Publications


List of Publications (last 3 years only). See full list of publications (2008-2018) here.

2018

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

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

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.

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., Bradbury I.R. 2018. Environmental extremes drive population structure at the northern range limit of Atlantic salmon in North America. Mol. Ecol. doi: 10.1111/mec.14849.

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.

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

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.

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.

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., Mar. 27 [epub ahead of print]

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

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

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.

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

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.

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

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

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.

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.

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.

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

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.

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., accepted Mar. 6.

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.

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

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.

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- V erlag.

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.

DesRoches, C.T., Inkpen, S.A. and Green, T.L. (2017) The eroding artificial/natural distinction? Some consequences for ecology and economics. In M. Nagatsu and A. Ruzzene (Eds.), Philosophy and the Social Sciences: A Dialogue, Bloomsbury Publishing, London, UK, in press.

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. Biology & Philosophy 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.

Mariscal, C. and Doolittle, W.F. (2017) Life and Life only: a radical alternative to life definitionism. Synthese, in press.

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.

Petkau, A., Mabon, P., Sieffert, C., Knox, N., Cabral, J., Weedmark, K., Zaheer, R., Katz, L.S., Nadon, C., Reimer, A., Taboada, E., Beiko, R.G., Hsiao, W., Brinkman, F., Graham, M. and Van Domselaar, G. (2017) SNVPhyl: A single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology. Microb. Genom. 3: e000116.

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

Robicheau, B.M., Susko, E., Harrigan, A.M. and Snyder, M. 2017. Ribosomal RNA genes contribute to the formation of pseudogenes and junk DNA in the human genome. Genome Biol. Evol. 9: 380-397.

Sibbald, S.J. and Archibald, J.M. (2017) More protist genomes needed. Nature Ecol. Evol. 1: 145.

Sibbald, S.J., Cenci, U., Colp, M., Eglit, Y., O'Kelly, C.J. and Archibald, J.M. (2017) Diversity and evolution of Paramoeba spp. and their kinetoplastid endosymbionts. J. Eukaryot. Microbiol. 64: 598-607.

Simpson, A.G.B. (2017) Jakobida. In Handbook of the Protists (Second Edition), Archibald, J.M., Simpson, A.G.B. & Slamovits C. (Eds.), pp. 973-1003, Springer Reference.

Simpson, A.G.B., Slamovits, C.H. and Archibald, J.M. (2017) Protist diversity and eukaryote phylogeny. (Introductory Chapter) In: Handbook of the Protists (Second Edition), Archibald, J.M., Simpson, A.G.B. & Slamovits, C. (Eds.), pp. 1-21, Springer Reference.

Spackeen, J.L., Sipler, R.E., Xu, K., Tatters A.O., Walworth, N.G., Bertrand, E.M., McQuaid, J.B., Hutchins, D.A., Allen, A.A. and Bronk, D. (2017) Interactive effects of elevated temperature and CO2 on nitrate, urea, and DIC uptake by a coastal California microbial community. Marine Ecology Progress Series, in press.

Stuart, Y.E., Inkpen, S.A., Hopkins, R. and Bolnick, D.I. (2017) Character displacement is an evolutionary pattern. So what causes it? Biol. J. Linnean Soc. 121: 711-715.

Sylvester, E.V.A., Bentzen, P., Bradbury, I.R., Clement, M., Pearce, J., Horne, J. and Beiko, R.G. (2017) Applications of random forest feature selection for fine-scale genetic population assignment. Evol. Appl. 11: 153-165.

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.

Tanifuji, G., Cenci, U., Moog, D., Dean, S., Nakayama, T., David, V., Fiala, I., Curtis, B.A., Sibbald, S.J., Onodera, N.T., Colp, M., Flegontov, P., Johnson-MacKinnon, J., McPhee, M., Inagaki, Y., Hashimoto, T., Kelly, S., Gull, K., Lukeš, J. and Archibald, J.M. (2017) Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis. Sci. Rep. 7: 11688.

Yurgel, S.N., Douglas, G.M., Comeau, A.M., Mammoliti, M., Dusault, A., Pecival, D. and Langille, M.G.I. (2017) Variation in bacterial and eukaryotic communities associated with natural and managed wild blueberry habitats. Phytobiomes 1: 102-113.

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. 95: 1161-1174.

Zhan, L., Paterson, I.G., Fraser, B.A., Watson, B., Bradbury, I.R., Nadukkalam Ravindran, P., Reznick, D., Beiko, R.G. and Bentzen, P. 2017. Megasat: automated inference of microsatellite genotypes from sequence data. Mol. Evol. Resourc. 17: 247-256.

