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.

The evolutionary dynamics and epidemiological history of hepatitis C virus genotype 6, including unique strains from the Li community of Hainan Island, China

“…Phylostems ( Doizy et al. 2020 ) was used to investigate temporal signaling in an ML tree of the gt6 Ref and gt6 Bai whole virus genome datasets.…”

“…Temporal signaling of the gt6 Ref and gt6 Bai whole virus genome datasets was firstly verified using Phylostems ( Doizy et al. 2020 ).…”

Suspicions of two bridgehead invasions ofXylella fastidiosasubsp.multiplexin France

“…At first, a Maximum Likelihood (ML) tree was constructed with RAxML 8.2.4 ( 78 ) using a rapid Bootstrap analysis, a General Time-Reversible model of evolution following a Γ distribution with four rate categories (GTRGAMMA) and 1,000 alternative runs. A linear regression test between sample age and root-to-tip distances was computed at each internal node of the ML tree using Phylostems ( 79 ). Temporal signal was considered present at nodes displaying a significant positive correlation.…”

Time‐calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen

“…We reconstructed a Maximum Likelihood tree of the global data set using RAxML v.8.2.9 (Kozlov et al, 2018). The presence of temporal signal in the data set was tested by computing the linear regression between sample age and root‐to‐tip distances at every internal node of the Maximum Likelihood tree (Doizy et al, 2020). The South West Indian Ocean clade root was the deepest node for which both the linear regression was statistically significant and was, therefore, assumed to contain detectable amounts of evolutionary change, making it suitable for tip‐dating inferences.…”