Phylogenetics PG_M0005

title:From Gene-Scale to Genome-Scale Phylogenetics: the Data Flood In, but the Challenges Remain
author:Antonis Rokas and Stylianos Chatzimanolis
year:2008
place of publish:
abstract:An important goal of phylogenetics is to be able to consistently and accurately reconstruct the historical patterns of cladogenesis
            among major organismic groups. Gene-scale phylogenetics is insufficient to attain this goal owing to the presence of poor
            resolution and incongruence in single- and few-gene phylogenies. The increasing availability of genomescale amounts of data
            promises to overcome the insufficiency of gene-scale phylogenetics and uncover the genealogical tapestry uniting all living
            organisms with unprecedented accuracy. Here, we argue that a vast increase in data size alone—although necessary—may not be
            sufficient to achieve the desired accuracy for three reasons: (i) the existence of short stems in the tree of life, (ii) the
            saturation of phylogenetic signal in molecular sequences, and (iii) the effect of systematic error on phylogenetic inference.
            Devising strategies to ameliorate the effect of such challenges on sequence evolution will be critical to the success of current
            efforts to reconstruct the tree of life.