2016

Archibald, J.M. (2016) One Plus One Equals One: Symbiosis and the Evolution of Complex Life. 224 pp. Oxford University Press. ISBN: 978-0-19-966059-9 [Paperback with new Afterward].

Baker, J.L., Dunn, K., Mingrone, J., Wood, B.A., Karpinski, B.A., Sherwood, C.C., Wildman, D.E., Maynard, T.M. and Bielawski, J.P. 2016. Functional divergence of the nuclear receptor NR2C1 as a modulator of pluripotentiality during hominid evolution. Genetics 203: 905-922.

Bielawski, J.P., Baker, J.L. and Mingrone, J. 2016. Inference of episodic changes in natural selection acting on protein coding sequences via CODEML. Curr. Protoc. Bioinformatics 54: 6.

Booth, A., Mariscal, C. and Doolittle, W.F. 2016. The modern synthesis in the light of microbial genomics. Ann. Rev. Microbiol. 70: 279-297.

Brunet, T.D. (2016) Aims and methods of biosteganography. J. Biotechnol. 226: 56-64.

Castro, S.I., Hleap, J.S., Cárdenas, H. and Blouin, C. (2016) Molecular organization of the 5S rDNA gene type II in elasmobranchs. RNA Biol. 13: 391-399.

Cenci, U., Moog, D., Curtis, B.A., Tanifuji, G., Eme, L., Lukes, J. and Archibald, J.M. 2016. Heme pathway evolution in kinetoplastid protists. BMC Evol. Biol. 16: 109.

Cenci, U., Ducatez, M., Kadouche, D., Colleoni, C. and Ball, S.G. (2016) Was the Chlamydial adaptative strategy to Tryptophan starvation an early determinant of plastid endosymbiosis? Front. Cell Infect. Microbiol. 6: 67.

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 how they all come together. J. Cell Sci. 129: 3695-3703.

David, V. and Archibald, J.M. (2016) Evolution: Plumbing the depths of diplonemid diversity. Curr. Biol. 26: R1290-1292.

de Vries, J., Stanton, A., Archibald, J.M. and Gould, S.B. 2016. Streptophyte terrestrialization in light of plastid evolution. Trends Plant Sci. 21: 467-476.

Dunn, K.A., Moore-Connors, J., MacIntyre, B., Stadnyk, A.W., Thomas, N.A., Noble, A., Mahdi, G., Rashid, M., Otley, A.R., Bielawski, J.P. and *Van Limbergen, J. (2016) Early changes in microbial community structure are associated with sustained remission after nutritional treatment of pediatric Crohn’s Disease. Inflamm. Bowel Dis. 22: 2853-2862.

Dunn, K.A., Moore-Connors, J., MacIntyre, B., Stadnyk, A.W., Thomas, N.A., Noble, A., Mahdi, G., Rashid, M., Otley, A.R., Bielawski, J.P. and *Van Limbergen, J. (2016) The gut microbiome of pediatric Crohn’s Disease patients differs from healthy controls in genes that can influence the balance between a healthy and dysregulated immune response. Inflamm. Bowel Dis. 22: 2607-2618.

Doolittle, W.F. and Brunet, T.D. 2016. What is the Tree of Life? PLoS Genet. 12: e1005912.

Eme, L. and Doolittle, W.F. 2016. Microbial evolution: xenology (apparently) trumps paralogy. Curr. Biol. 22: R1181-1183.

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. 26: 2729-2738.

Grisdale, C.J. and Archibald, J.M. (2016) Secondary and tertiary endosymbiosis. In: Reference Module in Life Sciences, Elsevier Publishing. 10.1016/B978-0-12-809633-8.13107-3.

Groussin, M., Boussau, B., Szöllosi, G.J., Eme, L., Gouy, M., Brochier-Armanet, C. and Daubin, V. (2016) Gene acquisitions from bacteria at the origins of major archaeal clades are vastly overestimated. Mol. Biol. Evol. 33: 305-310.

Hajibabaei, M., Baird, D.J., Fahner, N.A., Beiko, R. and Golding, G.B. (2016) A new way to contemplate Darwin's tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring. Philos Trans. R. Soc. Lond. B. Biol. Sci. 371: 20150330.

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.

Harding, T., Brown, M.W., Simpson, A.G. and Roger, A.J. (2016) Osmoadaptive strategy and its molecular signature in obligately halophilic heterotrophic protists. Genome Biol. Evol. 8: 2241-2258.

Hleap, J.S. and Blouin, C. 2016. The semantics of the modular architecture of protein structures. Curr. Prot. Peptide Sci. 17: 62-71.

Inkpen, S.A. and Doolittle, W.F. (2016) Molecular phylogenetics and the perennial problem of homology. J. Mol. Evol. 83: 184-192.

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