Genome sequencing
We used publicly available re-sequencing data from 14 eastern monarchs (8 males, 6 females) from Zhan et al. 2014 (Zhan et al. , 2014), which were collected in 2007-2009, and 30 newly re-sequenced western monarchs (15 males, 15 females), which were collected in January 2015 (Table S1). These numbers far exceed the number of genomes required to provide high power estimates of genetic differentiation (Willing, Dreyer & Van Oosterhout, 2012). The eastern monarchs from Zhan et al. were collected among multiple stopover points along the east coast and the Mexican overwintering sites (Fig. 1). Western monarchs were sampled from three overwintering locations along the California Coast: Big Sur, Oceano, and Carpinteria (Fig. 1). The newly sequenced western samples were sequenced on an Illumina HiSeq2000 platform. Paired-end libraries were prepared using an Illumina paired-end library kit. We combined 10 samples in a sequencing lane (2 x 100 bp) to generate 12X depth of coverage on average (Table S1). Sequences have been submitted to European Nucleotide Archive (ENA) project PRJEB33413.