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Items: 1 to 50 of 169

1.

Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes.

Heiss AA, Kolisko M, Ekelund F, Brown MW, Roger AJ, Simpson AGB.

R Soc Open Sci. 2018 Apr 4;5(4):171707. doi: 10.1098/rsos.171707. eCollection 2018 Apr.

2.

Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis.

Stairs CW, Eme L, Muñoz-Gómez SA, Cohen A, Dellaire G, Shepherd JN, Fawcett JP, Roger AJ.

Elife. 2018 Apr 26;7. pii: e34292. doi: 10.7554/eLife.34292.

3.

Accelerated Estimation of Frequency Classes in Site-Heterogeneous Profile Mixture Models.

Susko E, Lincker L, Roger AJ.

Mol Biol Evol. 2018 May 1;35(5):1266-1283. doi: 10.1093/molbev/msy026.

PMID:
29688541
4.

Demystifying Eukaryote Lateral Gene Transfer (Response to Martin 2017 DOI: 10.1002/bies.201700115).

Leger MM, Eme L, Stairs CW, Roger AJ.

Bioessays. 2018 May;40(5):e1700242. doi: 10.1002/bies.201700242. Epub 2018 Mar 15. Review.

PMID:
29543982
5.

Reply to 'Eukaryote lateral gene transfer is Lamarckian'.

Roger AJ.

Nat Ecol Evol. 2018 May;2(5):755. doi: 10.1038/s41559-018-0522-6. No abstract available.

PMID:
29535448
6.

Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group.

Brown MW, Heiss AA, Kamikawa R, Inagaki Y, Yabuki A, Tice AK, Shiratori T, Ishida KI, Hashimoto T, Simpson AGB, Roger AJ.

Genome Biol Evol. 2018 Feb 1;10(2):427-433. doi: 10.1093/gbe/evy014.

7.

The Origin and Diversification of Mitochondria.

Roger AJ, Muñoz-Gómez SA, Kamikawa R.

Curr Biol. 2017 Nov 6;27(21):R1177-R1192. doi: 10.1016/j.cub.2017.09.015. Review.

PMID:
29112874
8.

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation.

Wang HC, Minh BQ, Susko E, Roger AJ.

Syst Biol. 2018 Mar 1;67(2):216-235. doi: 10.1093/sysbio/syx068.

PMID:
28950365
9.

Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis.

Gentekaki E, Curtis BA, Stairs CW, Klimeš V, Eliáš M, Salas-Leiva DE, Herman EK, Eme L, Arias MC, Henrissat B, Hilliou F, Klute MJ, Suga H, Malik SB, Pightling AW, Kolisko M, Rachubinski RA, Schlacht A, Soanes DM, Tsaousis AD, Archibald JM, Ball SG, Dacks JB, Clark CG, van der Giezen M, Roger AJ.

PLoS Biol. 2017 Sep 11;15(9):e2003769. doi: 10.1371/journal.pbio.2003769. eCollection 2017 Sep.

10.

Adaptations to High Salt in a Halophilic Protist: Differential Expression and Gene Acquisitions through Duplications and Gene Transfers.

Harding T, Roger AJ, Simpson AGB.

Front Microbiol. 2017 May 29;8:944. doi: 10.3389/fmicb.2017.00944. eCollection 2017.

11.

Microbial Eukaryotes that Lack Sterols.

Takishita K, Chikaraishi Y, Tanifuji G, Ohkouchi N, Hashimoto T, Fujikura K, Roger AJ.

J Eukaryot Microbiol. 2017 Nov;64(6):897-900. doi: 10.1111/jeu.12426. Epub 2017 Jun 7.

PMID:
28509379
12.

Between a Pod and a Hard Test: The Deep Evolution of Amoebae.

Kang S, Tice AK, Spiegel FW, Silberman JD, Pánek T, Cepicka I, Kostka M, Kosakyan A, Alcântara DMC, Roger AJ, Shadwick LL, Smirnov A, Kudryavtsev A, Lahr DJG, Brown MW.

Mol Biol Evol. 2017 Sep 1;34(9):2258-2270. doi: 10.1093/molbev/msx162.

13.

Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes.

Leger MM, Kolisko M, Kamikawa R, Stairs CW, Kume K, Čepička I, Silberman JD, Andersson JO, Xu F, Yabuki A, Eme L, Zhang Q, Takishita K, Inagaki Y, Simpson AGB, Hashimoto T, Roger AJ.

