2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2015
Abstrakt

Matthew W. Hahn, Tijl {De Bie}, Jason E. Stajich, Chi Nguyen, Nello Cristianini. Estimating the tempo and mode of gene family evolution from comparative genomicdata. Genome research, 15(8):1153-1160. 2005.

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Abstract:

Comparison of whole genomes has revealed that changes in the size of gene
families among organisms is quite common. However, there are as yet no models of 
gene family evolution that make it possible to estimate ancestral states or to
infer upon which lineages gene families have contracted or expanded. In addition,
large differences in family size have generally been attributed to the effects of
natural selection, without a strong statistical basis for these conclusions. Here
we use a model of stochastic birth and death for gene family evolution and show
that it can be efficiently applied to multispecies genome comparisons. This model
takes into account the lengths of branches on phylogenetic trees, as well as
duplication and deletion rates, and hence provides expectations for divergence in
gene family size among lineages. The model offers both the opportunity to
identify large-scale patterns in genome evolution and the ability to make
stronger inferences regarding the role of natural selection in gene family
expansion or contraction. We apply our method to data from the genomes of five
yeast species to show its applicability.