-
1
-
-
58749090067
-
Uprooting Darwin’s tree
-
().:–
-
Lawton G, (2009) Uprooting Darwin’s tree. New Scientist201: 34–39.
-
(2009)
New Scientist
, vol.201
, pp. 34-39
-
-
Lawton, G.1
-
2
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
10381871, ().:–
-
Doolittle WF, (1999) Phylogenetic classification and the universal tree. Science284: 2124–2128. 10381871
-
(1999)
Science
, vol.284
, pp. 2124-2128
-
-
Doolittle, W.F.1
-
3
-
-
84876243684
-
The Tree of Life: metaphor, model, and heuristic device
-
23291311, ().:–
-
Mindell DP, (2013) The Tree of Life: metaphor, model, and heuristic device. Syst Biol62: 479–489. doi: 10.1093/sysbio/sys11523291311
-
(2013)
Syst Biol
, vol.62
, pp. 479-489
-
-
Mindell, D.P.1
-
4
-
-
84902507959
-
Is the Tree of Life the best metaphor, model or heuristic for phylogenetics?
-
24671618, ():–
-
Morrison DA, (2014) Is the Tree of Life the best metaphor, model or heuristic for phylogenetics?Syst Biol63: 628–638. doi: 10.1093/sysbio/syu02624671618
-
(2014)
Syst Biol
, vol.63
, pp. 628-638
-
-
Morrison, D.A.1
-
5
-
-
84872110525
-
Darwin and the Tree of Life: the roots of the evolutionary tree
-
().:–
-
Hellström NP, (2012) Darwin and the Tree of Life: the roots of the evolutionary tree. Arch Nat Hist39: 234–252.
-
(2012)
Arch Nat Hist
, vol.39
, pp. 234-252
-
-
Hellström, N.P.1
-
6
-
-
84964860909
-
-
Darwin C (1859)(Murray, London)
-
Darwin C (1859) On the Origin of Species (Murray, London).
-
-
-
-
7
-
-
33847790997
-
Pattern pluralism and the Tree of Life hypothesis
-
17261804, ().:–
-
Doolittle WF, Bapteste E, (2007) Pattern pluralism and the Tree of Life hypothesis. Proc Natl Acad Sci USA104: 2043–2049. 17261804
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 2043-2049
-
-
Doolittle, W.F.1
Bapteste, E.2
-
8
-
-
0000969425
-
Systematics and the Darwininan revolution
-
().:–
-
de Queiroz K, (1988) Systematics and the Darwininan revolution. Phil Sci55: 238–259.
-
(1988)
Phil Sci
, vol.55
, pp. 238-259
-
-
de Queiroz, K.1
-
9
-
-
0013092230
-
-
(), in, eds(,) pp.–
-
Zuckerkandl E, Pauling L, Bryson V, Vogel HJ, (1965) Evolutionary divergence and convergence in proteins, in Evolving Genes and Proteins, eds (Academic, New York) pp. 97–106.
-
(1965)
Evolving Genes and Proteins
, pp. 97-106
-
-
Zuckerkandl, E.1
Pauling, L.2
Bryson, V.3
Vogel, H.J.4
-
10
-
-
3042847118
-
The archaeal concept and the world it lives in: A retrospective
-
().:–
-
Woese CR, (2004) The archaeal concept and the world it lives in: A retrospective. Photsynth Res80: 361–372.
