Differential Evolution of Antiretroviral Restriction Factors in Pteropid Bats as Revealed by APOBEC3 Gene Complexity

Hayward, Joshua A; Tachedjian, Mary; Cui, Jie; Cheng, Adam Z; Johnson, Adam; Baker, Michelle L; Harris, Reuben S; Wang, Lin-Fa; Tachedjian, Gilda

To estimate the time of the expansion of A3Z1 genes in bat genome, molecular dating was performed using the Bayesian evolutionary method as implemented in BEAST v1.8.2 (Drummond et al. 2012) . All reference nucleotide sequences were aligned using MUSCLE and adjusted manually. A recombination test was then performed using the RDP, GENECONV and MaxChi methods implemented in RDP3 (Martin et al. 2010) . After removing recombinant sequences, all sequences were submitted to BEAST for estimation of the divergence time. Fossil node calibrations were taken from published literature (Kumar et al. 2017 Ma. Bayesian phylogeny was inferred using the GTR þ G substitution model, the Yule speciation tree prior and lognormal relaxed clock (Uncorrelated) prior. The BEAST processes were run for ten million generations until all relevant parameters converged [effective sample size (ESS)>200], with 10% of the Bayesian Markov chain Monte Carlo (MCMC) chains discarded as burn-in.