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).