-
(2004)
Photsynth Res
, vol.80
, pp. 361-372
-
-
Woese, C.R.1
-
11
-
-
84858962167
-
Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life
-
22308526, ().:–
-
Pace NR, Sapp J, Goldenfeld N, (2012) Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life. Proc Natl Acad Sci USA109: 1011–1018. doi: 10.1073/pnas.110971610922308526
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 1011-1018
-
-
Pace, N.R.1
Sapp, J.2
Goldenfeld, N.3
-
12
-
-
73649191344
-
Infectious heredity of multiple drug resistance in bacteria
-
13999115, ().:–
-
Watanabe T, (1963) Infectious heredity of multiple drug resistance in bacteria. Bact Rev27: 87–115. 13999115
-
(1963)
Bact Rev
, vol.27
, pp. 87-115
-
-
Watanabe, T.1
-
13
-
-
0027738868
-
Horizontal transfer of ATPase genes–the tree of life becomes a net of life
-
8155843, ().:–
-
Hilario E, Gogarten JP, (1993) Horizontal transfer of ATPase genes–the tree of life becomes a net of life. Biosystems31: 111–119. 8155843
-
(1993)
Biosystems
, vol.31
, pp. 111-119
-
-
Hilario, E.1
Gogarten, J.P.2
-
14
-
-
0031470387
-
Archaea and the prokaryote-to-eukaryote transition
-
9409149, ().:–
-
Brown JR, Doolittle WF, (1997) Archaea and the prokaryote-to-eukaryote transition. Microbiol Mol Biol Rev61: 456–502. 9409149
-
(1997)
Microbiol Mol Biol Rev
, vol.61
, pp. 456-502
-
-
Brown, J.R.1
Doolittle, W.F.2
-
15
-
-
0033609333
-
Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima
-
10360571, . ().:–
-
Nelson KE, Clayton RA, Gill SR, Gwinn MK, Dodson RJ, Haft DH, et al. (1999) Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature399: 323–329. 10360571
-
(1999)
Nature
, vol.399
, pp. 323-329
-
-
Nelson, K.E.1
Clayton, R.A.2
Gill, S.R.3
Gwinn, M.K.4
Dodson, R.J.5
Haft, D.H.6
-
16
-
-
33846476262
-
Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution
-
17213324, . ().(),–
-
Dagan T, Martin W, . (2007). Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc Natl Acad Sci USA104(3), 870–875. 17213324
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, Issue.3
, pp. 870-875
-
-
Dagan, T.1
Martin, W.2
-
17
-
-
1542272747
-
Comparative genomics, minimal gene-sets and the last universal common ancestor
-
().:–
-
Koonin EV, (2003) Comparative genomics, minimal gene-sets and the last universal common ancestor. Nature Revs Microbiol1: 127–136.
-
(2003)
Nature Revs Microbiol
, vol.1
, pp. 127-136
-
-
Koonin, E.V.1
-
18
-
-
10944248427
-
Computing prokaryotic gene ubiquity: rescuing the core from extinction
-
15574825, ().:–
-
Charlebois RL, Doolittle WF, (2004) Computing prokaryotic gene ubiquity: rescuing the core from extinction. Genome Res14: 2469–2477. 15574825
-
(2004)
Genome Res
, vol.14
, pp. 2469-2477
-
-
Charlebois, R.L.1
Doolittle, W.F.2
-
19
-
-
0033616714
-
Horizontal gene transfer among genomes: the complexity hypothesis
-
10097118, ().:–
-
Jain R, Rivera MC, Lake JA, (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA96: 3801–3806. 10097118
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 3801-3806
-
-
Jain, R.1
Rivera, M.C.2
Lake, J.A.3
-
20
-
-
79952840493
-
The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer
-
21149642, ().:–
-
Cohen O, Gophna U, Pupko T, (2011) The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Mol Biol Evol28: 1481–1489. doi: 10.1093/molbev/msq33321149642
-
(2011)
Mol Biol Evol
, vol.28
, pp. 1481-1489
-
-
Cohen, O.1
Gophna, U.2
Pupko, T.3
-
21
-
-
68149093715
-
Search for a Tree of Life in the thicket of the phylogenetic forest
-
19594957, ().:
-
Puigò P, Wolf YI, Koonin EV, (2009) Search for a Tree of Life in the thicket of the phylogenetic forest. J. Biol8: 59. doi: 10.1186/jbiol15919594957
-
(2009)
J. Biol
, vol.8
, pp. 59
-
-
Puigò, P.1
Wolf, Y.I.2
Koonin, E.V.3
-
22
-
-
84876334475
-
Seeing the Tree of Life behind the phylogenetic forest
-
23587361, ().:
-
Puigbò P, Wolf YI, Koonin EV, (2013) Seeing the Tree of Life behind the phylogenetic forest. BMC Biol11:46. doi: 10.1186/1741-7007-11-4623587361
-
(2013)
BMC Biol
, vol.11
, pp. 46
-
-
Puigbò, P.1
Wolf, Y.I.2
Koonin, E.V.3
-
23
-
-
84916892245
-
Ten years of pan-genome research
-
().:–
-
Vernikos G, Medini D, Riley DR, Tettelin H, (2015) Ten years of pan-genome research. Curr Op Microbiol23: 148–154.
