Publications


Select list of Publications (last 4 years only). See full list of publications (2008-2020) here.

2020

Alock et al. [14 authors incl. Beiko, R.G.] 2020. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 48: D517-D525.

Bretherton, L., Hillhouse, J., Kamalanathan, M., Finkel, Z.V., Irwin, A.J. and Quigg, A. 2020. Trait-dependent variability of the response of marine phytoplankton to oil and dispersant exposure. Marine Pollut. Bull. 153: 110906.

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.

Colp, M. and Archibald, J.M. 2020. The language of symbiosis: insights from protist biology. In: Cellular dialogs in the holobiont, Bosch, T.. and Hadfield, M. (eds.), CRC Press, in press.

Connors, J., Dunn, K.A., Allott, J., Bandsma, R., Rashid, M., Otley, A.R., Bielawski, J.P. and Van Limbergen, J. 2020. The relationship between fecal bile acids and microbiome community structure in pediatric Crohn’s disease. ISME J. 14: 702-713.

Doolittle, W.F. 2020. Evolution: Two domains of life or three? Curr. Biol. 30: R177-R179.

Finkel, Z.V., Liang, Y., Nanjappa, D., Bretherton, L., Brown, C.M., Quigg, A. and Irwin, A.J. 2020. A ribosomal sequence-based oil sensitivity index for phytoplankton groups. Marine Pollut. Bull. 151: 110798.

Gallot-Lavallée, L. and Archibald, J.M. 2020. Spotlight: Phagocytosis in a shape-shifting bacterium. Trends Microbiol., in press.

Gray, M.W., Burger, G., Derelle, R., Klimes, V., Leger, M.M., Sarrasin, M., Vlcek, C., Roger, A.J., Elias, M. and 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 Biol. 18: 22.

Gray, M.W. and Gopalan, V. 2020. Piece by piece: Building a ribozyme. J. Biol. Chem. 295: 2313-2323.

Jones, C.M.A., Connors, J., Dunn, K.A., Bielawski, J.P., Comeau, A.M., Langille, M.G.I. and *Van Limbergen, J. 2020. Bacterial taxa and functions are predictive of sustained remission following exclusive enteral nutrition in pediatric Crohn’s Disease. Inflamm. Bowel Dis., Jan. 21; pii: izaa001.

Novick, A. and Doolittle, W.F. 2020. Horizontal persistence and the complexity hypothesis. Biol. Philos. 35: 2.

Palau, M., Piqué, N., Comeau, A.M., Douglas, G.M., Ramírez-Lázaro, M.J., Lario, S., Calvet, X., Langille, M.G.I. and Miñana-Galbis, D. 2020. Detection of Helicobacter pylori microevolution and multiple infection from gastric biopsies by housekeeping gene amplicon sequencing. Pathogens 9(2), pii: E97.

Rotteveel, L. and Sterling, S.M. 2020. Five aluminum seasonality regimes identified in chronically acidified rivers of Nova Scotia. Environ. Sci. Technol. 54: 807-817.

Susko, E. and Roger, A.J. 2020. On the use of information criteria for model selection in phylogenetics. Mol. Biol. Evol. 37: 549-562.

Tanifuji, G., Kamikawa, R., Moore, C.E., Mills, T., Onodera, N.T., Kashiyama, Y., Archibald, J.M., Inagaki, Y. and Hashimoto, T. 2020. Comparative plastid genomics of Cryptomonas species reveals fine-scale genomic responses to loss of photosynthesis. Genome Biol. Evol. 12: 3926-3937.

2019

Asman, A.K.M., Curtis, B.A. and Archibald, J.M. 2019. Nucleomorph small RNAs in cryptophyte and chlorarachniophyte algae. Genome Biol. Evol. 11: 1117-1134.

