Signatures of the Anthropocene: Population Genomic Structure Detected in Pennsylvania Coyotes

Coyotes (Canis latrans) expanded across eastern North America in the last century and are ecological generalists capable of thriving across diverse habitats. Broad genetic surveillance has reported little spatial genetic patterning for this highly dispersive species. Here, we explore the genome-wide signatures of spatial patterns found in a 10-year study of 1199 coyotes from northeastern United States, with a temporal analysis of Pennsylvania coyotes. Despite their broad dispersal capability, we detected subtle but significant population structure, with two genetic clusters that have a weak clinal transition zone. This partitioning aligned qualitatively with patterns of human population density and activity. We inferred that gene flow between these genetic groups was associated with two different demographic expansions of coyotes eastward, south along the Great Lakes and separately along the northern Lakes towards northeastern United States. We identify Pennsylvania as a recent contact zone. Morphometric analyses revealed only modest differentiation between clusters and no robust temporal shifts, though a weak trend of increased body mass was noted in southwestern males. Collectively, our findings demonstrate that anthropogenic features likely influence fine-scale cryptic population structure, even in a highly dispersing and widespread mesopredator.