Genomics of museum samples reveal the evidence for recent effective population size increase in monarch butterflies.

Monarch butterflies are known to make one of the longest seasonal migrations of any insect species (Urquhart and Urquhart, 1977). Recent studies have raised concerns over the decline of the overwintering colony size by 84% since the last recorded maximum abundance in 1996 (Semmens et al., 2016). A combination of multiple factors such as habitat loss, milkweed loss (Hartzler, 2010; Pleasants, 2017), parasites, pesticides (Pleasants and Oberhauser, 2013), lack of floral food and extreme weather have been attributed to the decline of the overwintering monarch population (Belsky and Joshi, 2018). This decline was not observed in independent studies that had measured summer populations across the united states (Davis, 2012; Ries, Taron and Rendón-Salinas, 2015; Inamine et al., 2016). A comprehensive review of these studies which is pointing out to the census sizes of monarchs also show these dissimilar patterns between summer and winter counts (refer to Andy's paper). This contrasting census numbers of summer and overwintering numbers leads to a very interesting genetic question, if the effective population size of monarchs has been affected in recent years. Here we wanted to investigate if the decline in overwintering monarch population have directly impacted their genetic diversity and effective population size. In this study we have used whole genome re-sequencing reads of monarch butterflies collected at the Sierra Chincua Monarch Butterfly Sanctuary, Mexico in 1977 to understand the magnitude of change in their genetic diversity over time. We have used publicly available whole genome re-sequencing reads of contemporary eastern and western monarchs sampled between 2009 to 2015 to compare their genetic diversity and effective population sizes with the historic (1977) samples. We have then estimated the genetic differentiation generated between contemporary and historic monarchs due to a combination of genetic drift and local adaptations. Genes within these regions and their functions were identified to understand the recent patterns of evolution in monarch butterflies.