DesRoches, C.T., Inkpen, S.A. and Green, T.L. 2019 The eroding artificial/natural distinction? Some consequences for ecology and economics. In M. Nagatsu and A. Ruzzene (Eds.), Contemporary Philosophy and Social Science: An Interdisciplinary Dialogue, Bloomsbury Publishing, London, UK.

Dunn, K.A., Kenny, T., Gu., H. and Bielawski, J.P. 2019. Improved inference of site-specific positive selection under a generalized parametric codon model when there are multinucleotide mutations and multiple nonsynonymous rates. BMC Evol. Biol. 19: 22.

Grisdale, C.J., Smith, D.R. and Archibald, J.M. 2019. Relative mutation rates in nucleomorph-bearing algae. Genome Biol. Evol. 11: 1045-1053.

Hess, S., Eme, L., Roger, A.J. and Simpson, A.G.B. 2019. A natural toroidal microswimmer with a rotary eukaryotic flagellum. Nat. Microbiol. 4: 1620-1626.

Kim, J.I., Shin, H., Škaloud, P., Jung, J., Yoon, H.S., Archibald, J.M. & Shin, W. 2019. Comparative plastid genomics of Synurophyceae: inverted repeat dynamics and gene content variation. BMC Evol. Biol. 19: 20.

Levine, A., Wine, E., Assa, A., Sigall Boneh, R., Shaoul, R., Kori, M., Cohen, S., Peleg, S., Shamali, H., On, A., Millman, P., Abramas, L., Ziv-Baran,T., Grant, S., Abitbol, G., Dunn, K.A., Bielawski, J.P. and Van Limbergen, J. 2019. Crohn’s Disease Exclusion Diet Plus Partial Enteral Nutrition Induces Sustained Remission in a Randomized Controlled Trial. Gastroenterology 157: 440-450

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. 21; 8. pii: e42535.

Nadukkalam Ravindran, P., Bentzen, P., Bradbury, I.R. and Beiko, R.G. 2019. RADProc: A computationally efficient de novo locus assembler for population studies using RADseq data. Mol. Ecol. Resour. 19: 272-282.

Nearing, J.T., Connors, J., Whitehouse, S., Van Limbergen, J., Macdonald, T., Kulkarni, K. and Langille, M.G.I. 2019. Infectious complications are associated with alterations in the gut microbiome in pediatric patients with acute lymphoblastic leukemia. Front Cell. Infect. Microbiol. 9: 28.

Novick, A. and Doolittle, W.F. 2019. How microbes “jeopardize” the modern synthesis. PLoS Genet. 15: e1008166.

O’Malley, M.A., Leger, M.M., Wideman, J.G. and Ruiz-Trillo, I. 2019. Concepts of the last eukaryotic common ancestor. Nature Ecol. Evol. 3: 338-344.

Paight, C., Slamovits, C.H. Saffo, M.B. and Lane, C.E. 2019. Nephromyces encodes a urate metabolism pathway and predicted peroxisomes, demonstrating that these are not ancient losses of Apicomplexans. Genome Biol. Evol. 11: 41-53.

Saito, M.A., Bertrand, E.M. Duffy, M.E., Gaylord, D.A., Held, N.A., Hervey, W.J. 4th, Hettich, R.L., Jagtap, P.D., Janech, M.G., Kinkade, D.B., Leary, D.H., McIlvin, M.R., Moore, E.K., Morris, R.M., Neely, B.A., Nunn, B.L., Saunders, J.K., Shepherd, A.I., Symmonds, N.I. and Walsh, D.A. 2019. Progress and challenges in ocean metaproteomics and proposed best practices for data sharing. J. Proteome Res. 18: 1461-1476.

Sibbald, S.J., Hopkins, J.F., Filloramo, G.V. and Archibald, J.M. 2019. Ubiquitin fusion proteins in complex algae: implications for the spread of eukaryotic photosynthesis. BMC Genomics 20: 38.

Singh et al. [20 co-authors, incl. Langille, M.G.I.] 2019. Enhancement of the gut barrier integrity by a microbial metabolite through the Nrf2 pathway. Nat. Commun. 10: 89.

