From: Koonin, Eugene (NIH/NLM/NCBI) [E]
Sent: Friday, December 30, 2005 4:45 PM
To: NLM/NCBI List ncbi-seminar
Cc: Miklós Csürös
Subject: seminar 

Wednesday, Jan 4, 2006, 11 AM

Bldg. 38A, B2 conference room

 

Miklós Csürös 

 

University of Montreal, Quebec, Canada

 

Probabilistic gain-loss models for intron and gene content evolution

 

I will describe two probabilistic models with the

accompanying likelihood algorithms for the analysis of

intron evolution and the evolution of gene family size.

 

Recently completed genome sequences have been used for

comprehensive analyses of exon-intron organization in

orthologous genes of diverse organisms. Large sets of intron

presence-absence data require rigorous theoretical

frameworks in which different hypotheses can be compared and

validated. I describe a probabilistic model for intron gains

and losses along an evolutionary tree. The model parameters

are estimated using maximum likelihood. I propose a method

for estimating the number of introns lost or unobserved in

all extant organisms in a study, and show how to calculate

counts of intron gains and losses along the branches by

using posterior probabilities. The methods are used to

analyze the most comprehensive intron data set available

presently, consisting of 7236 intron sites from eight

eukaryotic organisms. The analysis shows a dynamic history

with frequent intron losses and gains, and fairly --- albeit

not as greatly as previously postulated --- intron-rich

ancestral organisms.

 

I introduce a Markov model for the evolution of a gene

family along a phylogeny. This work represents the first

tractable probabilistic model that simulatenously handles

the three main mechanisms that shape gene content:

horizontal gene transfer, gene duplication, and gene loss.

(The model assumes a linear birth-death-immigration process

along each edge.) The likelihood for the changes in the size

of a gene family across different organisms can be

calculated very efficiently, in quadratic time in the number

of all homologs. I illustrate the model by an application to

the evolution of gene content in Preoteobacteria using the

COG (Clusters of Orthologous Groups) database.

 

References:

M. Csuros. "Likely scenarios of intron evolution", 3rd RECOMB Satellite

Workshop on Comparative Genomics, DOI: http://dx.doi.org/10.1007/11554714_5.

http://www.iro.umontreal.ca/~csuros/papers/mle-introns.pdf.

 

M. Csuros and I. Miklos. "A probabilistic model for gene content evolution with 

duplication, loss, and horizontal transfer."

To appear at RECOMB 2006 (Conf. Research in Computational Molecular Biology).

http://www.iro.umontreal.ca/~csuros/papers/gld.pdf.

 

 

 

Eugene V. Koonin, PhD, Senior Investigator
National Center for Biotechnology Information
National Library of Medicine
National Institutes of Health
Bethesda, MD 20894
Telephone 301-435-5913 (office); 301-233-7294 (cellular)
Fax 301-435-7794