Molecular Evolution of MERS Coronavirus: Dromedaries as a Recent Intermediate Host or Long-Time Animal Reservoir?

Lau, Susanna K. P.; Wong, Antonio C. P.; Lau, Terrence C. K.; Woo, Patrick C. Y.

The number of synonymous substitutions per synonymous site, dS, and non-synonymous substitutions per non-synonymous site, dN, in S were calculated. Sites under positive selection were inferred using different methods as described in previous publications [21] [22] [23] [24] . First, single-likelihood ancestor counting (SLAC) and fixed effects likelihood (FEL) methods were used as implemented in DataMonkey server (Available online: http://www.datamonkey.org). The overall ω (dN/dS) value was calculated according to NJ trees under the custom (010121 with AIC of 16604.47594182065) substitution model. The ω (dN/dS) values for different clades and lineages were calculated according to NJ trees under either the F81 model or the custom substitution model (010121, 010011, 001020, or 000010 with various AIC). Positive selection for a site was considered to be statistically significant if p-value was <0.1. A mixed-effects model of evolution (MEME) was further used to identify positively selected sites under episodic diversifying selection in particular positions among different clades within a phylogenetic tree, even when positive selection was not evident across the entire tree.