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Here I put stuff of relevance in my PhD.

Sumary timeline[edit]


  • Doolittle and Bapteste speak for inclusion of network techniques.


  • Bapteste et al. find with heatmaps no congruency in ortholog gene sets, failing to support tree-thinking.


  • Charlebois and Doolittle "rescue the core from extinction".


  • Gogarten et al. kills 16S trees.
"... tree-like phylogenies are inadecuate to represent the pattern of prokaryotic evolution at any level."
  • Wolf et al. explicitly state the statistical central trend tree of life:
"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)


  • Woese vaguelly suggests the statistical central trend tree of life:
"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."


  • Maddison et al. describe the gene trees in the species trees.


SliceID SliceName
1 Bacterial species
2 Phylogeny
3 Sulfur oxidation
4 Metagenomics
5 Genome annotation
6 Tree of life
7 Standards
8 Anomaly zone
9 Genomes
10 Phylogenetic networks
11 Citation networks
12 Reproducibility
13 Substitution model selection
14 Orthology
15 Synteny
16 Bacterial systematics


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).

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).

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).

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).

Maddison, W. P. Gene trees in species trees. Systematic Biology 46, 523-536, doi:10.1093/sysbio/46.3.523 (1997).

Woese CR. Interpreting the universal phylogenetic tree. Proceedings of the National Academy of Sciences. 2000;97(15):8392.

Wolf YI, Rogozin IB, Grishin NV, Koonin EV. Genome trees and the tree of life. Trends in Genetics. 2002;18(9):472-9.