002). Cell evolution: mitochondria in hiding. Nature 418, 827-9.

O'Malley, M. A., Roger, A. J. and Doolittle, W. F. (2002). Can commercial protection be good for research? Nature 419, 111

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.

Inagaki, Y., Doolittle, W.F., Baldauf, S.L. and Roger, A.J. (2002) Lateral transfer of an EF-1a gene: origin and evolution of the large subunit of ATP sulfurylase in eubacteria. Curr. Biol. 12:772-776.

Andersson, J.O. and Roger, A.J. (2002) Evolutionary analyses of the small subunit of glutamate synthase: Gene order conservation, gene fusions and prokaryote-to-eukaryote lateral gene transfers. Euk. Cell. 1:304-310.

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 implications for the history of mitochondrial function in eukaryote evolution. Mol. Biol. Evol. 19:777-786

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.

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. Nucl. Acids Res. 30:532-544.

Andersson, J.O. and Roger A.J. (2002) A cyanobacterial gene in non-photosynthetic protists an early chloroplast acquisition in eukaryotes? Curr. Biol. 12:115-119.

2001:

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.

Morrison, H.G., Roger, A.J., Nystul, T. G., Gillin, F. D. and Sogin, M.L. (2001) Giardia lamblia expresses a proteobacterial-like DnaK homolog. Mol. Biol. Evol. 18:530-541.

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. * Co-first authors.

2000:

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.

1999:

Roger, A.J., Morrison, H.G. and Sogin, M.L. (1999) Primary structure and phylogenetic relationships of a malate dehydrogenase gene from Giardia lamblia . J. Mol. Evol. 48: 750- 755.

Dacks, J. and Roger, A.J. (1999) The first sexual lineage and the relevance of facultative sex. J. Mol. Evol. 48:779-783.

Roger, A.J., Sandblom, O., Doolittle, W.F. and Philippe, H. (1999) An evaluation of elongation factor 1alpha as a phylogenetic marker for eukaryotes. Mol. Biol. Evol. 16: 216-233.

Duncan, R., Faggart, M.A., Roger, A.J. and Cornell, N. W. (1999) Phylogenetic analysis of the 5-aminolevulinate synthase gene. Mol. Biol. Evol. 16: 383-396.

1998:

Roger, A.J., Svärd, S.G., Tovar, J., Clark, C.G., Smith, M.W., Gillin, F.D. and Sogin, M.L. (1998) A mitochondrial-like chaperonin 60 gene in Giardia lamblia : Evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria. Proc. Natl. Acad. Sci. USA 95: 229-234.

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.

Beaton, M.J., Roger, A.J. and Cavalier-Smith, T. (1998) Sequence analysis of the mitochondrial genome of Sarcophyton glaucum: conserved gene order among octocorals. J. Mol. Evol. 47:697-708.

Fast, N.M., Roger, A.J., Richardson, C. and Doolittle, W.F. (1998) U2 and U6 snRNA genes from the microsporidian Nosema locustae : Evidence for a functional spliceosome. Nucl. Acids Research 26: 3202-3207.

Wagner, M., Roger, A.J., Flax, J.L., Brusseau, G.A. and Stahl, D.A. (1998) Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. J. Bacteriol. 180: 2975-2982.

1996:

Roger, A.J., Clark, C.G. and Doolittle, W.F. (1996) A possible mitochondrial gene in the amitochondriate protist Trichomonas vaginalis . Proc. Natl. Acad. Sci. USA 93: 14618- 14622.

Roger, A.J., Smith, M.W., Doolittle, R.F. and Doolittle, W.F. (1996) Evidence for the Heterolobosea from phylogenetic analysis of genes encoding glyceraldehyde-3- phosphate dehydrogenase. J. Euk. Microbiol. 43: 475-485.

Rozario, C., Morin, L., Roger, A.J., Smith, M.W. and Müller, M. (1996) Primary structure and phylogenetic relationships of glyceraldehyde-3-phosphate dehydrogenase genes of free-living and parasitic diplomonad flagellates. J. Euk. Microbiol. 43: 330- 340.

Roger, A.J. and Brown, J.R. (1996) A chimeric origin for eukaryotes re-examined. Trends Biochem. Sci. 21: 370-371.

1995:

Clark, C.G. and Roger, A.J. (1995) Direct evidence for loss of mitochondria in Entamoeba histolytica. Proc. Natl. Acad. Sci. USA. 92:6518-6521.

Keeling, P.J. and Roger, A.J.* (1995) The selfish pursuit of sex. Nature 375:283. (*both authors contributed equally)

1994:

Roger, A.J., Keeling, P.J. and Doolittle, W.F. (1994) Introns, the broken transposons. J. Gen. Physiol. 49:27-37.

1993:

Roger, A.J. and Doolittle W.F. (1993) Why introns-in-pieces? Nature 364:289-299.

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.