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For: Csurös M, Miklós I. Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model. Mol Biol Evol 2009;26:2087-95. [PMID: 19570746 PMCID: PMC2726834 DOI: 10.1093/molbev/msp123] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
Number Cited by Other Article(s)
1
Forterre P. The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA. J Mol Evol 2024;92:550-583. [PMID: 39158619 DOI: 10.1007/s00239-024-10186-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/25/2024] [Indexed: 08/20/2024]
2
Krupovic M, Dolja VV, Koonin EV. The virome of the last eukaryotic common ancestor and eukaryogenesis. Nat Microbiol 2023;8:1008-1017. [PMID: 37127702 PMCID: PMC11130978 DOI: 10.1038/s41564-023-01378-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/29/2023] [Indexed: 05/03/2023]
3
Prondzinsky P, Toyoda S, McGlynn SE. The methanogen core and pangenome: conservation and variability across biology's growth temperature extremes. DNA Res 2023;30:dsac048. [PMID: 36454681 PMCID: PMC9886072 DOI: 10.1093/dnares/dsac048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/09/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022]  Open
4
Menet H, Daubin V, Tannier E. Phylogenetic reconciliation. PLoS Comput Biol 2022;18:e1010621. [PMID: 36327227 PMCID: PMC9632901 DOI: 10.1371/journal.pcbi.1010621] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]  Open
5
Csűrös M. Gain-loss-duplication models for copy number evolution on a phylogeny: Exact algorithms for computing the likelihood and its gradient. Theor Popul Biol 2022;145:80-94. [DOI: 10.1016/j.tpb.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 03/07/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
6
Genomic Insights into the Ecological Role and Evolution of a Novel Thermoplasmata Order, "Candidatus Sysuiplasmatales". Appl Environ Microbiol 2021;87:e0106521. [PMID: 34524897 DOI: 10.1128/aem.01065-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
7
Psomopoulos FE, van Helden J, Médigue C, Chasapi A, Ouzounis CA. Ancestral state reconstruction of metabolic pathways across pangenome ensembles. Microb Genom 2021;6. [PMID: 32924924 PMCID: PMC7725326 DOI: 10.1099/mgen.0.000429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
8
Fukunaga T, Iwasaki W. Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families. BIOINFORMATICS ADVANCES 2021;1:vbab014. [PMID: 36700099 PMCID: PMC9710636 DOI: 10.1093/bioadv/vbab014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 01/28/2023]
9
Comparative Genomics Provides Insights into the Genetic Diversity and Evolution of the DPANN Superphylum. mSystems 2021;6:e0060221. [PMID: 34254817 PMCID: PMC8407392 DOI: 10.1128/msystems.00602-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
10
Devos DP. Reconciling Asgardarchaeota Phylogenetic Proximity to Eukaryotes and Planctomycetes Cellular Features in the Evolution of Life. Mol Biol Evol 2021;38:3531-3542. [PMID: 34229349 PMCID: PMC8382908 DOI: 10.1093/molbev/msab186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
11
Banerjee R, Chaudhari NM, Lahiri A, Gautam A, Bhowmik D, Dutta C, Chattopadhyay S, Huson DH, Paul S. Interplay of Various Evolutionary Modes in Genome Diversification and Adaptive Evolution of the Family Sulfolobaceae. Front Microbiol 2021;12:639995. [PMID: 34248865 PMCID: PMC8267890 DOI: 10.3389/fmicb.2021.639995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 05/06/2021] [Indexed: 11/21/2022]  Open
12
Abram K, Udaondo Z, Bleker C, Wanchai V, Wassenaar TM, Robeson MS, Ussery DW. Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups. Commun Biol 2021;4:117. [PMID: 33500552 PMCID: PMC7838162 DOI: 10.1038/s42003-020-01626-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 12/21/2020] [Indexed: 01/30/2023]  Open
13
