Impervious surface cover and number of restaurants shape diet variation in an urban carnivore

In the past decade, studies have demonstrated that urban and nonurban wildlife populations exhibit differences in foraging behavior and diet. However, little is known about how environmental heterogeneity shapes dietary variation of organisms within cities. We examined the vertebrate prey components of 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 used DNA metabarcoding to quantify diet composition and individual niche differentiation. The highest contributor to coyote diet overall was anthropogenic food followed by small mammals. The most frequently detected species were domestic chicken, pocket gopher (Thomomys bottae), domestic pig, and raccoon (Procyon lotor). Diet composition varied significantly across territories and among individuals, with territories explaini..., , , # Impervious surface cover and number of restaurants shape diet variation in an urban carnivore

## SF-Coyote-Diet-Metabarcoding-main.zip

The zip file contains raw data files and scripts used to generate results for the above manuscript, which has been accepted in *Ecosphere* (December 5th, 2024). Below we provide descriptions of the files within each directory. 

### 1. Sequence-Processing

**Trimming-Reads.Rmd**: script to trim raw fastq files with cutadapt. High performance computing required.

**DADA2.Rmd**: script correct amplicon errors and infer amplicon sequence variants (ASVs) with DADA2 denoising algorithm. High performance computing required.

### 2. Assign-Taxonomy

**BLAST.Rmd**: script to create a local BLAST database of 12SV5 sequences of vertebrate genera recovered from pilot studies. Use the *blastn* feature of BLAST+ to assign ASVs via the custom database and append or correct as needed with the nucleotide database of NCBI available online. **12S_reference_lib.fasta**...