Rockefeller University

Program for the Human Environment

Area of Research: DNA Barcoding

New code for analyzing eDNA sequences using DADA2 pipeline

For the past year MIchael Coogan, now a grad student in marine science at the U. of New Hampshire, has helped Mark Stoeckle and PHE with improved software for our eDNA studies. See summary below. A pdf of the R code is available here. If you have questions, please write to Mark.

The goal is to adapt the DADA2 pipeline to Mark Stoeckle’s 12S experiment. Sample sequences will be identified using 12S reference file containing sequences of 262 unique vertebrates found around New York. The starting point is a set of Illumina-sequenced paired-end fastq files that have been split (or demultiplexed) by sample and which have barcodes/adapters already removed. The end product will be a sequence table, analogous to the ubiquitous “OTU table”, which records the number of times sample sequences were observed in each sample. The key difference between the output of DADA2 and standard OTU analyses is that DADA2 infers sample sequences exactly rather than clustering sequences into fuzzy OTUs which hide and complicate biological variation.

Fishing for DNA in the Hudson

In the morning of 3 November 2022, Jesse Ausubel summarized the work led by Mark Stoeckle about catching eDNA in the waters of New York City to learn about our local fish species. The site was the beautiful new Little Island in the Hudson River Estuary Park. We post the deck of slides which span from Central Park to the Hudson and East rivers to the Gowanus Canal and Coney Island. New York City enjoys the presence of dozens of fish species, ranging from eels to sturgeon.

Passing of Paul Waggoner

Our great friend and colleague, agronomist Paul E. Waggoner, died on 1 November 2022 in Seattle, surrounded by family and friends.   Paul’s wrote a crisp memoir of his own life, from Appanoose to Connecticut.  Jesse offered a tribute: Thriving Thrift: On the Occasion of Paul Waggoner Appreciation Day, 2013.

Jesse and Paul first met in 1981 during the work of the Carbon Dioxide Assessment Committee for which Paul wrote brilliant far-sighted chapters about “Agriculture and a climate changed by more carbon dioxide” and about “Effects of a carbon dioxide-induced climate change on water supplies in the Western United States.”  Jesse and Paul continued contact through the 1980s through the periodic seminars on climate change at Yale by William Nordhaus. 

Paul and Jesse also did most of the writing and editing for the section on Adaptation (pp. 499-657) in the 1992 NASEM report “Policy Implications of Global Warming.”

In 1992 Jesse asked Paul the question “How much land can 10 billion people spare for Nature” and this led to a superb, lengthy answer (PE Waggoner. How Much Land Can Ten Billion People Spare for Nature?  Task Force Report #121, Council for Agricultural Science and Technology, Ames IA 1994) and two decades more work on land-sparing and related issues of intensity of use of resources on land and in the sea. Paul was a universally helpful critic and editor as well as creative researcher and, perhaps most important, our best teacher about actual farming and plants.

Some papers we wrote together:

 JH Ausubel, IK Wernick, and PE Waggoner. Peak Farmland and the Prospect for Land Sparing. Population and Development Review 38 (Supplement): 217–238, 2012

Rautiainen, IK Wernick, PE Waggoner, JH Ausubel, PE Kauppi. A National and International Analysis of Changing Forest Density . PLoS ONE 6 (5): 2011

JH Ausubel, DT Crist, and PE Waggoner (eds.). First Census of Marine Life 2010: Highlights of a Decade of Discovery. CoML 2010

JH Ausubel, PE Waggoner. Dematerialization: variety, caution, and persistence . Proc Natl Acad Sci U S A 105 (35): 12774–12779, 2008 10.1073/pnas.0806099105 D

PE Waggoner, JH Ausubel. Quandaries of forest area, volume, biomass, and carbon explored with the forest identity . Pp. 13 pp in Connecticut Agricultural Experiment Station Bulletin 1011 2007

PE Kauppi, JH Ausubel, J-Y Fang, AS Mather, RA Sedjo, PE Waggoner. Returning forests analyzed with forest identity . Pp. 17574–17579 in Proc Natl Acad Sci U S A vol. 103, 2006 10.1073/pnas.0608343103

