Middle-Upper Pleistocene climate changes shaped the divergence and demography of Cycas guizhouensis (Cycadaceae): Evidence from DNA sequences and microsatellite markers

Climatic oscillations in the Pleistocene have had profound effects on the demography and genetic diversity of many extant species. Cycas guizhouensis Lan & R.F. Zou is an endemic and endangered species in Southwest China that is primarily distributed along the valleys of the Nanpan River. In this study, we used four chloroplast DNAs (cpDNA), three nuclear genes (nDNA) and 13 microsatellite (SSR) loci to investigate the genetic structure, divergence time and demographic history of 11 populations of C. guizhouensis. High genetic diversity and high levels of genetic differentiation among the populations were observed. Two evolutionary units were revealed based on network and Structure analysis. The divergence time estimations suggested that haplotypes of C. guizhouensis were diverged during the Middle-Upper Pleistocene. Additionally, the demographic histories deduced from different DNA sequences were discordant, but overall indicated that C. guizhouensis had experienced a recent population expansion during the post-glacial period. Microsatellite data revealed that there was a contraction in effective population size in the past. These genetic features allow conservation measures to be taken to ensure the protection of this endangered species from extinction.