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1
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0033603539
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Phylogenetic classification and the universal tree
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A recent review of developments in the fields of phylogenetics and bioinformatics as applied to the question of the root of the tree of life. An important aspect is the discussion of horizontal transfer, how this could affect the search for the root, and the issue of whether informational genes could potentially transfer between lineages as readily as operational genes are suggested to.
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Doolittle W.F. Phylogenetic classification and the universal tree. Science. 284:1999;2124-2128. A recent review of developments in the fields of phylogenetics and bioinformatics as applied to the question of the root of the tree of life. An important aspect is the discussion of horizontal transfer, how this could affect the search for the root, and the issue of whether informational genes could potentially transfer between lineages as readily as operational genes are suggested to.
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(1999)
Science
, vol.284
, pp. 2124-2128
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Doolittle, W.F.1
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2
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0025300402
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Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eukarya
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Woese C.R., Kandler O., Wheelis M.L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eukarya. Proc Natl Acad Sci USA. 87:1990;4576-4579.
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Proc Natl Acad Sci USA
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Woese, C.R.1
Kandler, O.2
Wheelis, M.L.3
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3
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0033616714
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Horizontal transfer among genomes: The complexity hypothesis
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The authors argue for extensive gene transfer between prokaryotes during evolution and that it is genes of the operational class that are transferred most frequently. They suggest that transfer of informational genes is hindered by the many intermolecular interactions in which these macromolecules are involved. Informational genes include those for transcription, translation, replication, and GTPases. Operational genes are those for nearly all of metabolism, including regulation.
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Jain R., Rivera M.C., Lake J.A. Horizontal transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA. 96:1999;3801-3806. The authors argue for extensive gene transfer between prokaryotes during evolution and that it is genes of the operational class that are transferred most frequently. They suggest that transfer of informational genes is hindered by the many intermolecular interactions in which these macromolecules are involved. Informational genes include those for transcription, translation, replication, and GTPases. Operational genes are those for nearly all of metabolism, including regulation.
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(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 3801-3806
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Jain, R.1
Rivera, M.C.2
Lake, J.A.3
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4
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0033609333
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Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima
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Another whole microbial genome sequence from TIGR. This paper considers especially the issue of horizontal gene transfer, concluding on the basis of conserved gene order that some horizontal transfer occurs between eubacteria and archaea.
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Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A.et al. Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature. 399:1999;323-329. Another whole microbial genome sequence from TIGR. This paper considers especially the issue of horizontal gene transfer, concluding on the basis of conserved gene order that some horizontal transfer occurs between eubacteria and archaea.
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(1999)
Nature
, vol.399
, pp. 323-329
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Nelson, K.E.1
Clayton, R.A.2
Gill, S.R.3
Gwinn, M.L.4
Dodson, R.J.5
Haft, D.H.6
Hickey, E.K.7
Peterson, J.D.8
Nelson, W.C.9
Ketchum, K.A.10
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5
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0031736121
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Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles
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Describes evidence that horizontal transfer from hyperthermophilic archaea to hyperthermophilic bacteria occurs more readily than to mesophilic bacteria. The authors conclude that this transfer may have been the defining event in the origin of hyperthermophilic bacteria.
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Aravind L., Tatusov R.L., Wolf Y.I., Walker D.R., Koonin E.V. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 14:1998;442-444. Describes evidence that horizontal transfer from hyperthermophilic archaea to hyperthermophilic bacteria occurs more readily than to mesophilic bacteria. The authors conclude that this transfer may have been the defining event in the origin of hyperthermophilic bacteria.
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(1998)
Trends Genet
, vol.14
, pp. 442-444
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Aravind, L.1
Tatusov, R.L.2
Wolf, Y.I.3
Walker, D.R.4
Koonin, E.V.5
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6
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0032568587
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Genomic evidence for two functionally distinct gene classes
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Using whole-genome data, the authors class genes as either operational or informational on the basis of function and demonstrate that the operational gene sets of bacteria and eukaryotes are more closely related than that of the archaea, whereas the archaea-eukaryote grouping holds for the informational gene set.
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Rivera M.C., Jain R., Moore J.E., Lake J.A. Genomic evidence for two functionally distinct gene classes. Proc Natl Acad Sci USA. 95:1998;6239-6244. Using whole-genome data, the authors class genes as either operational or informational on the basis of function and demonstrate that the operational gene sets of bacteria and eukaryotes are more closely related than that of the archaea, whereas the archaea-eukaryote grouping holds for the informational gene set.
