We identified the random clock model as optimal for our data (Table 1). The dated phylogenetic tree generated in the BEAST analysis under the random clock model and birth-death tree prior is indicated in Fig. 2. The relationships among Coptis species are well resolved with strong support (PP > 0.95) except for the node defining the sister relationship of C. quinquefolia Miq. and C. morii. Coptis contains two main clades (I and II). Based on our time estimates (Fig. 2), the stem and crown ages of Coptis are estimated at ca. 15.47 Ma (95% HPD: 11.47–19.37; node 1) and 9.55 Ma (95% HPD: 6.66–12.92; node 2), respectively. Within clade I, three western North American species clustered together and split from their eastern Asian sister group at ca. 7.78 Ma (95% HPD: 5.16–10.52; node 3). Japanese C. japonica Makino and C. lutescens Tamura are nested in the group of mainland Chinese species and the split of these two Japanese species and their sister group occurred at ca. 4.85 Ma (95% HPD: 2.98–6.80; node 4). Within clade II, Taiwanese C. morii and Japanese C. quinquefolia were grouped together with weak support (PP = 0.73). The split time of C. morii and C. quinquefolia was estimated to be at ca. 1.34 Ma (95% HPD: 0.69–2.18; node 5).Table 1Comparison of three clock models in BEAST analyses via Bayes factorsClock modelMarginal likelihoodExponentialLognormalRandomPS implementation Exponential− 8809.70–37.44−32.90 Lognormal− 8828.42−37.44–−70.34 Random− 8793.2532.9070.34SS implementation Exponential− 8810.29–37.62−33.72 Lognormal− 8829.10−37.62–−71.34 Random−8793.4333.7271.34–2ln Bayes factor (BF) was calculated by marginal likelihoods derived from path sampling (PS) and stepping-stone sampling (SS) implementations in BEAST. 2ln BF > 2.0 represents positive evidence, > 6.00 represents strong evidence, and > 10.00 represents very strong evidence Fig. 2Dated phylogeny of Coptis inferred from the combined plastid and nuclear data using BEAST under the random clock model and birth-death tree prior. Gray bars represent 95% highest posterior density intervals. Nodes of interests were marked as 1–5 in bold. All nodes are strongly supported (PP > 0.95) except for one node (in dashed line). Plio., Pliocene; Plt., Pleistocene