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.

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

News from the Quiet Ocean Experiment

Terry Collins artfully summarizes the progress in this news release about the International Quiet Ocean Experiment.  The news was picked up by

Agencia EFE: Artificial intelligence listens to the habits of marine life (in Spanish)

Independent (London):  Scientists eavesdrop on underwater creatures to gain insights on ocean life

Earth.Com: Monitoring ocean life through underwater soundscapes

Portal R7 (Brazil) Biólogos marinhos captam zumbido não identificado que pode ser uma nova espécie de peixe Marine biologists capture unidentified tinnitus that can be a new species of fish

Vice / Motherboard (USA) Scientists Recording Ocean Sounds Picked Up a Mysterious ‘Buzz’ They Can’t Identify

ORF Online (Austria) Unterwassermikrofone belauschen Fische Underwater microphones eavesdrop on fish

Scientias, Netherlands Moet je horen! Vissen maken fascinerende balts- en eetgeluiden, vooral bij volle maan You have to hear! Fish make fascinating balts and eating noises, especially at full moon

Mark & Jesse present NOAA ‘Omics seminar on eDNA abundance

Mark Stoeckle and Jesse Ausubel presented in the  NOAA ‘Omics Seminar Series on Marine fish eDNA Metabarcoding: Promising Developments and Early Applications.  The outline:

–eDNA abundance matters (relevant to detection, quantification, field design, laboratory protocols)

–Adding internal standard to metabarcoding PCRs quantifies eDNA (converts relative sequence reads to absolute eDNA copies)

–Current marine fish metabarcoding protocols ready for wider use (reasonably accurate index of fish abundance, especially for more abundant species)

–eDNA metabarcoding can overcome information hurdles for ecosystem-based management

recording is here , 40-minute presentation and 20-minute Q&A. Thanks to NOAA’s Katharine Egan and Nicole Miller.

Our paper on eDNA as bioassay of Anthropocene published

The new journal based in China, The Innovation, has published the Thaler-Ausubel-Stoeckle paper on Human and domesticated animal environmental DNA as bioassays of the Anthropocene in their “Out of the Box” category, where we like to be. We also post the pdf.

We thank Song Sun and Ke Chen for editorial assistance.

Summary: Human and domesticated animal sequences, commonly detected in environmental DNA (eDNA) metabarcoding studies, are routinely excluded from analysis. Here we suggest that reporting human and domesticated animal eDNA results might open new lines of investigation. For example, the relative abundance of human and domesticated animal eDNA as compared to that of wild vertebrate species might provide an index of human impact on local biota. Such an index could be applied to sites ranging from urban harbors to remote villages, and possibly to analyze historical samples. Various potential sources of contamination complicate the picture, but it should be possible to develop procedures that minimize risk of DNA introduction during collection and processing. Our near-term recommendation is to encourage inclusion of human and domesticated animal data in eDNA publications as an incentive for discovery, to lift quality controls, and to collectively contribute to new vistas that eDNA science might open.