Our dataset collection comprises files containing tree files and character matrices, serving as invaluable resources for researchers aiming to reproduce or extend the findings presented in our manuscript. panzootic_virus_metadata_lineage3.csv - metadata to make the trees (Figure 2) panzootic_virus.fa - the virus alignment file (Figure 2) panzootic_virus_rooted.treefile - the virus tree file (Figure 2) AA_gisaid_revANNA-ADR_05042022finalAL.xlsx - dataset for generation Figure 3 COVID_ToL,csv - metadata for mammal tree and trait matrix COVID_ToL_Infection.csv - metadata for mammal tree and trait matrix COVID_ToL_ACE2.csv - metadata for mammal tree and trait matrix COVID_ToL_CAT.csv - metadata for cat tree and trait matrix TopoFree_ND_MCC_SpeciesTree.rdata - Species tree file TopoFree_ND_MCC_SpeciesTree_ace_ACE2_ARD.rdata - Figure S3 TopoFree_ND_MCC_SpeciesTree_simmap_ACE2_ARD.rdata - Figure S2 TopoFree_ND_MCC_Famtree_V2.rdata - Family tree file TopoFree_ND_MCC_FamTree_V2_ace_ACE2.rdata - Figure S4 TopoFree_ND_MCC_Famtree_V2_simmap_ACE2.rdata - Figure 4 TopoFree_ND_CatTree.rdata - Cat tree file TopoFree_ND_MCC_CatTree_ace_Infection_ARD.rdata - Figure S6 TopoFree_ND_MCC_CatTree_simmap_Infection_ARD.rdata - Figure S5