Speaker: Bryan Kolaczkowski, Ph.D, Center for Ecology and Evolutionary Biology, University of Oregon
Time: 2:00-3:00pm, Wednesday, March 19th, 2008
Place: 321 Stanley Hall
Abstract:
One of the central questions in molecular evolution is, ‘How are
similarities and differences among species generated by evolutionary changes
in DNA and protein molecules?’ Answering this question requires not only
a detailed understanding of the evolutionary relationships among species but
also the ability to separate functionally important substitutions from those
that are largely neutral. Here I introduce a phylogenetic model of
site-specific evolutionary rate changes and describe how it can be used to 1)
improve the accuracy of inferred evolutionary relationships and 2) predict the
specific substitutions responsible for important functional shifts in protein
evolution. The motivation for the development of this model is the observation
that different positions in the molecule regularly change their rates of
evolution as they evolve. As I show, these changes in site-specific rates not
only interfere with accurate phylogenetic inference but also provide clues as
to which sites are likely to be responsible for shifts in molecular function.
The model incorporates site-specific rate changes by analyzing a sequence
alignment using a number of independently optimized branch length sets along
the tree rather than the single set of branch lengths used in current models. I
show that the incorporation of evolutionary rate changes produces more accurate
phylogenies than existing methods. The model can also be used to assign
specific sites in the alignment to particular branch length sets, providing an
estimate of site-specific evolutionary dynamics that can be exploited to
predict the functional importance of each site.
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