Wideman, J.G., Inkpen, S.A., Doolittle, W.F. and Redfield, R.J. 2019. Mutationism, not Lamarckism, captures the novelty of CRISPR-Cas. Biol. Philos. 34: 12.

Zorz, J., Willis, C., Comeau, A.M., Langille, M.G.I. Johnson, C.L., Li, W.K.W. and LaRoche, J. 2019. Drivers of regional bacterial community structure and diversity in the northwest Atlantic Ocean. Front Microbiol. 10: 281.

2018

Archibald, J.M. 2018. Evolution: scaling life’s tree. Nature 560: 26-27.

Archibald, J.M. 2018. Genomics. A Very Short Introduction. Paperback, 160 pp. Oxford Press. ISBN: 978-0-19-878620-7.

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.

Brunet, T.D.P. and Doolittle, W.F. (2018) The generality of constructive neutral evolution. Biol. Philos. 33: 2.

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.

Cheng, S., Melkonian, M., Smith, S.A., Brockington, S., Archibald, J.M., Delaux, P.M., Li, F.W., Melkonian, B., Mavrodiev, E.V., Sun, W., Fu, Y., Yang, H., Soltis, D.E., Graham, S.W., Soltis, P.S., Liu, X., Xu, X. and Wong, G.K. (2018) 10KP: A phylodiverse genome sequencing plan. Gigascience 7: 1-9.

de Vries, J. and Archibald, J.M. 2018. Plastid evolution: autonomy versus nuclear control. In: Advances in Botanical Research, Volume 85 (Plastid Genome Evolution). Chaw, S.-M. & Jansen, R. (eds.). Pp. 1-28.

de Vries, S., de Vries, J., von Dahlen, J.K., Gould, S.B., Archibald, J.M., Rose, L.E. and Slamovits, C.H. 2018. On plant defense signaling networks and early land plant evolution. Commun. Integr. Biol. 11: e1486168.

de Vries, J., Curtis, B.A., Gould, S.B. and Archibald, J.M. 2018. Embryophyte stress signalling evolved in the algal progenitors of land plants. Proc. Natl. Acad. Sci. USA 115: E3471-E3480.

de Vries, J. and Archibald, J.M. 2018. Quick guide: plastid genomes. Curr. Biol. 28: R336-R337.

de Vries, J. and Archibald, J.M. 2018. Plant evolution: landmarks on the path to terrestrial life. New Phytol. 217: 1428-1434.

Doolittle, W.F. and Inkpen, S.A. 2018. Processes and patterns of interaction as units of selection: An introduction to ITSNTS thinking. Proc. Natl. Acad. Sci. USA 115: 4006-4014.

Douglas, G.M., Hansen, R., Jones, C.M.A., Dunn, K.A., Comeau, A.M. Bielawski, J.P., Tayler, R., El-Omar, E.M., Russell, R.K., Hold, G.L., Langille, M.G.I. and Van Limbergen, J. 2018. Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn's disease. Microbiome 6: 13.

Harding, T. and Simpson, A.G.B. 2018. Recent Advances in Halophilic Protozoa Research. J. Eukaryot. Microbiol. 65(4):556-570.

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.

Hleap, J.S. and Blouin, C. (2018) The response to selection in glycoside hydrolase family 13 structures: a comparative quantitative genetics approach. PLoS One 13: e0196135.

Jones, C.T., Youssef, N., Susko, E. and Bielawski, J.P. 2018. Phenomenological load on model parameters can lead to false biological conclusions. Mol. Biol. Evol., 35: 1473-1488.

Kim, J.I., Yoon, H.S., Yi, G., Shin, W. and Archibald, J.M. (2018) Comparative mitochondrial genomics of cryptophyte algae: gene shuffling and dynamic mobile genetic elements. BMC Genomics 19: 275.

