Stony Brook University - School of Marine and Atmospheric Sciences
Joseph D. Warren
                                        Warren's photo

IG logo@warren.bioacoustics.lab

Joseph D. Warren
Associate Professor
School of Marine and Atmospheric Sciences
Stony Brook University

239 Montauk Hwy
Southampton, NY 11968


lab logo
twitter logo@warren_lab

Research: Bioacoustical Oceanography, Zooplankton Ecology

Scattering of sound by biological and physical oceanographic processes, Predator-prey relationships in zooplankton ecosystems,  Acoustic surveys of marine life, Biological and physical factors affecting zooplankton ecosystems, Antarctic krill ecosystem, Ocean observation systems.Zooplankton and nekton behavior and ecology. Survey design and technology.  Application of underwater acoustics to oceanographic problems. Use of sound by marine animals.  

 Harvey Mudd College - B.S. Engineering with Honors, 1994
 MIT/WHOI Joint Program - Ph.D. Applied Ocean Sciences, 2001

Some Recent Lab Publications (full list with links on Google Scholar, please contact me if a pdf is needed)

H.B. Blair, J. L. Miksis-Olds, J.D. Warren. (accepted) “Spatial variability of epi- and mesopelagic 38 kHz backscatter from fish and zooplankton across the southeastern US shelf break.” Marine Ecology Progress Series. doi:10.3354/meps13732

B.M. Lucca, P.H. Ressler, H.R. Harvey, J.D. Warren. (2021) “Individual variability in sub-Arctic krill material properties, lipid composition, and other scattering model inputs affect acoustic estimates of their population.” ICES Journal of Marine Science. doi:10.1093/icesjms/fsab045

K.C. Heim, L.H. Thorne, J.D. Warren, J.S. Link, J.A. Nye. (2021) “Marine ecosystem indicators are sensitive to ecosystem boundaries and spatial scale.” Ecological Indicators 125:107522. doi:10.1016/j.ecolind.2021.107522

D.E. Cade, S. Mduduzi Seakamela, K.P. Findlay, J. Fukunaga, S.R. Kahane-Rapport, J.D. Warren, J. Calambokidis, J.A. Fahlbusch, A.S. Friedlaender, E.L. Hazen, D. Kotze, S. McCue, M. Meÿer, W.K. Oestreich, M.G. Oudejans, C. Wilke, J. Godlbogen. (2021) “Predator-scale spatial analysis of intra-patch prey distribution reveals the energetic drivers of rorqual whale super group formation.”  Functional Ecology 35:894-908. doi:10.1111/1365-2435.13763

K. Owen, K. Saeki, J.D. Warren, A. Bocconcelli, D. Wiley, S.-I. Ohira, A. Bombosch, K. Toda, D.P. Zitterbart. (2021) “Natural dimethyl sulfide gradients would lead marine predators to higher prey biomass.” Communications Biology 4:149. doi:10.1038/s42003-021-01668-3

F. Caruso, L. Hickmott, J.D. Warren, P. Segre, G. Chiang, P. Bahamonde, S. Español-Jiménez, S. Li, A. Bocconcelli. (2020) “Diel differences in blue whale (Balaenoptera musculus) dive behavior increase nighttime risk of ship strikes in northern Chilean Patagonia.” Integrative Zoology. doi:10.1111/1749-4877.12501

C.G. Easson, K.M. Boswell, N. Tucker, J.D. Warren, J.V. Lopez. (2020) “Combined Acoustics and E-DNA Analysis Reflects Diel Vertical Migration of Mixed Consortia in the Gulf of Mexico.” Frontiers in Marine Science.  doi: 10.3389/fmars.2020.00552

S.S. Urmy* and J.D. Warren (2020) “Evaluating the target-tracking performance of scanning avian radars by augmenting data with simulated echoes.” Methods in Ecology and Evolution. doi: 10.1111/2041-210X.13365

K.M. Boswell, M. D’Elia, M.W. Johnston, J.A. Mohan, J.D. Warren, R.J.D. Wells, and T.T. Sutton. (2020) “Oceanographic structure and light levels drive patterns of sound scattering layers in a low-latitude oceanic system.” Frontiers in Marine Science. doi:10.3389/fmars.2020.00051

