Divergence time dating
Best-fit models of nucleotide substitution of chloroplast haplotypes
were chosen by jModelTest2 v2.1.6. The divergence times were estimated
by BEAST v1.8.4 (Drummond et al., 2016 ). Lacking fossil records,
secondary calibration points according to the diversification of
Rosaceae were applied to calibrate node ages. Divergence time dating was
calculated in two steps with two trees respectively. Five secondary
calibration points were applied to the first tree: Rosaceae Crown, 90.18
Mya (Zhang et al., 2017; Li et al., 2017); Amygdaleae, 84.84Mya (Zhang
et al., 2017); Spiraeeae, 84.30 Mya (Zhang et al., 2017); Roseae+Rubeae,
59.51 Mya (Zhang et al., 2017); Maleae Crown, 50.06 Mya (Zhang et al.,
2017; Li et al., 2017) to evaluate the divergence time of Prunus(node 1) and the time of Cerasus Crown (node 2). These two nodes
were subsequently used to calibrate the node ages in the second tree of
haplotypes of Cerasus serrulata . The GTR substitution model and
the uncorrelated log-normal relaxed clock and Yule process as for tree
prior were selected. MCMC was run for 1 ×107generations with sampling every 5,000 generations. The parameters were
checked in Tracer ver. 1.7.1 (Rambaut et al., 2018). Final phylogenetic
trees were edited in FigTree v. 1.4.