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Sequence-repeat polymorphisms exhibit the signature of recombination in lodgepole pine chloroplast DNA.

The chloroplast genome is widely used in plant systematic studies (Olmstead and Palmer 1994), in part because it is slowly evolving and is assumed to be nonrecombining (Clegg 1993). Microsatellite markers have also been identified within this genome (Powell et al. 1995; Provan et al. 1996; Vendramin et al. 1996; Newton et al. 1999), and these markers are sufficiently variable for phylogeographic studies within a species (Schaal et al. 1998; Newton et al. 1999; Marshall, Newton, and Ritland 2001). Lack of recombination reduces homoplasy, which in turn increases the precision of phylogenetic inference in such studies. However, recently there has emerged some evidence of recombination in another organelle, the mitochondrion. Lunt and Hyman (1997) found end products of mitochondrial genome recombination in the nematode Meloidogyne javanica. Saville, Kohli, and Anderson (1998) reported a discrepancy in the expected genotypic structure of mitochondrial DNA (mtDNA) sequences in the fungus Armillaria gallica relative to expectations under purely clonal transmission, consistent with observations of mitochondrial heteroplasmy. Using both sequence and restriction fragment length polymorphism data from humans, Awadalla, Eyre-Walker, and Maynard Smith (1999) found linkage disequilibria to decrease with increasing physical distance, consistent with mtDNA recombination. Phylogenetic trees constructed using similar data contained a larger number of homoplasies than expected on the basis of simulated data, which may indicate recombination (Eyre-Walker, Smith, and Maynard Smith 1999). Biologically, mtDNA recombination in humans is feasible, since mitochondria contain the necessary enzymes (Thyagarajan, Padua, and Campbell 1996), and a few paternal mitochondria are contributed to the egg during fertilization. The human mtDNA recombination issue is, however, still the subject of much debate (see EyreWalker 2000; Ingman et al. 2000). Here, we look for signatures of recombination in the chloroplast of lodgepole pine (Pinus contorta). Lodgepole pine is common in the forests of western North America, with a climactically and edaphically diverse natural range covering over 2.6 3 107 ha. A windpollinated outcrosser and aggressive pioneer, it is thought to have colonized its present range in a north-