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(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 6239-6244
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Rivera, M.C.1
Jain, R.2
Moore, J.E.3
Lake, J.A.4
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7
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0032900532
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Genome phylogeny based on gene content
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The authors use the gene content of 13 completely sequenced genomes for reconstructing the tree of life and rooting it. Unlike sequence-based phylogenies, the tree is built by examining similarities and differences in gene content, so that the presence or absence of a gene is counted as a character. The authors conclude that massive horizontal transfer events between distant groups is not supported by their results, and that their data largely support the 16S rRNA tree topology for the 13 genomes.
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Snel B., Bork P., Huynen M.A. Genome phylogeny based on gene content. Nat Genet. 21:1999;108-110. The authors use the gene content of 13 completely sequenced genomes for reconstructing the tree of life and rooting it. Unlike sequence-based phylogenies, the tree is built by examining similarities and differences in gene content, so that the presence or absence of a gene is counted as a character. The authors conclude that massive horizontal transfer events between distant groups is not supported by their results, and that their data largely support the 16S rRNA tree topology for the 13 genomes.
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(1999)
Nat Genet
, vol.21
, pp. 108-110
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Snel, B.1
Bork, P.2
Huynen, M.A.3
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0032499698
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The last universal common ancestor
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Woese C.R. The last universal common ancestor. Proc Natl Acad Sci USA. 95:1998;6854-6859.
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Proc Natl Acad Sci USA
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Woese, C.R.1
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0024358140
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Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes
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Proc Natl Acad Sci USA
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Kuma, K.-I.2
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Bowman, E.J.5
Bowman, B.J.6
Manolson, M.F.7
Poole, R.J.8
Date, T.9
Oshima, T.10
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11
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0033015732
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Archaea sister-group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies
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Uses a new method which applies the 'covarion' model to building a tree of life from signal recognition particle proteins. The authors conclude that the root is in the eukaryote branch and that earlier trees built with these sequences placing eubacteria as basal were as a result of long-branch attraction.
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Brinkmann H., Philippe H. Archaea sister-group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Mol Biol Evol. 16:1999;817-825. Uses a new method which applies the 'covarion' model to building a tree of life from signal recognition particle proteins. The authors conclude that the root is in the eukaryote branch and that earlier trees built with these sequences placing eubacteria as basal were as a result of long-branch attraction.
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(1999)
Mol Biol Evol
, vol.16
, pp. 817-825
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Brinkmann, H.1
Philippe, H.2
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12
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0032825223
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The root of the tree of life in light of the covarion model
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A description of a new method for applying the 'covarion' model to tree building that allows sites to alter their rate of evolution as secondary and tertiary structure evolves. Applied to the rooting of the tree of life, and with elongation factors, the authors conclude that the eubacteria are evolving at a higher rate than either archaea or eukaryotes, accounting for their basal position in earlier trees.
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Lopez P., Forterre P., Philippe H. The root of the tree of life in light of the covarion model. J Mol Evol. 49:1999;496-508. A description of a new method for applying the 'covarion' model to tree building that allows sites to alter their rate of evolution as secondary and tertiary structure evolves. Applied to the rooting of the tree of life, and with elongation factors, the authors conclude that the eubacteria are evolving at a higher rate than either archaea or eukaryotes, accounting for their basal position in earlier trees.
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(1999)
J Mol Evol
, vol.49
, pp. 496-508
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Lopez, P.1
Forterre, P.2
Philippe, H.3
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Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences
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Penny D., Foulds L.R., Hendy M.D. Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences. Nature. 297:1982;197-200.
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Nature
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Penny, D.1
Foulds, L.R.2
Hendy, M.D.3
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14
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0031737821
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How good are deep phylogenetic trees?
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A brief appraisal of the problems associated with building phylogenetic trees for deep divergences. Problems that are often ignored such as differences in evolutionary rate, sequence saturation, and fast-evolving lineages are addressed, and limitations of existing methods as well as possible solutions are described.
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Philippe H., Laurent J. How good are deep phylogenetic trees? Curr Opin Genet Dev. 8:1998;616-623. A brief appraisal of the problems associated with building phylogenetic trees for deep divergences. Problems that are often ignored such as differences in evolutionary rate, sequence saturation, and fast-evolving lineages are addressed, and limitations of existing methods as well as possible solutions are described.
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Curr Opin Genet Dev
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Philippe, H.1
Laurent, J.2
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Is there a phylogenetic signal in prokaryote proteins?
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Using a data set of 32 proteins, it is shown that one gene which has undergone horizontal transfer can heavily influence the construction of a phylogenetic tree, even for a data set of 32 proteins. Upon removal of the offending gene, the remainder of the data set contained little information.
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Teichmann S.A., Mitchison G. Is there a phylogenetic signal in prokaryote proteins? J Mol Evol. 49:1999;98-107. Using a data set of 32 proteins, it is shown that one gene which has undergone horizontal transfer can heavily influence the construction of a phylogenetic tree, even for a data set of 32 proteins. Upon removal of the offending gene, the remainder of the data set contained little information.
