We have some exciting initial results back from our pilot bobcat genotyping study and we are eager to share them with you.
Back in April, 5 volunteers and 3 Felidae staff members tested non-invasive methods to collect 106 fecal samples off trails in the Marin headlands and Muir Woods. We ended up sending 79 samples to our colleagues at Oregon State University: 32 classified as ‘likely bobcat,’ 33 classified as ‘possible bobcat,’ and 2 ‘unknown’ plus several negative control samples including 5 ‘likely coyote,’ 2 ‘likely grey fox’ and 5 domestic cat samples from the Marin Humane Society.
Our colleagues tested several methods to first determine whether or not samples were from bobcats, and then subsequently identify individuals from each confirmed bobcat sample. Of the 79 samples, all but 3 had DNA successfully extracted from them. All of these DNA samples were then tested using two different molecular protocols to determine whether the samples were from bobcats. Note that these protocols were technically binary in that they were either positive – indicating the sample came from a bobcat – or negative. Of the 65 likely or possible bobcat samples, 23 were strongly positive and thus confirmed as having come from bobcat, with an additional 7 that were weakly positive, i.e., positive using only one of the two methods.
All 30 of these positive samples were sent in for genotyping, a process that permits the identification of individual bobcats. From this lot, we determined full genotypes from 13 samples and partial genotypes from 8 samples. All of the 7 weakly positive samples and 2 of the strongly positive samples failed at this step. From the 13 full genotypes we acquired, we identified 8 individuals, several of which were sampled more than once (see map).
We have learned a number of important lessons from this successful pilot project and we are excited to move forward! Specifically, we now have optimized protocols for confirming whether a sample is from a bobcat and for identifying individual bobcats. This is important because these protocols are often location-specific. We also know approximately how many samples we need to collect to get a good idea of population size and diversity in the future.
Our next steps are two-fold. We first want to compare this data to our camera data. Cameras were set up in May so as to identify specific individuals based on spot patterns and we are currently looking to recruit 1-2 interns to help analyze this data. So if you are interested in helping with this project, please contact Cat Gallo (catherine@felidaefund.org). We will also be using this data to write an National Science Foundation (NSF) proposal to further study this population including collecting more samples and screening them for (1) toxic chemicals like rodenticides and (2) infectious diseases, especially those carried by humans and domestic animals. Going forward, we want to test the interaction between genotypes / family groups, toxin exposure and disease susceptibility.
We look forward to sharing more on this project as we continue to analyze the data.