The millions of monarchs (Danaus plexippus) that flit on fragile wings from the U.S.to a particular area of fir forest in Mexico—as far as 4,000 kilometers—are making the journey for the first time.

"They have never been to the overwintering sites before and have no relatives to follow," Steven Reppert, a neurobiologist at the University of Massachusetts Medical School, said in a prepared statement.

So how to do these insects know where to go? "There must be a genetic program underlying the butterflies' migratory behavior," Reppert said. In an effort to find more molecular-scale answers, Reppert and his team have drawn up the draft genome of the monarch, published online Wednesday in Cell. The 273-million basepair genome is the first of any butterfly and is considerably smaller than—and quite different from—that of the commercial silk moth (Bombyx mori), which has 432 million basepairs, suggesting rapid evolution in the Lepidoptera group, which includes both butterflies and moths.

Within the new genome, the research team found several gene groupings that help to explain how these insects know where to go. Compared with other sequenced insects, the butterflies had different genetic patterns in visual areas, which might help them to gather cues from the sun to guide their route. The research also found genetic clues about how their circadian clocks differ from those of other animals, which might help these long-distance fliers to respond differently to light during their travels.

"In terms of fundamental brain processes, those involved in the navigation mechanisms used for long-distance migration have been difficult to decipher," Reppert said. "Dissecting the genetic basis of long-distance migration in the monarch may help us understand these mechanisms not only in monarchs but more generally in other migrants, including migratory birds and sea turtles."

The genome sequence also provides some insight into why some monarchs migrate and others do not. Despite being the same species, interim generations do not make the long trip. But those that are destined to depart "have a striking increase in longevity, increased abdominal fat stores and cold tolerance and an overpowering drive to fly south," Zhan and colleagues wrote. The researchers discovered that a subset of regulatory molecules (microRNAs), buried in the genetic map, are expressed differently in the butterflies with such incurable wanderlust versus those that are content to stay local.