School of Marine and Atmospheric
Stony Brook University
239 Montauk Hwy
Southampton, NY 11968
Research: Bioacoustical Oceanography,
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
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.
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.
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
K. Owen, K. Saeki, J.D. Warren, A.
Bocconcelli, D. Wiley, S.-I. Ohira, A.
Bombosch, K. Toda, D.P. Zitterbart. (2021)
dimethyl sulfide gradients would lead
marine predators to higher prey biomass.
Communications Biology 4:149.
F. Caruso, L. Hickmott, J.D. Warren, P.
Segre, G. Chiang, P. Bahamonde, S.
Español-Jiménez, S. Li, A. Bocconcelli.
differences in blue whale (Balaenoptera
musculus) dive behavior increase
nighttime risk of ship strikes in
northern Chilean Patagonia.
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:
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:
K.M. Boswell, M. DElia, 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.
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.
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:
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.
P.S. Segre, A. Bocconcelli, L.S. Hickmott,
G. Howes, J.D. Warren, and G. Chiang.
hummingbird sightings in Chilean
Patagonia. The Wilson Journal of
Ornithology, 130(3): 796-799. doi:
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.
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:
Warren. 2012. Counting
in the sea using active acoustics.
Acoustics Today. Volume 8. Issue 3.
doi: 10.1121/1.4753914 [lay-language
article that gives a good background on
some of the research my lab does]
you interested in joining the
We have openings for
students, and post-docs.
Our projects generally involve
bioacoustics, zooplankton or
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
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.
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.
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
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
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
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
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!
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
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
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
photos and some student (and
species removal activities (i.e.
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).
thesis has produced two manuscripts and
both have already been submitted to
journals for publication -- way to go
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
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
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
Prof. Peterson and I had another great
group of students in our winter term
388: Tropical Marine Ecology (read
all about it in this year's course
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
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.
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
Congratulations to former lab member,
Krissy Forman whose work for her Masters
thesis on the variability of material
properties of zooplankton and nekton was
in the ICES Journal of Marine Science.
Stony Brook undergraduate
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.