Area of Research: Aquatic environmental DNA (eDNA)
New paper on eDNA as way to define marine regions
PLOS One publishes our new paper demonstrating the use of eDNA to define marine biogeography. This graphic summarizes key findings of the paper. The paper builds on our earlier work proving that loose DNA in seawater reveals both diversity AND abundance of marine life, in particular, fishes. Full title and abstract are below.
A potential tool for marine biogeography: eDNA-dominant fish species differ among coastal habitats and by season concordant with gear-based assessments Mark Y. Stoeckle , Jesse H. Ausubel, Greg Hinks, Stacy M. VanMorter Published: November 11, 2024 https://doi.org/10.1371/journal.pone.0313170
Abstract Effective ocean management asks for up-to-date knowledge of marine biogeography. Here we compare eDNA and gear-based assessments of marine fish populations using an approach that focuses on the commonest species. The protocol takes advantage of the “hollow curve” of species abundance distributions, with a minority of species comprising the great majority of individuals or biomass. We analyzed new and published teleost eDNA metabarcoding surveys from three neighboring northwest Atlantic coastal locations representing sandy, rocky, or estuary habitat. Fish eDNA followed a hollow curve species abundance distribution at each location—the 10 commonest taxa accounted for more than 90% of eDNA copies. Top ten taxa were designated eDNA-dominant species (eDDS) and categorized as habitat-associated (top 10 in one study) or as shared. eDDS by category were similarly abundant in concurrent bottom trawl and seine surveys. eDDS habitat category profiles correctly classified most (94%-100%) individual eDNA and capture measurements within surveys and recognized estuarine sites in other regional eDNA and seine studies. Using a category metric like that for habitats, eDDS demonstrated strong seasonal turnover concordant with trawl catch weights. eDNA seasonal profiles applied to historical trawl and seine records highlighted known long-term trends in mid-Atlantic fish populations. This study provides evidence that eDNA-abundant fish species differ among coastal habitats and by season consistent with gear-based assessments. Grouping abundant species by category facilitated comparisons among habitats and integration with established surveys. eDNA metabarcoding of dominant fish species potentially offers a useful tool for marine biogeography and ocean monitoring.
Economist magazine Back to Blue initiative refers to our oceans work
Adam Green, of the Economist magazine’s Back to Blue Initiative, interviews Jesse here about industrialization of the oceans.
And refers to our eDNA work in this article on Saving the Bays.
Short video about passive acoustic monitoring for ocean life
The International Quiet Ocean Experiment (IQOE) in 2023 gave birth to World Ocean Passive Acoustic Monitoring (WOPAM) Day. The excellent 2024 WOPAM Day video can be seen at https://x.com/GLUBS1/status/1798995048522277190. The full soundtrack for WOPAM Day 2024 is at: https://www.wo-pam.com/wopam-2024 (scroll down and see the link). Congratulations to Miles Parsons and other team members on extending the 2024 monitoring to about 400 sites around the world!
Jesse & Mark NOAA ‘Omics Webinar on eDNA-dominant fish species
NOAA has posted the video of their ‘Omics Seminar Series: eDNA-Dominant Marine Fish Species Characterize Coastal Habitats presented on 28 February, 2024 by Mark Stoeckle and Jesse Ausubel. The 1-hour seminar is full of new results and ideas about using eDNA data to characterize marine regions and features Mark’s excellent graphics.
Title: eDNA-Dominant Marine Fish Species Characterize Coastal Habitats: an eDNA-Based Classifier Approach to Aid Marine Biogeography and Ocean Monitoring by Mark Stoeckle & Jesse Ausubel
Abstract: A small minority of species typically account for the great majority of individuals or biomass. Here we characterize marine coastal habitats based on abundance of marine fish environmental DNA. We designate the ten most eDNA-abundant fish species in each habitat as eDNA-dominant species. eDNA-dominant species are similar within but differ among habitats and seasons and accord with abundance by traditional survey methods. “Classifiers” based on eDNA-dominant fish species could help map marine fish habitats and monitor changing oceans. Advantages include relatively low sampling requirements, a single technology applicable to diverse habitats, and ease of application to multiple datasets.
eDNA of Newtown Creek, industrial waterway separating Queens & Brooklyn
RockEDU summer students Priyam Shah and Michael Epelman, who just completed high school, teamed with mentor extraordinaire Mark Stoeckle to study the fishes of an NYC Superfund Site, Newtown Creek. Their excellent poster shows that eDNA detected a surprising diversity of fish in Newtown Creek, despite ongoing pollution and sewage overflow. The number and relative abundance of fish species differed among sites consistent with species habitat preference and pollution tolerance. Our data support eDNA as a cost-effective, non-destructive method for monitoring fish populations and assessing habitat restoration efforts in Newtown Creek and other Superfund sites
Remembrance of marine biologist Vera Alexander
A stalwart member of the International Scientific Steering Committee of the Census of Marine Life, Vera Alexander passed away at the age of 90 in Fairbanks AK in May. The Arctic Research Consortium US earlier offered this informative tribute.
Jesse worked closely with Vera during the Census of Marine Life from 1999-2010 and offers this remembrance of The Many Contributions of Vera Alexander.
First World Ocean Passive Acoustic Monitoring (WOPAM) day
A child of the International Quiet Ocean Experiment, today is the first World Ocean Passive Acoustics Monitoring (WOPAM) day. The IQOE leaders, including Miles Parsons and Steve Simpson, have prepared two very cool 90-second videos to initiate WOPAM day.
Downloadable at this site. 150 MB each, but they download quickly.
eDNA biodiversity survey of Charles River & Boston Harbor
For a 50th Harvard College Reunion Seminar on EO Wilson’s proposal to conserve half Earth, Jesse Ausubel and Mark Stoeckle, assisted by Elizabeth Munnell, conducted a survey of vertebrates in three locations in the Charles River and two in Boston Harbor. The 14 slides on The Charles River and Boston Harbor Then and Now tell a story of remarkable ecological recovery.
New software for visualizing the whole animal kingdom
Swiss bioinformatics wizard Wandrille Duchemin and PHE Guest Investigator David Thaler publish PyKleeBarcode: Enabling representation of the whole animal kingdom in information space in PLoS One. The computational advances in the paper open the way to calculating DNA-relatedness of all animal species, as the figure below for mammals suggests.
Fig 2. A. View of the structure matrix of the mammalian dataset and taxonomic structure of Mammalia. B. Phylogenetic tree structure of the taxonomic groups retrieved from NCBI taxonomy.
The paper builds on the pioneering work done earlier in the PHE by Larry Sirovich and Mark Stoeckle:
L Sirovich, MY Stoeckle, Y Zhang. A scalable method for analysis and display of DNA sequences. PLoS ONE 4 (10): e7051, 2009
L Sirovich, MY Stoeckle, Y Zhang. Structural analysis of biodiversity. PLoS ONE 5 (2): e9266, 2010
MY Stoeckle, C Coffran. TreeParser-Aided Klee Diagrams Display Taxonomic Clusters in DNA Barcode and Nuclear Gene Datasets . Nature Scientific Reports 3 (2635): 2013