S.S. Urmy and J.D. Warren (2019) “Seasonal changes in the biomass, distribution, and patchiness of zooplankton and fish in four lakes in the Sierra Nevada, California.” Freshwater Biology. doi:10.1111/fwb.13362

B.M. Lucca and J.D. Warren. (2019) “Fishery-independent observations of Atlantic menhaden abundance in the coastal waters south of New York” Fisheries Research 218: 229-236. doi:10.1016/j.fishres.2019.05.016

C. Wirth and J.D. Warren. (2019) “Overlapping use of an artificial reef by humans and an apex predator (Tursiops truncatus) in the New York Bight.” Marine Mammal Science 35(1): 271-283. doi:10.1111/mms.12515 [first published online: May 2018]

C. Wirth and J.D. Warren. (2018) “Spatial and temporal variation in toadfish (Opsanus tau) and cusk eel (Ophidion marginatum) mating choruses in eelgrass (Zostera marina) beds in a shallow, temperate estuary.” Bioacoustics. doi: 10.1080/09524622.2018.1542631

P.S. Segre, A. Bocconcelli, L.S. Hickmott, G. Howes, J.D. Warren, and G. Chiang. (2018) “Offshore hummingbird sightings in Chilean Patagonia.” The Wilson Journal of Ornithology, 130(3): 796-799. doi: 10.1676/17-066.1

B.M. Lucca and J.D. Warren. (2018) “Acoustically-measured distribution and abundance of Atlantic menhaden (Brevoortia tyrannus) in a shallow estuary in Long Island, NY” Estuaries and Coasts. doi:10.1007/s12237-018-0367-x

S.S. Urmy and J.D. Warren (2018) “Foraging hotspots of common and roseate terns: the influence of tidal currents, bathymetry, and prey density.” Marine Ecology Progress Series. 590: 227-245. doi:10.3354/meps12451

J.D. Warren. 2012. Counting critters in the sea using active acoustics. Acoustics Today. Volume 8. Issue 3. 25-34.
doi: 10.1121/1.4753914 [lay-language article that gives a good background on some of the research my lab does]


Are you interested in joining the lab ?

We have openings for undergraduates, graduate students, and post-docs.
Our projects generally involve bioacoustics, zooplankton or fish ecology.
Please read this for more information.

The spring semester has ended and we're ramping up for another summer of fieldwork in NY, the Gulf of Maine, and Massachusetts with offshore cruises in the Pacific and Mid-Atlantic Bight happening this fall. And two new graduate students will be starting this summer. Several new projects are beginning later this year so we have lots of openings for potential graduate students or post-docs, so please contact me for more details.

So there was a pandemic (I arrived back from Antarctica two days before Argentina stopped flights so that was cutting things a little close), but the lab kept chugging along with fieldwork actively occurring in NY and elsewhere.


This year's publications include: Brandyn Lucca's 2nd chapter from his MS thesis estimating forage fish abundance using acoustics in NY's coastal waters and the final publication from the NSF RAPID award we were a part of investigating wildfire effects on lake ecosystems was published in Freshwater Biology. We have the usual amount of fieldwork scheduled for this year: Jamaica, Chile, New York (X4), Antarctica, California, and the SE Coast of US. (I think I'm not forgetting anything).  We had a full lab this summer with 3 grad students and 7 undergrads working on processing samples and analyzing data. They even got some lab swag -- which was easy to acquire given a presidential candidate shares my last name.
warren lab
The year began with the departure of Dr. Sam Urmy who graduated (in Dec 2017) and began a post-doc at MBARI. But we accepted a new MS student (Marie Todey) who will be working on zooplankton and larval fish of the offshore waters of NY.  Colin Wirth defended his MS thesis and had two of his chapters get published in the same year! We had a slightly odd entry in my pub list: a short note detailing hummingbird observations that were made during a project studying the foraging behavior of blue whales in Patagonian Chile.  That's right - a study of the biggest animal on the planet produced a paper on one of the smallest animals! A heavy load of fieldwork continued for the group with research in: Fiji, South America, New York, Philippines, and the SE coast of the US.
sam in robeswirth defense

