Here I put stuff of relevance in my PhD.
- 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.
|6||Tree of life|
|13||Substitution model selection|
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.