2.10 Dating estimates
Dating analyses were performed in BEAST v1.10.4 (Suchard et al., 2018).
The phylogenetic tree was estimated altogether with time inference of
nodes. Isolation dates were used for tip-dating (Rieux & Balloux,
2016), with a relaxed clock model (uncorrelated lognormal rates across
branches). The prior for the clock rate (parameter ucln.mean ) was
set as [1e-9; 2e-7] substitutions/site/branch/year (s/s/b/y), a
conservative range encompassing values from previous studies (Lillebaek
et al., 2016; Pepperell et al., 2013; Kay et al., 2015; Eldholm et al.,
2015; Menardo et al., 2019). Markov Chain Monte Carlo (MCMC) chains were
run to avoid convergence to local optima, each run for
107 generations, or until convergence of parameters
and effective sample sizes (ESS) >= 200 (checked in Tracer
v1.7.1(Rambaut et al., 2018)). Burnin trees were discarded, and the
remaining ones were annotated using TreeAnnotator (Rambaut & Drummond,
2010), generating a maximum clade credibility tree with median heights.
Intervals for ages are reported for each node of the phylogenetic tree,
as [minimum between two runs and maximum between two runs], to be
conservative. The same five genomes of M. caprae described above
were used as outgroup.