JH Ausubel, PE Waggoner, IK Wernick. Foresters and DNA . Pp. 13–31 in Chapter 2 in Landscapes, Genomics and Transgenic Forests pp. 2006 CG Williams (ed), Published by Kluwer, Dordrecht

JH Ausubel, IK Wernick, AM Barret, PE Waggoner. Industrial ecology for leverage to let loose less cadmium. Prog Ind Ecol 3 (6): 522–537, 2006

MY Stoeckle, PE Waggoner, JH Ausubel. Barcoding Life, Illustrated: Goals, rationale, results (PDF). Consortium for the Barcode of Life (CBOL) 2005

MY Stoeckle, PE Waggoner, JH Ausubel. Barcoding Life: Ten Reasons (PDF). Consortium for the Barcode of Life (CBOL) 2004 Brochure

PE Waggoner, JH Ausubel. A Framework for Sustainability Science: A Renovated IPAT Identity (PDF). Proceedings of the National Academy of Sciences U S A 99 (12): 7860–7865, 2002  (See also a series of 6 Supplements at https://phe.rockefeller.edu/research/impact/)

PE Waggoner, JH Ausubel. How Much Will Feeding More and Wealthier People Encroach on Forests?.  Population and Development Review 27 (2): 239–257, 2001

CR Frink, PE Waggoner, JH Ausubel. Nitrogen on the Land: Overcoming the Worries – lifting fertilizer efficiency and preserving land for nonfarming uses Pollution Prevention Review 11 (3): 77–82, 2001

IK Wernick, PE Waggoner, JH Ausubel. The Forester’s Lever: Industrial Ecology and Wood Products Journal of Forestry 98 (10): 8–14, 2000

CR Frink, PE Waggoner, JH Ausubel. Nitrogen fertilizer: Retrospect and prospect. Pp. 1175–1180 in Proc Natl Acad Sci U S A vol. 96, 1999

IK Wernick, PE Waggoner, JH Ausubel. Searching for Leverage to Conserve Forests: The Industrial Ecology of Wood Products in the United States Journal of Industrial Ecology 1 (3): 125–145, 1997

PE Waggoner, JH Ausubel, IK Wernick. Lightening the Tread of Population on the Land: American Examples (PDF). Population and Development Review 22 (3): 531-45, 1996

2nd National eDNA workshop videos, slides

The proceedings from the 2nd National Workshop on Marine Enviromental eDNA 11-14 Sept 2022 in southern California have now been posted. Mark Stoeckle presented the opening Plenary.

Jesse Ausubel to receive 2022 Nierenberg Prize

Jesse Ausubel will be honored with the 2022 Nierenberg Prize for Science in the Public Interest. This award is presented annually by Scripps Institution of Oceanography at UC San Diego and the Nierenberg Family to honor the memory of William A. Nierenberg, an esteemed physicist and national science leader who served Scripps Oceanography as director for two decades. Previous awardees include atmospheric scientist Warren Washington, biochemist and Nobel Prize winner Jennifer Doudna, filmmaker Sir David Attenborough, and primatologist Dame Jane Goodall, among others.

eDNA degradation; 2nd National Workshop

PHE’s guest investigator David Thaler offers some stimulating ideas in a memo about ways of understanding and learning from degradation of aquatic eDNA. The title: How long has each particular species’ eDNA been outside the organism from which it came? Some thoughts on the possibility to obtain more information from eDNA analysis of water samples

Meanwhile, Jesse Ausubel and Mark Stoeckle are involved in the program for the 2nd US National Workshop on eDNA, 12-15 September in Southern California. PHE hosted the 1st US national meeting in 2018.

PHE eDNA student project a finalist in 2022 Genius Olympiad

Samara Davis’s salamander eDNA project is a finalist in 2022 Genius Olympiad.  Genius Olympiad is an international high school project competition about environmental issues founded and organized by Terra Science and Education and hosted by the Rochester Institute of Technology. The Olympiad will host projects in five general disciplines with an environmental focus.