Urbanization is associated with novel habitats, pathogens, and a general decline in species and genetic diversity. Most studies on the genetic diversity of urban species focus on neutral loci like microsatellites that may not reflect diversity in fitness-related traits. In this study, we will determine the role of urbanization on the major histocompatibility complex (MHC class I) in House Finches, Haemorhous mexicanus. We have collected blood samples from at least 30 House Finches in each urban, suburban, and rural area in and around Fresno, California, and Phoenix, Arizona. Firstly, we hypothesize that rural House Finches will vary in genetic diversity at MHC compared to their suburban and urban conspecifics because of putative anthropogenic barriers to gene flow. We have PCR-amplified the polymorphic peptide binding region of MHC class I and will sequence them on the Illumina MiSeq platform. We will discuss the number of MHC alleles, and the number of private alleles, and estimate indices of sequence polymorphisms between the three population units. In addition, we will discuss population divergence using Jost's D estimate and STRUCTURE. This study will ultimately shed light on the associations between urbanization and the evolution of an adaptive immune gene.

In the past decade, studies have demonstrated that several traits, including foraging behavior and diet, differ between urban and nonurban wildlife populations. However, little is known about how environmental heterogeneity shapes dietary variation of organisms within cities. We examined the diets of coyotes (Canis latrans) in San Francisco to quantify territory- and individual-level dietary differences and determine how within-city variation in land cover and land use affect coyote diet. We genotyped fecal samples for individual coyote identification and quantified diet with DNA metabarcoding. The highest contributor to coyote diet was anthropogenic food followed by small mammals. The most frequently detected species were domestic chicken, pocket gopher (Thomomys bottae), pig, and raccoon (Procyon lotor). Diet composition varied significantly across territories and among individuals. Within family groups, however, individual diets were relatively consistent. The representation of anthropogenic food in scats was correlated with impervious surface cover, suggesting that coyotes consumed more human food in more urbanized territories. The representation of invasive, human-commensal rodents in the diet was correlated with the number of food services in a territory. Overall, our results revealed substantial intraspecific variation in coyote diet associated with landscape heterogeneity and point to a diversifying effect of urbanization on population diet.

Urban developments and highways can isolate wildlife populations, subsequently decreasing their numbers and increasing matings between close relatives, which reduces genetic diversity. Low diversity can lead to genetic disorders and lower fitness, known as inbreeding depression. The mountain lion population in California’s Santa Monica Mountains (SMM) is isolated, increasing their risk of inbreeding and inbreeding depression. Inbreeding is traditionally measured with pedigree-based methods, which can underestimate inbreeding when founders are themselves partially inbred. To address this limitation, we conducted a genomic study to assess inbreeding directly based on runs of homozygosity (ROH) in >100 individual mountain lions collected 2002–2024 from the SMM and adjacent areas. We used genotyping-by-sequencing to estimate inbreeding from both pedigrees and ROH. Our analysis revealed that ROH consistently provided higher estimates of inbreeding compared to pedigree-based methods. This study has implications for the conservation of this vulnerable population, already showing physical signs of potential inbreeding depression, similar to the Florida Panthers. The results are crucial for mountain lion conservation, particularly in light of the Wallis Annenberg Wildlife Crossing, and data generated establishes a baseline for assessing this population’s future genetic health and fitness. This information is vital for understanding factors contributing to effective conservation planning.

Fewer than 5,000 federally endangered San Joaquin kit fox (Vulpes macrotis mutica) remain, largely due to habitat loss and fragmentation. Additionally, sarcoptic mange outbreaks in Bakersfield and Taft threaten these urban populations. To date, sarcoptic mange infestations have not been documented outside of the urban areas despite extensive surveillance, nor has it been observed in any other kit fox subspecies. We identified several non-urban populations that are relatively isolated and may be at increased risk of extinction due to inbreeding or disease. To assess the genomic impacts of fragmentation and disease, we sequenced whole genomes from kit foxes samples in urban (n = 5) and non-urban (n = 12) populations, comparing levels of inbreeding and genetic load. We also investigated immune-related genetic diversity (e.g., MHC, IFNG, IL2) between urban and non-urban populations, and between the San Joaquin kit fox and individuals from the closely related desert kit fox subspecies (n = 7), to explore potential links to sarcoptic mange susceptibility. Our findings provide insights into how genetic diversity and population connectivity may influence disease vulnerability and persistence in this endangered species.

The salt marsh harvest mouse (SMHM, Reithrodontomys raviventris) is a federally listed endangered species endemic to the coastal marshes of the San Francisco Bay Estuary. We combined range wide field survey data and conservation genomics to help identify population segments of particular concern. We resolved genetic units corresponding to the known subspecies. However, we also identified a previously unrecognized discrete genetic lineage near Richmond. Our survey of the species found that the population at Richmond is the last one remaining throughout all the central portion of the SMHM range. The populations in the central Bay were likely the first ones founded when the San Francisco Bay was reformed after the Pleistocene. Thus, these central populations are ancestral to those in the species strongholds in the south San Francisco Bay and to the north in San Pablo and Suisun Bays. Our analyses also indicated that the Richmond population had extremely low genetic diversity. The population is isolated on a small patch of habitat surrounded by urban features with minimal high tide escape habitat. It is in severe jeopardy of being wiped out by sea level rise, additional anthropogenic changes in the adjacent urban area, or through stochastic events.