Nat Ecol Evol. 2017 Apr 1;1(4):0092. doi: 10.1038/s41559-017-0092. No abstract available.

14.

Mitochondrial Genome Evolution and a Novel RNA Editing System in Deep-Branching Heteroloboseids.

Yang J, Harding T, Kamikawa R, Simpson AGB, Roger AJ.

Genome Biol Evol. 2017 May 1;9(5):1161-1174. doi: 10.1093/gbe/evx086.

15.

Lateral Gene Transfer in the Adaptation of the Anaerobic Parasite Blastocystis to the Gut.

Eme L, Gentekaki E, Curtis B, Archibald JM, Roger AJ.

Curr Biol. 2017 Mar 20;27(6):807-820. doi: 10.1016/j.cub.2017.02.003. Epub 2017 Mar 2.

16.

Nuclear genetic codes with a different meaning of the UAG and the UAA codon.

Pánek T, Žihala D, Sokol M, Derelle R, Klimeš V, Hradilová M, Zadrobílková E, Susko E, Roger AJ, Čepička I, Eliáš M.

BMC Biol. 2017 Feb 13;15(1):8. doi: 10.1186/s12915-017-0353-y.

17.

Corrigendum Correction to "Novel hydrogenosomes in the microaerophilic jakobid Stygiella incarcerata".

Leger MM, Eme L, Hug LA, Roger AJ.

Mol Biol Evol. 2017 Apr 1;34(4):1027. doi: 10.1093/molbev/msx059. No abstract available.

PMID:
28158607
18.

The Origin of Mitochondrial Cristae from Alphaproteobacteria.

Muñoz-Gómez SA, Wideman JG, Roger AJ, Slamovits CH.

Mol Biol Evol. 2017 Apr 1;34(4):943-956. doi: 10.1093/molbev/msw298. Review.

PMID:
28087774
19.

The Earliest Stages of Mitochondrial Adaptation to Low Oxygen Revealed in a Novel Rhizarian.

Gawryluk RMR, Kamikawa R, Stairs CW, Silberman JD, Brown MW, Roger AJ.

Curr Biol. 2016 Oct 24;26(20):2729-2738. doi: 10.1016/j.cub.2016.08.025. Epub 2016 Sep 22.

20.

Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes.

Novák L, Zubáčová Z, Karnkowska A, Kolisko M, Hroudová M, Stairs CW, Simpson AG, Keeling PJ, Roger AJ, Čepička I, Hampl V.

BMC Evol Biol. 2016 Oct 6;16(1):197.

21.

The changing view of eukaryogenesis - fossils, cells, lineages and how they all come together.

Dacks JB, Field MC, Buick R, Eme L, Gribaldo S, Roger AJ, Brochier-Armanet C, Devos DP.

J Cell Sci. 2016 Oct 15;129(20):3695-3703. Epub 2016 Sep 26. Review.

22.

Erratum to: On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1.

Xu F, Jerlström-Hultqvist J, Kolisko M, Simpson AG, Roger AJ, Svärd SG, Andersson JO.

BMC Biol. 2016 Sep 12;14(1):77. No abstract available.

23.

Leaving negative ancestors behind.

Muñoz-Gómez SA, Roger AJ.

Elife. 2016 Aug 31;5. pii: e20061. doi: 10.7554/eLife.20061.

24.

Split-specific bootstrap measures for quantifying phylogenetic stability and the influence of taxon selection.

Wang HC, Susko E, Roger AJ.

Mol Phylogenet Evol. 2016 Dec;105:114-125. doi: 10.1016/j.ympev.2016.08.017. Epub 2016 Aug 24.

PMID:
27568211
25.

On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1.

Xu F, Jerlström-Hultqvist J, Kolisko M, Simpson AG, Roger AJ, Svärd SG, Andersson JO.

BMC Biol. 2016 Aug 1;14:62. doi: 10.1186/s12915-016-0284-z. Erratum in: BMC Biol. 2016;14:77.

26.

Osmoadaptative Strategy and Its Molecular Signature in Obligately Halophilic Heterotrophic Protists.

Harding T, Brown MW, Simpson AG, Roger AJ.

Genome Biol Evol. 2016 Aug 3;8(7):2241-58. doi: 10.1093/gbe/evw152.

27.

Novel Hydrogenosomes in the Microaerophilic Jakobid Stygiella incarcerata.

