Additional File 4 The estimates of the mutation rate of Cupressus and the divergence timescales between the Asian species/lineage
We downloaded from GenBank and aligned three plastid DNA fragments (trnD-trnT, trnS-trnG and trnL-trnF) of three Cupressus species, three Juniperus species, three Calitropsis species, one species from Platycladus, Calocedrus, Chamaecyparis and Thuja. We used Thuja as outgroup in the BRAST analyses. We constrained the stem lineage of Chamaecyparis to be 99.63 millions years ago based on the fossil records of Cupressinocladus interruptus (similar to Chamaecyparis) in the late Cretaceous to Tertiary (Stockey RA, Kvaček J, Hill RS, Rothwell GW, Kvaček Z. 2005. Fossil record of Cupressaceae s.lat. In: Farjon A, eds. A monograph of Cupressaceae and Sciadopitys. Kew, UK: Royal Botanic Gardens, Kew, 54-68). We constrained the stem lineage of Juniperus Sect. Sabina (represented here by J. formosana and J. drupacea) to be 38.34 millions years ago based on the fossil record of J. pauli (similar to those species of Sect. Sabina) in the Eocene/Oligocene boundary (Kvaček Z. 2002. A new juniper from the Palaeogene of Central Europe. Feddes Repertorium 113: 492-502). The mutation rate of Cupressus was calculated to be 3.2 × 10-10 substitutions per site per year.
Additional File 4-figure 1: A preliminary estimation of the possible mutation rate (in blue) of Cupressus and fossil records (in read with millions years ago).
We then used the mutation rate to estimate the divergences of the Asian cypress species. The timescales of major nodes were showed as follows.
Additional File 4-figure 2: The divergence timescales of the Asian cypress lineage/species (in read with millions years ago).