Rockefeller University

Program for the Human Environment

Area of Research: DNA Barcoding

Science magazine on eDNA conference report

Science magazine runs a helpful story by Alex Fox on the final report from our 29-30 November 2018 National Conference on Marine eDNA:

The ocean is full of drifting DNA. The United States needs to collect it, researchers say

Also, a good new Japanese research paper is published on eDNA:

Effect of water temperature and fish biomass on environmental DNA shedding, degradation, and size distribution

and in Revelator 27 February 2019

How Do You Protect a Species You Can’t See? For manatees and other hard-to-spot species, the answer may lie in the minute particles of DNA they leave behind as they move through their environments.

Marine eDNA works–let’s get going!

Together with Monmouth University, we hosted the first National Conference on Marine Environmental DNA, November 29-30, 2018. The Conference included approximately 100 American ocean scientists and associated stakeholders, including representatives from academe, federal, state, and local governments, non-governmental organizations concerned with marine environment, and the private sector. The strong sense of the meeting was “eDNA works–let’s get going.” The Conference Final Report and press release summarize the meeting and outline concrete steps forward. 

Biology in Art

The Leonardo Da Vinci DNA Project opened our eyes to the possibilities (inevitability!) of exciting new discoveries by integrating new tools of genetics, molecular biology, and microbiology into studies of art history and practices in conservation of cultural heritage.  We were able to help arrange support for a joint project of the NYU Institute of Fine Arts and the research lab of the Metropolitan Museum of Art:

ART BIO MATTERS 2018 aims to assemble, for the first time, scientists, curators/art historians, and conservators for a stimulating forum to explore new directions in the study of biological materials in works of art. Through guided and balanced discussions, participants will identify connections between advanced DNA, mass-spectrometric, and antibody-based approaches and their own research questions, thereby, facilitating focused and mutually beneficial collaborations.

By many accounts, the conference 8-10 November 2018 was thrilling.  The website has lots of great materials and leads.  Congratulations to Julie Arslanoglu, Peggy Ellis, Matthew Teasdale, and the emerging community at the interface of biology and art!

GoFish

Go Fish

Our “GoFish” paper is published in PLOS ONE (Stoeckle MY, Mishu MD, Charlop-Powers Z. GoFish: a versatile nested PCR strategy for environmental DNA assays for marine vertebrates). From water collection to Sanger sequencing results, the assay can be carried out in three days. This approach will be a useful addition to current eDNA methods when analyzing presence/absence of known species, when turnaround time is important, and in educational settings.

GoFish for Environmental DNA!

Our “GoFish” paper is published in PLOS ONE (Stoeckle MY, Mishu MD, Charlop-Powers Z. GoFish: a versatile nested PCR strategy for environmental DNA assays for marine vertebrates). Excerpt from the abstract:

“GoFish assays amplify a mitochondrial 12S rDNA segment with vertebrate metabarcoding primers, followed by nested PCR with M13-tailed, species-specific primers. Sanger sequencing confirms positives detected by gel electrophoresis.

Unlike quantitative PCR (qPCR), GoFish does not require tissues of target and related species for assay development and a basic thermal cycler is sufficient. Unlike Illumina metabarcoding, indexing and batching samples are unnecessary and advanced bioinformatics expertise is not needed. From water collection to Sanger sequencing results, the assay can be carried out in three days.

The main limitations to this approach, which employs metabarcoding primers, are the same as for metabarcoding, namely, inability to distinguish species with shared target sequences and inconsistent amplification of rarer eDNA. 

This approach will be a useful addition to current eDNA methods when analyzing presence/absence of known species, when turnaround time is important, and in educational settings.”



DNA barcodes and Darwin

Our paper, “Why should mitochondria define species?“, is published open access in Human Evolution 2018; 33:1-40. It recently received a lot popular press attention claiming our work supports creationist views. This interpretation of our work is wrongheaded.

Our study is grounded in and strongly supports Darwinian evolution, including the understanding all life has evolved from a common biological origin over several billion years. Our study follows mainstream views of human evolution. We do not propose there was a single “Adam” or “Eve”. We do not propose any catastrophic events. We encourage interested persons to read our original article, not the recent press commentary.

National Geographic on eDNA

An article by Steve Leahy for National Geographic about our National Conference on Marine Environmental DNA 

New DNA tool ‘changes everything in marine science’

https://www.nationalgeographic.com/environment/2018/12/edna-environmental-dna-counts-fish-changes-marine-science/

Also in the news net:

Columbia Basin Fish and Wildlife Newsletter

Leading Practitioners Of eDNA Science Gather To Discuss New Tool’s Possibilities

cbbulletin.com

Thanks to every one of the 100 participants.  It was thrilling for all!

Also a good story in the Martha’s Vineyard Times about Linda Fairstein’s new book in which kids collect eDNA on Martha’s Vineyard.

And in the Martha’s Vineyard Gazette: Swimming With the Fishes, Naming Them Too,  Monday, December 3, 2018 – 1:58pm.

 

 

Mt paper supports Darwinian evolution

The article Why should mitochondria define species?
Stoeckle M.Y., Thaler D.S.
is grounded in and strongly supports Darwinian evolution, including the understanding all life has evolved from a common biological origin over several billion years.

The study follows mainstream views of human evolution. We do not propose there was a single “Adam” or “Eve”. We do not propose any catastrophic events.