In analyzing the genetic makeup of the hybrids, researchers used a technique which allows them to identify which parts of the plant's DNA came from the Lewis's monkey flower and which parts from the cardinal monkey flower. In this technique, sequences that differ between two species or individuals are amplified to yield RAPDs, or randomly amplified polymorhpic DNA. In eight different characteristics of the flowers, including color, size, and shape, researchers found a region in the DNA that contained a single responsible gene. Variations in this gene affected whether or not a flower would have Lewis's flower characteristics or cardinal flower characteristics. This evidence suggests that relatively few steps may be all that's required for new species to appear.
Source: "For A New Species, A Few Genes Are All That's Needed" by Carol Kaesuk Yoon, New York Times, September 5, 1995