Unambiguously aligned positions (Figs. S2, S3 and S4) were used for subsequent phylogenetic analyses. Maximum likelihood (ML) tree of IFITM gene family was reconstructed by PHYML2.4 implemented in Jmodeltest 0.1 package with the best-fitting model of F81+I+G that is selected using JmodelTest in the same package [65, 66] . The bootstrap analysis was performed with 1000 replications. Bayesian inference (Bayes) tree was reconstructed using MrBayes v3.1.2 [67] . Four independent Markov Chain Monte Carlo (MCMC) chains were used with the default temperature of 0.01. Four repetitions were run for 8,000,000 generations with tree and parameter sampling occurring every 1,000 generations. The first 25% of trees were discarded as burn-in, leaving 750 trees per run. Posterior probabilities for internal node were calculated from the posterior density of trees. Maximum parsimony (MP) tree was reconstructed by PAUP 4.0 with a bootstrap value of 1,000 repetitions [68] . To investigate whether gene conversion occurred in mammalian IR-IFITM genes, an analysis was performed using the GENECONV program [34] .