Several papers from the lab came out online this year (although they all ended up with 2018 publication dates for the print version) including: Brandyn Lucca's first MS thesis chapter in Estuaries and Coasts and Sam Urmy's second PhD thesis chapter in MEPS Brandyn also successfully defended his MS thesis (in 2016) and decided to continue his work in the lab as a doctoral student and our ALES lab field trip produced a great group shot if the lab members ever decide to form an alternative rock band.
lucca defenseales at pollock krasner

Congratulations to Ph.D. student Sam Urmy on the publication in Methods in Ecology and Evolution of his first doctoral thesis research chapter on using a marine radar to quantify the movement, abundance, and distribution of seabirds.

Congratulations to Maija Niemisto who completed her MS thesis investigating the fish and zooplankton of the Hudson River estuary this fall. Maija submitted her thesis to Stony Brook University two days before giving birth to her 2nd child!

Lots of field work for the lab this summer including: surveys of Atlantic menhaden (bunker) in the local bays and estuaries of Long Island; passive acoustic monitoring of soniforous animals in Shinnecock Bay and elsewhere; Brandyn and Joe's Excellent Bering Sea Krill Adventure; and much more.

Congratulations to Ph.D. student Sam Urmy on the publication in Geophysical Research Letters of his first ALES research paper. This project was in collaboration with colleagues at Miami University (OH), UC Davis, and TERC. It was part of a NSF RAPID award to study the effect of wildfire smoke on aquatic ecosystems.

Joe has been on sabbatical for the 2015-2016 academic year -- which so far has involved lots of field work (humpback whale and herring in SE Alaska, deep sea fish and zooplankton in the Gulf of Mexico, benthic habitat and passive acoustics in Jamaica, blue whale and krill foraging in the Gulf of Corcovado, Chile, more deep sea fishes in the Gulf of Mexico) and even more field work planned for this summer (Bering Sea in June, California trips in July and August).  Plus the lab is continuing our local New York area fish and zooplankton survey work.

Joe presented work from our winter-term travel course in Tropical Marine Ecology at this year's Benthic Ecology Meeting in Portland, Maine in March 2016. Graduate students Maija Niemisto and Brandyn Lucca recently presented their research at the NY AFS meeting in February 2016. Joe presented work from the Gulf of Mexico on the identity of the fish responsible for a specific deep sea scattering layer at the GOMRI meeting in Tampa, FL in February 2016.

2015 Adventures

ALES is gearing up for another busy field season with projects this summer involving: Tern foraging around Great Gull Island, surveys of artificial reefs south of Long Island, collecting mesopelagic acoustic backscatter data as part of the DEEPEND project in the Gulf of Mexico, and a variety of laboratory and estuary experiments involving passive and active acoustics.

Joe spent a few days in the Sierra Nevada continuing our portion of a NSF RAPID research study on the effects of the 2013 Yosemite Rimfire on lake ecosystems in the region. Beautiful weather, great group of folks from UC Davis / TERC, and lots of acoustic survey data!
Lake Cherry  Lake Eleanor

Congratulations to recent Master's graduate Kaylyn Becker on the publication of her first paper from her thesis research: a study on the material properties of many different types of zooplankton from the NE Pacific. These data are critical inputs for acoustic scattering models.

Summer 2014 research is off to a busy start. Graduate student Sam Urmy is spending several weeks on Great Gull Island (off the tip of the North Fork of Long Island) studying the foraging ecology of terns and their prey. He's even got his advisor doing field sampling for him (wait a minute, that's not how the advisor-student relationship is supposed to work, is it ?). Sam makes observations from a tower (below left) of terns (below middle) and concurrently, echosounder surveys are done in the area (below right) to assess prey densities -- which in this case are a good number of bluefish or schoolies (young striped bass) in The Race.  Sampling in a small boat in an area with very strong tidal currents can be quite fun (and wet). And in the next few months, we have work trips to Virginia, Yosemite, The Poconos, Molokai, and additional local sampling here on Long Island.

