Size homoplasy in chloroplast microsatellites of wild perennial relatives of soybean (Glycine subgenus Glycine)

Microsatellites are a rich and readily assayed source of variation for genetic and evolutionary studies. Recently, simple sequence repeats have been identified in the chloroplast genomes of pine (Powell et al. 1995b) and rice (Provan et al. 1996), and also in the cultivated soybean (Glycine max: Leguminosae) and its wild congeners (Powell et al. 1995a). The chloroplast genome has seen wide use in plant systematic studies, but its utility is often limited at lower taxonomic levels by the low amount of divergence frequently observed among closely related taxa (Olmstead and Palmer 1994). Hypervariable chloroplast microsatellites could therefore find wide use if they were shown to be reliable markers for chloroplast phylogeny. As is true with any character, the utility of a given microsatellite in revealing relationships is limited if identical states can arise independently in different taxa—if ‘‘size homoplasy’’ (Estoup et al. 1995) occurs. Size homoplasy can be assessed by comparing the distribution of microsatellite sizes with the phylogeny of the gene (in the coalescent sense) in which the microsatellite resides. For the effectively nonrecombining genome of the chloroplast, this phylogeny can be estimated using characters distributed throughout the entire chloroplast genome. Phylogenetic information of this sort is available for chloroplast genomes of the wild perennial relatives of soybean (Glycine subgenus Glycine). Three major chloroplast genome lineages (‘‘plastome’’ groups) were identified in species of the subgenus based on the occurrence of recognition sites for 29 restriction endonucleases distributed throughout the genome (Doyle, Doyle, and Brown 1990a). Further study with additional enzymes subdivided one of these lineages (Bplastome) into 27 distinct chloroplast haplotypes and showed that the haplotype phylogeny was not concordant with relationships among the diploid species bearing these chloroplast genomes (Doyle, Doyle, and Brown 1990b). Other studies used the same endonuclease site characters to associate B-plastome haplotypes found in polyploids of G. tabacina with those of putative diploid progenitors (Doyle et al. 1990a, 1990b). We studied two chloroplast microsatellites in 54 accessions bearing B-type chloroplast genomes, using DNA samples from previous studies; three G. tabacina polyploid individuals with A-type plastomes were also