Time-scaled Bayesian phylogenetic analyses
To construct time-scaled trees, Bayesian molecular clock analyses were
conducted using the Markov chain Monte Carlo (MCMC) method in BEAST
v.1.10.4 (Suchard et al., 2018). Phylogenies were reconstructed using a)
a Generalized Time-Reversible model (GTR) of nucleotide substitution
(Tavaré & Miura, 1986) with a gamma distribution of site heterogeneity
(also known as the Yang96 model (Yang, 1996)), b) a coalescent-based
Gaussian Markov random fields (GMRF) Skyride model for estimating
effective population size dynamics (Minin, Bloomquist, & Suchard,
2008), and c) an uncorrelated relaxed lognormal clock (Drummond, Ho,
Phillips, & Rambaut, 2006). The BEAGLE library was used to optimize
computational efficiency (Baele, Ayres, Rambaut, Suchard, & Lemey,
2019). Eight independent MCMC analyses were run for 200 million
generations, sampled every 20,000 runs, and parameter convergence and
effective sample size (ESS) (required to be >200) were
evaluated in Tracer v.1.7.1 (Rambaut, Drummond, Xie, Baele, & Suchard,
2018). Using LogCombiner v.1.10.4, at least 10% burn-in was removed
from each run and independent runs were combined to establish the
maximum clade credibility (MCC) tree, from which the last 500 trees from
the posterior distribution were extracted and used as the empirical tree
for all subsequent phylodynamic analyses (Pagel, Meade, & Barker,
2004). Trees were visualized using Figtree v1.4.4 (Rambaut A., 2018).