High levels of population differentiation for mitochondrial DNA haplotypes inPinus radiata, muricata, andattenuata.

We analyzed mitochondrial (mt) DNA restriction fragment length polymorphisms (RFLPs) associated with cytochrome oxidase, subunit I (coxI)-related gene sequences in 268 trees derived from 19 natural populations of three species of pines from California (USA): Monterey pine (Pinus radiata D. Don), bishop pine (P. Muricata D. Don), and knobcone pine (P. attenuata Lemm.). Total genomic DNA was digested with four restriction endonucleases and probed with a 750-bp fragment of the mitochondrialcoxI gene amplified fromP. attenuata via the polymerase chain reaction (PCR). ThecoxI gene is repeated at least 4 times in some populations, and all variants that we observed resulted from complex rearrangements rather than from point mutations. There was limited intrapopulation variation, but strong differentiation among populations. When applied to haplotype frequencies, Nei's gene diversity within populations (Hs) averaged 7% (±3), and Gst varied from 75% forP. Radiata to 96% forP. muricata. The high degree of population differentiation for mtDNA suggests that it can be a powerful marker of population differences, but its rapid rate of structural evolution appears to result from recombination among a limited number of repetitive elements-giving frequent homoplasious fragment phenotypes. The phylogenetic trees disagreed with results from chloroplast DNA, nuclear gene, and morphological studies.