Virus-host coevolution analysis.

Virus-host coevolution analysis was performed using the eMPRess tool (47,–50). A Newick format phylogenetic tree for hosts, a Newick format phylogenetic tree for viruses, and a tip mapping file for virus-hosts are needed to perform coevolution analysis in eMPRess. First, the Timescale phylogenetic tree for hosts was created using FaceTimeTree: The Timescale of Life (http://www.timetree.org/search/goto_timetree) (39). A group of species or a custom list of hosts was used to build the timescale phylogenetic tree for hosts. The resulting phylogenetic tree was exported in Newick format and stored. Next, the phylogenetic tree for the parvo-NS1 domains of viruses was created in MEGA7 using the evolutionary distances in the unweighted pair group method using average linkages (UPGMA) method using the equal input, gamma distribution (shape parameter = 5), and by removing all ambiguous positions for each sequence pair. The resulting phylogenetic tree was exported in Newick format and then stored. After this, the tip mapping files for each virus-host were created in the tip mapping format. The virus-host coevolution tanglegram was first generated in eMPRess using the Newick format phylogenetic tree for hosts, the phylogenetic tree in the Newick format for viruses, and the tip mapping files for virus hosts. Then, we looked at the event cost regions for coevolution. Next, two clusters were calculated to compute the reconciliations, and a virus-host coevolution tree was created for each cluster. The P value histogram for virus-host coevolution was then measured.