-
(2015)
Curr Op Microbiol
, vol.23
, pp. 148-154
-
-
Vernikos, G.1
Medini, D.2
Riley, D.R.3
Tettelin, H.4
-
24
-
-
84925517557
-
Insights from 20 years of bacterial genome sequencing
-
25722247, ().:–
-
Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, et al (2015) Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics15: 141–161. doi: 10.1007/s10142-015-0433-425722247
-
(2015)
Funct Integr Genomics
, vol.15
, pp. 141-161
-
-
Land, M.1
Hauser, L.2
Jun, S.R.3
Nookaew, I.4
Leuze, M.R.5
Ahn, T.H.6
-
25
-
-
84891763315
-
MetaRef: a pan-genomic database for comparative and community microbial genomics
-
24203705, . ().:–
-
Huang K, Brady A, Mahurkar A, White O, Gevers D, Huttenhower C, et al. (2014) MetaRef: a pan-genomic database for comparative and community microbial genomics. Nucleic Acids Res42: D617–D624. doi: 10.1093/nar/gkt107824203705
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D617-D624
-
-
Huang, K.1
Brady, A.2
Mahurkar, A.3
White, O.4
Gevers, D.5
Huttenhower, C.6
-
26
-
-
84864083035
-
The infinitely many genes model for the distributed genome of bacteria
-
().:–
-
Baumdicker F, Hess WR, Pfaffelhuber P, (2012) The infinitely many genes model for the distributed genome of bacteria. Genome Biol Evol4: 4434–456.
-
(2012)
Genome Biol Evol
, vol.4
, pp. 4434-4456
-
-
Baumdicker, F.1
Hess, W.R.2
Pfaffelhuber, P.3
-
27
-
-
84927050723
-
Prochlorococcus: the structure and function of collective diversity
-
().:–
-
Biller SJ, Berube PM, Lindell D, Chisholm SW, (2015) Prochlorococcus: the structure and function of collective diversity. Nature Rev Microbiol13: 13–27.
