A comparison of genetic diversity and differentiation in five Chinese pines using cpSSR and AFLP markers

Abstract

Gene diversity and genetic differentiation in five Chinese pines, Pinus henryi, P. tabulaeformis, P. yunnanensis, P. taiwanensis and P. massoniana, were compared using amplified fragment length polymorphism (AFLP) and simple chloroplast sequence repeat (cpSSR). High genetic differentiation and median gene diversity with cpSSR markers were found both at population and species level, while median differentiation and higher gene diversity in AFLP data. Measures of subdivision that consider similarity between haplotypes offered better information on the geographic structure of plants than the standard subdivisions. Among several methods analyzed in AFLPs, the square root method provided downwardly biased estimates of the genetic parameters, while the Lynch and Milligan method over-estimated genetic diversity due to a small sample size. The Bayesian statistic was the most accurate and popular method for these dominant species and its value of species differentiation (θB = 0.1035) was close to the parameter given by analysis of molecular variance (AMOVA).