Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

Abstract

Here, taking these three studies as a case in point, we discuss pitfalls that the simple addition of sequences cannot avoid, and show how the observed incongruence can be largely overcome and how improved bioinformatics methods can help reveal the full potential of phylogenomics. Two factors contribute significantly to the difficulty of reconstructing the correct phylogenetic tree for a set of sequences. First, if speciation events are closely spaced in time, the amount of phylogenetic signal is often small, leading to short internal tree branches that are difficult to resolve ,. Second, if th