-
(2015)
Nature Rev Microbiol
, vol.13
, pp. 13-27
-
-
Biller, S.J.1
Berube, P.M.2
Lindell, D.3
Chisholm, S.W.4
-
28
-
-
84926123404
-
Pangenome evidence for extensive interdomain horizontal transfer affecting loineage core and shell genes in uncultured planktonic Thaumarchaeota and Euryarchaeota
-
24923324, ().:–
-
Deschamps P, Zivanovic Y, Moreira D, Rodriguez-Valera F, Lopez-Garcia P, (2014) Pangenome evidence for extensive interdomain horizontal transfer affecting loineage core and shell genes in uncultured planktonic Thaumarchaeota and Euryarchaeota. Genome Biol Evol6: 1549–1563. doi: 10.1093/gbe/evu12724923324
-
(2014)
Genome Biol Evol
, vol.6
, pp. 1549-1563
-
-
Deschamps, P.1
Zivanovic, Y.2
Moreira, D.3
Rodriguez-Valera, F.4
Lopez-Garcia, P.5
-
29
-
-
84938909705
-
The pan-genome as a shared genomic resource: mutual cheating, cooperation and the black queen hypothesis
-
26284032, ().:
-
Fullmer MS, Soucy SM, Gogarten JP, (2015) The pan-genome as a shared genomic resource: mutual cheating, cooperation and the black queen hypothesis. Front Microbiol6:728. doi: 10.3389/fmicb.2015.0072826284032
-
(2015)
Front Microbiol
, vol.6
, pp. 728
-
-
Fullmer, M.S.1
Soucy, S.M.2
Gogarten, J.P.3
-
30
-
-
84860511582
-
The Black Queen hypothesis: evolution of dependencies through adaptive gene loss
-
22448042, (). pii:–
-
Morris JJ, Lenski R, Zinser ER, (2012) The Black Queen hypothesis: evolution of dependencies through adaptive gene loss. MBio3. pii: e00036–12doi: 10.1128/mBio.00036-1222448042
-
(2012)
MBio
, vol.3
, pp. 12-e00036
-
-
Morris, J.J.1
Lenski, R.2
Zinser, E.R.3
-
31
-
-
84926417610
-
Genomic expansion of domain Archaea highlights roles for organisms from new phyla in anaerobic carbon cycling
-
25702576, ().:–
-
Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, et al (2015) Genomic expansion of domain Archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr Biol25: 690–701. doi: 10.1016/j.cub.2015.01.01425702576
-
(2015)
Curr Biol
, vol.25
, pp. 690-701
-
-
Castelle, C.J.1
Wrighton, K.C.2
Thomas, B.C.3
Hug, L.A.4
Brown, C.T.5
Wilkins, M.J.6
-
32
-
-
84936942726
-
Unusual biology across a group comprising more than 15% of domain Bacteria
-
26083755, . ().:–
-
Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, et al. (2015) Unusual biology across a group comprising more than 15% of domain Bacteria. Nature523: 208–211. doi: 10.1038/nature1448626083755
-
(2015)
Nature
, vol.523
, pp. 208-211
-
-
Brown, C.T.1
Hug, L.A.2
Thomas, B.C.3
Sharon, I.4
Castelle, C.J.5
Singh, A.6
-
33
-
-
84881612486
-
Genome reduction as the dominant mode of evolution
-
23801028, ().:–
-
Wolf YI, Koonin EV, (2013) Genome reduction as the dominant mode of evolution. Bioessays35: 829–837. doi: 10.1002/bies.20130003723801028
-
(2013)
Bioessays
, vol.35
, pp. 829-837
-
-
Wolf, Y.I.1
Koonin, E.V.2
-
34
-
-
61349194462
-
Estimating the size of the bacterial pan-genome
-
19168257, ().:–
-
Lapierre P, Gogarten JP, (2009) Estimating the size of the bacterial pan-genome. Trends Genet25: 107–110. doi: 10.1016/j.tig.2008.12.00419168257
-
(2009)
Trends Genet
, vol.25
, pp. 107-110
-
-
Lapierre, P.1
Gogarten, J.P.2
-
35
-
-
1642339676
-
Cladogenesis, coalescence and the evolution of the three domains of life
-
15041172, ().:–
-
Zhaxybayeva O, Gogarten JP, (2004) Cladogenesis, coalescence and the evolution of the three domains of life. Trends Genet20: 182–187. 15041172
-
(2004)
Trends Genet
, vol.20
, pp. 182-187
-
-
Zhaxybayeva, O.1
Gogarten, J.P.2
-
36
-
-
0034027594
-
The nature of the universal ancestor and the evolution of the proteome
-
10851188, ().():–
-
Doolittle WF, (2000) The nature of the universal ancestor and the evolution of the proteome. Curr Opin Struct Biol. 10(3): 355–358. 10851188
-
(2000)
Curr Opin Struct Biol
, vol.10
, Issue.3
, pp. 355-358
-
-
Doolittle, W.F.1
-
37
-
-
84929145859
-
Ancient horizontal gene transfer and the last common ancestors
-
Fournier G. P., Andam C. P., Gogarten J. P., (2015). Ancient horizontal gene transfer and the last common ancestors. BMC evolutionary biology, 15(1), 70.