Leger MM, Eme L, Hug LA, Roger AJ.

Mol Biol Evol. 2016 Sep;33(9):2318-36. doi: 10.1093/molbev/msw103. Epub 2016 Jun 8. Erratum in: Mol Biol Evol. 2017 Apr 1;34(4):1027.

28.

Environmental Breviatea harbour mutualistic Arcobacter epibionts.

Hamann E, Gruber-Vodicka H, Kleiner M, Tegetmeyer HE, Riedel D, Littmann S, Chen J, Milucka J, Viehweger B, Becker KW, Dong X, Stairs CW, Hinrichs KU, Brown MW, Roger AJ, Strous M.

Nature. 2016 Jun 9;534(7606):254-8. doi: 10.1038/nature18297. Epub 2016 Jun 1.

29.

A Eukaryote without a Mitochondrial Organelle.

Karnkowska A, Vacek V, Zubáčová Z, Treitli SC, Petrželková R, Eme L, Novák L, Žárský V, Barlow LD, Herman EK, Soukal P, Hroudová M, Doležal P, Stairs CW, Roger AJ, Eliáš M, Dacks JB, Vlček Č, Hampl V.

Curr Biol. 2016 May 23;26(10):1274-84. doi: 10.1016/j.cub.2016.03.053. Epub 2016 May 12.

30.

Group II Intron-Mediated Trans-Splicing in the Gene-Rich Mitochondrial Genome of an Enigmatic Eukaryote, Diphylleia rotans.

Kamikawa R, Shiratori T, Ishida K, Miyashita H, Roger AJ.

Genome Biol Evol. 2016 Feb 1;8(2):458-66. doi: 10.1093/gbe/evw011.

31.

First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group.

Pánek T, Zadrobílková E, Walker G, Brown MW, Gentekaki E, Hroudová M, Kang S, Roger AJ, Tice AK, Vlček Č, Čepička I.

Mol Phylogenet Evol. 2016 May;98:41-51. doi: 10.1016/j.ympev.2016.01.011. Epub 2016 Jan 28.

PMID:
26826602
32.

Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi.

Torruella G, de Mendoza A, Grau-Bové X, Antó M, Chaplin MA, del Campo J, Eme L, Pérez-Cordón G, Whipps CM, Nichols KM, Paley R, Roger AJ, Sitjà-Bobadilla A, Donachie S, Ruiz-Trillo I.

Curr Biol. 2015 Sep 21;25(18):2404-10. doi: 10.1016/j.cub.2015.07.053. Epub 2015 Sep 10.

33.

Diversity and origins of anaerobic metabolism in mitochondria and related organelles.

Stairs CW, Leger MM, Roger AJ.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678):20140326. doi: 10.1098/rstb.2014.0326. Review.

34.

Gene fusion, fission, lateral transfer, and loss: Not-so-rare events in the evolution of eukaryotic ATP citrate lyase.

Gawryluk RM, Eme L, Roger AJ.

Mol Phylogenet Evol. 2015 Oct;91:12-6. doi: 10.1016/j.ympev.2015.05.010. Epub 2015 May 27.

PMID:
26025427
35.

An ancestral bacterial division system is widespread in eukaryotic mitochondria.

Leger MM, Petrů M, Žárský V, Eme L, Vlček Č, Harding T, Lang BF, Eliáš M, Doležal P, Roger AJ.

Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10239-46. doi: 10.1073/pnas.1421392112. Epub 2015 Mar 23.

36.

Lateral gene transfer and gene duplication played a key role in the evolution of Mastigamoeba balamuthi hydrogenosomes.

Nývltová E, Stairs CW, Hrdý I, Rídl J, Mach J, Pačes J, Roger AJ, Tachezy J.

Mol Biol Evol. 2015 Apr;32(4):1039-55. doi: 10.1093/molbev/msu408. Epub 2015 Jan 7.

37.

On the age of eukaryotes: evaluating evidence from fossils and molecular clocks.

Eme L, Sharpe SC, Brown MW, Roger AJ.

Cold Spring Harb Perspect Biol. 2014 Aug 1;6(8). pii: a016139. doi: 10.1101/cshperspect.a016139. Review.

38.

A large number of nuclear genes in the human parasite blastocystis require mRNA polyadenylation to create functional termination codons.

Klimeš V, Gentekaki E, Roger AJ, Eliáš M.

