Literature

Here I put stuff of relevance in my PhD.

2007

Doolittle and Bapteste speak for inclusion of network techniques.

2005

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

2004

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

2002

• Gogarten et al. kills 16S trees.

"... tree-like phylogenies are inadecuate to represent the pattern of prokaryotic evolution at any level."

1997

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

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).

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).