Land Plant Evolution: Phylogenetics and Beyond
Mishler, Brent D. , Kelch, Dean .
Phylogeny of land plants - Information from comparative genomics.
THE genomics revolution has impacted all fields of biology; from knowledge about proteins and cells, to the whole tree of life. Cross-genome comparisons using phylogenetic trees have the potential to provide insights into many open functional questions, including understanding the processes underlying genomic evolution, gene regulation, the complex relationship between phenotype and genomic changes, and the evolution of complex physiological pathways. There is also the potential for improving databases by adding a phylogenetic approach to gene naming. There is feedback the other direction as well: the new comparative genomic data will also greatly increase the accuracy of phylogenetic trees! There are phylogenetic questions for which nucleotide sequence data are poorly suited, because of their simple nature and tendency to evolve in a regular, more-or-less clocklike fashion. In particular, "deep" branching questions (with relatively short internodes of interest mixed with long terminal branches) are notoriously difficult; it is fortunate therefore, that fundamentally new kinds of structural genomic characters such as inversions, translocations, losses, duplications, and insertion/deletion of introns are increasingly available. As examples of synergistic role of genomics and phylogenetics, we will examine: (1) the process of "annotation" of a genome (with reference to the newly sequenced moss Physcomitrella). What does it mean to "identify" a gene, place it into a classification, and make inferences about its function? The phylogenetic concepts of orthology and paralogy are key to understanding gene family evolution. In turn, knowledge of gene family evolution is necessary to answer important questions about where new genes come from and how divergence in function happens as a lineage becomes more complex. Physcomitrella is perfectly placed phylogenetically to serve as a point of comparison for angiosperms. (2) the use of a structural-genomic data set from chloroplasts of land plants to help reconstruct basal relationships.
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1 - University of California, Berkeley, Department of Integrative Biology, 1001 Valley Life Sciences Bldg. #2465, Berkeley, California, 94720-2465, USA
2 - California Department of Food & Agriculture, 3294 Meadowview Road, Sacramento, California, 95832, USA
Presentation Type: Symposium or Colloquium Presentation
Date: Monday, July 31st, 2006
Time: 1:55 PM