Temporal matches between monarch butterfly and milkweed population changes over the past 25,000 years

In intimate ecological interactions, the interdependency of species may
result in correlated demographic histories. For species of conservation
concern, understanding the long-term dynamics of such interactions may
shed light on the drivers of population decline. Here we address the
demographic history of the monarch butterfly, Danaus plexippus, and its
dominant host plant, the common milkweed, Asclepias syriaca, using
broad-scale sampling and genomic inference. Because genetic resources for
milkweed have lagged behind those for monarchs, we first release a
chromosome-level genome assembly and annotation for common milkweed. Next,
we show that despite its enormous geographic range across eastern North
America, A. syriaca is best characterized as a single, roughly panmictic
population. Using Approximate Bayesian Computation via Random Forests
(ABC-RF), a machine learning method for reconstructing demographic
histories, we show that both monarchs and milkweed experienced population
expansion during the most recent recession of North American glaciers
10,000–20,000 years ago. Our data also identify concurrent population
expansions in both species during the large-scale clearing of eastern
forests (~200 years ago). Finally, we find no evidence that either species
experienced a reduction in effective population size over the past 75
years. Thus, the well-documented decline of monarch abundance over the
past 40 years is not visible in our genomic dataset, reflecting a possible
mismatch of the overwintering census population to effective population
size in this species.