Langille, M.G.I. (2018) Exploring linkages between taxonomic and functional profiles of the human microbiome. mSystems 3: pii: e00163-17.

Langille, M.G.I., Ravel, J. and Fricke, W.F. 2018. "Available upon request": not good enough for microbiome data. Microbiome 6: 8.

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.

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.

Lukeš, J., Jirsová, D., David, V., Wheeler, R. and Archibald, J.M. 2018. Massive mitochondrial DNA content in diplonemid and kinetoplastid protists. IUBMB Life 70: 1267-1274.

Mariscal, C. and Doolittle, W.F. (2018) Life and Life only: a radical alternative to life definitionism. Synthese, online 11 July; https://doi.org/10.1007/s11229-018-1852-2.

Nadukkalam Ravindran P., Bentzen P., Bradbury I.R. and Beiko R.G. 2018. PMERGE: Computational filtering of paralogous sequences from RAD-seq data. Ecol. Evol. 8(14):7002-7013.

Nowak, B.F. and Archibald, J.M. 2018. Opportunist but lethal: the mystery of Paramoebae. Trends Parasitol. 34: 404-419.

Paerl, R.W., Bertrand, E.M., Rowland, E., Schatt, P., Mehiri, M., Niehaus, T.D., Hanson, A.D., Riemann, L. and Yves-Bouget, F. (2018) Carboxythiazole is a key microbial nutrient currency and critical component of thiamine biosynthesis. Sci Rep. 8: 5940.

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.

Raina, J.B., Eme, L., Pollock, F.J., Spang, A., Archibald, J.M. and Williams, T.A. 2018. Symbiosis in the microbial world: from ecology to genome evolution. Biol Open. 7(2): pii: bio032524.

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

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

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

Stanley, R.R.E, DiBacco, C., Lowen, B., Beiko, R.G., Jeffery, N.W., Van Wyngaarden, M., Bentzen, P., Brickman, D., Benestan, L., Bernatchez, L., Johnson, C., Snelgrove, P.V.R., Wang, Z., Wringe, B.F. and Bradbury I.R. (2018) A climate-associated multispecies cryptic cline in the northwest Atlantic. Sci Adv. 4: eaaq0929.

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.

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.

Sylvester E.V.A., Beiko R.G, Bentzen P., Paterson I., Horne J.B., Watson B., Lehnert S., Duffy S., Clément M., Robertson M.J. and Bradbury I.R. 2018. Environmental extremes drive population structure at the northern range limit of Atlantic salmon in North America. Mol. Ecol. 27:4026-4040.

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.

Van Wyngaarden, M., Snelgrove, P.V.R., DiBacco, C., Hamilton, L.C., Rodriguez-Ezpeleta, N., Zhan, L., Beiko, R.G. and Bradbury, I.R. 2018. Oceanographic variation infuences spatial genomic structure in the sea scallop, P. magellanicus. Ecol. Evol. 8: 2824-2841

2017

Archibald, J.M. 2017. Evolution: Protein import in a nascent photosynthetic organelle. Curr. Biol. 27: R1004-R1006.

Archibald, J.M., Simpson, A.G.B. and Slamovits, C. 2017. Editors of Handbook of the Protists (2nd Edition of the Handbook of Protoctista by Margulis et al.), Springer.

Alarcón, M.E., Jara-F.A., Briones, R.C., Dubey, A.K. and Slamovits, C.H. (2017) Gregarine infection accelerates larval development of the cat flea Ctenocephalides felis (Bouché). Parasitol. 144: 419-425.

Berney, C. et al. [25 authors incl. Simpson, A.G.B.] (2017) UniEuk: Time to speak a common language in protistology. J. Eukaryot. Microbiol. 64: 407-411.

Browning, T.J., Achterberg, E.P., Rapp, I., Engel, A., Bertrand, E.M., Tagliabue, A. and Moore, C.M. (2017) Nutrient co-limitation at the boundary of an oceanic gyre. Nature 551: 242-246.

