PhyloSTemS: a new graphical tool to investigate temporal signal of
heterochronous sequences at various evolutionary scales
Abstract
Molecular tip-dating of phylogenetic trees is a growing discipline that
uses DNA sequences sampled at different points in time to co-estimate
the timing of evolutionary events with rates of molecular evolution.
Such inferences should only be performed when there is sufficient
temporal signal within the analysed dataset. Hence, it is important for
researchers to be able to test their dataset for the amount and
consistency of temporal signal prior to any tip-dating inference. For
this purpose, the most popular method considered to-date has been the
“root-to-tip regression” which consist in fitting a linear regression
of the number of substitutions accumulated from the root to the tips of
a phylogenetic tree as a function of sampling times. The main limitation
of the regression method, in its current implementation, relies in the
fact that the temporal signal can only be tested at the whole tree
evolutionary scale. To fill this methodological gap, we introduce
PhyloSTemS, a new graphical and user-friendly tool developed to
investigate temporal signal at every evolutionary scale of a
phylogenetic tree. PhyloSTemS allows detecting without a priori whether
any subset of a tree would contain sufficient temporal signal for
tip-based inference to be performed. We provide a “how to” guide by
running PhyloSTemS on empirical datasets and supply guidance for results
interpretation. PhyloSTems is freely available at
https://pvbmt-apps.cirad.fr/apps/phylostems.