Genetic diversity and population structure in Chrysolepis chrysophylla (golden chinquapin; Fagaceae): SSRs vs SNPs

Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP)
genotypes on the same plant samples of Chrysolepis chrysophylla (Fagaceae;
golden chinquapin) from 22 sites were used to determine genetic diversity
and population structure. One site of C. sempervirens allowed
interspecific vs. intraspecific comparison. SSRs and SNPs yielded many
similar results. Among-site variation contributed 13% to 17% of the
genetic variation and Fst estimates of 0.14 to 0.17 were in the range
expected among Fagaceae species rather than among populations within a
species. The northern sites tended to group separately on the first two
axes of multivariate scatterplots from southern sites. Sites in two
geographically isolated areas were divergent: 1) the Hood Canal,
Washington population was relatively more genetically distant from other
golden chinquapin sites than was our C. sempervirens site; 2) three
coastal southern California sites were moderately diverged. The Hood Canal
site had a negative inbreeding coefficient, fewer alleles, lower
heterozygosity, and differed from the Skamania County, Washington site as
well as all other sites. Hood Canal trees are distinguished by disjunct
geography and by these molecular results. This suggests that the golden
chinquapin near Hood Canal be treated as a management unit, and potential
conservation actions are discussed.