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
News
Quiet Ocean news
IQOE Newsletter #11 reports on the IQOE Science Committee meeting and Global Library on Underwater Sounds (GLUBS) workshop in Woods Hole in April in which Jesse participated, as well as the first World Ocean Passive Acoustic Monitoring Day in June. The newsletter also provides updates on the global hydrophone metadatabase, low-cost hydrophones, and effects of the COVID-19 pandemic on ocean sound.
New version of Loglet Lab released, LL5
The newest version of PHE’s Loglet Lab software, LL5 is now available to users online. Software improvements in LL5 include more tools for statistical analysis, cleaner graphs, and a ‘Get started’ section that guides new users step by step. We welcome users to try LL5 and send their feedback to david@model-lab.net.
Paper comparing epidemics of COVID and suppression in many countries & regions published by Burg & Ausubel
Nations and regions which implemented interventions sufficient to block community spread effectively experienced a rapid decline in confirmed cases. However, with lifting of interventions, rates rebounded to the previous high infection rates and attained a relatively stable empirical steady state. For COVID-19, societies so far appear to face a choice between relatively high oscillations involving waves of suppression and infection and lesser oscillations around an endemic setpoint.
Trajectories of COVID-19: A longitudinal analysis of many nations and subnational regions David Burg, Jesse H. Ausubel published 23 Jun 2023 PLOS ONE https://doi.org/10.1371/journal.pone.0281224
Trajectories of COVID-19: A longitudinal analysis of many nations and subnational regions
Abstract: The COVID-19 pandemic is the first to be rapidly and sequentially measured by nation-wide PCR community testing for the presence of the viral RNA at a global scale. We take advantage of the novel “natural experiment” where diverse nations and major subnational regions implemented various policies including social distancing and vaccination at different times with different levels of stringency and adherence. Initially, case numbers expand exponentially with doubling times of ~1–2 weeks. In the nations where interventions were not implemented or perhaps lees effectual, case numbers increased exponentially but then stabilized around 102-to-103 new infections (per km2 built-up area per day). Dynamics under effective interventions were perturbed and infections decayed to low levels. They rebounded concomitantly with the lifting of social distancing policies or pharmaceutical efficacy decline, converging on a stable equilibrium setpoint. Here we deploy a mathematical model which captures this V-shape behavior, incorporating a direct measure of intervention efficacy. Importantly, it allows the derivation of a maximal estimate for the basic reproductive number Ro (mean 1.6–1.8). We were able to test this approach by comparing the approximated “herd immunity” to the vaccination coverage observed that corresponded to rapid declines in community infections during 2021. The estimates reported here agree with the observed phenomena. Moreover, the decay (0.4–0.5) and rebound rates (0.2–0.3) were similar throughout the pandemic and among all the nations and regions studied. Finally, a longitudinal analysis comparing multiple national and regional results provides insights on the underlying epidemiology of SARS-CoV-2 and intervention efficacy, as well as evidence for the existence of an endemic steady state of COVID-19.
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.
First World Ocean Passive Acoustic Monitoring (WOPAM) day
A child of the International Quiet Ocean Experiment, today is the first World Ocean Passive Acoustics Monitoring (WOPAM) day. The IQOE leaders, including Miles Parsons and Steve Simpson, have prepared two very cool 90-second videos to initiate WOPAM day.
Downloadable at this site. 150 MB each, but they download quickly.
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:
GBIF: https://www.gbif.org/dataset/46488f96-b51e-4c06-9a02-8c4c900f7f78
OBIS: https://obis.org/dataset/fe2ed263-2b21-47d7-a79f-f9b911132398
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: https://www.gbif.org/occurrence/4126398311
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.