Phylogeography of Cephalotaxus oliveri (Cephalotaxaceae) in relation to habitat heterogeneity, physical barriers and the uplift of the Yungui Plateau

• Populations of C. oliveri in Yungui Plateau originated ca. 9.15 Ma, consistent with the uplift of Qinghai–Tibetan Plateau.
• Habitat heterogeneity and physical barriers deeply affected the population structure of C. oliveri.
• Mismatch distribution and haplotypes network provided evidences of recent demographic population expansion.
• The S-DIVA analysis indicated that the center of origin was in Central China.
• The comparison of haplotype distribution patterns indicated that the regions of HNHPS and HBLD were the potential refugia.

Habitat heterogeneity, physical barriers, and the uplift of the Yungui Plateau were found to deeply affect the phylogeographic pattern and evolutionary history of Cephalotaxus oliveri, a perennial conifer endemic to China. In this study, we explored the phylogeography using three chloroplast sequences (trnL–trnF, trnT–trnD and atpB–rbcL) in 22 natural populations of C. oliveri distributed throughout its range. The Yungui Plateau populations of C. oliveri were revealed to origin ca. 9.15 Ma by molecular clock estimation, which is consistent with rapid uplift of the Qinghai–Tibetan Plateau (QTP) ca. 8–10 Ma. Additionally, geological effects of the Yungui Plateau were suggested to promote the rapid intra-specific differentiation of C. oliveri in the Pliocene and Early Pleistocene. The relatively low level of genetic diversity (h = 0.719, θ = 1.17 × 10−3) and high population differentiation (NST = 0.771 and GST = 0.642) implied restricted gene flow among populations, which was confirmed by the Nested Clade Analysis (NCA). Mismatch distribution and haplotypes network provided evidences of recent demographic population expansion. Furthermore, the statistical dispersal–vicariance analysis indicated that the center of origin was in Central China. The comparison of haplotype distribution patterns indicated that the regions of HNHPS and HBLD were the potential refugia during the Pleistocene ice ages. Our results highlighted that habitat heterogeneity and physical barriers presenting in a species range can predict genetic patterns.

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