Project: Exploration of Novel Methods to Visualize Genome Evolution
Funded through NASA's Applied Information Systems Research Program (NNG04GP90G)
Interactive Webpages and Programs Developed under this Project
Publications that Resulted from this Research
- Maria S. Poptsova, J. Peter Gogarten (2007)
BranchClust: A phylogenetic algorithm for selecting gene families.
BMC Bioinformatics 8:120
This manuscript report a new phylogeny based algorithm to assemble gene families of orthologous genes. The algorithm is available at http://bioinformatics.org/branchclust/ . The algorithm works with large datasets (>200 genomes) and can be used to find orthologs and inparalogs withing superfamilies.
- Maria S. Poptsova, J. Peter Gogarten (2007)
The power of phylogenetic approaches to detect horizontally transferred genes.
BMC Evolutionary Biology 7:45
We describe the use of in silico transfer to test phylogenetic methods to identif transferred genes. The approach allows identifies the rate of false positives and of false negatives.
- Zhaxybayeva, O., Gogarten, J.P., Charlebois, R.L., Doolittle, W.F., Papke, R.T. (2006)
Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events.
Genome Res. 16(9):1099-108. Epub 2006 Aug 9 pubmed, Open Access
Introduces quartet decomposition analysis as tool to detect horizontally transferred genes. The work builds on the analysis of embedded quartets 2 , an approach that solves the taxon-sampling problem usually encountered in quartet-based analyses. The reliability of the quartet-based approach is assessed using simulated genome evolution. The quartet decomposition approach is applied to the evolution of cyanobacteria, we also discuss implications of the microbial species concept.
- Huang, J. and Gogarten, J.P. (2006)
Ancient horizontal gene transfer can benefit phylogenetic reconstruction.
Trends in Genetics 22 (7):361-6. Epub 2006 May 30 pubmed
This manuscripts reports on the usefulness of transferred genes in reconstructing organismal evolutionary history. Traditionally gene transfer is considered a complication in reconstructing a genomes history: if different parts of a genome have different histories, lumping the different genes together in a single analysis might result in phylogenies that represent neither the individual genes nor the genomes . However, transferred genes that are retained in the recipient lineage provide a shared derived character for the recipient lineage that characterizes this lineage as a natural group.
- Zhaxybayeva, O. and Gogarten, JP. (in press):
"Horizontal gene transfer, gene histories and the root of the tree of life"
Proceedings of the McMaster Astrobiology conference", Paul Higgs (ed.),
Cambridge University Press
We discuss horizontal gene transfer, coalescence of gene lineages, and the placement of the root of the tree of life based on ancient gene duplications. In discussing genome evolution, we extend population genetic concepts to early microbial evolution. While the most recent common ancestors (MRCA) of different genes existed in different organisms and at different times, most ancient duplicated genes place the MRCA between the archaeal and bacterial domains.
- Gogarten, J. P. and Townsend, J. P. (2005):
Horizontal gene transfer, genome innovation, and evolution
Nature Reviews in Microbiology 3(9) 679-687 (online version, pdf)
We review the role of gene transfer in microbial evolution, assess examples where frequent gene transfer has generated a signal that gave rise to the wrong organismal phylogenetic reconstruction. We introduce a nearly neutral theory for horizontal gene transfer, and promote the application of population genetic concepts to the evolution of higher taxonomic categories.
- Hamel, L., Zhaxybayeva, O., Gogarten J.P. (2005):
PentaPlot: A software tool for the illustration of genome mosaicism.
BMC Bioinformatics 2005,6:139
This manuscript introduces simple maps of gene families into tree space (an extension of ml mapping to 5 genomes) to identify genes that have different evolutionary histories.
Powerpoint slides from presentations that included data from this project (save and doubleclick, or open with powerpoint or powerpoint viewer; please give credit when using parts of these slides in your own work - thanks!):
- J.Peter Gogarten: "Organismal Evolution: Tree-of-Life or Tangled Web" invited seminar at the Seminar Series "Exceptions and the Unexpected", Swarthmore College, October 27, 2006
- Maria Poptsava: "Automated Assembly of Gene Families and Detection of Horizontally Transferred Genes" invited lecture at the The Life Science Society Computational Systems Bioinformatics Conference (CSB2006) Workshop on Comparative Genome Analysis of Bacterial Genomes and Applications in Stanford, CA, August 14-18, 2006
- J. Peter Gogarten: "Oxygen Producing Photosynthesis and the Molecular Record", Invited lecture at the Agouron Instute's Oxygen meeting, Santa Fe, April 6-10, 2006