When studying M. fuliginosus populations, the divergence times of bat alphaCoV and BtAdV were calculated using a Bayesian Markov Chain Monte Carlo (MCMC) approach, which was implemented using BEAST software, version 2.6.0 [40]. HKY+G and Coalescent constant size models were used to analyze the sequences of bat mitochondrial D-loop DNA, the RdRp fragment of bat alphaCoV, and the hexon fragment of BtAdV. The mean evolutionary rate of bat alphaCoV had previously been estimated to be 1.3 × 10−4 nucleotide substitutions/site/year based on the partial RdRp gene of coronaviruses [41]. Since no substitution rate was available for the hexon region of BtAdV, the substitution rate in the hexon gene of Human adenovirus-7, HAdV-7 (1.107 × 10−3 nucleotide substitutions/site/ year), which belongs to the same genus as BtAdV, was applied to calculate the divergence time of BtAdV found in this study [42]. The divergence time of the bats was estimated, based on an evolutionary rate for mitochondrial D-loop of 20% nucleotide substitution/site/million years. The MCMC run was 3× 107 steps long, with sampling every 300 steps. The convergence of the MCMC run was checked using Tracer version 1.7.1. Higher ESS values for most of phylogenetic parameters were shown after discarding 95% of the sampled data as burn-in, but they are still very low. Thus, we carried out a MCMC run once again and found that the second MCMC run reached to the same values for each phylogenetic parameter as the first run. Because the MCMC run took a long time at once (more than one week) due to a huge number of bat D-loop sequences, we copied the last 5% of tree data ten times and combined them as a single tree file using the software, LogCombiner version 2.6.0. The Bayesian phylogenetic trees were constructed with Tree Annotator software, version 2.6.0 based on the combined tree data.

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