Caron, D.A. et al. [15 authors incl. Archibald, J.M.] (2017) Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nat. Rev. Microbiol. 15: 6-20.

Cenci, U., Moog, D. and Archibald, J.M. (2017) Origin and spread of plastids by endosymbiosis. In M. Grube, L. Muggia & J. Seckbach (Eds.), Algal and Cyanobacteria Symbioses, pp. 43-81, Springer-Verlag.

Chan, C.X., Beiko, R.G. and Ragan, M.A. 2017. Scaling up the phylogenetic detection of lateral gene transfer events. Methods Mol. Biol. 1525: 421-432.

Comeau, A.M., Douglas, G.M. and Langille, M.G. 2017. Microbiome Helper: a custom and streamlined workflow for microbiome research. mSystems 2: e00127-16.

de Vries, J., Archibald, J.M. and Gould, S.B. (2017) The carboxy terminus of YCF1 contains a motif conserved throughout >500Myr of streptophyte evolution. Genome Biol. Evol. 9: 473-479.

de Vries, J. and Archibald, J.M. 2017. Endosymbiosis: Did plastids evolve from a freshwater cyanobacterium? Curr. Biol. 27: R103-R105.

de Vries, J., de Vries, S., Slamovits, C.H., Rose, L.E. and Archibald, J.M. 2017. How embryophytic is the biosynthesis of phenylpropanoids and their derivatives in streptophyte algae? Plant Cell Physiol. 58: 934-945.

Doolittle, W.F. 2017. Darwinizing Gaia. J. Theoret. Biol. 434: 11-19.

Doolittle, W.F. 2017. Making the most of clade selection. Phil. Sci. 84: 275-295.

Doolittle, W.F. and Brunet, T.D.P. (2017) On causal roles and selected effects: our genome is mostly junk. BMC Biol. 15: 116.

Doolittle, W.F. and Booth, A. (2017) It’s the song, not the singer: an exploration of holobiosis and evolutionary theory. Biol. Philos.32: 5-24.

Finlayson-Trick, E.C.L., Getz, L.J., Slaine, P.D., Thornbury, M., Lamoureux, E., Cook, J., Langille, M.G.I., Murray, L.E., McCormick, C., *Rohde, J.R. and Cheng, Z. (2017) Taxonomic differences of gut microbiomes drive cellulolytic enzymatic potential within hind-gut fermenting mammals. PLoS One 12: e0189404.

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.

Gray, M.W. 2017. Lynn Margulis and the endosymbiont hypothesis: 50 years later. Mol. Biol. Cell 28: 1285-1287.

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.

Hall, M.W., Singh, N., Ng, K.F., Lam, D.K., Goldberg, M.B., Tenenbaum, H.C., Neufeld, J.D., Beiko, R.G. and Senadheera, D.B. (2017) Inter-personal diversity and temporal dynamics of dental, tongue, and salivary microbiota in the healthy oral cavity. NPJ Biofilms Microbiomes 3, Article Number 2.

Hall, M.W., Rohwer, R.R., Perrie, J., McMahon, K.D. and Beiko, R.G. 2017. Ananke: temporal clustering reveals ecological dynamics of microbial communities. PeerJ 5: e3812.

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.

Heiss, A.A., Brown, M.W. and Simpson, A.G.B. (2017) Apusomonadida. In Handbook of the Protists (Second Edition), Archibald, J.M., Simpson, A.G.B. & Slamovits, C. (Eds.), pp. 1619-1645, Springer Reference.

Hoef-Emden, K. and Archibald, J.M. (2017) Cryptophyta (Cryptomonads). In Handbook of the Protists (Second Edition), J.M. Archibald, A.G. Simpson & C. Slamovits (Eds), pp. 851-891, Springer Reference.