Genome Biol Evol. 2014 Jul 10;6(8):1956-61. doi: 10.1093/gbe/evu146.

39.

Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae.

Tanifuji G, Onodera NT, Brown MW, Curtis BA, Roger AJ, Ka-Shu Wong G, Melkonian M, Archibald JM.

BMC Genomics. 2014 May 15;15:374. doi: 10.1186/1471-2164-15-374.

40.

A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia.

Stairs CW, Eme L, Brown MW, Mutsaers C, Susko E, Dellaire G, Soanes DM, van der Giezen M, Roger AJ.

Curr Biol. 2014 Jun 2;24(11):1176-86. doi: 10.1016/j.cub.2014.04.033. Epub 2014 May 22.

41.

Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages.

Gentekaki E, Kolisko M, Boscaro V, Bright KJ, Dini F, Di Giuseppe G, Gong Y, Miceli C, Modeo L, Molestina RE, Petroni G, Pucciarelli S, Roger AJ, Strom SL, Lynn DH.

Mol Phylogenet Evol. 2014 Sep;78:36-42. doi: 10.1016/j.ympev.2014.04.020. Epub 2014 May 6.

PMID:
24814356
42.

Gene content evolution in Discobid mitochondria deduced from the phylogenetic position and complete mitochondrial genome of Tsukubamonas globosa.

Kamikawa R, Kolisko M, Nishimura Y, Yabuki A, Brown MW, Ishikawa SA, Ishida K, Roger AJ, Hashimoto T, Inagaki Y.

Genome Biol Evol. 2014 Feb;6(2):306-15. doi: 10.1093/gbe/evu015.

43.

An amino acid substitution-selection model adjusts residue fitness to improve phylogenetic estimation.

Wang HC, Susko E, Roger AJ.

Mol Biol Evol. 2014 Apr;31(4):779-92. doi: 10.1093/molbev/msu044. Epub 2014 Jan 16.

PMID:
24441033
44.

Evolution of the cytosolic iron-sulfur cluster assembly machinery in Blastocystis species and other microbial eukaryotes.

Tsaousis AD, Gentekaki E, Eme L, Gaston D, Roger AJ.

Eukaryot Cell. 2014 Jan;13(1):143-53. doi: 10.1128/EC.00158-13. Epub 2013 Nov 15.

45.

Evidence for a hydrogenosomal-type anaerobic ATP generation pathway in Acanthamoeba castellanii.

Leger MM, Gawryluk RM, Gray MW, Roger AJ.

PLoS One. 2013 Sep 27;8(9):e69532. doi: 10.1371/journal.pone.0069532. eCollection 2013.

46.

Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads.

Brown MW, Sharpe SC, Silberman JD, Heiss AA, Lang BF, Simpson AG, Roger AJ.

Proc Biol Sci. 2013 Aug 28;280(1769):20131755. doi: 10.1098/rspb.2013.1755. Print 2013 Oct 22.

47.

The Capsaspora genome reveals a complex unicellular prehistory of animals.

Suga H, Chen Z, de Mendoza A, Sebé-Pedrós A, Brown MW, Kramer E, Carr M, Kerner P, Vervoort M, Sánchez-Pons N, Torruella G, Derelle R, Manning G, Lang BF, Russ C, Haas BJ, Roger AJ, Nusbaum C, Ruiz-Trillo I.

Nat Commun. 2013;4:2325. doi: 10.1038/ncomms3325.

48.

Functional divergence and convergent evolution in the plastid-targeted glyceraldehyde-3-phosphate dehydrogenases of diverse eukaryotic algae.

Gaston D, Roger AJ.

PLoS One. 2013 Jul 30;8(7):e70396. doi: 10.1371/journal.pone.0070396. Print 2013.

49.

Parallel re-modeling of EF-1α function: divergent EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes.

Kamikawa R, Brown MW, Nishimura Y, Sako Y, Heiss AA, Yubuki N, Gawryluk R, Simpson AG, Roger AJ, Hashimoto T, Inagaki Y.

BMC Evol Biol. 2013 Jun 26;13:131. doi: 10.1186/1471-2148-13-131.

50.

The site-wise log-likelihood score is a good predictor of genes under positive selection.

Wang HC, Susko E, Roger AJ.

J Mol Evol. 2013 May;76(5):280-94. doi: 10.1007/s00239-013-9557-0. Epub 2013 Apr 18.

PMID:
23595859

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