Cophylogeny represents a framework to understand how ecological and evolutionary process influence lineage diversification. The recently developed algorithm Random Tanglegram Partitions provides a directly interpretable statistic to quantify the strength of cophylogenetic signal and incorporates phylogenetic uncertainty into its estimation, and maps onto a tanglegram the contribution to cophylogenetic signal of individual host-symbiont associations. We introduce Rtapas, 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 internal nodes that maximize phylogenetic congruence. This new package extends the original implementation with a new algorithm that examines the contribution to phylogenetic incongruence of each host-symbiont association and adds ParaFit, a method designed to test for topological congruence between two phylogenies, to the list of global-fit methods than can be applied. Rtapas facilitates and speeds up cophylogenetic analysis, as it can handle large phylogenies (100+ terminals) in affordable computational time as illustrated with two real-world examples. Rtapas can particularly cater for the need for causal inference in cophylogeny in two domains: (i) Analysis of complex and intricate host-symbiont evolutionary histories and (ii) assessment of topological (in)congruence between phylogenies produced with different DNA markers and specifically identify subsets of loci for phylogenetic analysis that are most likely to reflect gene-tree evolutionary histories.

Supplementary Figures and Tables SuppMat.pdf Amphipod_trematode_example Phylogenetic trees, association matrix and R script to perform the amphipod-trematode example Amph_Trem.zip Nuclear_organellar_example Phylogenetic trees and R script to carry out the nuclear-organellar example in Orchids Nucl_Plast.zip Mamals_Fleas_example Phylogenetic trees, association matrix and R script to carry out the mammals-fleas example Mam_Fleas.zipFunding provided by: Ministerio de Ciencia e InnovaciónCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100004837Award Number: Funding provided by: Sainsbury Orchid Fellowship*Crossref Funder Registry ID: Award Number: