The draft genome was expected to provide a solid background for population genetics studies between migratory and nonmigratory populations. In fact, results of population genetic studies have been surprising. Because monarchs (D. plexippus) occur worldwide, it was possible to perform whole-genome sequencing on 80 monarchs from diverse populations from across the globe, including both migratory and nonmigratory ones, and to analyze genome-wide single nucleotide polymorphism (SNP) variation to reveal the evolutionary history of monarchs and their migration (Zhan et al., 2014). The monarch butterfly appears to have originated in North America and had a migratory ancestor, with the migration dating back at least one million years. Approximately 20,000 years ago, after the last glacial maximum, the North American population expanded and the migration extended further northward from Mexico to ultimately fill out its current northern range.

Genomic regions strongly associated with migration have been identified (Zhan et al., 2014). These make up 2.1% of the genome and comprise more than 500 genes, including those involved in morphogenesis and neurogenesis. A single 21-kb genomic segment stood out as showing signatures of divergent selection. The gene showing the most marked divergence encodes collagen type IV α-1, which is important for muscle function. Further gene expression and metabolic studies suggested greater flight efficiency among migratory monarchs as one of the hallmarks of the migration. It is still unclear whether other genes at the loci under selection could be involved in navigation. An RNAseq study of transcriptional differences between migrants, remigrants, and nonmigrants should help sort out which of the 500 candidate genes should be subjected to a more rigorous functional assessment.