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| | Here I put stuff of relevance in my PhD. | | Here I put stuff of relevance in my PhD. |
| − | ==Sumary timeline==
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| − | ===2007===
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| − | *Doolittle and Bapteste speak for inclusion of network techniques.
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| − | ===2005=== | + | ==2002== |
| − | *Bapteste et al. find with heatmaps no congruency in ortholog gene sets, failing to support tree-thinking. | + | *Gogarten et al. kills 16S. |
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| − | ===2004===
| + | ==1997== |
| − | *Charlebois and Doolittle "rescue the core from extinction".
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| − | ===2002===
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| − | *Gogarten et al. kills 16S trees.
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| − | <blockquote> "... tree-like phylogenies are inadecuate to represent the pattern of prokaryotic evolution at any level." </blockquote>
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| − | *Wolf et al. explicitly state the statistical central trend tree of life:
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| − | <blockquote> "However, the concept of the Tree of Life is bound to change in the post-genomic world. It cannot be thought as a definitive 'species tree' (something that does not even exist in reality) but only as a ''central trend'' in the ritch patchwork of evolutionary history, replete with gene loss and horizontal transfer events." (emphasis added) </blockquote>
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| − | ===2000===
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| − | *Woese vaguelly suggests the statistical central trend tree of life:
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| − | <blockquote> "Their aboriginal evolutionary histories have been severely jumbled by horizontal gene flow, yet, in the aggregate, their phylogenetic trees retain clear vestiges of the ground structure of the universal tree." </blockquote>
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| − | ===1997===
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| | *Maddison et al. describe the gene trees in the species trees. | | *Maddison et al. describe the gene trees in the species trees. |
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| − | ==Slices==
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| − | {| class="wikitable"
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| − | | SliceID || SliceName
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| − | |-
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| − | | 1 || Bacterial species
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| − | |-
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| − | | 2 || Phylogeny
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| − | |-
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| − | | 3 || Sulfur oxidation
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| − | |-
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| − | | 4 || Metagenomics
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| − | |-
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| − | | 5 || Genome annotation
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| − | |-
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| − | | 6 || Tree of life
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| − | |-
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| − | | 7 || Standards
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| − | |-
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| − | | 8 || Anomaly zone
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| − | |-
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| − | | 9 || Genomes
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| − | |-
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| − | | 10 || Phylogenetic networks
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| − | |-
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| − | | 11 || Citation networks
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| − | |-
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| − | | 12 || Reproducibility
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| − | |-
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| − | | 13 || Substitution model selection
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| − | |-
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| − | | 14 || Orthology
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| − | |-
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| − | | 15 || Synteny
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| − | |-
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| − | | 16 || Bacterial systematics
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| − | |}
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| | ==References== | | ==References== |
| − | Bapteste, E. et al. Do orthologous gene phylogenies really support tree-thinking? BMC Evolutionary Biology 5, 1-10, doi:10.1186/1471-2148-5-33 (2005).
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| − | Charlebois, R. L. & Doolittle, W. F. Computing prokaryotic gene ubiquity: Rescuing the core from extinction. Genome Research 14, 2469-2477, doi:10.1101/gr.3024704 (2004).
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| − | Doolittle, W. F. & Bapteste, E. Pattern pluralism and the Tree of Life hypothesis. Proceedings of the National Academy of Sciences of USA 104, 2043-2049 (2007).
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| | Gogarten, J. P., Doolittle, W. F. & Lawrence, J. G. Prokaryotic evolution in light of gene transfer. Molecular Biology and Evolution 19, 2226-2238, doi:10.1093/oxfordjournals.molbev.a004046 (2002). | | Gogarten, J. P., Doolittle, W. F. & Lawrence, J. G. Prokaryotic evolution in light of gene transfer. Molecular Biology and Evolution 19, 2226-2238, doi:10.1093/oxfordjournals.molbev.a004046 (2002). |
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| | Maddison, W. P. Gene trees in species trees. Systematic Biology 46, 523-536, doi:10.1093/sysbio/46.3.523 (1997). | | Maddison, W. P. Gene trees in species trees. Systematic Biology 46, 523-536, doi:10.1093/sysbio/46.3.523 (1997). |
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| − | Woese CR. Interpreting the universal phylogenetic tree. Proceedings of the National Academy of Sciences. 2000;97(15):8392.
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| − | Wolf YI, Rogozin IB, Grishin NV, Koonin EV. Genome trees and the tree of life. Trends in Genetics. 2002;18(9):472-9.
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