Global patterns in coronavirus diversity

Anthony, Simon J.; Johnson, Christine K.; Greig, Denise J.; Kramer, Sarah; Che, Xiaoyu; Wells, Heather; Hicks, Allison L.; Joly, Damien O.; Wolfe, Nathan D.; Daszak, Peter; Karesh, William; Lipkin, W. I.; Morse, Stephen S.; Mazet, Jonna A. K.; Goldstein, Tracey

The Jane (Conow et al. 2010 ) software tool was used for cophylogenetic reconstructions. This approach applies an a priori 'cost scheme' to different evolutionary events in order to test the degree of congruence between two trees (virus and host). These 'events' include cospeciation, duplication, host switching, and failure to diverge (or sorting) (Charleston 1998; Conow et al. 2010) , which are used to create a minimal-cost reconstruction of the evolutionary history between the viruses and hosts. Another cophylogeny program, CoRe-PA (Merkle et al. 2010) , uses a parameter-adaptive approach to estimate an appropriate cost scheme without any prior value assignment. For our analysis, we used Jane with the default pre-determined cost scheme where cospeciation is the null hypothesis and, therefore, the 'cheapest' event, with the assumption that host switching would theoretically be more costly than genetic drift within a species to which a virus is already adapted. Analysis was repeated with varied cost values in Jane to test for sensitivity to our cost scheme, as well as in CoRe-PA for robustness, and event types and costs from each reconstruction were compared between the two programs. As these changes ultimately did not significantly influence the outcome of the analysis, exact event assignments used in the final analysis were inferred solely from Jane with the default cost scheme.