PhyloTempo: A Set of R Scripts for Assessing and Visualizing Temporal Clustering in Genealogies Inferred from Serially Sampled Viral Sequences

Abstract

Serially-sampled nucleotide sequences can be used to infer demographic history of evolving viral populations. The shape of a phylogenetic tree often reflects the interplay between evolutionary and ecological processes. Several approaches exist to analyze the topology and traits of a phylogenetic tree, by means of tree balance, branching patterns and comparative properties. The temporal clustering (TC) statistic is a new topological measure, based on ancestral character reconstruction, which characterizes the temporal structure of a phylogeny. Here, PhyloTempo is the first implementation of the TC in the R language, integrating several other topological measures in a user-friendly graphical framework. The comparison of the TC statistic with other measures provides multifaceted insights on the dynamic processes shaping the evolution of pathogenic viruses. The features and applicability of PhyloTempo were tested on serially-sampled intra-host human and simian immunodeficiency virus population data sets. PhyloTempo is distributed under the GNU general public license at https://sourceforge.net/projects/phylotempo/.

Phylogenetic tree shapes resolve disease transmission patterns

“…We use two measures of the ‘staircase-ness’ of phylogenies defined by Norström et al [21]: (i) the portion of sub-trees that are imbalanced (i.e. that have different numbers of descending tips on the left and right sides) and (ii) the average of $\min (T_{li},T_{ri)}/\max (T_{li,}{T}_{ri})$ over the internal nodes of the tree.…”

The impact of super-spreaders in COVID-19: mapping genome variation worldwide

“…• Staircase-ness: defined as the portion of imbalance nodes (Norström et al 2012). It shows much lower values for chain out-breaks.…”

Phylogenetic tree shapes resolve disease transmission patterns

“…We calculated the maximum width of each tree divided by its maximum depth (max d , the maximum depth of any leaf in the tree). Maximum difference in widths We compared in the trees. This summary reflects the maximum absolute difference in widths from one depth to the next, over all depths d i in the tree. Cherries A cherry configuration is a node with two leaf descendants. Staircase-ness We use two measures of the “staircase-ness” of phylogenies defined by Nord-strom et al [Norström et al, 2012]: (1) the portion of sub-trees that are imbalanced (ie that have different numbers of descending tips on the left and right sides) and (2) the average of over the internal nodes of the tree.…”

“…Staircase-ness We use two measures of the “staircase-ness” of phylogenies defined by Nord-strom et al [Norström et al, 2012]: (1) the portion of sub-trees that are imbalanced (ie that have different numbers of descending tips on the left and right sides) and (2) the average of over the internal nodes of the tree.…”

“…This motivates asking the question: does tree shape carry epidemiological information? Recent work indicates that tree shape reveals aspects of the evolution of viral pathogens [Norström et al, 2012, Leventhal et al, 2012, Robinson et al, 2013, Poon et al, 2013, Frost and Volz, 2013], but to date we do not have methods to exploit tree shape in an analysis of pathogen transmission dynamics, built upon simulated data and validated using real-world outbreak data.…”