Table 1.
Results of the ILD, CADM, and CONCATERPILLAR tests.
Table 2.
Datasets used for phylogenetic analyses and model settings as determined in jModeltest 2.0 and MrModeltest 2.3 using Akaike Information Criterion (AIC).
Figure 1.
The ML tree of gymnosperms constructed from combined LFY and NLY CDS sequences.
Numbers associated with branches are bootstrap percentages higher than 50%. The cycads were used as functional outgroups.
Figure 2.
Comparison of ML trees of gymnosperms constructed using LFY + NLY sequences.
A and C, All three codon positions were used; B and D, 1st and 2nd codon positions were used. A and B, Angiopteris lygodiifolia was used as outgroup; C and D, The cycads were used as functional outgroups. Numbers associated with branches are bootstrap percentages of ML higher than 50% and Bayesian posterior probabilities greater than 0.90, respectively.
Figure 3.
The ML trees of cycads inferred from sequence analysis of combined LFY and NLY sequences.
A, CDS; B, CDS+Intron. Numbers associated with branches are bootstrap percentages of ML and MP higher than 50% and Bayesian posterior probabilities greater than 0.90, respectively. Ginkgo biloba was used as outgroup in Fig. 3A.
Figure 4.
ML trees of Podocarpaceae constructed from sequence analysis of combined LFY and NLY sequences.
A, CDS; B, CDS+Intron. Numbers associated with branches are bootstrap percentages of ML and MP higher than 50% and Bayesian posterior probabilities greater than 0.90, respectively. Araucaria heterophylla and Agathis robusa were used as outgroups in Fig. 4A.
Figure 5.
Divergence times of gymnosperms estimated from combined LFY and NLY CDS sequences using BEAST.
A time scale is shown at the bottom. A–K indicate fossil calibration points. 1–10, A, D, E and G indicate some nodes of interest. Median ages of nodes are shown, with horizontal bars indicating the 95% highest posterior density intervals.
Figure 6.
The ML trees of Taxaceae+Cephalotaxaceae constructed from CDS sequences.
A, combined LFY and NLY; B, LFY; C, NLY. Numbers associated with branches are bootstrap percentages of ML and MP higher than 50% and Bayesian posterior probabilities greater than 0.90, respectively. Taiwania cryptomerioides and Cunninghamia lanceolata were used as outgroups.
Figure 7.
A lineage-through-time plot showing divergence time distribution of the gymnosperm genera.
The divergence times was based on the median ages of the nodes from the BEAST analysis (see Fig. 5).
Figure 8.
Comparison of divergence times of the coniferous genera between the Southern and Northern Hemispheres.
A, boxplot comparison of all genera; B, dot plot comparison of each genus. The calculation of divergence times was based on the median ages of the nodes from the BEAST analysis as shown in Fig. 5.