Zwaenepoel A, Van de Peer Y. Model-Based Detection of Whole-Genome Duplications in a Phylogeny. Mol Biol Evol 2020;37:2734-2746. [PMID: 32359154 DOI: 10.1093/molbev/msaa111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
14
Hunnicutt KE, Tiley GP, Williams RC, Larsen PA, Blanco MB, Rasoloarison RM, Campbell CR, Zhu K, Weisrock DW, Matsunami H, Yoder AD. Comparative Genomic Analysis of the Pheromone Receptor Class 1 Family (V1R) Reveals Extreme Complexity in Mouse Lemurs (Genus, Microcebus) and a Chromosomal Hotspot across Mammals. Genome Biol Evol 2020;12:3562-3579. [PMID: 31555816 PMCID: PMC6944220 DOI: 10.1093/gbe/evz200] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2019] [Indexed: 12/14/2022]  Open
15
Armaleo D, Müller O, Lutzoni F, Andrésson ÓS, Blanc G, Bode HB, Collart FR, Dal Grande F, Dietrich F, Grigoriev IV, Joneson S, Kuo A, Larsen PE, Logsdon JM, Lopez D, Martin F, May SP, McDonald TR, Merchant SS, Miao V, Morin E, Oono R, Pellegrini M, Rubinstein N, Sanchez-Puerta MV, Savelkoul E, Schmitt I, Slot JC, Soanes D, Szövényi P, Talbot NJ, Veneault-Fourrey C, Xavier BB. The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata. BMC Genomics 2019;20:605. [PMID: 31337355 PMCID: PMC6652019 DOI: 10.1186/s12864-019-5629-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 03/20/2019] [Indexed: 12/14/2022]  Open
16
Zwaenepoel A, Van de Peer Y. Inference of Ancient Whole-Genome Duplications and the Evolution of Gene Duplication and Loss Rates. Mol Biol Evol 2019;36:1384-1404. [PMID: 31004147 DOI: 10.1093/molbev/msz088] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
17
Koonin EV, Yutin N. Multiple evolutionary origins of giant viruses. F1000Res 2018;7:F1000 Faculty Rev-1840. [PMID: 30542614 PMCID: PMC6259494 DOI: 10.12688/f1000research.16248.1] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/15/2018] [Indexed: 12/12/2022]  Open
18
Genome size evolution in the Archaea. Emerg Top Life Sci 2018;2:595-605. [PMID: 33525826 PMCID: PMC7289037 DOI: 10.1042/etls20180021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/26/2018] [Accepted: 09/28/2018] [Indexed: 11/17/2022]
19
Davidson P, Eutsey R, Redler B, Hiller NL, Laub MT, Durand D. Flexibility and constraint: Evolutionary remodeling of the sporulation initiation pathway in Firmicutes. PLoS Genet 2018;14:e1007470. [PMID: 30212463 PMCID: PMC6136694 DOI: 10.1371/journal.pgen.1007470] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 06/04/2018] [Indexed: 12/16/2022]  Open
20
Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis. Sci Rep 2018;8:2393. [PMID: 29403020 PMCID: PMC5799301 DOI: 10.1038/s41598-018-20889-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/25/2018] [Indexed: 12/24/2022]  Open
21
The Tree of Life. MOLECULAR MECHANISMS OF MICROBIAL EVOLUTION 2018. [DOI: 10.1007/978-3-319-69078-0_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
22
Brito PH, Chevreux B, Serra CR, Schyns G, Henriques AO, Pereira-Leal JB. Genetic Competence Drives Genome Diversity in Bacillus subtilis. Genome Biol Evol 2018;10:108-124. [PMID: 29272410 PMCID: PMC5765554 DOI: 10.1093/gbe/evx270] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2017] [Indexed: 12/18/2022]  Open
23
Schulz F, Yutin N, Ivanova NN, Ortega DR, Lee TK, Vierheilig J, Daims H, Horn M, Wagner M, Jensen GJ, Kyrpides NC, Koonin EV, Woyke T. Giant viruses with an expanded complement of translation system components. Science 2017;356:82-85. [PMID: 28386012 DOI: 10.1126/science.aal4657] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/18/2017] [Accepted: 03/15/2017] [Indexed: 12/24/2022]
24
Williams TA, Szöllősi GJ, Spang A, Foster PG, Heaps SE, Boussau B, Ettema TJG, Embley TM. Integrative modeling of gene and genome evolution roots the archaeal tree of life. Proc Natl Acad Sci U S A 2017;114:E4602-E4611. [PMID: 28533395 PMCID: PMC5468678 DOI: 10.1073/pnas.1618463114] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
