Gaining Insights on San Francisco’s Urban Coyotes Through Noninvasive Genetic Analysis

The ability of individuals to move among habitat patches and disperse to other locations is fundamental to population connectivity. Without such mobility, gene flow between populations is reduced or eliminated. When populations colonize new habitats, such as in urban areas, they can become isolated from the original population. In urban areas, dispersal and migration may be reduced, and individuals may have difficulties migrating throughout urban spaces if they are unable to navigate the novel environment. Isolation of small founder populations can lead to genetic bottlenecks, genetic drift, and inbreeding, especially if the colonizing population does not grow rapidly. Nonrandom breeding among individuals within urban ecosystems is expected to cause differences in genetic makeup of sub-populations, further exacerbating the possibility for inbreeding.

My research, funded by a Christine Stevens Wildlife Award, focused on the population of coyotes that reestablished habitat in the city of San Francisco in 2002. The effects of urban dwelling on the genetics of this population is not well understood and difficult to study in the human-dense environment using traditional methods such as telemetry and trapping. The use of noninvasive genetic methods provides a potentially powerful means of addressing several fundamental questions about urban wildlife. Understanding relatedness and movement of coyotes throughout San Francisco can aid in monitoring this population and in anticipating and mitigating potential coyote-human conflicts.

I conducted genotyping and relatedness analyses on over 1,400 coyote scat samples collected 2019–2022 from parks and green spaces throughout San Francisco. I successfully genotyped 828 of these samples and was able to assign them to 176 individuals (83 of whom were identified in at least two to as many as 30 samples, with the remaining 93 individuals identified from a single sample). Using these genotyped individuals, I constructed pedigrees for some of the families located in the city. These pedigrees have allowed me to determine movement patterns from potential natal sites based on the assigned parents, who typically do not move as much as dispersing animals since they have an established territory. During 2021, I documented at least eight family groups in San Francisco, identified breeders, and built a city-wide coyote population pedigree. For the next phase of my research, I will be using genomic methods to determine source populations and to investigate levels of inbreeding within San Francisco’s coyote population.

This project has laid a foundation for future monitoring of San Francisco coyotes and demonstrates the practical use of noninvasive genetic methods in areas where traditional monitoring methods are infeasible. 

This study was funded by the Christine Stevens Wildlife Awards program. Learn more about this program or view additional studies.