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.

Ocean Biodiversity Information System publishes fish eDNA (genomic) data set, based on work by Stoeckle et al

Way back in 1999,  Jesse Ausubel, Fred Grassle, Mark Costello, Edward van den Berghe, James Edwards and others began to envisage an on-line ocean biogeographical information system (OBIS) to enable researchers and resource managers, within a few years, to select any area or volume of water on a global map and bring up information as to what has been reported to live there.  Developed as the data portal for the Census of Marine Life program (2000-2010), by 2010 OBIS had several million what/where records for over 120,000 species.   OBIS now contains over 109 million records from over 180,000 species, about 70% of described marine species, and offers wonderful data access, archiving, and visualization.

Today, thanks to software wizardry and persistence of Dr. Steven Formel, Science Analytics and Synthesis team within the U.S. Geological Survey, and PHE’s Mark Stoeckle, OBIS and the Global Biodiversity Information Facility (GBIF) contain their pioneering eDNA (marine genomic) datasets, derived from the paper Mark co-authored about  fish diversity in coastal New Jersey.

Here are links to the datasets:



OBIS and GBIF expose slightly different sets of metadata.  One can even access a single ASV from a single library.  Here is an example; the DNA-derived data are in the table at the bottom: 

Thanks, Steve and Mark, for making this a historic day in the advancement of marine bioinformatics.

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

Guest investigator David Thaler co-authors paper with novel idea for biological diaries

Published Open Access in Frontiers in Epidemiology: The Coronavirus Calendar (CoronaCal): a simplifiedSARS-CoV-2 test system for sampling and retrospective analysis  by Manija A. Kazmi, David S. Thaler, Karina C. Åberg, Jordan M. Mattheisen, Thomas Huber and Thomas P. Sakmar

The paper concludes that sampling saliva on simple paper provides a useful method to study the natural history and epidemiology of COVID-19 (and probably many other microbes). The “CoronaCal” collection and testing method is easy to implement, inexpensive, non-invasive and scalable. The approach can inform the historical and epidemiological understanding of infections in individuals and populations.

The idea for the paper arose from efforts in the Leonardo Da Vinci DNA Project about stable preservation of genetic material on paper.

Burg & Ausubel publish “Jewish population trajectories between the Jordan River and the Mediterranean Sea”

Continuing our exploration of human populations with logistic wavelets, David Burg and Jesse Ausubel publish Jewish population trajectories between the Jordan River and the Mediterranean Sea Open Access in the journal Israel Affairs, DOI: 10.1080/13537121.2023.2206247

ABSTRACT This article re-examines Jewish population in what is now Israel using historical estimates from Ottoman, Mandatory British and United Nations sources and recent data from the Israeli census bureau. A logistic model generates backward extrapolations and forward projections. The model quantifies three waves of Jewish immigration totalling about 3.5 million. Subtracting immigrant data from total population numbers gives the main empirical trajectory for non- immigrant native-born population. A multi-logistic model combining migrant and native populations projects a Jewish population of about 10 million in 2050, a level low in the range of estimates made by others.

Some other relevant papers

IK Wernick. Jews in Time and Space (PDF). International Journal of Anthropology 31 (1-2): 93–109, 2016

PS Meyer, Ausubel JH. Carrying Capacity: A Model with Logistically Varying Limits (PDF). Technological Forecasting and Social Change 61 (3): 209–214, 1999

C Marchetti, PS Meyer, JH Ausubel. Human Population Dynamics Revisited with the Logistic Model: How Much Can Be Modeled and Predicted? Pp. 1–30 in Technological Forecasting and Social Change vol. 53, 1996