Nuclear DNA diversity, population differentiation, and phylogenetic relationships in the California closed-cone pines based on RAPD and allozyme markers

We studied nuclear gene diversity and population differentiation using 91-9 8 randomly amplified polymorphic DNA (RAPD) loci in the California closed-c one pines knobcone (Pinus attenuata Lemm.), bishop (P. muricata D. Don), an d Monterey (P. radiata D. Don) pines. A total of 384 trees from 13 populati ons were analyzed for RAPDs and another sample of 242 trees from 12 of thes e 13 populations were analyzed at 32-36 allozyme loci, using a published da ta set. Twenty-eight of 30 (93%) comigrating RAPD fragments tested were fou nd to be homologous by Southern hybridization in all three species. Using a n enriched mitochondrial DNA (mtDNA) preparation and a chloroplast DNA (cpD NA) library as probes, two fragments of cpDNA origin, and one of mtDNA orig in present among RAPD profiles were excluded from analysis of nuclear gene diversity. RAPD markers revealed moderately higher intrapopulation gene div ersity and substantially higher total genetic diversity and population diff erentiation than did allozyme markers for each species. We performed a simu lation study using allozyme data, which showed that the dominant and bialle lic nature of RAPD markers could explain the differences observed in differ entiation parameters, but not in gene diversity; RAPD phenotypes appear to represent more underlying gene diversity than do allozyme phenotypes. Resul ts of joint phylogenetic analyses of both the RAPD and allozyme markers str ongly supported a common ancestor for P. radiata and P. attenuata pines, an d south-to-north migration histories for all three species.