From: Rogozin, Igor (NIH/NLM/NCBI) [E]
Sent: Monday, May 14, 2007 11:13 AM
To: NLM/NCBI List ncbi-seminar
Subject: CBB seminar, May 15 at 11 AM, B2 Library room

Tuesday, May 15, at 11 AM Bldg. 38A, B2 NCBI Library Rare amino acid replacements:
 a new class of characters for genome-wide phylogenetic studies 
Igor B. Rogozin National Center for Biotechnology Information, National Library of Medicine, 
National Institutes of Health, Bethesda, MD 20894, USA 

As the number of sequenced genomes from diverse walks of life rapidly increases, phylogenetic analysis
 is entering a new era: reconstruction of the evolutionary history of organisms on the basis of full-scale 
comparison of their genomes. In addition to brute force, genome-wide analysis of alignments, rare genomic 
changes (RGCs) that are thought to comprise derived shared characters of individual clades are increasingly
 used in genome-wide phylogenetic studies. We propose a new type of RGCs designated RGC_CAMs (after Conserved
 Amino acids-Multiple substitutions), which are inferred using a genome-scale analysis of protein and underly
ing nucleotide sequence alignments. The RGC_CAM approach utilizes amino acid residues conserved in 
major eukaryotic lineages, with the exception of a few species comprising a putative clade, and selects 
for phylogenetic inference only those amino acid replacements that require 2 or 3 nucleotide substitutions, 
in order to reduce homoplasy. The RGC_CAM analysis was combined with a procedure for rigorous statistical
 testing of competing phylogenetic hypotheses. The RGC_CAM method is shown to be robust to branch length 
differences and taxon sampling. When applied to animal phylogeny, the RGC_CAM approach strongly supports
 the coelomate clade that unites chordates with arthropods as opposed to the ecdysozoan 
(molting animals) clade. This conclusion runs against the view of animal evolution that is currently 
prevailing in the evo-devo community. The final solution to the coelomate-ecdysozoa controversy will
 require a much larger set of complete genome sequences representing diverse animal taxa. It is expected 
that RGC_CAM and other RGC-based methods will be crucial for these future, definitive phylogenetic studies.