Genome-wide comparative analysis of phylogenetic trees and search for trends in the phylogenetic forest

Monday, October 24, 2011 — Poster Session I
Noon – 2:00 p.m.	Natcher Conference Center	NLM	BIOINFO-13

* FARE Award Winner

Authors

• P Puigbo
• YI Wolf
• EV Koonin

Abstract

Comparative genomics has revealed extensive horizontal gene transfer (HGT) among prokaryotes (Archaea and Bacteria), a development that is often considered to undermine the 'tree of life'(TOL) concept, suggesting that the TOL should be replaced by a ‘net of life’ as the paradigm of prokaryote evolution. However, the possibility remains that a statistical central trend still exists in the phylogenetic 'forest of life' (FOL).The FOL encompasses the complete set of phylogenetic trees for all genes from all genomes. However, a comprehensive analysis of the entire FOL is computationally prohibitive. Therefore, we constructed and analyzed all trees of the FOL for 100 prokaryotic species, which consists of 6,901 phylogenetic trees, including 102 nearly universal trees (NUTs). In this study, we describe new, cutting-edge methodologies (e.g.: a new metric to compare phylogenetic trees that takes into account bootstrap values, a new measure of tree inconsistency to assess how representative of the entire FOL is the topology of a given tree and a novel algorithm for detecting tree-like and net-like evolutionary trends in the phylogenetic FOL) and introduce new concepts in prokaryote evolution (e.g.: TOL as central trend discernible throughout the evolution of prokaryotes and routes of tree-like and net-like evolution).

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