Rockefeller University

Program for the Human Environment

News

AFP coverage of mt DNA paper

Thanks to Marlowe Hood of Agence France Press (AFP) for an extensive article about Why should mitochondria define species? by Mark Stoeckle and David Thaler. Editing of Mr. Hood’s article resulted in a couple of inaccuracies.

While the opening sentence suggests that a handheld barcoding device already exists, such a convenient device remains a few years away, although the process of obtaining barcodes is now standardized, routine, and quick.

The fourth paragraph inquires about diversity increasing with time.  Diversity does increase with time.  What the paper shows is that while time matters, the population size achieved over the interval of time does not matter.

The 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.

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.

 

 

More coverage of Why mitochondria define species

The article Why should mitochondria define species?
Stoeckle M.Y., Thaler D.S.
is now fully open access:
DOI: 10.14673/HE2018121037

Coverage in Tekniikan Maailma, Finland: (Widespread genetic research revealed: Human genetic diversity is low – Two people do not differ by more than two percent) https://tekniikanmaailma.fi/laaja-perimatutkimus-paljasti-ihmisen-geneettinen-monimuotoisuus-on-vahaista-kaksi-ihmista-ei-eroa-toisistaan-enempaa-kuin-kaksi-pulua/

and Nachrichten Welt, Germany: Alles andere als besonders: Die winzigen DNA-Unterschiede der Menschheit sind “Durchschnitt” im Tierreich https://nach-welt.com/technik/alles-andere-als-besonders-die-winzigen-dna-unterschiede-der-menschheit-sind-durchschnitt-im-tierreich/

The 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.

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.

 

 

More fishing for DNA on Martha’s Vineyard

We (Mark Stoeckle and Jesse Ausubel) post new results from water sampling in October 2017 for eDNA on the island of Martha’s Vineyard.  We tested for freshwater fish (light green rows), saltwater fish (blue rows), and other vertebrates (taupe rows).  We tested in four more locations, Upper Lagoon Pond (Oak Bluffs), Mill Brook just below Mill Pond (West Tisbury), Old Millpond (West Tisbury), and Priester’s Pond (North Tisbury).  Priester’s Pond is about two miles north of Mill Pond and feeds into it.  We compared these four locations to two places we tested in 2016, Look’s Pond (freshwater, West Tisbury) and Tisbury Great Pond (saltwater) into which it feeds.

In each case, we sieved DNA from about a cup of water scooped within reach of the shore. The numbers in the columns are the number of DNA “reads” obtained from each sample for each species.  One can think of the number of reads or fragments of DNA as indicative of the abundance of DNA of that species and probably indicative of the abundance of the species itself, although different species of animals shed DNA at different rates.

The first two columns on the left show the results from 2016, for example, lots of American eel DNA in Look’s Pond.  In 2017 the Bella Bennett of the Martha’s Vineyard Times covered our initial findings about eDNA on the Island: https://www.mvtimes.com/2017/08/02/fishing-for-dna/

We found some cool things in the new locations.  For example, Mill Pond has DNA of river otters, which are hard critters to see.  The Mill Brook, Millpond, and Priester’s Pond all have muskrat DNA, and all abound in frog DNA.  DNA from all the fish in Priester’s Pond also occurs downstream in Millpond but Millpond has pickerel and eel DNA absent from Priester’s.   The brook has DNA for small stream species such as darters and killifish but not for brown bullhead (similar to catfish) or pickerel, which may need the pond habitat.

We found a mix of DNA for salt and freshwater fish in Upper Lagoon Pond.  We were happy to find menhaden and herring DNA, which means the “herring ladder” gets used.  Most remarkably, we found striped bass DNA in Upper Lagoon Pond, confirming a wild “fish” story from 2016: https://www.mvtimes.com/2016/06/01/late-night-splash-dark-holds-surprise/

We continue to be thrilled by ways that eDNA allows us to discover the animals in the water around us.  For more, see https://phe.rockefeller.edu/blog/2018/01/11/edna-seasonal-fish-abundance-study/ and  https://phe.rockefeller.edu/blog/2017/04/12/fishing-for-dna-paper-published/ .

