Bioinformatický seminár

Tue 25 Sep. 2012, 17:20

Title: Jimmy Yang, Tandy Warnow (2011) Fast and accurate methods for phylogenomic analyses
Speaker: Kuko Kováč

BACKGROUND: Species phylogenies are not estimated directly, but rather through
phylogenetic analyses of different gene datasets. However, true gene trees can
differ from the true species tree (and hence from one another) due to biological 
processes such as horizontal gene transfer, incomplete lineage sorting, and gene 
duplication and loss, so that no single gene tree is a reliable estimate of the
species tree. Several methods have been developed to estimate species trees from 
estimated gene trees, differing according to the specific algorithmic technique
used and the biological model used to explain differences between species and
gene trees. Relatively little is known about the relative performance of these
methods. RESULTS: We report on a study evaluating several different methods for
estimating species trees from sequence datasets, simulating sequence evolution
under a complex model including indels (insertions and deletions), substitutions,
and incomplete lineage sorting. The most important finding of our study is that
some fast and simple methods are nearly as accurate as the most accurate methods,
which employ sophisticated statistical methods and are computationally quite
intensive. We also observe that methods that explicitly consider errors in the
estimated gene trees produce more accurate trees than methods that assume the
estimated gene trees are correct. CONCLUSIONS: Our study shows that highly
accurate estimations of species trees are achievable, even when gene trees differ
from each other and from the species tree, and that these estimations can be
obtained using fairly simple and computationally tractable methods.