Introduction
Seasonal migration is common in nature (Dingle, 2014) and allows many different animals to escape deteriorating habitats, escape predators and parasites, and benefit from seasonally available resources in multiple regions (Dingle, 1972; Alerstam, Hedenstrom & Åkesson, 2003; Alerstam, 2006; McKinnon et al. , 2010; Altizer, Bartel & Han, 2011; Fricke, Hencecroth & Hoerner, 2011; Dingle, 2014). Migration is likely to be polygenic (Dingle, 1991) and studies have demonstrated that genes involved in muscle development, energy metabolism and circadian rhythm tend to show genetic divergence or differential expression patterns between migratory and non-migratory individuals (McFarlan, Bonen & Guglielmo, 2009; O’Malley, Ford & Hard, 2010; Postel, Thompson, Barker, Viney & Morris, 2010; Trivedi, Kumar, Rani & Kumar, 2014). While it is clear that migration imposes selection for specific gene variants or transcription levels, the interplay between animal migration and genome evolution remain understudied. Genomes may be affected by migration in varying ways. Populations of the same species often vary in their migratory propensity, with some populations migrating and others not, or with populations migrating over different distances and to different destinations. This could result in spatial or temporal separation between different migrants, and consequently reduced gene flow and increased genome-wide genetic differentiation, as found in beluga whales and noctule bats (O’Corry-Crowe, Suydam, Rosenberg, Frost & Dizon, 1997; Petit & Mayer, 2000). Alternatively, the use of common breeding or overwintering grounds can result in a lack of genome-wide differentiation, even if differential selection acts on individuals during part of the year (Dallimer & Jones, 2002; Dallimer, Jones, Pemberton & Cheke, 2003). An extreme example occurs in Pacific salmon, in which the genetic differentiation between early (premature) and late (typical, mature) migrants is restricted to a single gene, GREB1L(Prince et al. , 2017); while selection acts on this gene seasonally, large amounts of gene flow homogenize the remainder of the genome. Insights into the genetic basis of animal migration thus require genome-wide studies, to identify genes that are under selection against a potential background of variable gene flow (Bensch, Andersson & Åkesson, 1999; Liedvogel, Åkesson & Bensch, 2011).
Eastern North American monarch butterflies undergo one of the most well-known and spectacular migrations of the animal kingdom (Gustafsson, Agrawal, Lewenstein & Wolf, 2015; Reppert & de Roode, 2018), with up to hundreds of millions of butterflies migrating up to 4,500 km to reach their overwintering sites in central Mexico (Urquhart & Urquhart, 1978; Brower, 1995; Flockhart et al. , 2017). Monarch caterpillars are specialist feeders of milkweed host plants, which die back seasonally in North America, thereby preventing monarchs from breeding throughout the year. In the fall, developing monarch caterpillars respond to changing temperature, shortening day length and senescing host plants to enter a state of reproductive diapause (Goehring & Oberhauser, 2002), which enables them to survive the 6-8 months that it takes to migrate south, overwinter, and re-migrate north in the spring (Herman & Tatar, 2001). Prior to spring re-migration, overwintering monarchs complete reproductive development and mate at the Mexican overwintering sites or in their recolonized breeding areas (Herman, Brower & Calvert, 1989). Monarchs recolonize the southern parts of the United States and lay eggs on re-emerging milkweed, and 2-4 successive generations of reproductive monarchs recolonize their entire 4.5 million km2 breeding range (Flockhart et al. , 2013).
While monarchs are best known for this long-distance migration from eastern North America to Mexico, monarchs that inhabit breeding grounds west of the Rocky Mountains migrate shorter distances to overwinter in groves of Eucalyptus and native conifers along California’s Pacific Coast (Nagano et al. , 1993; James et al. , 2018). Whereas eastern monarchs may fly over 4,500km to reach the Mexican overwintering sites, western monarchs reach the California Coast by flying as little as 500km, with the greatest recorded distances being 1,600km (Yang, Ostrovsky, Rogers & Welker, 2016). Whether these dramatic differences in migration distance are the result of differential selection, or plasticity from genotype by environment interaction remains unknown. Eastern and western North American butterflies have divergent wing morphology (Altizer & Davis, 2010; Freedman & Dingle, 2018), and it is often assumed that they form distinct genetic populations (Brower et al. , 1995; NatureServe, 2019). However, observational studies (Brower & Pyle, 2004) and limited allozyme and microsatellite studies (Shephard, Hughes & Zalucki, 2002; Lyons et al. , 2012) have indicated large amounts of genetic exchange between eastern and western monarchs. This lack of genome-wide genetic differentiation suggests that migratory differences may instead be driven by restricted loci or differential environment-induced gene expression (Liedvogel et al. , 2011). Here, we compare flight performance of eastern and western monarchs, carry out an analysis of 43 genomes (Fig. 1), and measure the expression of a small number of candidate genes in eastern and western monarchs during flight trials.