Association between chloroplast and mitochondrial lineages in oaks

Patterns of chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) variationwere studied in 378 populations of oak trees sampled throughout thesouthern half of France. Six cpDNA haplotypes detected in a previousEuropean survey and three new cpDNA haplotypes were found in this region.Two mitochondrial polymorphisms detected earlier by restriction analysis ofPCR-amplified fragments alone, or in combination with single-strandconformation polymorphism (SSCP), were compared with the cpDNA data.Sequencing revealed the nature of the two mitochondrial mutations: asingle-base substitution and a 4-bp inversion associated with a 22-bphairpin secondary structure. The single-base substitution was then analyzedby allele-specific amplification. Results for the two cytoplasmic genomeswere combined, which allowed the identification of 12 cpDNA-mtDNAhaplotypes. The 4-bp mtDNA inversion has appeared independently indifferent cpDNA lineages. Given the peculiar nature of this mtDNA mutation,we suggest that intramolecular recombination leading to repeated inversionsof the 4-bp sequence (rather than paternal leakage of one of the twogenomes) is responsible for this pattern. Furthermore, the geographiclocations of the unusual cpDNA-mtDNA associations (due to the inversion)usually do not match the zones of contact between divergent haplotypes. Inaddition, in southern France, the groupings of populations based on themtDNA substitution were strictly congruent with those based on cpDNA.Because many populations that are polymorphic for both cpDNA and mtDNA haveremained in contact since postglacial recolonization in this area withoutproducing any new combination of cytoplasms involving the mitochondrialsubstitution, we conclude that paternal leakage is not a significant factorat this timescale. Such results confirm and expand our earlier conclusionsbased on controlled crosses.