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

The migratory monarch butterfly (Danaus plexippus) has garnered substantial interest and concern due to drastic and 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 the 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. As a result, these data are of critical importance to the current and future management of the species in North America.
We employed a temporal approach that combined newly generated whole genome sequencing data with that from previous studies to estimate trends in heterozygosity, genetic load, and runs of homozygosity (ROH), between 2007 and 2024. We also estimated recent effective population size (Ne) from populations collected in 2023 and 2024. We found that individual heterozygosity estimates are remarkably conserved, despite concurrent census size declines across populations. We also failed to find evidence of inbreeding, with few individuals having large ROH, and stability in estimates of realized and potential load. Furthermore, we found that estimates of Ne from both populations remain high and stable (4.3 – 4.6 x 106 individuals) for the 200 most recent generations (~40 years). The results thus far suggest that despite declines in census size, eastern and monarch populations have conserved their genetic diversity throughout the period of time studied, and do not show signatures of genetically depauperate populations.