2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2014
Abstrakt

Yu Lin, Fei Hu, Jijun Tang, Bernard M. E. Moret. Maximum likelihood phylogenetic reconstruction from high-resolution whole-genome data and a tree of 68 eukaryotes. Pacific Symposium on Biocomputing, :285-286. 2013.

Download preprint: not available

Download from publisher: http://dx.doi.org/10.1142/9789814447973_0028 PubMed

Related web page: not available

Bibliography entry: BibTeX

Abstract:

The rapid accumulation of whole-genome data has renewed interest in the study of 
the evolution of genomic architecture, under such events as rearrangements,
duplications, losses. Comparative genomics, evolutionary biology, and cancer
research all require tools to elucidate the mechanisms, history, and consequences
of those evolutionary events, while phylogenetics could use whole-genome data to 
enhance its picture of the Tree of Life. Current approaches in the area of
phylogenetic analysis are limited to very small collections of closely related
genomes using low-resolution data (typically a few hundred syntenic blocks);
moreover, these approaches typically do not include duplication and loss events. 
We describe a maximum likelihood (ML) approach for phylogenetic analysis that
takes into account genome rearrangements as well as duplications, insertions, and
losses. Our approach can handle high-resolution genomes (with 40,000 or more
markers) and can use in the same analysis genomes with very different numbers of 
markers. Because our approach uses a standard ML reconstruction program (RAxML), 
it scales up to large trees. We present the results of extensive testing on both 
simulated and real data showing that our approach returns very accurate results
very quickly. In particular, we analyze a dataset of 68 high-resolution
eukaryotic genomes, with from 3,000 to 42,000 genes, from the eGOB database; the 
analysis, including bootstrapping, takes just 3 hours on a desktop system and
returns a tree in agreement with all well supported branches, while also
suggesting resolutions for some disputed placements.