Temporal genomics of the monarch butterfly (Danaus plexippus): An assessment of genetic diversity in response to population size decline

The monarch butterfly (Danaus plexippus) has garnered substantial concern due to on-going declines. Two populations exist in North America, with differing migratory routes, and are demarcated by the Rocky Mountains. Western monarchs over-winter in coastal groves of California and Baja California, while eastern monarchs over-winter in central Mexico. Genetic diversity metrics can provide insight on the genetic health of these populations, of the species overall, and their potential adaptive capacity. Consequently, these data are of critical importance to the current and future management of the species in North America. 

We employed a temporal approach that leverages whole genome sequencing data to estimate trends in heterozygosity and runs of homozygosity (ROH), between 1901 and 2024. We also estimated recent effective population size (N_e) from individuals collected in 2023 and 2024. We found that individual heterozygosity estimates are remarkably conserved for most of the sampled period, with an 18 % decline in average heterozygosity across the two most recent time periods. We also failed to find evidence of marked inbreeding, with few individuals having large ROH. However, there was an excess of ROH for the 2023-2024 time-period, suggesting a recent increase in inbreeding.  We found that estimates of N_e remained high and stable (> 4.0 x 10⁶ individuals) for most of the last ~ 60 years, with evidence of declines in N_e within the last 25 years. These results suggest that genetic diversity has declined, and inbreeding has increased, but only very recently.