Rtapas: An R package to assess cophylogenetic signal between two evolutionary histories

Abstract

Cophylogeny represents a framework to understand how ecological and evolutionary process influence lineage diversification. However, linking patterns to mechanisms remains a major challenge. The recently developed Random Tanglegram Partitions provides a directly interpretable statistic to quantify the strength of cophylogenetic signal, maps onto a tanglegram the contribution to phylogenetic signal of individual host-symbiont associations, and can incorporate phylogenetic uncertainty into estimation of cophylogenetic signal. We introduce Rtapas (v1.2), an R package to perform Random Tanglegram Partitions. Rtapas applies a given global-fit method to random partial tanglegrams of a fixed size to identify the associations, terminals, and nodes that maximize phylogenetic congruence. Rtapas extends the original implementation with a new algorithm that tests phylogenetic incongruence and adds ParaFit, a method designed to test for topological congruence between two phylogenies using patristic distances, to the list of global-fit methods than can be applied. Rtapas can particularly cater for the need for causal inference in cophylogeny as demonstrated herein using to two real-world systems. One involves assessing topological (in)congruence between phylogenies produced with different DNA markers and identifying the particular associations that contribute most to topological incongruence, whereas the other implies analyzing the evolutionary histories of symbiont partners in a large dataset. Rtapas facilitates and speeds up cophylogenetic analysis, as it can handle large phylogenies reducing computational time, and is directly applicable to any scenario that may show phylogenetic congruence (or incongruence).

Deep-mining of vertebrate genomes reveals an unexpected diversity of endogenous viral elements

“…For the inference of the time tree of ectodomains, we used orthology of the tarsier elements and their estimated ages (based on LTR divergence, Supplementary excel file 2) to calibrate internal nodes in the tree, and used a prior distribution on the root of the tree assuming that the retroelements present in cartilaginous fish/tetrapods codiverged with their gnathostome hosts (prior mean 462, prior 95% CI: 436-489 MYA). Cophylogenetic analysis for benyviruses was performed and plotted in RTapas using the maximum incongruence algorithm (81). We predicted select paramyxovirus and nairovirus protein structures for de novo using AlphaFold2 (82) as implemented in ColabFold (83).…”