Sam's towerternsechogram

Spring 2014 fieldwork in the lab began with the SV Clearwater getting back in the water and collecting acoustic data as it moves up and down the Hudson River. Sam Urmy continued our fieldwork as part of a NSF-RAPID study examining the effects of the Yosemite Rimfire on lake ecology by treking into Yosemite in April. This busy spring in the lab was capped off by trips to the Acoustical Society of America meeting in Providence, RI and the ICES Working Group on Fisheries Acoustics, Science, and Technology in New Bedford, MA in early May. We presented five talks between the two meetings so congrats to Kaylyn Becker (who made Joe give her talk since she decided to go on her honeymoon instead of attending the meetings) and Sam Urmy (who gave two talks with no overlap in content -- something his advisor didn't do).

ALES has branched into the world of passive acoustic monitoring in 2014. We deployed a passive acoustic recorder at two different reef sites on the north coast of Jamaica during Stony Brook University's winter-term Tropical Marine Ecology course. We'll be looking at whether there are differences in the two locations in terms of fish activity as well as human activity (fishing boats). You can also check out videos of this year's best student photos and some student (and faculty) invasive species removal activities (i.e. spearfishing lionfish).

becker defense image
Congratulations to Kaylyn Becker who received her Master's degree in December. Kaylyn collected the first measurements on the material properties (density and sound speed) of Humboldt squid, Pacific hake, two species of myctophids, and several different zooplankton species.  These data are critically important inputs into acoustic scattering models which are used by fisheries scientists to estimate standing stock of commercially important species like Pacific hake (which most people have eaten as a fast food fish sandwich or fish sticks).

Kaylyn's thesis has produced two manuscripts and both have already been submitted to journals for publication -- way to go Kaylyn!

The spring ALES lab outing to the Long Island Ducks game was a quacking success (except for those who had to study for finals.  The Ducks didn't win, but we have a new Titration Helmet (which came with popcorn in it) for the lab. Thanks to all the undergrads and grad students for a great semester of research.

I wrote a lay-language article for Acoustics Today [15 MB file!] about how active acoustics is used to assess fish and zooplankton. For those interested in a general overview to my research field, this is a great place to start.

Congratulations to former lab member, Joy Smith whose paper in the ICES Journal of Marine Science about developing a target strength model for Bering Sea euphausiids is the 2nd published paper from her Masters thesis.

The ALES group is back in NY getting ready for our next set of projects and working on analyzing data from our recent projects in Australia (working with the SURFAH group), Alaska, the NE Pacific, and Antarctica, catching up on sample processing, paper and report writing, and -maybe- sneaking in some surf if we get some decent waves here in Long Island. Joe recently traveled to Penn State to teach the active acoustics section of the SeaBASS week-long graduate course in bioacoustics.

Prof. Peterson and I had another great group of students in our winter term course MAR 388: Tropical Marine Ecology (read all about it in this year's  course blog).

Check out our lab blog from our past several research cruises in the Pacific Ocean (Aug 2012) and in Antarctica (Nov/Dec 2010 and 2011).

Recent presentations by members of our lab include: 2012 Ocean Sciences meeting in Salt Lake City, Utah (February 2012);  ICES WGFAST meeting in Reykjavik, Iceland and shortly afterwards to the Acoustic Challenges in Aquatic Ecosystem Assessment Workshop sponsored by the Acoustical Society of America and the American Fisheries Society in Seattle, WA (both May 2011); the 5th International Zooplankton Production Symposium  in Pucon, Chile (March 2011).  It was a great meeting with ~ 300 zooplankton scientists from around the globe in attendance. I also found a local bakery which made alfajores which were delicious.

Congratulations to former lab member, Joy Smith whose work for her Masters thesis on the variability of material properties of Bering Sea zooplankton was published in the Journal of the Acoustical Society of America.

Congratulations to former lab member, Krissy Forman whose work for her Masters thesis on the variability of material properties of zooplankton and nekton was published in the ICES Journal of Marine Science.

                                  Attention Stony Brook undergraduate MAR/MVB/ENS majors:                                  

I am looking for students to assist in the analysis of zooplankton samples from Cape Cod and Antarctica. You will be able to receive academic credit or pay for working in my lab. If interested, please contact me.

Check out some summaries of what folks are currently working on as well as past projects