-
(2015)
BMC evolutionary biology
, vol.15
, Issue.1
, pp. 70
-
-
Fournier, G.P.1
Andam, C.P.2
Gogarten, J.P.3
-
38
-
-
0032499698
-
The universal ancestor
-
9618502, ().:–
-
Woese C, (1998) The universal ancestor. Proc Natl Acad Sci USA95: 6854–6859. 9618502
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 6854-6859
-
-
Woese, C.1
-
39
-
-
84949255558
-
Toward the Darwinian transition: switching between distributed and speciated states in a simple model of early life
-
().:
-
Arnoldt H, Strogatz SH, Timme M, (2015) Toward the Darwinian transition: switching between distributed and speciated states in a simple model of early life. Physical Rev E92: 052909.
-
(2015)
Physical Rev E
, vol.92
, pp. 052909
-
-
Arnoldt, H.1
Strogatz, S.H.2
Timme, M.3
-
40
-
-
79953647279
-
Trees before and after Darwin
-
().:–
-
Tassy P, (2011) Trees before and after Darwin. J Zool Syst Evol Res49: 89–101.
-
(2011)
J Zool Syst Evol Res
, vol.49
, pp. 89-101
-
-
Tassy, P.1
-
41
-
-
84937109171
-
The universal tree of life: an update
-
26257711, ().:
-
Forterre P, (2015) The universal tree of life: an update. Front Microbiol6: 717. doi: 10.3389/fmicb.2015.0071726257711
-
(2015)
Front Microbiol
, vol.6
, pp. 717
-
-
Forterre, P.1
-
42
-
-
84864615070
-
Low species barrriers in halophilic archaea and the formation of recombinant hybrids
-
22748314, ().:–
-
Naor A, Lapierre P, Mevarech M, Papke RT, Gophna U, (2012) Low species barrriers in halophilic archaea and the formation of recombinant hybrids. Curr Biol22: 1444–1448. doi: 10.1016/j.cub.2012.05.05622748314
-
(2012)
Curr Biol
, vol.22
, pp. 1444-1448
-
-
Naor, A.1
Lapierre, P.2
Mevarech, M.3
Papke, R.T.4
Gophna, U.5
-
43
-
-
84922775800
-
Origins of major archaeal clades correspond to gene acquisitions from bacteria
-
25317564, ().:–
-
Nelson-Sathi S, Sousa FL, Roettger M, Lozada-Chavez N, Thiergart T, Janssen A, et al (2015) Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature517: 77–80. doi: 10.1038/nature1380525317564
-
(2015)
Nature
, vol.517
, pp. 77-80
-
-
Nelson-Sathi, S.1
Sousa, F.L.2
Roettger, M.3
Lozada-Chavez, N.4
Thiergart, T.5
Janssen, A.6
-
44
-
-
84964665909
-
Gene acquisitions from bacteria at the origins of major archaeal clades are vastly overestimnated
-
()
-
Groussin M, Boussau B, Szöllzösi Eme L, Guoy M, Brochier-Armanet et al (2015) Gene acquisitions from bacteria at the origins of major archaeal clades are vastly overestimnated. Mol Biol Evoldoi: 10.1093/molbev/msv249
-
(2015)
Mol Biol Evol
-
-
Groussin, M.1
Boussau, B.2
Szöllzösi3
Eme, L.4
Guoy, M.5
Brochier-Armanet6
-
45
-
-
60349111236
-
Darwin was right
-
. ().:–
-
Dennett D, Coyne J, Dawkins R, Myers P, . (2009) Darwin was right. The New Scientist201: 22–24.
-
(2009)
The New Scientist
, vol.201
, pp. 22-24
-
-
Dennett, D.1
Coyne, J.2
Dawkins, R.3
Myers, P.4
|