Delmore et al. (2016) use NGS to find migration genes in light-logger-equipped Swainson’s thrushes. As amazingly as it may sound, they do find a migration-associated candidate region on chromosome 4. This would thus mean that this region of the genome may hold genes that trigger individuals to go either west or east of the Rocky mountains during their migration to Central America. They have worked in an area where hybrids and backcrosses occur which may have been key to find such a genotype-phenotype association in otherwise genetically well-differentiated subspecies.
Figure 2A from Delmore et al. (2016) showing the association between SNPs at chromosome 4 and the phenotype of interest - migratory direction in Swainson’s thrushes.