Neutrality Test, Mismatch Analysis, and the Extended Bayesian
Skyline Plot
Statistics for Tajima’s D, Fu and Li’s D * and F * were
presented in Table 2. Mismatch distribution analyses for C.
bifida displayed a unimodal graph for AC5 and PPRC , but
multimodal graphs for cpDNA, PHYP , AAT and SAMS(Supplementary Figure S1). But for C. micholitzii , mismatch
distribution analyses showed a unimodal graph for PHYP and AC5 ,
but multimodal graphs for cpDNA, PPRC , AAT and SAMS(Supplementary Figure S1). A unimodal curve is indicative of recent
population expansion, whereas a multimodal curve is indicative of a
population at demographic equilibrium. Extended Bayesian Skyline Plots
(EBSP) of the two species simiulated by BEAST were shown in Figure 7.
The EBSP of C. bifida showed that a weak bottleneck effect had
occurred since about 0.25 Mya until now. During 0.25 Mya to 0.08 Mya,C. bifida experienced population contraction, and while from
about 0.08 Mya to present it experienced population expansion (Figure
7a). For C. micholitzii , EBSP result showed that after a long
stable population size, there was a continuous population expansion from
about 0.1 Mya to present (Figure 7b).