eDNA Fish Study at Hudson River Park

In this study, Hudson River Park staff, interns and local students collected water samples from Hudson River Park’s Pier 25, Pier 66 and Pier 84. These samples were taken biweekly throughout the year and filtered to collect DNA. Cold Spring Harbor Laboratory then extracted and amplified the desired barcode region, a section of the 12S ribosomal RNA, using polymerase chain reaction (PCR). After confirming the region was copied, the DNA was sequenced using “Next Generation Sequencing.” The sequencing produces so much data that a sophisticated program is needed to check its quality and analyze the results. The bioinformatics program compares all of the sequences to a fish database, identifying the species of fish and counting the fish DNA sequences for each species. To learn more about this project and how we process eDNA, you can click here.

eDNA Sampling Sites in Hudson River Park
Fish DNA in Hudson River park
* This fish is found in the Hudson, but not expected in Hudson River Park's Estuarine Sanctuary. The DNA may have come from upstream.
** This fish is not expected in the region. The DNA may be a contaminant from sewer runoff.

This chart shows the average percentage of fish DNA reads for each fish species in 88 water samples collected in 2019 and 2021. Samples were collected from surface water at Hudson River Park’s Piers 25, 66 and 84. The sequencing data from samples at each collection site are displayed in two charts: 1) Most common fish DNA in samples and 2) Less common fish DNA in samples.
The percentage of fish DNA was calculated by comparing the number of reads for each species to the total for all fish in each sample. The amount of DNA for each species is not a direct measure of the abundance of that species, but rather indicates a species’ presence in a general area. Other species detected in small numbers in these samples include winter flounder, summer flounder, cunner and bluefish.

* This fish is found in the Hudson, but not expected in Hudson River Park's Estuarine Sanctuary. The DNA may have come from upstream.
** This fish is not expected in the region. The DNA may be a contaminant from sewer runoff.

This chart shows the average percentage of fish DNA reads for each fish species in 88 water samples collected in 2019 and 2021. Samples were collected from surface water at Hudson River Park’s Piers 25, 66 and 84. The sequencing data from samples at each collection site are displayed in two charts: 1) Most common fish DNA in samples and 2) Less common fish DNA in samples.
The percentage of fish DNA was calculated by comparing the number of reads for each species to the total for all fish in each sample. The amount of DNA for each species is not a direct measure of the abundance of that species, but rather indicates a species’ presence in a general area. Other species detected in small numbers in these samples include winter flounder, summer flounder, cunner and bluefish.