As a first step to mapping quantitative trait loci for mating system d
ifferences, a genetic linkage map was generated from an interspecific
backcross between Mimulus guttatus and Mimulus platycalyx. The linkage
map consists of 99 RAPD and two isozyme markers. Eighty-one of these
markers were mapped to 15 linkage groups, spanning 1437 contiguous cen
tiMorgans, and covering 58% of the estimated genome. The genome length
of Mimulus is estimated at 2474 +/- 35 cM; bootstrapping indicates th
at only ca. 40 markers are needed to give an accurate estimate of geno
me length. Further statistical analyses indicate that many RAPD marker
s cannot be ordered with certainty and that uncertain linkage groups t
end to map nonlinearly even under commonly used mapping functions. Str
ategies for speeding up the mapping process for a wild species and pos
sible applications of a partial linkage map in evolutionary studies ar
e discussed.