Inkpen, S.A. (2017) Demarcating nature, defining ecology: Creating a rationale for the study of nature’s ‘primitive conditions’. Perspect. Sci. 25: 355-92.

Inkpen, S.A. (2017) Are humans disturbing conditions in ecology? Biol. Philos 32: 51-71.

Inkpen, S.A., Douglas, G.M., Brunet, T.D.P., Leuschen, K., Doolittle, W.F. and Langille, M.G.I. (2017) The coupling of taxonomy and function in microbiomes. Biol. Philos. 32: 1225-1243.

Jeffery, N.W., DiBacco, C., Van Wyngaarden, M., Hamilton, L.C., Stanley, R.R.E., McKenzie, C., Nadukkalam Ravindran, P., Beiko, R.G. and Bradbury, I.R. (2017). RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic. Ecol. Evol. 7: 2513-2524.

Jeffery, N.W., Stanley, R.R.E., Wringe, B.F., Guijarro-Sabaniel, J., Bourret, V., Bernatchez, L., Bentzen, P., Beiko, R.G., Gilbey, J., Clément, M. and Bradbury, I.R. (2017) Range-wide parallel climate- associated genomic clines in Atlantic salmon. R. Soc. Open Sci. 4: 171394.

Jones, C.T., Youssef, N., Susko, E. and Bielawski, J.P. 2017. Shifting balance on a static mutation-selection landscape: a novel scenario of positive selection. Mol. Biol. Evol. 34: 391-407.

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.

Kamikawa, R., Moog, D., Zauner, S., Tanifuji, G., Ishida, K.I., Miyashita, H., Mayama, S., Hashimoto, T., Maier, U.G., Archibald, J.M. and Inagaki, Y. (2017) A non-photosynthetic diatom reveals early steps of reductive evolution in plastids. Mol. Biol. Evol. 34: 2355-2366.

Kim, J.I., Moore, C.E., Archibald, J.M., Bhattacharya, D., Yi, G., Yoon, H.S. and Shin, W. (2017) Evolutionary dynamics of Cryptophyte plastid genomes. Genome Biol. Evol. 9: 1859-1872.

Leander, B.S., Lax, G., Karnkowska, A. and Simpson, A.G.B. (2017) Euglenida. In Handbook of the Protists (Second Edition), Archibald, J.M., Simpson, A.G.B. & Slamovits, C. (Eds.), pp. 1047-1088, Springer Reference.

Lamoureux, E.V., Grandy, S.A. and Langille, M.G.I. 2017. Moderate exercise has limited but distinguishable effects on the mouse microbiome. mSystems 2: e00006-17.

Leger, M.M. et al. (17 authors, incl. Roger, A.J.) 2017. Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes. Nature Ecol. Evol. 1: 0092.

MacLellan, A., Moore-Connors, J., Grant, S., Cahill, L., Langille, M.G.I. and Van Limbergen, J. 2017. The impact of exclusive enteral nutrition on the gut microbiome in Crohn's disease: A review. Nutrients 9: E0447.

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.

Muñoz-Gómez, S.A., Mejía-Franco, F.G., Durnin, K., Colp, M., Grisdale, C.J., Archibald J.M. and Slamovits, C.H. (2017) The new red algal subphylum Proteorhodophytina comprises the largest and most divergent plastid genomes known. Curr. Biol. 27: 1677-1684.

Panek, T., Simpson, A.G.B., Brown, M.W. and Dyer, B.D. (2017) Heterolobosea. In Handbook of the Protists (Second Edition), Archibald, J.M., Simpson, A.G.B. & Slamovits, C. (Eds.), pp. 1005-1046, Springer Reference.

Panek, T., Zihala, D., Sokol, M., Derelle, R., Klimes, V., Hradilova, M., Zadrobilkova, E., Susko, E., Roger, A.J., Cepicka, I. and Elias, M. 2017. Nuclear genetic codes with a different meaning of the UAG and the UAA codon. BMC Biol. 15: 8.

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