Document Type

Honors Thesis


Marine Science


Kristina Cammen

Committee Members

James Brophy, Sindhu Manjesh, Julia Sunnarborg

Graduation Year

May 2022

Publication Date

Spring 5-2022


As technology and science progresses, the methodology behind observing, monitoring, and sampling marine mammals advances as well. One such technique is environmental DNA or eDNA, which entails extracting organismal DNA from water samples without ever handling or disturbing the organism. It is a cost-efficient and non-invasive method that can be utilized in the sampling of seal haulout sites as is its purpose for this research. Another method, using the DNA analysis of seal fecal samples, is a less invasive method that can also be utilized to monitor and assess marine mammals. Through collecting both fecal and water samples from gray seal haulout sites in Cape Cod, Massachusetts, these two differing, but equally progressive methods can be compared to one another. The water samples collected from the seal haulout sites were paired for DNA analysis with the fecal samples collected from the beaches where gray seals are hauled out in Cape Cod. DNA was then extracted from both the water samples and fecal samples, followed by sequencing a portion of the gray seal mitochondrial control region in all the samples. This allowed for the comparison of the haplotypes detected in fecal samples to those detected in water samples as a comparison of these two non-invasive approaches for assessing marine mammal genetic diversity. We obtained sequences from 25 fecal samples. Sequences from all but 2 of the 25 samples were found to match with one of the sequences in the reference dataset. Our study identified 2 new haplotypes that had not been previously identified in the population. When compared to the water sample sequences, we found 19 matches out of the 25 fecal sample sequences. In all of these cases, the fecal haplotype was detected in water samples collected during the same survey (at the same haulout on the same day), though in many cases a given fecal haplotype was also detected in water samples from multiple surveys. Although future studies are needed to further confirm the efficiency and non-invasiveness of the eDNA approach, our study suggests that it can provide similar information to a fecal sample sequence analysis, but in a less invasive way.