Colloquium

Tuesday, April 1, 2008

4:00 PM, BAC 219

Speaker: John Karro, Department of Computer Science and Systems Analysis, Miami University, Oxford, Ohio

Host: David Groggel

Title: Modeling the Process of Random Change in the Mammalian Genome

Abstract: The evolution of any species is driven by random changes to its genome: first a change in an organism’s DNA must occur, then that change must propagate throughout the population. Understanding and modeling this first process (the initial random change) is an important step in understanding the molecular history of a genome, but formulating a model is extremely difficult. The lack of historical data poses one challenge, and the highly variable nature of the rate at which these changes occur further complicates the problem. Even when we consider only non-functional DNA (e.g. DNA not subject to the forces of natural selection), we find that: different species undergo genomic change at substantially different rates; any given species has been subjected to substantially different rates at different periods in time; even different portions of the same genome can be subject to very different rates.

In this talk I will discuss our recent work in developing a model for the mutation process at the genomic level. Using a Markov chain for a first approximation, I will outline how this model has been modified as the required assumptions have been relaxed, and how the increasingly complex models are fit to data produced by the sequencing of the human genome (as well as other species). In the process I will discuss what the application of these models has shown us about the mammalian genome, in terms of its structure, its history and its predicted evolutionary future.

This talk is designed for researchers in statistics and mathematics; no biological background will be assumed or required. (Though some might be inflicted.)