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(1999)
J Mol Evol
, vol.49
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Teichmann, S.A.1
Mitchison, G.2
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16
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0033214077
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Where is the root of the universal tree of life?
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An overview of problems associated with rooting the tree of life, along with arguments favouring prokaryotes being derived from a mesophilic ancestor that was eukaryote-like in many respects. The paper also reviews details of how eukaryotes and prokaryotes have arisen from such an ancestor.
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Forterre P., Philippe H. Where is the root of the universal tree of life? Bioessays. 21:1999;871-879. An overview of problems associated with rooting the tree of life, along with arguments favouring prokaryotes being derived from a mesophilic ancestor that was eukaryote-like in many respects. The paper also reviews details of how eukaryotes and prokaryotes have arisen from such an ancestor.
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(1999)
Bioessays
, vol.21
, pp. 871-879
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Forterre, P.1
Philippe, H.2
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17
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0031852105
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A covariotide model describes the evolution of oxygenic photosynthesis
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A mathematical test is introduced that can detect some cases where sites in a sequence are evolving under different constraints in different parts of the tree. It is well known in structural biology that two- and three-dimensional structrures of macromoles evolve over time (as predicted under W Fitch's covarion model); however, standard tree-building methods assume a site is always under the same contrstraints.
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Lockhart P.J., Steel M.A., Barbrook A.C., Huson D.H., Howe C.J. A covariotide model describes the evolution of oxygenic photosynthesis. Mol Biol Evol. 15:1998;1183-1188. A mathematical test is introduced that can detect some cases where sites in a sequence are evolving under different constraints in different parts of the tree. It is well known in structural biology that two- and three-dimensional structrures of macromoles evolve over time (as predicted under W Fitch's covarion model); however, standard tree-building methods assume a site is always under the same contrstraints.
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(1998)
Mol Biol Evol
, vol.15
, pp. 1183-1188
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Lockhart, P.J.1
Steel, M.A.2
Barbrook, A.C.3
Huson, D.H.4
Howe, C.J.5
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19
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0031964398
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Relics from the RNA world
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An updated model of the RNA-world, describing arguments, both old and new, for the placing of various RNAs in the RNA-world, what gaps there are in our present understanding of this period, plus a review of ancient genome architecture from the viewpoint of information theory. The paper also describes a novel way of viewing the evolutionary transition from RNA to protein catalysts and explains why some RNAs have persisted while others have not.
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Jeffares D.C., Poole A.M., Penny D. Relics from the RNA world. J Mol Evol. 46:1998;18-36. An updated model of the RNA-world, describing arguments, both old and new, for the placing of various RNAs in the RNA-world, what gaps there are in our present understanding of this period, plus a review of ancient genome architecture from the viewpoint of information theory. The paper also describes a novel way of viewing the evolutionary transition from RNA to protein catalysts and explains why some RNAs have persisted while others have not.
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(1998)
J Mol Evol
, vol.46
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Jeffares, D.C.1
Poole, A.M.2
Penny, D.3
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20
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0031984372
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The path from the RNA world
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Here we attempted to establish what was known about the evolutionary transitions in going from an RNA-world to the emergence of the three domains of life. Included is a discussion of the origins of protein synthesis, the first proteins, messenger RNA, as well as aspects of the origins of DNA. Notably, we put forth a new hypothesis on the origin of introns, which we call 'introns-first'. Also discussed is the validity of using RNA-world relics for 'rooting' the tree of life. We conclude that the data we assemble are incompatible with a prokaryote-like Last Universal Common Ancestor.
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Poole A.M., Jeffares D.C., Penny D. The path from the RNA world. J Mol Evol. 46:1998;1-17. Here we attempted to establish what was known about the evolutionary transitions in going from an RNA-world to the emergence of the three domains of life. Included is a discussion of the origins of protein synthesis, the first proteins, messenger RNA, as well as aspects of the origins of DNA. Notably, we put forth a new hypothesis on the origin of introns, which we call 'introns-first'. Also discussed is the validity of using RNA-world relics for 'rooting' the tree of life. We conclude that the data we assemble are incompatible with a prokaryote-like Last Universal Common Ancestor.
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(1998)
J Mol Evol
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Poole, A.M.1
Jeffares, D.C.2
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21
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Early evolution: Prokaryotes, the new kids on the block
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We argue for re-evaluating the nature of the Last Universal Common Ancestor. Emphasises the importance of continuity of function in evolution, and suggests that our understanding of the RNA-world and the Last Universal Common Ancestor should be mututally compatible. It proposes a feedback process (the Darwin-Eigen cycle) where improved accuracy of replication permits a larger genome size, which permits coding for more features, which permit more accurate replication.