25
Nagy LG, Szöllősi G. Fungal Phylogeny in the Age of Genomics: Insights Into Phylogenetic Inference From Genome-Scale Datasets. ADVANCES IN GENETICS 2017;100:49-72. [DOI: 10.1016/bs.adgen.2017.09.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
26
Arguments Reinforcing the Three-Domain View of Diversified Cellular Life. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016;2016:1851865. [PMID: 28050162 PMCID: PMC5165138 DOI: 10.1155/2016/1851865] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/18/2016] [Accepted: 11/03/2016] [Indexed: 11/18/2022]
27
Koonin EV. Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions. F1000Res 2016;5. [PMID: 27508073 PMCID: PMC4962295 DOI: 10.12688/f1000research.8737.1] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/18/2016] [Indexed: 01/01/2023]  Open
28
Eme L, Doolittle WF. Archaea. Curr Biol 2016;25:R851-5. [PMID: 26439345 DOI: 10.1016/j.cub.2015.05.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
29
Koonin EV. Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier? Philos Trans R Soc Lond B Biol Sci 2016;370:20140333. [PMID: 26323764 PMCID: PMC4571572 DOI: 10.1098/rstb.2014.0333] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
30
Mariscal C, Doolittle WF. Eukaryotes first: how could that be? Philos Trans R Soc Lond B Biol Sci 2016;370:20140322. [PMID: 26323754 DOI: 10.1098/rstb.2014.0322] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
31
Vakirlis N, Sarilar V, Drillon G, Fleiss A, Agier N, Meyniel JP, Blanpain L, Carbone A, Devillers H, Dubois K, Gillet-Markowska A, Graziani S, Huu-Vang N, Poirel M, Reisser C, Schott J, Schacherer J, Lafontaine I, Llorente B, Neuvéglise C, Fischer G. Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus. Genome Res 2016;26:918-32. [PMID: 27247244 PMCID: PMC4937564 DOI: 10.1101/gr.204420.116] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/28/2016] [Indexed: 12/22/2022]
32
O'Malley MA, Wideman JG, Ruiz-Trillo I. Losing Complexity: The Role of Simplification in Macroevolution. Trends Ecol Evol 2016;31:608-621. [PMID: 27212432 DOI: 10.1016/j.tree.2016.04.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/18/2016] [Accepted: 04/19/2016] [Indexed: 10/21/2022]
33
Tiley GP, Ané C, Burleigh JG. Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data. Genome Biol Evol 2016;8:1023-37. [PMID: 26988251 PMCID: PMC4860690 DOI: 10.1093/gbe/evw058] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
34
Zamani-Dahaj SA, Okasha M, Kosakowski J, Higgs PG. Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss. Mol Biol Evol 2016;33:1843-57. [DOI: 10.1093/molbev/msw062] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
35
Tekaia F. Inferring Orthologs: Open Questions and Perspectives. GENOMICS INSIGHTS 2016;9:17-28. [PMID: 26966373 PMCID: PMC4778853 DOI: 10.4137/gei.s37925] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 12/30/2015] [Accepted: 01/02/2016] [Indexed: 01/25/2023]
36
Zhao J, Teufel AI, Liberles DA, Liu L. A generalized birth and death process for modeling the fates of gene duplication. BMC Evol Biol 2015;15:275. [PMID: 26643106 PMCID: PMC4672517 DOI: 10.1186/s12862-015-0539-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/10/2015] [Indexed: 01/15/2023]  Open
37
Jeong H, Sung S, Kwon T, Seo M, Caetano-Anollés K, Choi SH, Cho S, Nasir A, Kim H. HGTree: database of horizontally transferred genes determined by tree reconciliation. Nucleic Acids Res 2015;44:D610-9. [PMID: 26578597 PMCID: PMC4702880 DOI: 10.1093/nar/gkv1245] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/01/2015] [Indexed: 01/13/2023]  Open
38
