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

## TL;DR

Coyotes in Pennsylvania show subtle genetic differences linked to human activity, revealing hidden population structure despite their wide dispersal.

## Contribution

The study reveals cryptic genetic structure in coyotes associated with human population density and expansion routes.

## Key findings

- Two genetic clusters with a weak clinal transition zone were detected in Pennsylvania coyotes.
- Population structure aligned with human density and distinct eastward expansion routes.
- A weak trend of increased body mass was observed in southwestern male coyotes.

## Abstract

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.

Coyotes rapidly expanded across eastern North America and are highly dispersive ecological generalists, leading prior studies to report little spatial genetic structure. Using genome‐wide data from 1199 coyotes sampled over a decade in the northeastern United States, we detected subtle but significant population structure, with two weakly clinal genetic clusters meeting in Pennsylvania and aligned with patterns of human density and distinct eastward expansion routes. These results show that anthropogenic landscapes can shape fine‐scale, cryptic population structure even in a widespread, highly mobile mesopredator.