 

Mark Stoeckle mitochondria paper in Human Evolution

Mark Stoeckle and David Thaler publish “Why should mitochondria define species?” open-access (DOI: 10.14673/HE2018121037) in the journal Human Evolution following a study of mitochondrial DNA from about 5 million specimens covering about 100,000 animal species. The paper argues that humans are far from special: humanity’s tiny mt DNA differences are “average” in the animal kingdom. Moreover, as with humans, over 90% of animal species today likely originated 100,000–200,000 years ago.

RealClearScience runs a good article about Stoeckle-Thaler, “What Can ‘DNA Barcodes’ Tell Us About Evolution and Ourselves?”

The 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.

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.

Other coverage:

The Independent, UK Genetic differences between people across the world are no greater than differences between pigeons https://uk.news.yahoo.com/genetic-differences-between-people-across-184451249.html?guccounter=2

Europa Press, newswire, Spain La diferencia genética entre humanos, en el promedio de las especies https://www.europapress.es/ciencia/laboratorio/noticia-diferencia-genetica-humanos-promedio-especies-20180521172546.html

Agencia EFE, Spain Demostrado, no eres nada excepcional (Demonstrated, you’re nothing exceptional https://sevilla.abc.es/ciencia/abci-demostrado-no-eres-nada-excepcional-201805211531_noticia.html

RIA Novosti (newswire), Russia: Scientists have not found differences in the genetic diversity of humans and animals) https://ria.ru/science/20180521/1521018801.html?referrer_block=index_archive_1

Astounding family lobster

 Lifewatch has named Jesse Ausubel’s ‘terrible claw’ lobster as one of the ten astounding species of the last decade (2007-2017).  Hooray for Dinochelus ausubeli! Thanks to the colleagues who made this happen.

Ten astounding marine species of the last decade (2007-2017)

  • Deep-sea lyre sponge – Chondrocladia lyra
  • Palauan primitive cave eel – Protanguilla palau 
  • Deep-sea acochlidiacean slug – Bathyhedyle boucheti  
  • Tree syllid worm – Ramisyllis multicaudata 
  • Starry sea wanderer jelly – Marivagia stellata  
  • The Hoff crab – Kiwa tyleri 
  • Squidworm – Teuthidodrilus samae 
  • Jesse Ausubel’s ‘terrible claw’ lobster – Dinochelus ausubeli  
  • The ‘living fossil’ octocoral – Nanipora kamurai 
  • Scaly-foot snail – Chrysomallon squamiferum

Robert Kates passed away, 89

Our beloved geographer colleague and friend Robert Kates passed away 21 April 2018 at the age of 89.  Jesse met Bob in 1978 during preparations for the first UN World Climate Conference and they work closely together on studies of the impacts of climate variability and change for the next 20 years.  Together they conceived and led the climate project of the Scientific Committee on Problems of the Environment (SCOPE) during the early 1980s, much of which was reported in RW Kates, JH Ausubel, M Berberian (eds), Climate Impact Assessment, SCOPE 27, Chichester: Wiley, 625pp., 1985.  Bob also contributed an excellent chapter to Daedalus 125(3), 1996, The Liberation of the Environment, “Population, Technology, and the Human Environment: A Thread through Time,” pp. 43-72, edited by Jesse.

Environment reporter Andy Revkin offers sound and sensitive thoughts and links to some of Bob’s late work.

We look forward to a seminar sure to be organized to celebrate his wonderful work and humanity.

POGO report

The Task Force on Ocean Biological Observations of the Partnership for Observation of the Global Oceans (POGO) has completed its Report.  Jesse Ausubel served on the Task Force, whose report explores new genomic, acoustic, and optical approaches, and their synergies, especially in relation to the deep ocean, and some organizational strategies to speed progress.

“The oceanographic community is beginning to develop sensors, instruments, platforms and systems that will eventually make large scale and long-term ocean biological observation possible. There are developments in imaging, acoustic measurement and genomic sensing that show great promise for the future. Each development is in a different stage of maturity and there is great enthusiasm within the communities for investment in these capabilities. But we see no organization that is consistently fostering these capabilities. We believe that POGO has the long-term perspective, the ocean observation focus, the international scope, and the organizational convening power to take on a focus on ocean biological observation..”

Animal species and mitochondria

We post to BioRXiv, the pre-print server for biology:
Why Should Mitochondria Define Species?
Mark Y. Stoeckle, David S. Thaler

Comments on the paper are most welcome.The 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.

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.