Koonin EV. Archaeal ancestors of eukaryotes: not so elusive any more. BMC Biol 2015;13:84. [PMID: 26437773 PMCID: PMC4594999 DOI: 10.1186/s12915-015-0194-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
39
Fullmer MS, Soucy SM, Gogarten JP. The pan-genome as a shared genomic resource: mutual cheating, cooperation and the black queen hypothesis. Front Microbiol 2015;6:728. [PMID: 26284032 PMCID: PMC4523029 DOI: 10.3389/fmicb.2015.00728] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/03/2015] [Indexed: 11/13/2022]  Open
40
Forterre P. The universal tree of life: an update. Front Microbiol 2015;6:717. [PMID: 26257711 PMCID: PMC4508532 DOI: 10.3389/fmicb.2015.00717] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 06/29/2015] [Indexed: 12/03/2022]  Open
41
Lei W, Fang W, Lin Q, Zhou X, Chen X. Characterization of a non-classical MHC class II gene in the vulnerable Chinese egret (Egretta eulophotes). Immunogenetics 2015;67:463-72. [PMID: 26033691 DOI: 10.1007/s00251-015-0846-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 05/16/2015] [Indexed: 11/28/2022]
42
The two-domain tree of life is linked to a new root for the Archaea. Proc Natl Acad Sci U S A 2015;112:6670-5. [PMID: 25964353 DOI: 10.1073/pnas.1420858112] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
43
Ravenhall M, Škunca N, Lassalle F, Dessimoz C. Inferring horizontal gene transfer. PLoS Comput Biol 2015;11:e1004095. [PMID: 26020646 PMCID: PMC4462595 DOI: 10.1371/journal.pcbi.1004095] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
44
Koonin EV. The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life. J Mol Evol 2015;80:244-50. [PMID: 25894542 PMCID: PMC4472940 DOI: 10.1007/s00239-015-9679-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 04/08/2015] [Indexed: 11/05/2024]
45
Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales. Life (Basel) 2015;5:818-40. [PMID: 25764277 PMCID: PMC4390880 DOI: 10.3390/life5010818] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/25/2015] [Accepted: 02/28/2015] [Indexed: 11/18/2022]  Open
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Atkinson GC. The evolutionary and functional diversity of classical and lesser-known cytoplasmic and organellar translational GTPases across the tree of life. BMC Genomics 2015;16:78. [PMID: 25756599 PMCID: PMC4342817 DOI: 10.1186/s12864-015-1289-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/27/2015] [Indexed: 12/24/2022]  Open
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Richards VP, Palmer SR, Pavinski Bitar PD, Qin X, Weinstock GM, Highlander SK, Town CD, Burne RA, Stanhope MJ. Phylogenomics and the dynamic genome evolution of the genus Streptococcus. Genome Biol Evol 2015;6:741-53. [PMID: 24625962 PMCID: PMC4007547 DOI: 10.1093/gbe/evu048] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
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Petitjean C, Deschamps P, López-García P, Moreira D, Brochier-Armanet C. Extending the conserved phylogenetic core of archaea disentangles the evolution of the third domain of life. Mol Biol Evol 2015;32:1242-54. [PMID: 25660375 DOI: 10.1093/molbev/msv015] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
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Luo H. Evolutionary origin of a streamlined marine bacterioplankton lineage. ISME JOURNAL 2014;9:1423-33. [PMID: 25431989 DOI: 10.1038/ismej.2014.227] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/23/2014] [Accepted: 10/30/2014] [Indexed: 12/31/2022]
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Stolzer M, Wasserman L, Durand D. Robustness of birth-death and gain models for inferring evolutionary events. BMC Genomics 2014;15 Suppl 6:S9. [PMID: 25572914 PMCID: PMC4239551 DOI: 10.1186/1471-2164-15-s6-s9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
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