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Poole A.M., Jeffares D.C., Penny D. Early evolution: prokaryotes, the new kids on the block. Bioessays. 21:1999;880-889. We argue for re-evaluating the nature of the Last Universal Common Ancestor. Emphasises the importance of continuity of function in evolution, and suggests that our understanding of the RNA-world and the Last Universal Common Ancestor should be mututally compatible. It proposes a feedback process (the Darwin-Eigen cycle) where improved accuracy of replication permits a larger genome size, which permits coding for more features, which permit more accurate replication.
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Bioessays
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Poole, A.M.1
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The authors compare the GC content of modern organisms in order to understand more on the nature of the LUCA and concludes that the ancestral GC content was too low for it to have been hyperthermophilic. A similar ancestral GC content was found using only the thermophilic organisms in the dataset.
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Galtier N., Tourasse N., Gouy M. A nonhyperthermophilic common ancestor to extant life forms. Science. 283:1999;220-221. The authors compare the GC content of modern organisms in order to understand more on the nature of the LUCA and concludes that the ancestral GC content was too low for it to have been hyperthermophilic. A similar ancestral GC content was found using only the thermophilic organisms in the dataset.
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The stability of the RNA bases: Implications for the origin of life
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The half-lives of RNA bases at temperatures characteristic of hyperthermohiles is shown to be too rapid for bases to accumulate in a prebiotic world. The authors conclude that life must originate at low temperatures or that theories for the high temperature origin of life must exclude the four bases in RNA.
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Levy M., Miller S.L. The stability of the RNA bases: implications for the origin of life. Proc Natl Acad Sci USA. 95:1998;7933-7938. The half-lives of RNA bases at temperatures characteristic of hyperthermohiles is shown to be too rapid for bases to accumulate in a prebiotic world. The authors conclude that life must originate at low temperatures or that theories for the high temperature origin of life must exclude the four bases in RNA.
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Archean molecular fossils and the early rise of eukaryotes
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Identification of molecular biomarkers in 2700-million-year-old Archaean shales in Australia argues for the presence of photosynthetic organisms hundreds of millions of years before the atmosphere became oxidising. Perhaps more strikingly, the research also points to the presence of eukaryotes at this time, pushing back the earliest identification of these organisms by 600 million years.
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Brocks J.J., Logan G.A., Buick R., Summons R.E. Archean molecular fossils and the early rise of eukaryotes. Science. 285:1999;1033-1036. Identification of molecular biomarkers in 2700-million-year-old Archaean shales in Australia argues for the presence of photosynthetic organisms hundreds of millions of years before the atmosphere became oxidising. Perhaps more strikingly, the research also points to the presence of eukaryotes at this time, pushing back the earliest identification of these organisms by 600 million years.
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0032512051
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The genome sequence of Rickettsia prowazekii and the origin of mitochondria
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The first complete genome for an α proteobacterium and thereby among the closest ancestors to mitochondria. The work demonstrates the effects of Müller's ratchet (accumulation of deleterious alleles in the absence of recombination) on the evolution of intracellular obligate microbes.
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Andersson S.G.E., Zomorodipour A., Andersson J.O., Sicheritz-Pontén T., Alsmark U.C.M., Podowski R.M., Näslund A.K., Eriksson A-S., Winkler H.H., Kurland C.G. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature. 396:1998;133-140. The first complete genome for an α proteobacterium and thereby among the closest ancestors to mitochondria. The work demonstrates the effects of Müller's ratchet (accumulation of deleterious alleles in the absence of recombination) on the evolution of intracellular obligate microbes.
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Nature
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Andersson, S.G.E.1
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Alsmark, U.C.M.5
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Gene transfer to the nucleus and the evolution of chloroplasts
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Using whole genomes, mostly of chloroplasts, the paper demonstrates patterns of gene loss and of gene transfer to the nucleus. They find independent gene losses in multiple lineages and identify a large set (44) of chloroplast genes which had transferred from chloroplast to nucleus. It is concluded that gene loss and transfer in organelles is best explained in terms of Müller's ratchet.
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Martin W., Stoebe B., Goremykin V., Hansmann S., Hasegawa M., Kowallik K.V. Gene transfer to the nucleus and the evolution of chloroplasts. Nature. 393:1998;162-165. Using whole genomes, mostly of chloroplasts, the paper demonstrates patterns of gene loss and of gene transfer to the nucleus. They find independent gene losses in multiple lineages and identify a large set (44) of chloroplast genes which had transferred from chloroplast to nucleus. It is concluded that gene loss and transfer in organelles is best explained in terms of Müller's ratchet.
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Nature
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Martin, W.1
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